bandeau pegase 2023

Scientific publication

Scientific publication

Unit publications on the Hal-INRAE institutional portal.

Last scientifics articles

HAL : Dernières publications

  • [hal-04538081] Relationship between feed efficiency and gut microbiota in laying chickens under contrasting feeding conditions

    The gut microbiota is known to play an important role in energy harvest and is likely to affect feed efficiency. In this study, we used 16S metabarcoding sequencing to analyse the caecal microbiota of laying hens from feed‑efficient and non‑efficient lines obtained by divergent selection for residual feed intake. The two lines were fed either a commercial wheat‑soybean based diet (CTR) or a lowenergy, high‑fibre corn‑sunflower diet (LE). The analysis revealed a significant line x diet interaction, highlighting distinct differences in microbial community composition between the two lines when hens were fed the CTR diet, and more muted differences when hens were fed the LE diet. Our results are consistent with the hypothesis that a richer and more diverse microbiota may play a role in enhancing feed efficiency, albeit in a diet‑dependent manner. The taxonomic differences observed in the microbial composition seem to correlate with alterations in starch and fibre digestion as well as in the production of short‑chain fatty acids. As a result, we hypothesise that efficient hens are able to optimise nutrient absorption through the activity of fibrolytic bacteria such as Alistipes or Anaerosporobacter, which, via their production of propionate, influence various aspects of host metabolism. (Maria Bernard) 09 Apr 2024
  • [hal-04495275] Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability

    Highlights: • Improving jointly health and welfare of farm animals raises new research questions. • An integrated measure of animal health through their lifespan has to be developed. • Synergies and tensions between health, welfare and production need to be investigated. • Improving animal health and welfare challenges in industrial and territorial dimensions. • Livestock farmer and citizen expectations towards animal condition need consideration. Abstract: The need to integrate more clearly societal expectations on livestock farming has led the authors of this article to consider that livestock farming systems must be redesigned to position health and welfare at the heart of their objectives. This article proposes a vision of the advances in knowledge required at different scales to contribute to this transformation. After defining health and welfare of animals, the article emphasises the need to consider health in a broader perspective, to deepen the question of positive emotional experiences regarding welfare, and raises the question of how to assess these two elements on farms. The positive interactions between health and welfare are presented. Some possible tensions between them are also discussed, in particular when improving welfare by providing a more stimulating and richer environment such as access to outdoor increases the risk of infectious diseases. Jointly improving health and welfare of animals poses a number of questions at various scales, from the animal level to the production chain. At the animal level, the authors highlight the need to explore: the long-term links between better welfare and physiological balance, the role of microbiota, the psycho-neuro-endocrine mechanisms linking positive mental state and health, and the trade-off between the physiological functions of production, reproduction and immunity. At the farm level, in addition to studying the relationships at the group level between welfare, health and production, the paper supports the idea of co-constructing innovative systems with livestock farmers, as well as analysing the cost, acceptability and impact of improved systems on their working conditions and well-being. At the production chain or territory levels, various questions are raised. These include studying the best strategies to improve animal health and welfare while preserving economic viability, the labelling of products and the consumers’ willingness to pay, the consequences of heterogeneity in animal traits on the processing of animal products, and the spatial distribution of livestock farming and the organisation of the production and value chain. At the level of the citizen and consumer, one of the challenges is to better inter-relate sanitary and health perspectives on the one hand, and welfare concerns on the other hand. There is also a need to improve citizens’ knowledge on livestock farming, and to develop more intense and constructive exchanges between livestock farmers, the livestock industry and citizens. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research. (Christian Ducrot) 08 Mar 2024
  • [hal-04309414] Assessment of beef sensory attributes and physicochemical characteristics: A comparative study of intermediate versus normal ultimate pH striploin cuts

    The quality of beef, defined by key attributes such as the intrinsic sensory qualities texture, flavour, and juiciness, is shaped by various intrinsic and extrinsic factors. This study conducted a detailed examination of Nellore beef, focusing on two categories based on ultimate pH (pHu) levels: intermediate (pHu ≥ 5.8) and normal (pHu < 5.6) beef. A comprehensive approach was taken, involving twenty trained assessors who applied the Optimised Descriptive Profile (ODP) method to evaluate grilled striploin steak samples. In parallel, consumer preferences were measured through a hedonic test and a Check-all-that-apply (CATA) task, involving 135 participants. The ODP results revealed that the intermediate pHu samples were juicier (P < 0.05) compared to the normal pHu group. The CATA analysis highlighted differences in both intermediate and normal pHu beef, especially in juiciness, a crucial factor for consumer satisfaction. Notably, variations in deoxymyoglobin content linked to ageing were observed, with higher levels at the 3rd day compared to the 28th day, especially in the intermediate pHu samples (P < 0.05). Moreover, colour-related aspects such as L*, b*, chroma (C*), and oxymyoglobin were significantly influenced (P < 0.05) by both the pHu category and ageing time. Regarding consumer acceptance, the study found no significant difference in perception between the intermediate and normal pHu groups (P > 0.05). These findings revealed the complex interactions between pHu levels, sensory characteristics, and consumer preferences in beef quality, offering valuable insights for both the industry and research community. (Iliani Patinho) 04 Dec 2023
  • [hal-04283002] Nitrogen offset potential in a multi-year farmlet-scale study; milk and herbage production from grazed perennial ryegrass/white clover swards

    The objective of this study was to quantify the farm gate nitrogen (N) off-set potential of perennial ryegrass (Lolium perenne L.; PRG) white clover (Trifolium repens L.; WC) swards by comparing the herbage and milk production from dairy farmlets that were simulations of full farming systems. A study was established where 120 cows were randomly assigned to 4 farmlets of 10.9 ha (stocking rate: 2.75 cow/ha), comprised of 20 paddocks each. Cows were fed 526 kg DM of concentrate on average each year. The 4 grazing treatments were PRG-only at 150 or 250 kg N/ha and PRG-WC at 150 or 250 kg N/ha. Cows remained in their treatment group for an entire grazing season and were re-randomized as they calved across treatments each year. As cows calved in the Spring as standard practice in Ireland, they were rotationally grazed from early-February both day and night (weather permitting) to mid-November, to a target post-grazing sward height of 4.0 cm. Mean sward WC content was 18.1 and 15.4% for the 150 and 250 kg N/ha WC treatments, respectively over the 3 year period. When WC was included, lowering the N rate did not reduce pre-grazing yield, pre-grazing height or herbage removed but did so significantly when WC was absent. Total annual herbage DM production was 13,771, 15,242, 14,721 and 15,667 kg DM/ha, for the 4 treatments; PRG-only swards receiving 150 kg N/ha or 250 kg N/ha and a PRG-WC sward receiving 150 kg N/ha or 250 kg N/ha respectively. In addition, when WC was present, compressed post-grazing sward heights were lower (4.10 vs. 4.21 cm) and herbage allowance (approximately 17 kg/cow feed allocation per cow per day) higher than the high N control (+ 0.7 kg of DM/cow per day). There was a significant increase in milk production, both per cow and per ha (P > 0.001), when WC was included into PRG swards. Over the 3-year study, cows grazing PRG-WC had greater milk (+ 304 kg) and milk solids (MSo; + 31 kg fat + protein) yields than cows grazing PRG-only swards. This significant increase in milk production suggests the inclusion of WC in grazing systems can be effectively used to increase milk production per cow and per ha and help offset nitrogen use. This result offers potential to increase farm gate NUE, and reduce the N surplus compared with PRG-dominant sward grazing systems receiving 250 kg N/ha without negatively impacting on MSo yield or herbage production and increasing farm profit by €478/ha. (Á. Murray) 13 Nov 2023
  • [hal-04415987] Meat Omics: Trends and applications of Omics strategies in meat research

    In this thematic issue, the potential of Omics methods currently applied to meat research have been demonstrated through seventeen papers that grouped seven reviews and ten original research papers. Overall, the papers described cutting-edge Omics methods to study several key aspects of meat quality, which were mainly dominated using proteomics (both traditional and label-free shotgun approaches), followed by metabolomics, lipidomics and new emerging approaches such as Rapid Evaporative Ionization Mass Spectrometry (REIMS) fingerprinting. (Mohammed Gagaoua) 26 Jan 2024
  • [hal-04533050] Genetic background of body reserves in laying hens through backfat thickness phenotyping

    In this study, we pursued three primary objectives: firstly to test and validate the phenotyping of backfat thickness as an indicator of the overall fatness of laying hens; secondly, to estimate genetic parameters for this trait; thirdly, to study the phenotypic and genetic relationships between this trait and other traits related to production and body composition. To address these questions, hens from two lines under divergent selection for residual feed intake, were phenotyped for body weight, body composition traits (backfat, total fat volume, and blood adipokines levels), and egg number. Linear mixed models enabled to estimate variance components and calculate genetic parameters. The two lines largely differed in body fatness: the efficient line had larger backfat and lower chemerin levels compared to the inefficient line. However, there were no significantly differences between the two lines concerning body weight, total fat volume, other blood adipokines levels (adiponectin, ghrelin, and visfatin), and egg production. The genetic parameter estimation revealed moderate heritability (0.38 and 0.42) for backfat and body weight, high heritability (higher than 0.80) for blood adipokines levels and low heritability (0.24 and 0.27) for egg production and total fat volume. The backfat and total fat volume were genetically highly and positively correlated (0.91). The body weight and total fat volume were also highly positively correlated (0.67). However, backfat and body weight were moderately positively correlated (0.39). The genetic correlation between backfat and egg number was moderate and negative. In conclusion, backfat could provide additional genetic information to that of the body weight as a selection criterion for body reserves. However, its correlation with laying performance should be taken into account to avoid undesired responses to selection (Nicolas Bédère) 04 Apr 2024
  • [hal-04448073] Bioaccessibility and associated concepts: Need for a consensus

    Background: The definition of the term 'bioaccessibility' is not clear. In the fields of Nutrition and Food Sciences, the term bioaccessibility was introduced in the context of micronutrients, which can lead to some confusion when applied to macronutrients, the latter requiring hydrolysis (sometimes included in the definition of bioaccessibility). Scope: In the context of macronutrient digestion, particularly in plant-based food where cell walls play a significant role, it seems coherent to differentiate between the release of nutrients from the food matrix, hydrolysis and absorption. Key findings and Conclusions: We concluded that the terms bioaccessibility, digestibility and bioavailability have been misused over time and have lost some of their meaning. Therefore, in this study, we suggest a definition for “bioaccessibility” and related vocabulary, as well as a possible classification of the biochemical events occurring during food or feed digestion. It is critical to use precise, specific vocabulary to describe the mechanisms involved while food transits through the different compartments of the gastro-intestinal tract. This goes hand in hand with a recent realisation of the importance of the food matrix, which has an impact on the breakdown of food in the digestive tract and thus on human and animal health. (Myriam M.L. Grundy) 09 Feb 2024
  • [hal-04527102] The genetics of resilience and its relationships with egg production traits and antibody traits in chickens

    Background Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have been suggested, but they need further evaluation to determine whether they are indeed predictive of improved resilience, such as disease resilience. This study investigated different resilience indicators based on deviations between expected and observed egg production (EP) by exploring their genetic parameters, their possible trade-offs with production traits, and their relationships with antibody traits in chickens. Methods Egg production in a nucleus breeding herd environment based on 1-week-, 2-week-, or 3-week-intervals of two purebred chicken lines, a white egg-laying (33,825 chickens) and a brown egg-laying line (34,397 chickens), were used to determine deviations between observed EP and expected average batch EP, and between observed EP and expected individual EP. These deviations were used to calculate three types of resilience indicators for two life periods of each individual: natural logarithm-transformed variance (ln(variance)), skewness, and lag-one autocorrelation (autocorrelation) of deviations from 25 to 83 weeks of age and from 83 weeks of age to end of life. Then, we estimated their genetic correlations with EP traits and with two antibody traits. Results The most promising resilience indicators were those based on 1-week-intervals, as they had the highest heritability estimates (0.02–0.12) and high genetic correlations (above 0.60) with the same resilience indicators based on longer intervals. The three types of resilience indicators differed genetically from each other, which indicates that they possibly capture different aspects of resilience. Genetic correlations of the resilience indicator traits based on 1-week-intervals with EP traits were favorable or zero, which means that trade-off effects were marginal. The resilience indicator traits based on 1-week-intervals also showed no genetic correlations with the antibody traits, which suggests that they are not informative for improved immunity or vice versa in the nucleus environment. Conclusions This paper gives direction towards the evaluation and implementation of resilience indicators, i.e. to further investigate resilience indicator traits based on 1-week-intervals, in breeding programs for selecting genetically more resilient layer chickens. (Tom Berghof) 04 Apr 2024
  • [hal-04437975] Potential applications of biosurfactants in animal production and meat research

    Muscle foods are perishable products that are subject to several contaminations such as microbial and/or chemical (lipid and protein oxidation) alterations, which result in their deterioration and quality loss. Several processing strategies are used to preserve and improve the stability, shelf-life and quality of meat and meat products, from which natural preservative agents are gaining interest from both industrials and consumers as green and eco-friendly strategies. Among these natural preservatives, biosurfactants are emerging molecules. Their natural origin and biodegradability make them appealing for use in the food industry. In meat research, biosurfactants are of great interest as antimicrobial and antioxidant agents to reduce meat spoilage and wastage as well as for improving the shelf-life of the products. We aimed to discuss the potential applications of biosurfactants with a focus on their antimicrobial and antioxidant activity within the objectives of reducing meat quality deterioration and improving the image quality (acceptability by consumers) of meat and meat products. Additionally, further perspectives under the context of practical applications of biosurfactants in meat emulsification have been discussed, serving as a reference to feed knowledge gaps in this emerging topic of research. Further studies and evaluations of biosurfactants in meat research are needed to establish more evidence of their potential benefits, applicability and feasibility at a larger scale. (Cerine Yasmine Boulahlib) 05 Feb 2024
  • [hal-04283061] Genetic covariance components for measures of nitrogen utilization in grazing dairy cows

    Improved nitrogen utilization of dairy production systems should improve not only the economic output of the systems but also the environmental metrics. One strategy to improve efficiency is through breeding programs. Improving a trait through breeding is conditional on the presence of exploitable genetic variability. Using a database of 1,291 deeply phenotyped grazing dairy cows, the genetic variability for 2 definitions of nitrogen utilization was studied: nitrogen use efficiency (i.e., nitrogen output in milk and meat divided by nitrogen available) and nitrogen balance (i.e., nitrogen available less nitrogen output in milk and meat). Variance components for both variables were estimated using animal repeatability linear mixed models. Genetic variability was detected for both nitrogen utilization metrics, even though their heritability estimates were low (<0.10). Validation of genetic evaluations revealed that animals divergent for nitrogen use efficiency or nitrogen balance indeed differed phenotypically, further demonstrating that breeding for improved nitrogen efficiency should result in a shift in the population mean toward better efficiency. Nitrogen use efficiency and nitrogen balance were not genetically correlated with each other (<|0.28|), and neither metric was correlated with milk urea nitrogen (<|0.12|). Nitrogen balance was unfavorably correlated to milk yield, showing the importance of including the nitrogen utilization metrics in a breeding index to improve nitrogen utilization without negatively impacting milk yield. In conclusion, improvement of nitrogen utilization through breeding is possible, even if more nitrogen utilization phenotypic data need to be collected to improve the selection accuracy considering the low heritability estimates. (E. Tavernier) 13 Nov 2023
  • [hal-04536609] Decreased lactose percentage in milk associated with quarter health disorder and hyperketolactia, a proxy for negative energy balance, in dairy cows

    Several studies have described variations in lactose content (LC) in dairy cows during udder quarter health disorder or negative energy balance (NEB). However, their joint effects on LC have never been described. This was the aim of a longitudinal observational study performed on 5 Quebec dairy farms using automatic milking systems. Quarter milk samples were collected every 14 d from 5 to 300 DIM. Quarter health status was described by combining SCC level (SCC- or SCC+: < or ≥100,000 cells/mL) and infectious status (Patho- or Patho+: presence or absence of pathogens on a milk culture). Cows with NEB in early lactation (DIM <70) were identified using milk β-hydroxybutyrate (BHB) content: 0.15 mM = BHB-; 0.15 - 0.19 mM = BHB+; > 0.19 mM = BHB++. A total of 14,505 quarter cisternal milk samples were collected from 380 lactating cows. The quarter LC was analyzed using a mixed linear regression model with the following fixed effects: quarter health status, parity, time interval between last milking and sampling, quarter milk yield (in kg/d), DIM, and herd. A random quarter intercept with a repeated measures correlation structure and a cow random intercept were also specified. The LC of SCC+ quarters was lower (-0.17 ± 0.013% pts) compared with LC of SCC- quarters for both primiparous and multiparous cows. Over the 162 bacterial species identified, only 8 species had a prevalence greater than 4.0%, and just 5 of them were associated with a reduction in LC: Staphylococcus aureus, Staph. chromogenes, Streptococcus dysgalactiae, Staph. epidermidis, and Staph. simulans. Cows identified as BHB+ and BHB++ in early lactation had a lower LC (-0.05 ± 0.019% and -0.13 ± 0.020% pts, respectively) compared with BHB- cows. For BHB++ cows, in both parity groups the decrease in LC (-0.20 ± 0.025% pts) was higher in SCC+ quarters compared with SCC- quarters. Moreover, the additive effect of the quarter health status and NEB on milk LC was greater with larger increases in BHB. Our findings highlight the necessity to jointly take into consideration both quarter health status and milk BHB concentration when using LC as a biomarker for NEB. (Auxane Hamon) 08 Apr 2024
  • [hal-04510660] Sensitivity analysis of the INRA 2018 feeding system for ruminants by a one-at-a-time approach: Effects of dietary input variables on predictions of multiple responses of dairy cattle

    In the INRA 2018 feeding system for ruminants, the prediction of multiple animal responses is based on the integration of the characteristics of the animal and the available feedstuff characteristics, as well as the rationing objectives. In this framework, the characterization of feedstuffs in terms of net energy, digestible protein, and fill units requirs information on their chemical composition, digestibility, and degradability. Despite the importance of these feed characteristics, a comprehensive assessment of their impact on the responses predicted by the INRA 2018 feeding system has not been carried out. Thus, our study investigated how variables predicted by the INRA feeding system (i.e., outputs) for dairy cows are affected by variation in feed characterization (i.e., inputs). Five input variables were selected for the sensitivity analysis (SA): CP, OM apparent digestibility (OMd), GE, effective degradability of nitrogen assuming a passage rate of 6%/h (ED6_N) and true intestinal digestibility (dr_N) of nitrogen. A one-at-a-time SA was performed on predicted digestive, productive and environmental output variables for dairy cows with 6 contrasted diets. These 6 diets were formulated to meet 95% of the potential daily milk production (37.5 kg) of a multiparous cow at wk 14 of lactation. Then, the values of the 5 key input variables of each feedstuff were randomly sampled around the INRA 2018 feed table values (reference point). The response of the output variable to the variation of the input variable was quantified and compared using the tangent value at the reference point and the normalized sensitivity coefficient. Among the major final output variables, CP and dr_N had the greatest impact on nitrogen (N) excretion in urine (as a proportion of total fecal and urinary N excretion, UN/TN), OMd and GE had the greatest impact on N utilization efficiency (N in milk as proportion of intake N, NUE), and ED6_N had the greatest impact on milk protein yield (MPY). Additionally, CP, GE, and dr_N had the least effect on methane emission, OMd had the least effect on UN/TN, and ED6_N had the least effect on NUE. The responses of most output variables to ED6_N and dr_N variations were highly dependent on diet, and were related to the ratio between PDI (i.e., metabolizable protein) and UFL (i.e., NEL) at the reference point of each diet. In conclusion, we were able to analyze the response of output variables to the variations of the input variables, using the tangent and its normalized value at the reference point. The predicted final outputs were more impacted by variations in CP, GE, and OMd. The other 2 input variables, ED6_N and dr_N, had a smaller effect on the final output variables, but the responses varied between the diets according to their PDI/UFL ratio. Among the final output variables affected by ED6_N, MPY was the most impacted, but when quantified this impact was at an acceptable level. Our present study was conducted using 6 representative diets for dairy cattle fed at their potential, but should be completed by the analysis of more diverse conditions. (Seoyoung Jeon) 19 Mar 2024
  • [hal-04364631] Pea cell wall polysaccharides and their structural integrity influence protein bioaccessibility and hydrolysis

    Pea cell walls have been shown to encapsulate nutrients inside cells, thereby limiting their hydrolysis by digestive enzymes. However, it is unknown how the cell wall performs this barrier function. In particular, this could be due to the presence of specific polysaccharides or, most probably, the organisation of the components within the cell wall. This study aimed to investigate how cell walls prevented protein hydrolysis. To address this objective, isolated cells were obtained using different treatments thought to affect cell walls differently (incubations in water, salt or EDTA solutions) and digested in vitro using a three-phase (oral, gastric and intestinal) model. Purified polysaccharides (cellulose, rhamnogalacturonan I and xyloglucan) and solutions obtained from the incubation of pea fibres and flour were also used in our digestion experiments. We found that protein bioaccessibility (here defined as the amount of protein released from the pea cells) and hydrolysis was lower after the gastric phase for the isolated cells prepared with the salt solution compared to the other treatments. Regardless of the treatment, between 47% and 93% of proteins were released from the cells (bioaccessible) and hydrolysed, respectively. Therefore, after prolonged incubation time proteases seem to be able to penetrate the cells during digestion. In terms of purified polysaccharides, rhamnogalacturonan I had the greatest effect on protein hydrolysis. Incubation solutions made from the pea fibres reduced proteolysis to a greater extent than the pea flour. The present study showed that pea cell walls delay protein digestion mainly via its structural organisation within the cell wall, with purified polysaccharides having a more limited effect. (Maxence Noel) 27 Dec 2023
  • [hal-04502991] Meat by-products as a source of bioactive peptides and functional ingredients: Regulatory and safety barriers to valorization

    Proposals for sustainable use of meat industry waste and by-products have seen a remarkable growth in recent decade. This paper aims to shed light on the often-overlooked realm of meat by-products, positioning them as an invaluable source of bioactive peptides and functional ingredients. It emphasized on the first part the main strategies for valorization of meat industry by-products into diverse bioactive peptides, and then it introduces in the second part the diverse and current methods of identification and characterization of bioactive peptides and protein hydrolysates. While the promise of these macromolecules is immense, the paper focuses and takes an in-depth look in the third part at the regulatory and safety barriers hindering their efficient valorization. By addressing regulatory and safety concerns, this review aims to pave the way for a more sustainable and responsible utilization of meat by-products, ensuring not only the economic viability of the meat sector, but also fostering a holistic and safe approach towards enhanced food and animal production sustainability. (Mohammed Gagaoua) 13 Mar 2024
  • [hal-04536587] The fate of Cu and Zn along the feed-animal-excreta-effluent continuum in swine systems according to feed and effluent treatment strategies

    Copper (Cu) and zinc (Zn) have negative environmental impacts as they accumulate in the soil after pig manure is spread. Cu and Zn are essential elements in pig nutrition but due to their low retention rate, more than 90% of ingested Cu and Zn are excreted. A better understanding of the behaviour of these elements throughout the animal-manure-soil continuum according to feed composition and manure management chain is thus required to propose alternative ways to reduce these environmental impacts. The aim of this study was to determine the fate of Cu and Zn throughout this continuum by studying the effect of Cu and Zn contents in animal feed and in the manure management chain based on anaerobic digestion and composting. Faeces were collected from 24 finishing pigs fed with 4 different Cu and Zn dietary levels and sources of supplementation. Samples of faeces were exposed to mesophilic anaerobic digestion or to 5-week composting with straw. Concentrations of Cu and Zn in the faeces were highly dependent on dietary supplies and ranged from 38 to 188 mg Cu/kg DM and from 191 to 728 mg Zn/kg DM. Degradation of a significant fraction of organic matter during treatment led to a significant increase in Cu and Zn concentration relative to the product's dry matter (DM) content, which. Cu and Zn concentrations relative to DM content were twice as high after treatment whatever the content and the form of Cu and Zn dietary supplementation. Otherwise, effluent treatment tended to reduce the possible availability of Cu and Zn in final organic products according to water-extractible contents. This study clearly shows that feed management is the main lever for reducing the amount of Cu and Zn amount in pig effluents and hence in the soil. Appropriate treatment could also facilitate the supply of organic fertilisers to areas with soil deficiency, but feed strategies need to be adapted to the treatment chain to enable the production of good quality organic products that respect EU regulations. (Emma Gourlez) 08 Apr 2024
  • [hal-04299155] Challenges and future perspectives for the European grading of pig carcasses – A quality view

    This study sought to evaluate pig carcass grading, describing the existing approaches and definitions, and highlighting the vision for overall quality grading. In particular, the current state of pig carcass grading in the European Union (SEUROP system), its weaknesses, and the challenges to achieve more uniformity and harmonization across member states were described, and a broader understanding of pig carcass value, which includes a vision for the inclusion of meat quality aspects in the grading, was discussed. Finally, the noninvasive methods for the on-line evaluation of pig carcass and meat quality (hereafter referred to as pork quality), and the conditions for their application were discussed. As the way pigs are raised (especially in terms of animal welfare and environmental impact), and more importantly, their perception of pork quality, is becoming increasingly important to consumers, the ideal grading of pigs should comprise pork quality aspects. As a result, a forwardlooking "overall quality" approach to pork grading was proposed herein, in which grading systems would be based on the shared vision for pork quality (carcass and meat quality) among stakeholders in the pig industry and driven by consumer expectations with respect to the product. Emerging new technologies provide the technical foundation for such perspective; however, integrating all knowledge and technologies for their practical application to an "overall quality" grading approach is a major challenge. Nonetheless, such approach aligns with the recent vision of Industry 5.0, i.e. a model for the next level of industrialization that is human-centric, resilient, and sustainable. (Marjeta Čandek-Potokar) 22 Nov 2023
  • [hal-04456512] Biopreservation of pre-processed fresh fish by bio-based coatings

    The demand for pre-processed fresh fishery products is growing due to their convenience for subsequent processing and cooking. However, when improperly stored, the combined impacts of microbial deterioration and chemical reactions render them inedible, leading to significant food waste. To tackle this issue, several approaches have been proposed, among which bio-based edible coating provides a promising solution with a green approach. Edible coatings are formed of bio-based polymers, particularly using macromolecules such as proteins and polysaccharides that are biodegradable, edible, and can serve as carriers for naturally sourced active agents. Coatings made from a variety of proteins and polysaccharides with the main focus on gelatin and chitosan to preserve pre-processed fish products are discussed in this review along with their properties from the microbial, physicochemical, and sensory perspectives. Coating carriers and composite natural preservatives as well as formula optimization and investigation of coating mechanisms, challenges, and potential research prospects have been further reviewed. Overall, edible coatings with active substances can be used to efficiently preserve freshly pre-processed fish. The underlying mechanisms are multiple, and the applications were mainly for preventing or reducing moisture loss and purge accumulation, postponing microbial spoilage, and restricting the growth of pathogenic microorganisms, slowing and/or inhibiting lipid, protein, and pigment oxidation, and extending the shelf-life along with improving sensory properties. Edible coatings are viewed as ecologically friendly and sustainable packaging alternatives for the preservation of pre-processed fish products. (Don Hettiarachchige Udana Eranda) 19 Feb 2024
  • [hal-04389098] Calculating herbage utilization and intake by dairy cows under subtropical conditions using conventional field measurement techniques or the HerbValo method

    This study aimed to evaluate the HerbValo method in comparison to conventional field measurement techniques as a tool for estimating the herbage utilization and dry matter (DM) intake by grazing dairy cows under subtropical conditions. It was carried out during 18 months in a commercial farm of Southern Brazil. The herbage utilization was estimated monthly in two to four randomly selected paddocks (total n = 40) using the rising-plate meter or the double-sampling technique. In parallel, the herbage utilization was estimated by the HerbValo method, which is based on simple descriptions of the herd, supplements, pasture and grazing management. Values of herbage utilization estimated by field techniques were linearly (P < 0.01) related to those estimated by HerbValo, with no effect of pasture type (tropical vs. temperate) on the origin or on the slope of the regression (slope = 0.97; origin = -0.1; R-2 = 0.81; rsd = 0.17 t DM/ha). At cow x day level, values of herbage intake estimated by field techniques were also linearly related to those estimated by HerbValo (P < 0.01; R-2 = 0.82; rsd = 1.30 kg DM/cow/day). A negative linear relationship (P < 0.01) between herbage and supplement intake was obtained for both field (slope = -1.06; R-2 = 0.72; rsd = 1.64) and HerbValo (slope = -0.92; R-2 = 0.82; rsd = 1.08) approaches. Herbage utilization and intake by a dairy herd in a subtropical grazing-based system can be reliably estimated by the HerbValo method with the advantage of not requiring direct field pasture measurements. (Letícia Wlodarski) 11 Jan 2024
  • [hal-04495509] Quel modèle pour couvrir ses besoins dans le cadre d’une alimentation durable ? Focus sur les protéines et le calcium. Synthèse du workshop SFN en partenariat avec Bel donné en visioconférence le mercredi 21 juin 2023

    La société se trouve confrontée à de nouveaux enjeux planétaires rendant nécessaires des modifications de nos systèmes alimentaires. La SFN, avec le soutien financier de Bel, a organisé un webinaire sur les modèles de régimes alimentaires permettant de couvrir les besoins nutritionnels dans le cadre d’une alimentation durable, avec un focus sur les protéines et le calcium. Cette session s’est tenue en digital le 21 juin 2023. (Bernard Guy-Grand) 08 Mar 2024
  • [hal-04455106] One-shot technology for 3D imaging of large animals: perspectives for ruminant management

    In numerous systems of animal production, there is increasing interest in the use of 3D imaging technology on farms for its ability to easily and safely measure traits of interest on living animals. With this information, it is possible to evaluate multiple morphological indicators of interest, either directly or indirectly, and follow them through time. Several tools for this purpose were developed, but one of their main weaknesses was their sensitivity to light and animal movement, which limited their potential for large-scale application on farms. To address this, a new device, called Deffilait3D and based on depth camera technology, was developed. In tests on 31 Holstein dairy cows and 13 Holstein heifers, the values generated for most measured indicators were highly repeatable and reproducible, with coefficients of variation lower than 4%. A comparison of measurements obtained from both Deffilait3D and previous validated system, called Morpho3D, revealed a high degree of similarity for most selected traits, e.g., less than 0.2% variation for animal volume and 1.2% for chest depth, with the highest degree of difference (8%) noted for animal surface area. Previously published equations used to estimate body weight with the Morpho3D device were equally valid using Deffilait3D. This new device was able to record 3D images regardless of the movement of animals and it is affected only by direct daylight. The on-going step is now to develop methods for automated analysis and extraction from images, which should enable the rapid development of new tools and potentially lead to the large-scale adoption of this type of device on commercial farms. (Yannick Le Cozler) 13 Feb 2024
  • [hal-04449380] Multi-tissue metabolic and transcriptomic responses to a short-term heat stress in swine

    Background Heat stress (HS) is an increasing threat for pig production with a wide range of impacts. When submitted to high temperatures, pigs will use a variety of strategies to alleviate the effect of HS. While systemic adaptations are well known, tissue-specific changes remain poorly understood. In this study, thirty-two pigs were submitted to a 5-day HS at 32 °C. Results Transcriptomic and metabolomic analyses were performed on several tissues. The results revealed differentially expressed genes and metabolites in different tissues. Specifically, 481, 1774, 71, 1572, 17, 164, and 169 genes were differentially expressed in muscle, adipose tissue, liver, blood, thyroid, pituitary, and adrenal glands, respectively. Regulatory glands (pituitary, thyroid, and adrenal) had a lower number of regulated genes, perhaps indicating an earlier sensitivity to HS. In addition, 7, 8, 2, and 8 metabolites were differentially produced in muscle, liver, plasma, and urine, respectively. The study also focused on the oxidative stress pathway in muscle and liver by performing a correlation analysis between genes and metabolites. Conclusions This study has identified various adaptation mechanisms in swine that enable them to cope with heat stress (HS). These mechanisms include a global decrease in energetic metabolism, as well as changes in metabolic precursors that are linked with protein and lipid catabolism and anabolism. Notably, the adaptation mechanisms differ significantly between regulatory (pituitary, thyroid and adrenal glands) and effector tissues (muscle, adipose tissue, liver and blood). Our findings provide new insights into the comprehension of HS adaptation mechanisms in swine. (Guilhem Huau) 12 Feb 2024
  • [hal-04438202] Data quantifying the behaviour of macro and trace elements along the feed – manure – treated waste continuum in pig production

    Manure from animal production is commonly spread on agricultural soil as an organic fertiliser to provide macro and trace elements to crops. However, some trace elements can accumulate in the soil and become toxic to plants and microorganisms. These elements include copper (Cu) and zinc (Zn), which can be applied in large quantities when pig manure is spread. The feeding strategy and manure management (e.g. through treatment chains) are two mechanisms identified to better control the use of these elements, but their fate from the feed to the soil in pig production remains poorly documented. Better understanding the fate of Cu and Zn, as well as that of other trace and macro elements, along the feed – excreta – waste chain is required to develop alternative ways to reduce their environmental impacts. This dataset provides insight into the composition (Cu, Zn and other trace and macro elements) of organic products along two contrasting manure management chains: (1) only storage or (2) in-building separation, anaerobic digestion (AD) of solids, and digestate drying. Feed, raw slurry, liquid and solid phases after separation of the manure and AD products were sampled and then analysed to measure their total compound contents. (Emma Gourlez) 08 Feb 2024
  • [hal-04399175] Proteomics and bioinformatics analyses based on two-dimensional electrophoresis and LC-MS/MS for the primary characterization of protein changes in chicken breast meat from divergent farming systems: Organic versus antibiotic-free

    Proteomics is a key analytical method in meat research thanks to its potential in investigating the proteins at interplay in post-mortem muscles. This study aimed to characterize the differences in early post-mortem muscle proteomes of chickens raised under two farming systems: organic versus antibiotic-free. Forty post-mortem Pectoralis major muscle samples from two chicken strains (Ross 308 versus Ranger Classic) reared under organic versus antibiotic-free farming systems were characterized and compared using two-dimensional electrophoresis and LC-MS/MS mass spectrometry. Within antibiotic-free and organic farming systems, 14 and 16 proteins were differentially abundant between Ross 308 and Ranger Classic, respectively. Within Ross 308 and Ranger Classic chicken strains, 12 and 18 proteins were differentially abundant between organic and antibiotic-free, respectively. Bioinformatics was applied to investigate the molecular pathways at interplay, which highlighted the key role of muscle structure and energy metabolism. Antibiotic-free and organic farming systems can significantly impact the muscle proteome of chicken breast meat. This paper further proposes a primary list of putative protein biomarkers that can be used for chicken meat or farming system authenticity. (Laura Alessandroni) 18 Jan 2024
  • [hal-04356432] Epigenetics, genes and the environment: what importance for breeding practices and selection methods in poultry?

    Epigenetics is commonly defined as the set of molecular mechanisms involved in gene expression regulation that are reversible and transmissible during development, and sometimes between generations, without altering the DNA sequence. Several epigenetic marks involved in chromatin regulation are now well known, such as the methylation of DNA cytosines, histone post -translational modifications, and non -coding RNA. Thanks to the technological development of high -throughput DNA sequencing, epigenetic marks can now be investigated at the whole-genome scale. It is also well known that the epigenome (the whole set of epigenetic marks in a tissue) is sensitive to environmental fluctuations, including temperature or nutrition, and can be considered as a mediator between the genes and the environment. Phenotypic programming strategies based on epigenetic mechanisms could thus be used as a lever to adjust the phenotype of individuals with their living conditions. Moreover, over the last decades, genetic selection has contributed to a considerable improvement in animal performances. Although the genetic component can be estimated with some accuracy, a large part of the phenotypic variability, considered to be of environmental origin, is not directly accessible by genetic approaches. In a context of diversification of production environments (climate change, production methods that are more respectful of welfare and the environment...), it is necessary to understand the impact of the environment on phenotypic variation via epigenetic marks, to optimize breeding systems and to predict the phenotype of an animal. Like genomic selection a few years ago, the contribution of epigenetic research could contribute to more efficient and sustainable production systems in poultry farming. (Vincent Coustham) 20 Dec 2023
  • [hal-04323941] Nouvelles références sur l'herbe valorisée au pâturage grâce à la méthode HerbValo

    L'outil HerbValo a été créé pour calculer la quantité d'herbe valorisée dans les parcelles pâturées sans avoir à y réaliser de mesures. Plus de 400 parcelles ont été suivies avec cette méthode en 2018 et 2019 pour créer un premier référentiel de l'herbe valorisée à l'échelle des régions partenaires et décrire la variabilité observée. En moyenne, ce sont 6,1t MS (Matière Sèche) d'herbe qui ont été valorisées par hectare et par an sur les parcelles suivies avec une variabilité importante (coefficient de variation interparcelles de 43 %). La région, la profondeur de sol, l'âge de la prairie et la présence d'au moins une fauche par an sont les principaux facteurs qui expliquent cette variabilité. La méthode HerbValo s'est révélée plus robuste que la méthode de la biomasse disparue pour estimer l'herbe valorisée, offrant ainsi des perspectives d'utilisation moins chronophages pour disposer de cette valeur tant en fermes expérimentales que commerciales. (Stéphanie Guibert) 05 Dec 2023
  • [hal-04315092] Can healthy diets be achieved worldwide in 2050 without farmland expansion?

    This paper analyses to what extent it would be possible to ensure food availability to the world population by 2050 with two objectives: healthy diets and no farmland expansion. Assumptions were made to project exogenous demand and supply variables. Climate change impacts on crop yields, grazing use intensities and maximum cultivable areas were taken into account. Cropland and pastureland needs were then estimated for 21 regions using a global biomass balance model. Simulation results established for two sets of crop yield projections (‘moderate’ versus ‘high’ growth) show that several regions (India, Rest of Asia, Near- and Middle-East countries and North Africa, as well as West Africa in the case of ‘moderate’ yield growth) would be constrained by their maximum cultivable areas with no deforestation. Our scenarios would be technically infeasible because of additional pastureland needs notably in sub-Saharan Africa. As a consequence, we analyse to what extent additional levers could reduce pastureland needs in sub-Saharan Africa. (Agneta Forslund) 30 Nov 2023
  • [hal-04131807] Restriction site-associated DNA sequencing technologies as an alternative to low-density SNP chips for genomic selection: a simulation study in layer chickens

    To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for routine use for genomic selection. An alternative and cost-efficient solution is to use restriction site-associated DNA sequencing (RADseq) techniques to sequence only a fraction of the genome using restriction enzymes. From this perspective, use of RADseq techniques followed by an imputation step on HD chip as alternatives to LD chips for genomic selection was studied in a pure layer line. Results Genome reduction and sequencing fragments were identified on reference genome using four restriction enzymes (EcoRI, TaqI, AvaII and PstI) and a double-digest RADseq (ddRADseq) method (TaqI-PstI). The SNPs contained in these fragments were detected from the 20X sequence data of the individuals in our population. Imputation accuracy on HD chip with these genotypes was assessed as the mean correlation between true and imputed genotypes. Several production traits were evaluated using single-step GBLUP methodology. The impact of imputation errors on the ranking of the selection candidates was assessed by comparing a genomic evaluation based on ancestry using true HD or imputed HD genotyping. The relative accuracy of genomic estimated breeding values (GEBVs) was investigated by considering the GEBVs estimated on offspring as a reference. With AvaII or PstI and ddRADseq with TaqI and PstI, more than 10 K SNPs were detected in common with the HD SNP chip, resulting in an imputation accuracy greater than 0.97. The impact of imputation errors on genomic evaluation of the breeders was reduced, with a Spearman correlation greater than 0.99. Finally, the relative accuracy of GEBVs was equivalent. Conclusions RADseq approaches can be interesting alternatives to low-density SNP chips for genomic selection. With more than 10 K SNPs in common with the SNPs of the HD SNP chip, good imputation and genomic evaluation results can be obtained. However, with real data, heterogeneity between individuals with missing data must be considered. (Florian Herry) 17 Jun 2023
  • [hal-04370809] Estimation of carcass chemical composition in beef-on-dairy cattle using dual-energy X-ray absorptiometry (DXA) scans of cold half-carcass or 11th rib cut

    The aim of the present study was to estimate the chemical composition (water, lipid, protein, mineral, and energy contents) of carcasses measured postmortem using dual-energy X-ray absorptiometry (DXA) scans of cold half-carcass or 11th rib cut. One hundred and twenty beefon-dairy (dam: Swiss Brown, sire: Angus, Limousin, or Simmental) bulls (n = 66), heifers (n = 42), and steers (n = 12) were included in the study. The reference carcass composition measured after grinding, homogenization, and chemical analyses was estimated from DXA variables using simple or multiple linear regressions with model training on 70% (n = 84) and validation on 30% (n = 36) of the observations. In the validation step, the estimates of water and protein masses from the half-carcass (R 2 = 0.998 and 0.997; root mean square error of prediction [RMSEP], 1.0 and 0.5 kg, respectively) and 11th rib DXA scans (R 2 = 0.997 and 0.996; RMSEP, 1.5 and 0.5 kg, respectively) were precise. Lipid mass was estimated precisely from the half-carcass DXA scan (R 2 = 0.990; RMSEP = 1.0 kg) with a slightly lower precision from the 11th rib DXA scan (R 2 = 0.968; RMSEP = 1.7 kg). Mineral mass was estimated from half-carcass (R² = 0.975 and RMSEP = 0.3 kg) and 11th rib DXA scans (R 2 = 0.947 and RMSEP = 0.4 kg). For the energy content, the R 2 values ranged from 0.989 (11th rib DXA scan) to 0.996 (half-carcass DXA scan), and the RMSEP ranged from 36 (half-carcass) to 55 MJ (11th rib). The proportions of water, lipids, and energy in the carcasses were also precisely estimated (R 2 ≥ 0.882) using either the half-carcass (RMSEP ≤ 1.0%) or 11th rib-cut DXA scans (RMSEP ≤ 1.3%). Precision was lower for the protein and mineral proportions (R 2 ≤ 0.794, RMSEP ≤ 0.5%). The cattle category (sex and breed of sire) effect was observed only in some estimative models for proportions from the 11th rib cut. In conclusion, DXA imaging of either a cold half-carcass or 11th rib cut is a precise method for estimating the chemical composition of carcasses from beef-on-dairy cattle. (Caroline Xavier) 03 Jan 2024
  • [hal-04409031] Getting to grips with Resilience: Towards large-scale phenotyping of this complex trait

    [...] (Nicolas N.C. Friggens) 22 Jan 2024
  • [hal-04193855] Datasets on the nutritional and environmental (including biodiversity) characteristics of food products consumed in France

    Analysing the nutritional and environmental impacts of our current diets and promoting sustainable dietary shifts require quantified data on the characteristics of foods. We have jointly studied environmental and nutritional performances of more than 200 generic foods consumed in France, by combining and completing different databases. Several environmental issues calculated by Life Cycle Assessment (LCA) were selected, including impacts on biodiversity. This required to (1) model diets for given subpopulations; (2) adapt the LCA database of food products, Agribalyse 3.0, to link selected food and environmental inventories (3) compile characterization factors to assess impacts on biodiversity. Additionally, modifying Agribalyse 3.0 required to also modify the characterization method on Land Competition. This data paper compiles all the data used to obtain the results presented in the companion article entitled: Environmental trade-offs of fulfilling nutritionally adequacy with reduced animal protein share for French adult populations [1]; i.e. (i) the characterization methods used, (ii) the modifications made to Agribalyse 3.0 and (iii) the nutrient content and quantities consumed of generic foods (iv) the optimized quantities of simulated diets reaching nutrient recommendations with low share of animal-based proteins. It also comprises (iv) Life Cycle Impact Assessment for all Agribalyse 3.0 processes of food having a CIQUAL code (2,497 processes). (Samuel Le Féon) 01 Sep 2023
  • [hal-04455809] 107. The AHOL (Animal Health Ontology for Livestock) ontology for integrating data on the main diseases of farmed animals: An example in the pig sector

    An ontology is a way of representing a set of concepts and the relationships between these concepts in a specific field. At present, ontologies are reliable and effective tools for processing and analysing a large number of scientific data with a standardized language and the formalization of knowledge into structured oriented graphs. The design of the data (unique identifiers, relationships, interoperability, etc.) and their characterization (relevance, up-to-date and recognised by the scientific community) are considered. The role of these ontologies is becoming increasingly important due to the increasing number of reports collected every day by the scientific community. The AHOL (Animal Health Ontology for Livestock) ontology has been developed by INRAE with the objective to define and organise the characteristics of farmed animal diseases, as no ontology dealing with these data is currently available to the general public. AHOL is now available on the Web and provides data on 105 swine diseases with their symptoms and pathogens. Each of these three elements is classified in a separate tree structure to facilitate the consultation and search for information. Development is underway to facilitate the search for information by including synonyms (for diseases, symptoms) in the search bar. Eventually, the AHOL ontology will also provide the ability to navigate among diseases of different species (pigs, poultry, rabbits, ruminants, horses, fish). It will then be a useful and effective tool for animal health professionals and students, for use in e-learning for example, and can be integrated into the global ontology network already in place, notably ATOL (Animal Trait Ontology for Livestock) (M. Leblanc-Maridor) 13 Feb 2024
  • [hal-04217636] Fourth report on chicken genes and chromosomes 2022

    [...] (Jacqueline Smith) 26 Oct 2023
  • [hal-04178183] Quality of animal-source foods: lessons from a collective scientific expertise

    This article critically reviews the state of knowledge on the quality of animal-source foods according to animal production and food processing conditions, including consumer expectations-behaviours and the effects of consumption of animal-source foods on human health. Quality has been defined through seven core attributes: safety, commercial, sensory, nutritional, technological, convenience, and image. Image covers ethical cultural and environmental dimensions associated with the origin of the food and the way it is produced and processed. This framework enables to highlight the priorities given to the different quality attributes. It also helps to identify potential antagonisms and synergies among quality attributes, between production and processing stages, and among stakeholders. Primacy is essentially given to commercial quality attributes, especially for standard-commodity animal-source foods. This primacy has strongly influenced genetic selection and farming practices in all livestock commodity chains and enabled substantial quantitative gains, although at the expense of other quality traits. Focal issues are the destructuring of chicken muscle that compromises sensory, nutritional and image quality attributes, and the fate of males in the egg and dairy sectors, which have heavily specialized their animals. Quality can be gained but can also be lost throughout the farm-to-fork continuum. Our review highlights critical factors and periods throughout animal production and food processing routes, such as on-farm practices, notably animal feeding, pre-slaughter and slaughter phases, food processing techniques, and food formulation. It also reveals on-farm and processing factors that create antagonisms among quality attributes, such as the castration of male pigs, the substitution of marine-source feed by plant-based feed in fish, and the use of sodium nitrite in meat processing. These antagonisms require scientific data to identify trade-offs among quality attributes and/or solutions to help overcome these tensions. There are also food products that value synergies between quality attributes and between production and processing phases, particularly Geographical Indications. Human epidemiological studies have found associations between consumption of animal-source foods and increased or decreased risk for chronic non-communicable diseases. These associations have informed public health recommendations. However, they have not yet considered animal production and food processing conditions. A concerted and collaborative effort is needed from scientists working in animal science, food process engineering, consumer science, human nutrition and epidemiology in order to address this research gap. Avenues for research and main options for policy action are discussed. (Sophie Prache) 07 Aug 2023
  • [hal-04037306] Stress at slaughter: a key factor in the determination of meat quality?

    With these papers, this Special Issue illustrates the effects of stress on various meat quality traits in very different settings and species, including pigs, catfish, game species, fowl, and cattle. The stressors described were of very different types, often with both a psychological and physical origin. This knowledge should help designing protocols trying to unravel the complex factors that determine meat quality traits, by including stress measurements of the animals from which the meat will be studied. The reduction in stress before slaughter is likely to improve meat quality. The reduction in stress before slaughter should certainly be the objective for ethical reasons. (Claudia Terlouw) 20 Mar 2023
  • [hal-03965647] A blend of functional amino acids and grape polyphenols improves the pig capacity to cope with an inflammatory challenge caused by poor hygiene of housing conditions

    Background: Dietary supplementation with a blend of functional amino acids (AA) and grape extract polyphenols contributes to preserve intestinal health and growth performance of piglets during the post-weaning period. In the present experiment, we assessed if a supplementation with a mix of AA and grape extract polyphenols during the post-weaning period would persist to improve the pig capacity to cope with a subsequent challenge caused by poor hygiene of housing conditions. Eighty pigs weaned at 28 days of age were fed a standard diet supplemented (AAP) or not (CNT) with 0.2% of a blend of AA (glutamine, arginine, cystine, valine, isoleucine, and leucine) and grape extract polyphenols during the post-weaning period (from week 0 to 6). At week 6, pigs were transferred to a growing unit where 50% of pigs previously fed AAP and CNT diets were housed in good and the other 50% in poor hygiene conditions for 3 weeks (from week 7 to 9; challenge period). All pigs were fed a standard growing diet that was not supplemented with AAP. We measured pig growth performance, plasma indicators of inflammation, digestive integrity, and oxidative status, and scored fecal consistency. Differences were considered significant at P ≤ 0.05. Results One week post-weaning, pigs fed AAP had lower plasma concentrations of haptoglobin than CNT pigs ( P = 0.03). Six weeks post-weaning, plasma concentrations of diamine oxidase (DAO) were lower ( P = 0.03) whereas those of vitamin E and A were greater ( P ≤ 0.05) in pigs fed AAP compared to CNT pigs. The prevalence of diarrhea was higher in CNT pigs compared to AAP pigs ( P < 0.01). During the challenge period, only pigs previously fed CNT diet had lower growth rate in poor than good conditions ( P ≤ 0.05). They had also greater plasma concentrations of haptoglobin and oxidative stress index (OSI) and lower plasma concentrations of vitamin E in poor than good hygiene conditions ( P ≤ 0.05). Conclusions Pigs fed AAP diet during post-weaning had less diarrhea and plasma concentrations of a digestive integrity marker, as well as greater plasma concentrations of antioxidant indicators during the post-weaning period. The beneficial effects of AAP supplementation persisted after the post-weaning period as evidenced by the absence of effects of the hygiene challenge on growth and health indicators in pigs previously fed APP. This clearly indicated a greater ability of pigs fed AAP to cope with the poor hygiene conditions. (Alícia Zem Fraga) 31 Jan 2023
  • [hal-03899905] A marginal abatement cost curve for climate change mitigation by additional carbon storage in French agricultural land

    Following the Paris agreement in 2015, the European Union (EU) set a carbon neutrality objective by 2050, and so did France. The French agricultural sector can contribute as a carbon sink through carbon storage in biomass and soil, in addition to reducing GHG emissions. The objective of this study is to quantitatively assess the additional storage potential and cost of a set of eight carbon-storing practices. The impacts of these agricultural practices on soil organic carbon storage and crop production are assessed at a very fine spatial scale, using crop and grassland models. The associated area base, GHG budget, and implementation costs are assessed and aggregated at the region level. The economic model BANCO uses this information to derive the marginal abatement cost curve for France and identify the combination of carbon storing practices that minimizes the total cost of achieving a given national net GHG mitigation target. We find that a substantial amount of carbon, 36.2 to 52.9 MtCO2e yr-1, can be stored in soil and biomass for reasonable carbon prices of 55 and 250 € tCO2e-1, respectively (corresponding to current and 2030 French carbon value for climate action), mainly by developing agroforestry and hedges, generalising cover crops, and introducing or extending temporary grasslands in crop sequences. This finding questions the 3-5 times lower target of 10 MtCO2e.yr-1 retained for the agricultural carbon sink by the French climate neutrality strategy. Overall, this would decrease total French GHG emissions by 9.2 to 13.8%, respectively (reference year 2019). (Laure Bamière) 15 Dec 2022
  • [hal-03929067] On the use of impedance detuning for gastrointestinal segment tracking of ingestible capsules

    During their travel through the gastrointestinal (GI) tract, ingestible antennas encounter detuning in their impedance response due to varying electromagnetic (EM) properties of the surrounding tissues. This communication investigates the possibility of using this impedance detuning to detect in which segment of the GI tract—stomach, small intestine, or large intestine—the capsule is located. Meandered dipole antennas operating in the 433 MHz industrial, scientific, and medical (ISM) band are designed for this purpose. The antennas conform to the inner surface of 3-D printed polylactic acid (PLA) capsules with a shell thickness of 0.6 or 0.4 mm. The impedance response is first optimized numerically in a homogeneous cylindrical phantom with time-averaged EM properties. The magnitude and the phase of the reflection coefficient are then obtained in different tissues and compared with simulations and measurements. The experimental demonstration is carried out first using tissue-mimicking liquids and then in a recently deceased ex vivo porcine model. The minimum change in the phase between different GI tissues was determined to be around 10° in the porcine model, indicating that the changes in the impedance response, particularly the changes in the phase, provide sufficient information to follow the position of the capsule in the GI tract. (Erdem Cil) 14 Mar 2023
  • [hal-04284310] MiRNome variations in milk fractions during feed restrictions of different intensities in dairy cows

    Background: In dairy cows, diet is one factor that can affect their milk production and composition. However, the effect of feed restriction on milk miRNome has not yet been described. Indeed, milk is the body fluid with the highest RNA concentration, which includes numerous microRNA. Its presence in the four different milk fractions, whole milk, fat globules, mammary epithelial cells and extracellular vesicles, is still poorly documented. This study aimed to describe the effects of different feed restrictions on the miRNome composition of different milk fractions. Results: Two feed restrictions were applied to lactating dairy cows, one of high intensity and one of moderate intensity. 2,896 mature microRNA were identified in the different milk fractions studied, including 1,493 that were already known in the bovine species. Among the 1,096 microRNA that were sufficiently abundant to be informative, the abundance of 1,027 of them varied between fractions: 36 of those were exclusive to one milk fraction. Feed restriction affected the abundance of 155 microRNA, with whole milk and milk extracellular vesicles being the most affected, whereas milk fat globules and exfoliated mammary epithelial cells were little or not affected at all. The high intensity feed restriction led to more microRNA variations in milk than moderate restriction. The target prediction of known microRNA that varied under feed restriction suggested the modification of some key pathways for lactation related to milk fat and protein metabolisms, cell cycle, and stress responses. Conclusions: This study highlighted that the miRNome of each milk fraction is specific, with mostly the same microRNA composition but with variations in abundance between fractions. These specific miRNomes were affected differently by feed restrictions, the intensity of which appeared to be a major factor modulating milk miRNomes. These findings offer opportunities for future research on the use of milk miRNA as biomarkers of energy status in dairy cows, which is affected by feed restrictions. (Antoine Leduc) 14 Nov 2023
  • [hal-03875179] A proteomic approach to identify biomarkers of foal meat quality: A focus on tenderness, color and intramuscular fat traits

    Foal meat is considered a healthy alternative to other meat sources and more environmentally sustainable. However, its quality is highly variable and there is lack of knowledge about the molecular mechanisms underlying its determination. Genotype and diet play a relevant role as the main factors that can allow a control of the final quality and the use of high-throughput analytical methods such as proteomics is a way to achieve this lofty goal. This research aimed to study-two breeds (Burguete and Jaca Navarra) supplemented with two different finishing diets: conventional concentrate and straw (C) vs silage and organic feed (S). The proteomic approach built a library of 294 proteins that were subjected to several statistical and bioinformatic analyses. Burguete breed finished with concentrate produced higher meat quality in terms of tenderness, intramuscular fat and color lightness mainly due to the high abundance of energy metabolic proteins. Tenderness was correlated to myofibrillar proteins (ACTA1, MYBPH, MYL1 and TNNC1) and energy metabolic proteins (ALDOA, CKM, TPI1 and PGMA2). Regarding color, the main pathways were energy metabolism, involving several glycolytic enzymes (ALDOA, PKM, PFKM and CKM). Oxidative stress and response to stress proteins (HSPA1A, SOD2 and PRDX2) were further involved in color variation. Moreover, we revealed that several proteins were related to the intramuscular fat accordingly to the breed. This study proposed several candidate protein biomarkers for foal meat quality that are worthy to evaluate in the future. (María López-Pedrouso) 28 Nov 2022
  • [hal-04179736] Muscle proteome of crossbred cattle that received vitamin A at birth: impacts on meat quality traits

    This study aimed to evaluate the skeletal muscle proteome of calves that received an intramuscular application of vitamin A at birth and its impacts on meat quality. Forty male crossbred calves were used from birth to feedlot finishing. On the day of birth, 20 calves were injected intramuscularly with a single dose of 300,000 IU of vitamin A and the other 20 animals received placebo (control). After weaning at 210 days, the animals of the two treatments were feedlot finished for 180 days. Longissimus muscle samples were collected for proteome analysis and meat quality assessment. There was a trend (P = 0.07) towards more tender meat in animals that received vitamin A compared to control (WBSF = 3.92 ± 0.16 kg vs. 4.23 ± 0.15). Meat color, pH and cooking loss were not affected (P > 0.05). Vitamin A treatment resulted in a more than 50% increase in intramuscular fat (IMF) content (P < 0.05) compared to control (4.10 ± 0.35% vs. 2.57 ± 0.27%). The intramuscular injection of vitamin A affected the post-mortem muscle proteome and the protein-protein interactions. A greater abundance of proteins involved in three main pathways were observed these being energy metabolism (GAPDH, ENO3, TPI1, CKM, and COX5A), muscle contraction (ACTB, ACTC1, ACTG1, ACTG2, ACTA1, ACTA2, ACTN1, ACTN2, ACTN3, TPM1, TPM2, TPM3, MYH1, PDLIM3, and TNNT3), protein binding, transport, and signaling (TUBA4A, VIM, TBA1B, and EEF1A2). A greater abundance of oxidative stress and cellular defense proteins (HSPA8 and DNAJC18) was specifically observed in the control treatment. Vitamin A upregulated key biological processes related to energy metabolism, which favored IMF accumulation during the finishing phase. (Rayssa Scapol) 11 Aug 2023
  • [hal-04157753] Les approches complémentaires à l'expérimentation animale en agronomie et clinique vétérinaire : solutions et limites

    Le recours aux modèles animaux en recherche biologique soulève de nombreux questionnements de la société en général mais aussi chez les acteurs même de cette recherche. Au cours des siècles précédents la reconnaissance de l'animal comme un être sensible a pris beaucoup de temps. L' évolution des mentalités de la société depuis l'Antiquité jusqu'à nos jours a permis cette reconnaissance. Le cadre réglementaire de l' expérimentation animale a fortement évolué depuis une vingtaine d'années, associé à une réflexion éthique qui s' est traduite depuis 1990 par la mise en place de comités d' éthique. Des progrès restent encore à faire mais les applications de la Directive européenne de 2010 devraient contribuer encore à l'amélioration de la condition animale en recherche expérimentale. Le but de cette revue est d' exposer les différentes étapes ayant menées à la notion de « conscience animale », définie comme l' expérience subjective que les animaux ont de leur environnement, de leur propre corps et/ou de leurs propres connaissances, et à la nécessité de développer de nouveaux outils permettant de diminuer l' expérimentation animale. (Marie-Hélène Perruchot) 10 Jul 2023
  • [hal-04199735] Effects over time of different types of sounds on gestating sows’ behavior

    Noise can alter the behavior and welfare of pigs, although they have good adaptive abilities. The objective of this study was to determine the relationship between different regularly emitted sounds and the behavior of gestating sows as well as their potential time of habituation to these sounds. Two groups of gestating sows (n = 15, n = 17) were involved in the experiment over two consecutive weeks. During the first week, (“Base week”), no sound was emitted, while the following week ("Test week") one sound among 40 sounds grouped into 4 types (alarm, animal, metallic, and human) was emitted randomly every 10 min during the observed periods. The sows posture (lying, sitting, standing) and behavior (sleeping, observing, in the automations) were observed thanks to manual video analysis during a resting period (PM: 13:30 h – 18:30 h) and a feeding period (Night: 23:00 h – 04:00 h) on Mondays (for Base and Test weeks – Test1) and on Wednesday (only for Test week – Test2). Sows' location in the different areas of the room, posture, and behaviour were recorded. The sows spent less time sleeping during Test1 than Base but this behavior increased again during Test2. The number of behavior changes increased during Test1 and decreased in Test2. In Test1 during the PM time, the number of area, posture and behavior changes was higher during the emissions of Alarm sounds than during the emission of other sounds, but no difference among the type of sounds was observed during the Night. During the emission of Human sounds in Test2, the sows spent more time sitting and observing, and less time sleeping than with the emission of other sounds. They also changed position more during PM of Test2 with the emission of human sounds. To conclude, frequent emission of short sounds, even below 85 decibels, can reduce to time spent sleeping and cause behavior changes. However, gestating sows can habituate to the sound stimuli and return to normal behavior by the second day of testing. The effects of different types of sounds on sow behavior and posture are not yet fully understood and require further research based on the sounds characteristics. (Charlotte Gaillard) 08 Sep 2023
  • [hal-04235874] Prediction of the daily nutrient requirements of gestating sows based on sensor data and machine-learning algorithms

    Precision feeding is a strategy for supplying an amount and composition of feed as close that are as possible to each animal’s nutrient requirements, with the aim of reducing feed costs and environmental losses. Usually, the nutrient requirements of gestating sows are provided by a nutrition model that requires input data such as sow and herd characteristics, but also an estimation of future farrowing performances. New sensors and automatons, such as automatic feeders and drinkers, have been developed on pig farms over the last decade, and have produced large amounts of data. This study evaluated machine-learning methods for predicting the daily nutrient requirements of gestating sows, based only on sensor data, according to various configurations of digital farms. The data of 73 gestating sows was recorded using sensors such as electronic feeders and drinker stations, connected weight scales, accelerometers, and cameras. Nine machine-learning algorithms were trained on various dataset scenarios according to different digital farm configurations (one or two sensors), in order to predict the daily metabolizable energy and standardized ileal digestible lysine requirements for each sow. The prediction results were compared to those predicted by the InraPorc model, a mechanistic model for the precision feeding of gestating sows. The scenario predictions were also evaluated with or without the housing conditions and sow characteristics at artificial insemination usually integrated into the InraPorc model. Adding housing and sow characteristics to sensor data improved the mean average percentage error by 5.58% for lysine and by 2.22% for energy. The higher correlation coefficient values for lysine (0.99) and for energy (0.95) were obtained for scenarios involving an automatic feeder system (daily duration and number of visits with or without consumption) only. The scenarios including an automatic feeder combined with another sensor gave good performance results. For the scenarios using sow and housing characteristics and automatic feeder only, the root mean square error was lower with Gradient Tree Boosting (0.91 MJ/d for energy and 0.08 g/d for lysine) compared with those obtained using linear regression (2.75 MJ/d and 1.07 g/d). The results of this study show that the daily nutrient requirements of gestating sows can be predicted accurately using data provided by sensors and machine-learning methods. It paves the way to simpler solutions for precision feeding. (Maëva Durand) 10 Oct 2023
  • [hal-04236303] Current innovative approaches in reducing polycyclic aromatic hydrocarbons (PAHs) in processed meat and meat products

    The presence of polycyclic aromatic hydrocarbons (PAHs) in processed meat and meat products is a global concern as they are known to be carcinogenic, mutagenic, teratogenic, and genotoxic to living beings. PAHs are generated in processed meat through different thermo-processing techniques, such as smoking, grilling, barbecuing, roasting, and frying, which involve abnormal high-temperature treatments and extruded fuels. These carbonaceous compounds with two or more cyclic benzene rings are highly stable and toxic, and their generation is enhanced by faulty thermal processing techniques, contaminated raw materials, and environmental pollution. Based on their degree of toxicity, Benzo[a]pyrene (B[a]P) is recognized as the most probable human carcinogen among different fractions of PAHs by the European Commission Regulation (EC-No.1881/2006). Furthermore, the association between dietary PAHs exposures and their role as carcinogen in human beings has been reported clinically. Therefore, it is necessary to focus on prevention and control of PAHs formation in processed meat products through various strategies to avert public health concerns and safety issues. Accordingly, several approaches have been used to reduce the risk of PAHs formation by employing safe processing systems, harmless cooking methods, marination by natural plant components, use of biological methods etc. to eliminate or reduce the harmful effects of PAHs in the food system. This review provides a comprehensive insight into the occurrence and formation of PAHs in meat and meat products and their toxicological effects on human beings. Furthermore, the different cost-effective and environment friendly methods that have been employed as “green strategies” to mitigate PAHs in meat and meat products at both household and commercial levels are discussed. (Arun Das) 10 Oct 2023
  • [hal-03901379] An evaluation of detailed animal characteristics influencing the lactation production efficiency of spring-calving, pasture-based dairy cattle

    Selection for feed efficiency, the ratio of output (e.g., milk yield) to feed intake, has traditionally been limited on commercial dairy farms by the necessity for detailed individual animal intake and performance data within large animal populations. The objective of the experiment was to evaluate the effects of individual animal characteristics (animal breed, genetic potential, milk production, body weight (BW), daily total dry matter intake (TDMI), and energy balance) on a cost-effective production efficiency parameter calculated as the annual fat and protein (milk solids) production per unit of mid-lactation BW (MSperBWlact). A total of 1,788 individual animal intake records measured at various stages of lactation (early, mid, and late lactation) from 207 Holstein-Friesian and 200 Jersey × Holstein-Friesian cows were used. The derived efficiency traits included daily kilograms of milk solids produced per 100 kg of BW (dMSperBWint) and daily kilograms of milk solids produced per kilogram of TDMI (dMSperTDMI). The TDMI per 100 kg of BW was also calculated (TDMI/BWint) at each stage of lactation. Animals were subsequently either ranked as the top 25% (Heff) or bottom 25% (Leff) based on their lactation production efficiency (MSperBWlact). Dairy cow breed significantly affected animal characteristics over the entire lactation and during specific periods of intake measurements. Jersey crossbred animals produced more milk, based on a lower TDMI, and achieved an increased intake per kilogram of BW. Similarly, Heff produced more milk over longer lactations, weighed less, were older, and achieved a higher TDMI compared with the Leff animals. Both Jersey × Holstein-Friesian and Heff cows achieved superior production efficiency due to lower maintenance energy requirements, and consequentially increased milk solids production per kilogram of BW and per kilogram of TDMI at all stages of lactation. Indeed, within breed, Heff animals weighed 20 kg less and produced 15% more milk solids over the total lactation than Leff. In addition, Heff achieved increased daily milk solids yield (+0.16 kg) and milk solids yield per kilogram of TDMI (+ 0.23 kg/kg DM) during intake measurement periods. Moreover, the strong and consistently positive correlations between MSperBWlact and detailed production efficiency traits (dMSperBWint, dMSperTDMI) reported here demonstrate that MSperBWlact is a robust measure that can be applied within commercial grazing dairy systems to increase the selection intensity for highly efficient animals. (S.H. Evers) 15 Dec 2022
  • [hal-03920179] Combining pig genetic and feeding strategies improves the sensory, nutritional and technological quality of pork in the context of relocation of feed resources

    Genetic and feeding factors were combined to improve various quality attributes of pork. Thirty Duroc (D) and thirty Pietrain NN (P) female crossbreeds received a control (C) or an R diet including extruded faba bean and linseed, from 30 to 115 kg. Growth, feed efficiency and slaughter weight were higher for P vs. D pigs and for R vs. C pigs. D pigs had fatter carcasses than P, whereas feeding did not affect carcass fatness. Compared with P, loin meat from D pigs had lower drip, higher ultimate pH and lipid content, and higher marbling, tenderness and juiciness scores (P < 0.05). R feeding did not modify sensory traits but improved pork nutritional value by markedly reducing n-6:n-3 and saturated:n-3 fatty acid ratios (P < 0.001). Combining D genotype and R diet is a favorable strategy for sensory, nutritional, technological properties and societal image of pork through relocation of feed resources, but requires a better market valorization to be implemented. (Bénédicte Lebret) 03 Jan 2023
  • [hal-03977449] An in vitro and in vivo approach to characterise digesta from pigs fed different forms of pea flour

    In vitro models of digestion are useful tools to explore the behaviour of dietary fibre sources in gastrointestinal conditions. In order to evaluate the validity of our digestion model, digesta obtained in vivo and in vitro were characterised and the impact of cell wall integrity on protein bioaccessibility and digestibility evaluated. Six cannulated barrows [Pietrain × (Large White × Landrace)] were included in a 2x2 Latin square design where they were fed two diets identical in chemical composition but differing in nutrient bioaccessibility. Pea was given either as flour (R1, most proteins encapsulated by intact cell walls) or reconstituted flour (R2, mixture of proteins and purified, broken cell walls). Digesta were collected at the duodenal and ileal cannulas at regular interval and after slaughtering, following ingestion of either R1 or R2. The two diets were also digested in vitro using a static gastrointestinal model. The original pea ingredients as well as the digesta collected in vivo and in vitro were characterised (i.e., particle size measurement, microscopy observations and gel electrophoresis) and then compared with each other. The degradation of the pea ingredients differed greatly between the two forms of flour, where particles filled with nutrients were recovered at the latest stage of R1 intestinal digestion as observed with the particle size distribution and the microscopy images. These results were consistent with the in vivo and in vitro digestibility analysis that showed lower protein hydrolysis for R1 than R2 (about 19% difference in protein digestion regardless of the method). Overall, great similarities were found between the digesta collected in vivo and in vitro, especially regarding the particle size measurements. To summarise, a substantial proportion of the proteins contained in R1 was retained within the pea cells following gastrointestinal digestion. These encapsulated proteins reduced the amount of amino acids and small peptides available for absorption. This mechanism will have consequences on postprandial metabolism of amino acids and bacterial population based on the delivery form of the dietary fibre. (Myriam M.-L. Grundy) 16 Mar 2023
  • [hal-04199873] The color of fresh pork: Consumers expectations, underlying farm-to-fork factors, myoglobin chemistry and contribution of proteomics to decipher the biochemical mechanisms

    The color of fresh pork is a crucial quality attribute that significantly influences consumer perception and purchase decisions. This review first explores consumer expectations and discrimination regarding pork color, as well as an overview of the underlying factors that, from farm-to-fork, contribute to its variation. Understanding the husbandry factors, peri- and post-mortem factors and consumer preferences is essential for the pork industry to meet market demands effectively. This review then delves into current knowledge of pork myoglobin chemistry, its modifications and pork discoloration. Pork myoglobin, which has certain peculiarities comparted to other meat species, plays a weak role in determining pork color, and a thorough understanding of the biochemical changes it undergoes is crucial to understand and improve color stability. Furthermore, the growing role of proteomics as a high-throughput approach and its application as a powerful research tool in meat research, mainly to decipher the biochemical mechanisms involved in pork color determination and identify protein biomarkers, are highlighted. Based on an integrative muscle biology approach, the available proteomics studies on pork color have enabled us to provide the first repertoire of pork color biomarkers, to shortlist and propose a list of proteins for evaluation, and to provide valuable insights into the interconnected biochemical processes implicated in pork color determination. By highlighting the contributions of proteomics in elucidating the biochemical mechanisms underlying pork color determination, the knowledge gained hold significant potential for the pork industry to effectively meet market demands, enhance product quality, and ensure consistent and appealing pork color. (Mohammed Gagaoua) 08 Sep 2023
  • [hal-04020965] Towards the discovery of goat meat quality biomarkers using label-free proteomics

    This study aimed to identify for the first time protein biomarkers of meat quality traits from Longissimus thoracis (LT) muscle of goats (Capra hircus). Male goats of similar age and weight reared under extensive rearing conditions were used to relate the LT muscle proteome with multiple meat quality traits. The early post-mortem muscle proteome analyzed using label-free proteomics was compared among three texture clusters built using hierarchical clustering analysis. Twenty-five proteins were differentially abundant and their mining using bioinformatics revealed three major biological pathways to be involved: 10 muscle structure proteins (MYL1, MYL4, MYLPF, MYL6B, MYH1, MYH2, ACTA1, ACTBL2, FHL1 and MYOZ1); 6 energy metabolism proteins (ALDOA, PGAM2, ATP5F1A, GAPDH, PGM1 and ATP5IF1), and two heat shock proteins: HSPB1 (small) and HSPA8 (large). Seven other miscellaneous proteins belonging to pathways such as regulation, proteolysis, apoptosis, transport and binding, tRNA processing or calmodulin-binding were further identified to play a role in the variability of goat meat quality. The differentially abundant proteins were correlated with the goat meat quality traits in addition to multivariate regression models built to propose the first regression equations of each quality trait. This study is the first to highlight in a multi-trait quality comparison the early post-mortem changes in the goat LT muscle proteome. It also evidenced the mechanisms underpinning the development of several quality traits of interest in goat meat production along the major biochemical pathways at interplay. (Melisa Lamri) 12 Sep 2023
  • [hal-04087298] Les prairies pour répondre aux multiples enjeux de l'élevage

    Face aux nombreuses crises affectant l’élevage (écologiques, climatiques, économiques, sociétales,…), les prairies contribuent à fournir une réponse positive et reconnue pour consolider l’élevage des herbivores. Cet article met en évidence les atouts des prairies et les perspectives de travail, au regard de l’évolution des enjeux associés à l’élevage. Les connaissances sur le fonctionnement des prairies et leur gestion ont fortement progressé. Leurs intérêts environnementaux, pour la santé des animaux, en termes de qualité nutritionnelle et organoleptique des produits animaux ou de résilience face aux aléas climatiques et économiques sont intéressants. Ces éléments devraient nous inciter à conforter, voire accroitre dans certaines zones et certains systèmes, leur place dans des élevages ruminants durables de demain et acceptables par la société. (Audrey A. Michaud) 03 May 2023
  • [hal-04186616] Extrusion of lupines with or without addition of reducing sugars: Effects on the formation of Maillard reaction compounds, partition of nitrogen and Nε-carboxymethyl-lysine, and performance of dairy cows

    The extrusion of leguminous seeds induces the formation of Maillard reaction compounds (MRC) as a product of protein advanced glycation and oxidation, which lowers protein degradability in the rumen. However, the quantitative relationship between the parameters of pretreatment (i.e., addition of reducing sugars) and extrusion, and the formation of MRC has not been established yet. Moreover, the fate of the main stable MRC, Nε-carboxymethyl-lysine (CML), in the excretory routes has never been investigated in ruminants. We aimed to test the effects of the temperature of extrusion of white lupines with or without addition of reducing sugars on the formation of MRC, crude protein (CP) degradability in the rumen, N use efficiency for milk production (milk N/N intake), and performance of dairy cows. Two experiments with a replicated 4 × 4 Latin square design were conducted simultaneously with 16 (3 rumen-cannulated) multiparous Holstein cows to measure indicators of ruminal CP degradability (ruminal NH3 concentration, branched-chain volatile fatty acids), metabolizable protein supply (plasma essential AA concentration), N use efficiency (N isotopic discrimination), and dairy performance. In parallel, apparent total-tract digestibility of dry matter, organic matter, neutral detergent fibers, N, total Lys and CML, and partition of N and CML were measured with 4 cows in both experiments. The diets consisted on a DM basis of 20% raw or extruded lupines and 80% basal mixed ration of corn silage, silage and hay from permanent grasslands, pelleted concentrate, and a vitaminized mineral mix. Expected output temperatures of lupine extrusion were 115°C, 135°C, and 150°C, without and with the addition of reducing sugars before extrusion. The extrusion numerically reduced the in vitro ruminal CP degradability of the lupines, and consequently increased the predicted supply of CP to the small intestine. Nitrogen balance and urinary N excretion did not differ among dietary treatments in either experiment. Milk yield and N use efficiency for milk production increased with extrusion of lupines at 150°C without addition of reducing sugars compared with raw lupines. Nitrogen isotopic discrimination between dietary and animal proteins (the difference between δ15N in plasma and δ15N in the diet) were lower with lupines extruded at 150°C without and with addition of reducing sugars. Regardless of sugar addition, milk true protein yield was not affected, but milk urea concentration and fat:protein ratio were lower with lupines extruded at 150°C than with raw lupines. In the CML partition study, we observed that on average 26% of the apparently digested CML was excreted in urine, and a much lower proportion (0.63% on average) of the apparently digested CML was secreted in milk, with no differences among dietary treatments. In conclusion, we showed that the extrusion of white lupines without or with addition of reducing sugars numerically reduced enzymatic CP degradability, with limited effects on N partition, but increased milk yield and N use efficiency at the highest temperature of extrusion without addition of reducing sugars. (E. Manzocchi) 01 Apr 2024
  • [hal-04369504] Poultry meat quality preservation by plant extracts: an overview

    Poultry meat is appreciated by consumers for its nutritional value, low fat content, versatility of use in various cuisines and affordable prices. However, its susceptibility to spoilage due to multiple pre‑slaughter and processing factors poses challenges for the meat industry, especially in developing countries. To improve the safety of poultry products, synthetic preservatives like nitrites, butylated hydroxytoluene and sulphites are used. Currently, these additives / preservatives have, however, raised concerns about their impact on human health, prompting a shift from consumers toward natural alternatives, such as medicinal and aromatic plants. Therefore, this paper delves into the potential of plant extracts as natural preservatives for improving the quality and shelf‑life of chicken meat and processed products. It provides an overview of the various plant extracts and essential oils that have demonstrated antimicrobial, antioxidant and enzyme inhibitory properties, without compromising the sensory attributes of the products. Different incorporation methods are discussed, including direct incorporation or marination in aqueous and/or alcoholic extracts, and the use of essential oils, including for in vivo animal feed supplementation. Overall, each method influences the final product quality differently. We further summarised the current knowledge about the mechanisms of action of the plant extracts tested, even though they are not fully elucidated. Despite the benefits of these compounds, some challenges have to be addressed, including standardising the composition of the extracts, harmonising the sensitivity of the bioactive compounds with the processing conditions, ensuring cost effectiveness and obtaining regulatory approvals for their use. The scaling up of production to meet industry demands also presents some technical challenges. Overall, the application of natural plant preservatives not only enhances chicken meat quality, but also could support the meat industry to align with the evolving consumer expectations for sustainable food products. (Ines Feknous) 02 Jan 2024
  • [hal-04261526] Proteomics as an emerging tool in equine meat research: an overview

    Proteomics tools in the field of equine meat research have been very recently applied to explore the changes in the post‑mortem muscle proteome and to discover biomarkers to monitor the variations in its different meat quality traits. The current advances achieved by proteomics in equine meat research are reviewed. Different proteomics techniques (sodium dodecyl sulphate‑polyacrylamide gel electrophoresis; two‑dimensional polyacrylamide gel electrophoresis; fluorescent two‑dimensional difference gel electrophoresis; targeted proteomics; tandem‑mass tag labeled proteomics; data‑independent analysis proteomics) have been applied in the study of the equine muscle/meat. The studies revealed the biochemical pathways involved in the development of several donkey and horse (foal) meat quality variation. The current knowledge would be useful to develop high‑quality products. (Antonella Della Malva) 27 Oct 2023
  • [hal-04271916] Egg production in nests and nesting behaviour: genetic correlations with egg quality and BW for laying hens on the floor

    In laying hen production, cage-free housing is growing rapidly to provide living conditions that meet hens’ needs. Unlike cages, this housing requires nests for automatic collection of eggs, as eggs laid outside nests must be collected by hand. Selecting hens for nest-related traits, such as egg production in nests and nesting behaviour, could help meet the requirements of cage-free housing. However, genetic correlations between these traits and major traits of breeding programmes, such as egg quality or BW, are poorly known. In addition, the genetic determinism of major traits has rarely been studied under cage-free conditions. The objective of the present study was to estimate the heritability of egg quality and BW measured on the floor and their genetic correlations with nest-related traits. Egg production in nests was based on the laying rate in nests, laying rhythm (clutch number and mean oviposition time), and nest acceptance. Nesting behaviour was based on nest preference (mean distance between nests used for laying) and mean laying duration (time spent in the nest for laying). Nest-related traits were recorded from 24 to 64 weeks of age. BW and egg quality were measured at 50 and 55 weeks of age, respectively. Nest-related traits and identification of the eggs laid by each hen (for individual measurements of egg quality) were obtained using individual electronic nests used by hens raised in groups and on the floor. The phenotypes of 1 455 Rhode Island Red and 1 538 White Leghorn hens were analysed. Heritability coefficients and genetic correlations were estimated using a multi-trait animal model for each line. Heritability estimates for egg quality and BW were moderate to high for both lines (0.17–0.74). Overall, weak genetic correlations were estimated between nest-related traits and egg quality or BW for both lines. However, strong and antagonistic genetic correlations were estimated between eggshell strength and laying rate in the nests (−0.46 to −0.42) or laying rhythm (+0.46 to +0.68) for both lines. Several moderate-to-strong genetic correlations were found for White Leghorn between nest-related traits and egg weight, eggshell shape, albumen height, and BW. This study shows that nest-related traits can be used to select hens better adapted to cage-free housing without degrading overall egg quality and BW. It also shows that some traits, like the eggshell strength, must be carefully monitored if these new traits are included in breeding goals. These results must now be confirmed for other populations and larger datasets. (L. Bécot) 28 Feb 2024
  • [hal-04197492] Using recombinant superoxide dismutase to control oxidative stress in the gastrointestinal tract of cyclic heat-stressed pigs

    Climate change is associated with an increased frequency and intensity of heat waves, posing a threat of heat stress to pig production. Heat stress compromises the efficiency of pig production partly due to causing oxidative stress, intestinal dysfunction, and inflammatory responses. Superoxide dismutase is an antioxidant enzyme reported to reduce oxidative stress and inflammation. Therefore, this experiment aimed to investigate whether recombinant superoxide dismutase (rSOD) could ameliorate oxidative stress and inflammatory responses in heat-stressed grower pigs. Sixty-four female pigs (Large White × Landrace, 27.8 ± 1.65 kg, mean ± SD) were randomly allocated to a control diet (standard grower feed, CON) or the control diet supplemented with 50 IU recombinant superoxide dismutase (rSOD) for 14 days. After acclimation to the diet, pigs were then housed under thermoneutral (TN, 20 °C, 35–50% relative humidity) or cyclic heat stress conditions (CHS, at 35 °C: 9 a.m. to 5 p.m. and 28 °C: 5 p.m. to 9 a.m., 35–50% relative humidity) for 3 days. Heat stress increased respiration rate (RR), skin and rectal temperature (RR and RT) (p < 0.001 for all), and reduced plasma thyroid hormone concentration (p < 0.001). The amount of oxidized glutathione (GSH:GSSG) was increased in the jejunum and ileum of CHS pigs. In the jejunum, rSOD also increased the amount of oxidized glutathione in both TN and CHS pigs, without any change in endogenous SOD activity. In the ileum, rSOD prevented increases in oxidized glutathione formation in the CHS pigs only. Taken together, this may reflect increased oxidative stress in both the jejunum and ileum in CHS pigs. Alternatively, rSOD increased the conversion of reduced to oxidized glutathione independently of CHS, possibly reflecting an increased overall SOD activity due to the addition of exogenous SOD. In conclusion, the use of in-feed SOD enzymes at a dose of 50 IU/kg may be a useful strategy for preventing oxidative stress in pigs. (Hieu Huu Le) 06 Sep 2023
  • [hal-04091374] Plasma 1H-NMR metabolic and amino acid profiles of newborn piglets from two lines divergently selected for residual feed intake

    Together with environmental factors, physiological maturity at birth is a major determinant for neonatal survival and postnatal development in mammalian species. Maturity at birth is the outcome of complex mechanisms of intra-uterine development and maturation during the end of gestation. In pig production, piglet preweaning mortality averages 20% of the litter and thus, maturity is a major welfare and economic concern. Here, we used both targeted and untargeted metabolomic approaches to provide a deeper understanding of the maturity in a model of lines of pigs divergently selected on residual feed intake (RFI), previously shown to have contrasted signs of maturity at birth. Analyses were conducted on plasma metabolome of piglets at birth and integrated with other phenotypic characteristics associated to maturity. We confirmed proline and myo-inositol, previously described for their association with delayed growth, as potential markers of maturity. Urea cycle and energy metabolism were found more regulated in piglets from high and low RFI lines, respectively, suggesting a better thermoregulation ability for the low RFI (with higher feed efficiency) piglets. (Laurence Liaubet) 08 May 2023
  • [hal-04071316] The use of pigs vocalisation structure to assess the quality of human-pig relationship

    Studying human-animal interactions in domestic species and how they affect the establishment of a positive Human-Animal Relationship (HAR) may help us improve animal welfare and better understand the evolution of interspecific interactions associated with the domestication process. Understanding and describing the quality of an HAR requires information on several aspects of the animal biology and emotional states (social, spatial and postural behaviours, physiological and cognitive states). Growing evidence shows that acoustic features of animal vocalisations may be indicators of emotional states. Here, we tested the hypothesis that vocal structure may indicate the quality of HAR. At weaning, 30 piglets were positively handled by an experimenter who talked to and physically interacted with them three times a day, while 30 other piglets only received the contact necessary for proper husbandry. After two weeks, we recorded the behaviours and vocalisations produced in the presence of the static experimenter for 5 min. We repeated this test two weeks later, after a conditioning period during which human presence with additional positive contacts was used as a reward for all piglets. We hypothesized this conditioning period would lead to a positive human-piglet relationship for all piglets. As expected, piglets that were positively handled at weaning expressed a higher attraction toward the experimenter, and, after the conditioning, piglets that were not positively handled at weaning expressed a similar level of attraction than the positively handled ones. Piglets positively handled at weaning produced shorter grunts than the other ones, regardless of the context of recording, which may indicate a more positive affect. During reunions with the static experimenter, a more positive HAR was associated with a decrease in vocal reactivity to human proximity. However, during reunions with the experimenter providing additional positive contacts and over the conditioning, spatial proximity to the human systematically triggered shorter and higher pitched grunts, which may indicate a more positive emotional state. Results first show that changes in vocal structure are consistent with indicators of positive states in the presence of a human. Second, these changes are stronger when the human positively interact with the piglets, supposedly emphasizing a higher positive arousal state during these interactions. We show that vocalisation structure may be a promising indicator of the quality of human-pig relationship. (Avelyne S Villain) 17 Apr 2023
  • [hal-03876258] Association between body condition genomic values and feed intake, milk production, and body weight in French Holstein cows

    Body condition score (BCS) offers a good estimate of the amount of stored fat on the body, and its variations can be used as a proxy for energy balance. Many countries have implemented a genomic evaluation of BCS, including France, where estimated breeding values are based on an individual BCS determination during the first lactation. In this article, we investigate the degree to which this genomic estimated breeding value based on a single phenotype record per cow might reflect different profiles of body reserves throughout lactation and be used to predict, and perhaps limit, their mobilization during early lactation. We also investigate whether selection on BCS affects other traits. A data set including 686 lactations of 435 Holstein cows from 3 experimental farms not used in the reference population for genomic evaluation was used to estimate the effects of the BCS direct genomic value (iBCS) on BCS, body weight, feed intake, milk production, and fat and protein contents throughout the lactation period. For each trait, the model included different iBCS regressions and an effect of the direct genomic value of the trait itself when available. It thus appeared that cows with a positive iBCS always had a higher BCS than negative iBCS cows, whatever the lactation stage, and that this difference increased during the first 6 mo to reach a difference of 0.8 point. A similar effect was seen regarding body weight, but it was the opposite for milk production, with negative iBCS cows producing slightly more milk (difference of about 3% over lactation). Feed intake increased slightly faster at the beginning of lactation for cows with positive iBCS. Therefore, iBCS is a promising tool that could help to limit intense mobilization during early lactation. Should feed efficiency be included in the breeding goal, greater attention should be paid to BCS to avoid further body mobilization in early lactation. (Rachel Lefebvre) 28 Nov 2022
  • [hal-04001621] Targeting environmental and technical parameters through eco-efficiency criteria for iberian pig farms in the dehesa ecosystem

    Eco-efficiency could be defined as the simultaneous ability to achieve acceptable economic results with the least possible environmental degradation. Its analysis in crop and livestock production systems has become a hot topic among politicians and scientists. Pig pasture production systems are in high commercial demand because they are associated with high quality and environmentally friendly products. This work aimed to assess the eco-efficiency of pig farms and subsequently explore the determinants of inefficiency in the dehesa ecosystem in the southwest of the Iberian Peninsula. Farmers from 35 randomly selected farms were interviewed to obtain farm-level data. The eco-efficiency level was calculated through a joined data envelopment analysis (DEA) and life cycle assessment (LCA) approach. Subsequently, a truncated Tobit model was applied to determine factors associated with inefficiency. The results of the research revealed that Iberian pig farms are highly eco-efficient. The estimated average eco-efficiency score is 0.919 and ranges from 0.479 to 1, suggesting that the average farm could increase its value by about 8.1%. This means that the aggregate environmental pressures could be reduced by approximately this proportion (8%) while maintaining the same input level. The determinants related to social and demographic characteristics that positively affected eco-efficiency were the number of children, while years of farm activity and educational level had a negative effect. On the other hand, farm’s characteristics and the type of management, the percentage of own surface area, the percentage of livestock use, and the high proportion of pigs fattened in montanera, positively affected the eco-efficiency level. (Javier García-Gudiño) 23 Feb 2023
  • [hal-04000680] Feed restriction as a tool for further studies describing the mechanisms underlying lipolysis in milk in dairy cows

    Milk lipolysis is defined as the hydrolysis of triglycerides, which are the main component of milk fat. Short-chain fatty acids (FAs) released in milk are responsible for rancid flavour. In addition, the presence of partial glycerides impairs the functional properties of milk, such as foaming and creaming abilities. Milk lipolysis, a key criterion used to assess milk quality, depends on animal parameters and breeding factors. Low-energy diets are associated with higher levels of spontaneous lipolysis, particularly in late lactation. In this study, dairy cows were fed a restricted diet (i.e. 65% of their ad libitum DM intake (DMI)) to induce spontaneous lipolysis in milk and to study milk composition associated with lipolysis. Two groups of 22 cows each received a control diet (100% of ad libitum DMI) or the restricted diet according to a 2 x 2 crossover design. The restricted diet was fed for five days. As expected, feed restriction increased milk spontaneous lipolysis which was associated with an increase in lipoprotein lipase activity. At the same time, milk yield and protein content decreased and no effect was observed on milk fat content. The increase in spontaneous lipolysis was associated with an increase in milk fat globules diameter, without influencing casein micelles diameter. Feed restriction altered the parameters of dairy cow metabolism, with increases in plasma non-esterified FAs, triglycerides and urea, indicating body fat mobilisation and protein catabolism associated with feed restriction. Feed restriction also altered hormonal parameters, with decreases in plasma insulin, insulin-like growth factor 1 and prolactin. As expected, lipolysis was higher in evening milk and was associated with a larger diameter of milk fat globules. This zootechnical approach will be completed with proteomic, lipidomic and transcriptomic studies of milk and/or mammary gland of animals selected for their extreme lipolysis. (Catherine Hurtaud) 22 Feb 2023
  • [hal-04020710] Effects of thermal conditions on gestating sows’ behaviors and energy requirements

    Room temperature and individual behavior may influence the energy requirements of gestating sows. These factors are not yet integrated on a daily and individual basis in the calculation of these requirements. The objective of this study was to quantify the effect of temperatures on the sows’ behaviors, especially on the level of physical activity, and on the energy requirements of gestating sows. Over four consecutive weeks, the temperature of two gestation rooms was maintained at medium temperatures (16.7 °C and 18.5 °C, respectively, for room 1 and room 2) for the first and third week, at low temperatures (14.4 °C and 15.3 °C) for the second week, and at high temperatures (31.6 °C and 31.9 °C) for the fourth week. Individual behavior was manually recorded based on videos and the data used to estimate the physical activity and social interactions of 37 gestating sows separated into two groups. The videos were analyzed over two periods of 5 h (“Feeding period” from 2300 to 0400 hours, “Resting period” from 1330 to 1830 hours). The energy requirements were calculated by the InraPorc model, modified for gestating sows, on the basis of a thermo-neutral situation and an average activity of 4 h standing per day for all the sows. The sows of one group were less active in high than low temperatures (83 vs. 103 min standing or walking over 5 h, P < 0.001). Isolation for high temperatures or huddling for low temperatures could be observed when sows were lying down. The sows spent more time lying laterally with high temperatures than low temperatures (66% vs. 52% of time spent lying, respectively, P < 0.001). Both groups reacted differently to high temperatures, in one the sows changed their activity (lying more) whereas in the other they drank more water compared to medium temperatures (11 vs. 8.5 L/d, P = 0.01). In one group, with high temperatures the sows were fed above their requirements (they should have received 110 g of feed per day per sow less, P < 0.001) and with low temperatures the same group should have received 50 g/d per sow more to fulfill their requirements. For the second group of sows, the temperatures did not significantly affect the feed requirements. In conclusion, daily ambient temperature and individual physical activity seem to be relevant information to add in nutritional models to improve precision feeding. (Justine Abarnou) 09 Mar 2023
  • [hal-03892083] Exogenous porcine somatotropin administered to late pregnant gilts alters liver and muscle functionalities in pig foetuses

    Neonatal maturity depends on the maternal capacity to provide nutrients for fetal growth. This study aimed to investigate the effects of systemic administration of recombinant porcine somatotropin (pST), one of the main regulators of growth and metabolism, to pregnant gilts during late gestation on circulating nutrients and expression levels of genes in liver and skeletal muscle of their 110-day old fetuses. Gilts received either daily injections of sterile water (control [CTL] group, n = 15) or of 5 mg of pST (pST group, n = 17) from days 90 to 109 of gestation. At day 110 postconceptus, pairs of fetuses (one of small and one of average size within a litter) were selected. Circulating fructose concentrations were greater but circulating concentrations of urea were lower in pST than in CTL fetuses. Expression levels of genes involved in carbohydrate and lipid metabolism were more affected by pST treatment in liver than in muscle. Hepatic molecular changes suggest an inhibition of energy-consuming processes (glycogen and lipid biosynthesis) and the activation of energy-producing pathway (mitochondrial oxidation) in pST compared to CTL fetuses. Expression levels of some genes involved in intracellular degradation of proteins were greater in the liver of pST fetuses, and combined with lower uremia, this suggests a higher utilization of protein sources in pST fetuses than in CTL fetuses. In muscle, molecular changes were mainly observed in the IGF-insulin axis. Altogether, pST-treated gilts seem to have a greater ability to support fetal liver development by the reorientation of energy and protein metabolism. (Florence Gondret) 29 Dec 2022
  • [hal-04093060] Phytochemicals as natural additives for quality preservation and improvement of muscle foods: a focus on fish and fish products

    Fish and fish products offer a wide variety of nutritional and health benefits, thanks to the desirable protein and quality. Nevertheless, their quality is prone to degradation due to microbial contamination, oxidation and enzymatic reactions during the storage period. This results in the development of unsuitable flavor and rancid odor hence affecting the freshness, texture and sensory acceptability. Various processing methods such as drying, chilling, freezing etc. are employed, but they seemed to be insufficient to prevent such deterioration. Therefore, additives are added to maintain and/or improve the quality and extend the shelf-life of muscle foods, including fish products. In recent years, natural food additives are well perceived by consumers over synthetic ones. Perceived naturalness is mainly related to healthiness. Natural products, such as plant-derived phytochemicals (phenolics, essential oils, carotenoids, lignins and other molecules), having antioxidant and antimicrobial properties offer plenty of opportunities to overcome protein degradation, lipid peroxidation and also to inhibit microbial growth, thereby improving the quality and shelf-life of food products. This review intends to critically address the potential of phytochemicals as natural food additives to prevent the deterioration of the quality and safety of fish products, and thus providing healthy and safe final products to the consumers. (Olipriya Biswas) 09 May 2023
  • [hal-04084869] Fixing molecular complexes in BioPAX standards to enrich interactions and detect redundancies using Semantic Web Technologies

    Motivation: Molecular complexes play a major role in the regulation of biological pathways. The Biological Pathway Exchange format (BioPAX) facilitates the integration of data sources describing interactions some of which involving complexes. The BioPAX specification explicitly prevents complexes to have any component that is another complex (unless this component is a black-box complex whose composition is unknown). However, we observed that the well-curated Reactome pathway database contains such recursive complexes of complexes. We propose reproductible and semantically-rich SPARQL queries for identifying and fixing invalid complexes in BioPAX databases, and evaluate the consequences of fixing these non-conformities in the Reactome database. Results: For the Homo sapiens version of Reactome, we identify 5,833 recursively defined complexes out of the 14,987 complexes (39%). This situation is not specific to the human dataset, as all tested species of Reactome exhibit between 30% (Plasmodium falciparum) and 40% (Sus scrofa, Bos taurus, Canis familiaris, Gallus gallus) of recursive complexes. As an additional consequence, the procedure also allows the detection of complex redundancies. Overall, this method improves the conformity and the automated analysis of the graph by repairing the topology of the complexes in the graph. This will allow to apply further reasoning methods on better consistent data. Availability We provide a jupyter notebook detailing the analysis Supplementary information Supplementary data are available at Bioinformatics online. (Camille Juigné) 03 May 2023
  • [hal-04184535] Intrinsic and extrinsic factors impacting fresh goat meat quality: an overview

    Goat meat, known also as chevon or caprine meat, is an important source of protein and essential nutrients in many regions worldwide. To ensure high-quality goat meat production, it is crucial to understand the intrinsic and extrinsic factors that influence its sensory, technological and nutritional properties. This review aims to provide an overview of the factors affecting goat meat quality throughout the production and processing chain. The importance of different factors influencing goat meat quality were described. First, the focus was made on the intrinsic factors, including the effects of age at slaughter, gender (sex), breeds, slaughter weight, and the contractile and metabolic properties of the muscle by discussing their impact in terms of their influence on important intrinsic quality traits such as tenderness, flavor, color and overall quality of goat meat. Furthermore, the extrinsic factors such as production systems, husbandry practices, feeding strategies, types of feed and roughages, antioxidants, feeding systems, climate, season, and environmental conditions were examined in addition to the pre-slaughter treatments, transport conditions, and stress experienced by goats at the time of slaughter. Overall, this review synthesizes current knowledge on both the intrinsic and extrinsic factors affecting goat meat quality. The findings emphasize the importance of a better understanding and optimizing of these factors at each stage of production and processing to ensure the consistent delivery of high-quality goat meat. Further research in these areas will contribute to the development of improved practices and technologies in the goat meat industry. (Mohammed Gagaoua) 22 Aug 2023
  • [hal-04378868] The effect of spring grass availability and silage supplementation on dairy cow performance and dry matter intake during early lactation

    The objectives of this study were to investigate the effect of level and timing of silage supplementation during early lactation on animal performance and dry matter intake (DMI). Two farm-lets were established with a high (1253 kg DM/ha) and low (862 kg DM/ha) grass availability at turnout. In spring, cows were assigned to one of two treatments as they calved over 2 years; high grass (HG) and low grass (LG). During period 1 (week 1–6), cows on the HG treatment were offered a high daily herbage allowance (DHA) with low silage and the LG treatment were offered a low DHA with high silage. In period 2 (week 7–12), half of the cows from the HG treatment in P1 switched to the LG treatment in P2 and vice versa as 20 LG cows in P1 switched to the HG treatment in P2. Cows on the HG treatment in P2 received a high DHA with no silage and the LG treatment received a low DHA with 3 kg DM/cow silage. Grass DMI was significantly higher for the HG treatment during both periods (+1.6 and +3.4 kg DM/cow/day, respectively). The HG treatment produced +0.9 kg milk/cow/day and had a higher protein concentration (+1.1 g/kg milk) compared to cows on the LG treatment during period 2. Differences in animal performance observed in period 2 were maintained throughout the 8-week carryover period. (Sarah Walsh) 08 Jan 2024
  • [hal-04235911] Combining sheep and beef cattle in a pasture-based system minorly influenced muscle and fat colour and dorsal fat firmness but increased fat skatole content in lambs

    A recent long-term system-level experiment, using grassland-based organic systems established as separate farmlets, showed that combining sheep and beef cattle within a mixed (MIX) system promoted self-sufficient production of grass-fed meat and improved economic and environmental performance in the sheep enterprise compared to a sheep-only (SH) system. In the present study, we used all male lambs produced over the first year in this experiment to evaluate the effect of this farming practice on some lamb carcass and meat sensory quality traits. Lambing took place at the end of February and lambs were pasture-fed from 1 month of age on average until slaughter, unless they were not ready for slaughter at 3–4 weeks before the start of the mating period in October, in which case they were finished indoors on a concentrate-based diet. All MIX lambs (n = 33) were finished at pasture. One SH lamb (out of a total of 85) had to be finished indoors with a concentrate-based diet. MIX lambs had a higher growth rate than SH lambs (P < 0.001), resulting in a lower lamb age at slaughter in MIX than in SH (150 vs 173 days, P < 0.001). Carcass weight and degree of fatness, kidney fat weight and dorsal fat thickness did not differ between systems. Kidney fat skatole concentration was higher in MIX than in SH (median value reaching 0.15 µg/g liquid fat and 0.11 µg/g liquid fat in MIX and SH, respectively, P < 0.05). This was most likely due to MIX lambs being slaughtered at a younger age and therefore eating younger grass. There were minor differences between MIX and SH lambs in dorsal fat firmness and in colour coordinates of longissimus thoracis et lumborum muscle. We conclude that while combining sheep and beef cattle within a mixed system offers advantages in terms of self-sufficient production of grass-fed meat and system economic and environmental performance, it could come at a cost to lamb flavour. (Sophie Prache) 28 Feb 2024
  • [hal-04087047] Reply to F Mariotti et al.

    [...] (Florent Vieux) 02 May 2023
  • [hal-04174264] La prairie pâturée : un gisement de protéines à portée de gueules de vaches !

    Le pâturage des prairies temporaires et permanentes constitue un levier majeur de renforcement de l’autonomie protéique des systèmes d’élevage avec à la clé des économies significatives de concentrés azotés. Une analyse récente conduite sur l’Unité Expérimentale INRAE du Pin-au-Haras (système laitier conventionnel avec fertilisation azotée) et la ferme expérimentale de Thorigné d’Anjou (système allaitant en agriculture biologique) a permis de préciser la contribution des prairies pâturées à la valorisation des protéines tout au long d’une saison de pâturage. Dans le cas du Pin-au-haras, les prairies permanentes présentent un niveau de valorisation en kg de MAT/ha/an supérieur de 20% aux prairies temporaires avec respectivement 1,88 t de MAT/ha/an exportées sur les prairies permanentes contre 1,48 t de MAT/ha/an dans le cas des prairies temporaires. Dans le cas des prairies à flore variée de Thorigné, le rendement en MAT valorisé au cours de la saison de pâturage par le troupeau allaitant est de 975 kg de MAT/ha/an. Différents leviers, relevant notamment des pratiques de pâturage permettent d’allonger la saison de pâturage et ainsi maximiser ce gisement de protéines. Encore faut-il se donner les moyens d’exploiter et valoriser cette ressource bon marché et renouvelable par le pâturage : sa régression dans certains systèmes de plaine interroge ! (Patrice Pierre) 31 Jul 2023
  • [hal-04182700] Impact of sampling location and aging on the Longissimus thoracis et lumborum muscle proteome of dry-aged beef

    This study aimed to explore the differences in the proteome and molecular pathways between two sampling locations (external, internal) of bovine Longissimus thoracis et lumborum (LTL) muscles at 0, 21, and 28 days of dry-aging (i.e.3, 24, and 31 days post-mortem). It further assessed the impact of aging on the proteome changes and the biological processes at interplay. Proteins related to defence response to bacterium and regulation of viral entry into host cell were identified to be more abundant on the external location before dry-aging, which may be associated to the oxidative conditions and microbial activity to which post-mortem muscle is exposed during dressing, chilling, and/or quartering of the carcasses. This highlights the relevance of sampling from interior tissues when searching for meat quality biomarkers. As dry-aging progressed, the proteome and related biological processes changed differently between sampling locations; proteins related to cell-cell adhesion and ATP metabolic processes pathways were revealed in the external location at 21 and 28 days, respectively. On the other hand, the impact of aging on the proteome of the interior samples, evidenced that muscle contraction and structure together with energy metabolism were the major pathways driving dry-aging. Additionally, aging impacted other pathways in the interior tissues, such as regulation of calcium import, neutrophil activation, and regeneration. Overall, the differences in the proteome allowed discriminating the three dry-aging times, regardless of the sampling location. Several proteins were proposed for validation as robust biomarkers to monitor the aging process (tenderization) of dry-aged beef: TTN, GRM4, EEF1A1, LDB3, CILP2, TNNT3, GAPDH, SERPINI1, and OMD. (Sara Álvarez) 04 Sep 2023
  • [hal-04320323] Weaned piglet’s reactivity to humans, tonic immobility and behaviour in a spatial maze test is affected by gestating sows’ relationship to humans and positive handling at weaning

    Fear of human can impact negatively offspring's behaviour and cognition whereas early positive handling has positive impacts. The aim of this study was to evaluate the crossed effects of trans-generational transfer and familiarisation with human on piglets' behaviour. Sows were classified into two categories (Fearful, n = 11 and Docile, n = 13) based on whether they avoided human contact or not during a human approach test at 71 days of gestation. Fear of human was not related to salivary cortisol levels of the sows (F =2.72, P = 0.10). Fearful sows' piglets stood immobilized longer (Chisq= 6.24, P = 0.01), as well females (8.70, P = 0.003) during a tonic immobility test (TIT) at 7 days but not at 15 days. The behaviour of two male and two female piglets per sow (n = 96) was studied after weaning (28 days). We found no effect of sow's reaction to human on piglets' emotionality expressed during an open-field test (OFT) at 32-33 days. However, during a Human voluntary approach test (VHAT) piglets born from fearful sows were more fearful than piglets born from docile sows (Chisq=8.23, P = 0.004,). Half of the piglets (n = 48, 1 male and 1 female per sow) were then familiarised with human while the others received minimum contact. We found no main or crossed effect of sow's reaction to human and piglet's treatment on piglets' emotionality during an OFT, nor on their exploratory behaviour during VHAT at 46-47 days. Piglets' born from fearful sows were less attracted to human during VHAT2 (Chisq=8.33, P = 0.004) and familiarised piglets were more attracted (Chisq=15.05, P < 0.001). Piglets born from docile sows found the reward faster in a spatial maze test than those born from fearful sows. Both sows HAR and piglet familiarisation with human seemed to specifically affect human related behaviours without affecting their general emotionality, but also behaviour in a spatial maze test. (Mathilde Lanthony) 04 Dec 2023
  • [hal-04092080] Genetic relationships between weight loss in early lactation and daily milk production throughout the lactation in Holstein cows

    After calving, high-yielding dairy cows mobilize body reserves for energy, sometimes to the detriment of health and fertility. This study aimed to estimate the genetic correlation between body weight loss until nadir and daily milk production (MY24) in first-(L1) and second-lactation (L2) Holstein cows. The data set included 859,020 MY24 records and 570,651 daily raw body weight (BWr) phenotypes from 3,989 L1 cows, and 665,361 MY24 records and 449,449 BWr phenotypes from 3,060 L2 cows, recorded on 36 French commercial farms equipped with milking robots that included an automatic weighing platform. To avoid any bias due to change in digestive content, BWr was adjusted for variations in feed intake, estimated from milk production and BWr. Adjusted body weight was denoted BW. The genetic parameters of BW and MY24 in L1 and L2 cows were estimated using a 4-trait random regression model. In this model, the random effects were fitted by second-order Legendre polynomials on a weekly basis from wk 1 to 44. Nadir of BW was found to be earlier than reported in the literature, at 29 d in milk, and BW loss from calving to nadir was also lower than generally assumed, close to 29 kg. To estimate genetic correlations between body weight loss and production, we defined BWL5 as the loss of weight between wk 1 and 5 after calving. Genetic correlations between BWL5 and MY24 ranged from −0.26 to 0.05 in L1 and from −0.11 to 0.10 in L2, according to days in milk. These moderate to low values suggest that it may be possible to select for milk production without increasing early body mobilization. (T. Tribout) 09 May 2023
  • [hal-04229429] Effects of corn silage supplementation strategy and grazing intensity on herbage intake, milk production, and behavior of dairy cows

    Effects of corn silage supplementation on milk production of grazing dairy cows depend in part on the substitution rate between the 2 forages, which may be influenced by grazing management. The aim of this study was to compare 2 grazing management strategies for measuring substitution rate between herbage and corn silage, in interaction with grazing intensity. Six treatments were compared, with 2 grazing intensities and 3 supplementation strategies investigated at both grazing intensities. The 2 grazing intensities were severe and light grazing, defined by either (1) herbage allowance (HA) of 15 (severe) or 30 (light) kg dry matter (DM)/cow per d at 3 cm above ground level or (2) postgrazing sward height, depending on the supplementation strategy. The 3 supplementation strategies were as follows: (U) an unsupplemented treatment, (A) 5 kg DM/d of corn silage offered at a similar HA as in U, and (H) 5 kg DM/d of corn silage offered at a similar postgrazing sward height as in U. Thirty-six multiparous Holstein cows were used in a randomized complete block design and divided in 2 groups for the entire experiment, one for each grazing intensity. Within each grazing intensity group, the corn silage supplementation strategy was studied using a 3 × 3 Greco-Latin square design, with 3 periods of 14 d. Supplementing cows with corn silage increased total DM intake only for severe grazing by 1.7 kg DM/d. The substitution rate between corn silage and grazed herbage was lower for severe than for light grazing, averaging 0.63 and 1.23, respectively. Herbage dry matter intake was lower by 1.2 kg/d for strategy H than A, leading to lower substitution rates (0.81 vs. 0.99, respectively), irrespective of grazing intensity. Milk production increased with silage supplementation for severe grazing (+1.0 kg/d milk) and was unaffected by silage supplementation for light grazing (−0.4 kg/d milk). The milk production response to corn silage supplementation averaged +0.23 and −0.08 kg of milk per kg DM of silage for severe and light grazing, respectively. Fat-corrected milk production tended to be lower by 0.4 kg/d for strategy H than A, leading to lower milk production response (+0.00 vs. +0.12 kg of milk per kg DM of silage, respectively). Milk protein concentration increased with silage supplementation for severe grazing (+1.0 g/kg) but decreased with silage supplementation for light grazing (−0.6 g/kg). Milk fat concentration did not differ among treatments. On average, daily grazing time (−47 min/d, i.e., −9%) and herbage intake rate (−4.9 g of DM/min, i.e., −14%) decreased when cows were supplemented, with greater grazing time reduction at severe than light grazing, and greater herbage intake rate reduction at light than severe grazing. In conclusion, the greater substitution rate and the lower 4% fat-corrected milk production when corn silage was provided at a similar postgrazing sward height rather than at a similar HA to those of unsupplemented cows explain why supplementing grazing dairy cows with conserved forages has no strong effect in practice from a production point of view. (M.F. Miguel) 05 Oct 2023
  • [hal-04177970] Change in fat skatole and indole content in lambs switched from a concentrate-based diet indoors to alfalfa grazing for various durations before slaughter

    Meat from lambs fattened on alfalfa is at risk of excessive pastoral flavours due to high levels of in-fat volatile indolic compounds (especially, skatole). Skatole has also been identified as a potential marker of interest for authenticating pasture-fed lamb meat. Here, we investigated the change in skatole and indole concentrations in kidney fat from lambs switched from an indoor-fed concentrate based diet to outdoor alfalfa grazing for various durations (0, 21, 42, 63 days) before slaughter. The study used a total of 219 lambs over 3 consecutive years. Kidney-fat skatole and indole concentrations increased from as early as 21 days on alfalfa, and then reached a plateau. Similarly, the proportion of lambs that had a kidney fat-skatole concentration above 0.15 μg/g liquid fat, a value that has been established as a sensory rejection threshold for pork, increased significantly from as early as 21 days on alfalfa and then reached a plateau. This value was reached or exceeded in a significant proportion of lambs fattened on alfalfa pastures (45.1%). However, skatole was not detected in kidney fat from 20 out of 164 alfalfa-fattened lambs (i.e., 12.2%) but was detected in 15 out of 55 concentrate-fed lambs (i.e., 27.3%). We thus conclude that while skatole content in kidney fat can inform on dietary changes made shortly before slaughter, it does not have the discrimination power needed to reliably authenticate pasture-fed lamb meat, let alone duration of finishing on pasture. (Sophie Prache) 07 Aug 2023
  • [hal-04170840] Protein signatures of spontaneous lipolysis and lipoprotein lipase activity in cow’s milk

    Spontaneous milk lipolysis refers to the breakdown of triacylglycerols in milk. Lipolysis impacts the organoleptic value of milk by causing off-flavours and reduces the technological properties of milk. Lipolysis is caused by lipoprotein lipase (LPL), a tightly regulated enzyme in milk. Our objective was to identify robust biomarkers of lipolysis and putative regulators of LPL enzyme in bovine milk. To achieve this goal, we used feed restriction as a lever to generate highly contrasted samples with regard to milk lipolysis. We combined statistical methods on proteomics data, milk lipolysis and LPL activity values. Following this strategy, we identified CD5L and GP2 as robust biomarkers of high lipolysis in cow milk. We also identified HID1, SURF4 and CUL9 as putative inhibitors of the lipolytic process in the milk. We thus proposed 5 putative biomarkers to be considered in future tools to manage milk lipolysis. (Mylène Delosière) 08 Sep 2023
  • [hal-04143637] Preservative effects of composite biopreservatives on goat meat during chilled storage: Insights into meat quality, high-throughput sequencing and molecular docking

    To investigate the preservative effect of composite biopreservatives on goat meat during chilled storage, three biopreservatives (chitosan, tea polyphenols and grape seed extract) were selected. Meat samples were soaked in composite biopreservatives at previously optimized concentrations, prior to storage at 4 • C for 12 days. Meat quality parameters including pH, TBARS, TVB-N, color, sensory index and total viable count were evaluated. 16S rDNA high-throughput sequencing combined with bioinformatics was used to assess the changes in the bacterial community, while molecular docking permitted the investigation of molecular interaction between gyrase, catechins, and anthocyanins. Treatment by composite biopreservatives contributed to the stability and maintenance of meat quality, notably by significantly reducing TBARS and maintaining meat color and sensory scores. Pseudomonadales, Bacillales and Flavobacteriales were effectively inhibited as the main spoilage bacteria in goat meat during chilled storage. Molecular docking revealed that catechins and anthocyanins could bind to DNA gyrase by hydrogen bonds and hydrophobic interactions, thus inhibiting DNA synthesis and bacterial growth. Hence, the composite biopreseratives exerted a preservative impact on the chilled goat meat. (Jin Wang) 27 Jun 2023
  • [hal-04290811] A three year comparison of once-a-day and twice-a-day milking in a seasonal calving pasture-based systems

    Globally, the majority of dairy cows are milked twice-a-day (TAD), however, in pasture-based production systems such as in Ireland the idea of milking once-a-day (OAD) is being considered for reasons such as improved work life balance. The immediate effects within a lactation, as well as the multi-lactation consequences of OAD, compared with TAD milking, require understanding. The objective of this randomized experiment was to compare OAD and TAD milking, over a 3 year period, by examining the differences in milk production and composition, bodyweight, body condition score, dry matter intake, udder characteristics, locomotion score and milking time. Over the 3 years 83 cows were enrolled in the experiment; 32, 44 and 48 cows in years 1, 2 and 3 of the experiment, respectively. Each year 23% of the herd were primiparous animals, while the remainder were second lactation or greater in parity. All cows were milked in the morning at 07:00, only cows milked TAD were milked a second time each day at 16:00. Cows rotationally grazed pastures for the duration of the lactating period and were housed during the nonlactating period. Milking cows OAD reduced cumulative milk yield by 26% and milk solids yield (kg fat + kg protein) by 21%, across the 3 years of the experiment when compared with cows milked TAD which produced 4126 and 365 kg/cow, respectively. A contributory factor to the reduced production was a shorter lactation length (9.7 d) of the cows milked OAD compared with TAD (294 d). Milk fat % of cows milked TAD was similar for all 3 years of the study (5.05%) while milk fat % of the cows milked OAD increased year on year, with each year being greater than the previous year (5.02, 5.32 and 5.70% for year 1, 2 and 3; respectively). Milk protein % was greater (+0.19%) for cows milked OAD compared with TAD which was 3.78%. Compared with cows milked TAD, total dry matter intake for cows milked OAD was 22% less at the start of lactation (<167 d), but as the lactation progressed (>167 d) there was no difference in DMI between treatments. Similar to the literature milking cows OAD significantly increased average SCS; both during (+16%) and at the end of lactation (+19%), compared with milking cows TAD which were 4.69 and 4.79, respectively. There were positive aspects associated with OAD milking such as greater bodyweight, body condition score and fertility performance. Milking OAD reduced both milking time per cow per day (reductions ranged from 34% in first 4 mo of lactation to 43% during mo 5 to 9 of lactation) and milking time per liter of milk (-3.5 s/liter) throughout lactation leading to less labor inputs on farm which can have positive implications for farmer work life balance. The significant time saving and potential savings in costs (e.g., electricity) need to be considered in conjunction with the milk production reduction when considering OAD milking for the entire lactation. (John Paul Murphy) 17 Nov 2023
  • [hal-04068634] Effect of live yeast supplementation and feeding frequency in male finishing pigs subjected to heat stress

    In growing pigs, reduced growth during heat stress (HS) is mainly related to decreased feed intake. The study aimed to determine whether the reported positive effects of live yeast (LY) supplementation in HS pigs were due to a modified feeding behaviour or energy metabolism, and if these can be replicated by imposing an increased meal frequency. The effect of LY supplementation (0 (NS) v . 100 (LY) g/ton of feed), and of feeding window (FW) (unlimited or Unli, 2FW of 1 h each and 8FW of 15 min each) were measured in entire male finishing pigs ( n 36). Ambient temperature was at 22°C during the thermoneutral (TN) period (5 d) and at 28°C during the HS period (5 d). Heat exposure decreased DM intake (DMI) and retained energy (RE) (–627 and −460 kJ·kg BW –0·60 · d –1 , respectively; P < 0·01). During HS, LY supplementation in Unli pigs decreased inter-meal intervals ( P = 0·02) attenuating HS effect on DMI which tended to improve RE ( P = 0·09). NS – 8FW had higher DMI and RE than NS – 2FW ( P < 0·05) but protein deposition (PD) were similar. Supplemented pigs had higher PD during HS regardless of FW (+18 g · d –1 ; P = 0·03). Comparing the 2FW groups, improved heat tolerance of LY-supplemented pigs were due to improved insulin sensitivity ( P < 0·05) and latent heat loss capacity after a meal ( P < 0·05) allowing them to increase their DMI (via an increased number of meals) and thus their energy efficiency. Imposing an increased meal frequency improved DMI in HS pigs but did not replicate positive effects of LY on PD. (Aira Maye Serviento) 14 Apr 2023
  • [hal-04011704] Nest preference and laying duration traits to select against floor eggs in laying hens

    Background: Floor eggs, which are defined as eggs that hens lay off-nest, are a major issue in cage-free layer poultry systems. They create additional work for farmers because they must be collected by hand. They are also usually soiled or broken, which results in economic losses. Nonetheless, knowledge about the genetics of nesting behavior is limited. The aim of this study was to estimate genetic parameters for traits related to nest preference for laying and to time spent in the nests used for laying (laying duration). Methods: Two pure lines of laying hens were studied: 927 Rhode Island Red and 980 White Leghorn. Electronic nests were used to record the nesting behavior of these hens in floor pens from 24 to 64 weeks of age. Nest preference was studied based on the mean distance between nests used for laying and the percentage of nests used for laying. Laying duration was studied based on mean laying duration, mean duration in the nest before laying, and mean duration in the nest after laying. Genetic parameters were estimated for each line using a restricted maximum-likelihood method applied to a pedigree-based multi-trait animal model. Results: Estimates of genetic parameters were similar for the two lines. Estimates of heritability ranged from 0.18 to 0.37 for nest preference traits and from 0.54 to 0.70 for laying duration traits. Estimates of genetic correlations of these traits with clutch number or mean oviposition time were favorable. Positive genetic correlations were estimated between nest preference and laying rate in the nests or nest acceptance for laying (+ 0.06 to + 0.37). Conclusions: These results show that genetics influences traits related to nest preference and laying duration. Selecting hens that have no preference for particular nests and spend little time laying in the nests could help optimize nest use, reduce their occupation rate, and thus decrease the incidence of floor eggs in cage-free systems. Genetic correlations of these traits with other traits of interest related to hen welfare and egg quality have yet to be estimated. (Lorry Bécot) 02 Mar 2023
  • [hal-04047138] Can a urease inhibitor improve the efficacy of nitrogen use under perennial ryegrass temperate grazing conditions?

    This study sought to compare the efficiency of different nitrogen (N) fertilizer forms applied to perennial ryegrass swards that were rotationally grazed by dairy cows or sheep under Irish conditions for two or three years. A 3 × 2 factorial random complete block design plot arrangement was used to compare calcium ammonium nitrate (CAN), urea and urea + N-(n-butyl) thiophosphoric triamide (urea + NBPT) at 150 and 250 kg N/ha per year. Zero nitrogen plots were also added to allow for N efficiency to be calculated. The study was conducted at four sites, giving three years of data collection at two sites and two years at the other two sites. All four sites observed similar responses to N fertilizer type and N fertilizer rate. Significant differences were observed between the 150 kg N/ha and 250 kg N/ha treatments for pre-grazing herbage yield (1346 and 1588 kg DM/ha, respectively; P < 0.001) and total herbage production (12 290 and 14 448 kg DM/ha, respectively; P < 0.001). There was no difference but a tendency for pre-grazing herbage yield to be higher for CAN and urea + NBPT than urea (1485, 1480 and 1436 kg DM/ha, for CAN, urea + NBPT and urea, respectively; P = 0.091). Total herbage production was significantly higher for CAN and urea + NBPT than urea (13 478, 13 542 and 13 087 kg DM/ha, respectively; P = 0.004). In conclusion, there was an overall benefit detected over the 10 site-years from using urea protected with NBPT v. using urea. (Áine Murray) 27 Mar 2023
  • [hal-04279631] Nitrogen balance in dairy cows fed low-nitrogen diets based on various proportions of fresh grass and maize silage

    To ensure sustainable and efficient production, dairy farms must reduce their environmental impacts and nitrogen losses, which are sources of pollution, while increasing their feed self-sufficiency. Grass-based dairy systems, frequently combine fresh grass with maize silage when grass is scarce or during dietary transitions. However, the effects of combining fresh grass and maize silage on cow performance and N excretion are poorly known. This study aimed to quantify the effects of increasing the proportion of maize silage in a fresh grass diet on cow N flows and metabolism, in the context of grass-based dairy systems. Four proportions of maize silage in a fresh grass diet (objectives of 0, 17, 34 and 51% DM of maize silage) were investigated. The experiment was performed in a 4 × 3 Latin square design using eight lactating cows during three 3-week periods. DM intake (DMI), milk yield, faeces and urine outputs, and their N concentrations were measured for each cow. The fresh grass CP concentration was lower than planned (106 ± 13.0 g/kg DM). This resulted in very low dietary CP concentration, which decreased from 108 to 86 g/kg DM when maize silage in the diet increased from 0 to 51% DM, respectively. DM intake and milk yield both decreased linearly by 3.3 kg/day from 0 to 51% DM of maize silage in the diet. Thus, N intake decreased linearly by 100 g/day from 0 to 51% DM of maize silage in the diet. The N concentration of milk was highest for the diet with 0% DM of maize silage. Nitrogen excreted in faeces and urine decreased linearly by 29 and 23 g/day, respectively, from 0 to 51% DM of maize silage in the diet. The low dietary N concentration resulted in low ruminal NH3-N concentrations (8 mg/L, on average) and urinary urea excretion (down to 8% urea N in urinary N). Increasing the proportion of maize silage in an unusually low-N grass diet, without protein-rich concentrates, induced highly N-deficient diets with minimal N losses in faeces and urine but large and unsustainable decreases in DMI and milk yield. (M. Ferreira) 28 Feb 2024
  • [hal-04346676] Devenir des jeunes ruminants laitiers : comment concilier élevage et attentes sociétales

    Dans les conditions naturelles, les jeunes ruminants développent un lien privilégié avec leur mère dans les heures qui suivent la naissance, lien qui perdure bien au-delà de l’allaitement. Or, sur les 5,5 millions de jeunes ruminants (veaux, chevreaux et agneaux) qui naissent chaque année en France dans des élevages laitiers, la grande majorité sont séparés de leur mère à la naissance et allaités « artificiellement » au seau. La séparation mère-jeune précoce interpelle les citoyens et certains éleveurs quant au respect du bien-être de l’animal. L’allaitement artificiel des femelles de renouvellement jusqu’au sevrage permet d’assurer, à un coût maîtrisé, un développement mammaire optimal et un bon potentiel laitier. Cependant, l’allaitement par les mères ou par des nourrices se développe, principalement en élevage bovin. Ce type d’allaitement entraîne généralement des quantités de lait commercialisables moindres, mais la croissance, la santé et le bien-être des veaux sont améliorés. Des questions se posent aussi sur le devenir des jeunes, mâles pour l’essentiel, non conservés pour le renouvellement du troupeau. Ceux-ci quittent généralement l’élevage quelques semaines après la naissance pour être engraissés dans des ateliers spécialisés, voire exportés. Là aussi, afin de répondre aux nouvelles attentes des consommateurs et pallier le faible intérêt économique de ces débouchés, éleveurs et filières recherchent des solutions alternatives telles que l’engraissement à la ferme, de nouveaux modes d’élevage ou de nouveaux débouchés. Ces pratiques alternatives – allaitement naturel ou engraissement sur place des jeunes mâles – pourraient se développer grâce à une identification de leurs produits (lait, viande) et au consentement du consommateur à les payer plus cher que des produits standards. (Dominique Pomiès) 15 Dec 2023
  • [hal-04068768] Proteomic approaches to characterize biochemistry of fresh beef color

    Color of retail fresh beef is the most important quality influencing the consumers' purchase decisions at the point of sale. Discolored fresh beef cuts are either discarded or converted to low-value products, before the microbial quality is compromised, resulting in huge economic loss to meat industry. The interinfluential interactions between myoglobin, small biomolecules, proteome, and cellular components in postmortem skeletal muscles govern the color stability of fresh beef. This review examines the novel applications of high-throughput tools in mass spectrometry and proteomics to elucidate the fundamental basis of these interactions and to explain the underpinning mechanisms of fresh beef color. Advanced proteomic research indicates that a multitude of factors endogenous to skeletal muscles critically influence the biochemistry of myoglobin and color stability in fresh beef. Additionally, this review highlights the potential of muscle proteome components and myoglobin modifications as novel biomarkers for fresh beef color. (Surendranath Suman) 08 Sep 2023
  • [hal-04126195] In-depth characterization of myofibrillar muscle proteome changes in lambs fed hazelnut skin by-products

    This study investigated the effect of hazelnut skin by-products supplementation on lamb myofibrillar proteome changes during post-mortem storage (0, 4, and 7 days). Gel-based proteomics and bioinformatics approaches were applied to reveal the underlying biochemical pathways and their importance in lamb meat texture development. Twenty-two Valle del Belice male lambs were randomly assigned to two dietary treatments: control (C) for lambs fed with maize-barley diet, and hazelnut skin (H) for lambs fed hazelnut skin by-product as maize partial replacer in the concentrate diet (150 g/kg DM basis). A greater myofibrillar fragmentation index (MFI) was found in meat from the C group at day 0 of storage (91.33 vs 98.38 in H and C groups, respectively). Conversely, starting from 4 days of storage, higher MFI values were observed in meat from lambs fed hazelnut skin (113.74 and 116.1 vs 99.28 and 107.26 in H and C groups at 4 and 7 days, respectively). Myofibrillar proteome changes estimated by SDS-PAGE and immunoblotting revealed a degradation of desmin (P<0.01) and troponin T (P<0.001) intact proteins, and an increase in the abundance of the appearing 30 kDa fragment (P<0.001) after 4 days of storage in meat from H than the C group. In-depth proteomics and bioinformatics revealed 44 proteoforms (26 unique proteins), mainly involved in actin filament-based process/cytoskeleton organization, energy metabolism, and heat shock proteins, as the major interconnected pathways impacted by hazelnut by-product feeding strategy on lamb meat quality. Twelve proteins were proposed in this trial as potential biomarkers of lamb meat texture as a consequence of hazelnut skin by-products supplementation. (Antonella Della Malva) 12 Sep 2023
  • [hal-04047303] Evaluating net energy and protein feed conversion efficiency for dairy ruminant systems in France

    Modern systems of animal production are facing increasing challenges on issues such as animal welfare, product quality, and environmental impact. Ruminants in particular are often regarded as being inefficient with respect to feed conversion for both protein and energy. Efficiency is defined as the ratio between resources and production; when applied to dairy production systems, it corresponds to the total amount of feed (kg of dry matter of roughages and concentrates) consumed per kg of milk and meat produced. This ratio underlines the biological ability of dairy cows, ewes, and goats to convert feed into products that are edible by humans while maintaining other physiological functions. Feeds consumed by animals can be “human-edible”, i.e. directly usable for human nutrition (cereals, legumes, maize silage), or not (grasslands, wild grass areas). Calculations of livestock efficiency are strongly influenced by whether or not they consider, and distinguish between, the consumption of human-edible or -inedible plant resources (roughages and concentrates) as well as the production of edible and/or inedible animal products (e.g., milk, meat, wool, leather). An improved understanding of the inedible fraction of both energy and protein in animal feed will be invaluable in analyses of feed-food competition, especially in ruminants. In this study, we investigated the feed conversion efficiency (FCE) of dairy ruminant systems in France (cow, goat, ewe) with respect to both energy and protein. We hypothesized that FCE would be influenced by the composition of the diet and its grass content, as well as, by animal type. Data from a French database (Diapason) provided information on land, labor, herds, and production from 2012 to 2016 for 274 dairy goat farms, 108 dairy ewe farms, and 498 dairy cow farms. These herds consumed feeds that were human-edible (cereals, legumes, maize silage) as well as -inedible (grasslands, wild grass areas). We estimated that French dairy systems are, on average, net consumers of energy and net producers of protein, with higher efficiencies for grass-based systems compared to maize-based systems. At the national scale, average net protein efficiencies were 1.16, 1.12, and 1.88 for ewes, goats, and cows, respectively. These results on the net FCE in dairy systems will promote a more objective quantification of their contribution to food security, which should be taken into account in assessments of feed-food competition and its impact on human nutrition. When combined with other factors such as greenhouse gas emissions and land and resource use, such considerations will help to inform discussions of the future of livestock production. (B. Rouillé) 27 Mar 2023
  • [hal-04040702] A dataset to study group-housed sows' individual behaviours and production responses to different short-term events

    The relational database SOWELL was created to better understand the behaviour and individual responses of gestating sows facing different short-term events induced: a competitive situation for feed, hot and cold thermal conditions, a sound event, an enrichment (straw, ropes and bags available) and an impoverishment (no straw, no objects) of the pen. The data were collected on 102 crossbred sows equipped with activity sensors, group-housed in video-recorded pens (16–18 sows per pen), with access to automatons. Feeding and drinking behaviours were extracted from the electronic feeders and drinkers’ recordings. Social behaviours, physical activities and locations in the pen were recorded thanks to manual video analysis labelling at the individual scale. Accelerometer fixed on the sows’ ears also recorded individual physical activities. The physical activity was also determined at a group scale by automatic video analysis using deep learning techniques. BWs, back fat thickness, and body condition (cleanliness, body damages) were recorded weekly during the whole gestation. Last gestation room data regarding environmental conditions (temperature, humidity, noise level) were recorded using automatic sensors. The database can fulfil different research purposes, namely sows’ nutrition for example to better calculate the energy requirements regarding environmental factors, or also on welfare or health during gestation by providing indicators. (Maëva Durand) 22 Mar 2023
  • [hal-04040968] Effects of a competitive feeding situation on the behaviour and energy requirements of gestating sows

    In groups of gestating sows, accessing feed supply may be a source of tension and induce aggressiveness and fights. Using electronic sow feeders (ESF) could help to ensure that each sow eats its entire ration in a grouphoused pen. The objective of this study was to evaluate the impact of a competitive feeding situation related to the management of the ESF, on the overall behaviour, physical activity, and energy requirements of gestating sows. A total of 32 sows, divided into two groups, were involved in the study. The feed competition was created by closing the access of one of the two feeders available in each gestation room for 5 consecutive days. This situation was repeated twice, each time preceded by one control week during which both feeders were available. Automatons, accelerometers and manual video analysis recorded each sow's feeding, drinking and social behaviour, their physical activity, occupation and location in the pen. Linear mixed effect models were used, including the fixed effects of treatment (feed competition or control), repetition (first or second period), group (2 modalities), social ranking (3 modalities), their interactions, and the random effect of sow. During competitive feeding situations, the number of negative interactions doubled (P < 0.001), the sows spending more time standing in the morning (P < 0.001) and in the areas located further away from the feeder (P = 0.005). The number of and time spent for nutritive visits were not affected by treatment, whereas the number and duration of non-nutritive visits decreased (P < 0.001) during feed competition. This later effect was more marked in low-and high-ranking sows (interaction, P < 0.01). During feed competition sow spent less time sleeping (P < 0.01) and more time exploring the feeder (P < 0.001), these effects being less marked in period 2. The calculated metabolizable energy (ME) requirement, and therefore the quantity of feed required, increased during feed competition (P < 0.001), the effect being greater during the second period than the first (interaction P = 0.04). Moreover, ME requirement was greater for higher compared to lower-ranking sows (P < 0.001). The treatment had no significant effect on body weight and back-fat-thickness, neither on health criteria. To conclude, these results indicate that short-term dysfunction of ESF affect the overall behaviour of sows and increase negative interactions and energy requirements, without affecting their performances or health. (Maëva Durand) 22 Mar 2023
  • [hal-04290823] Cow-level factors associated with nitrogen utilization in grazing dairy cows using a cross-sectional analysis of a large database

    Reducing nitrogen pollution while maintaining milk production is a major challenge of dairy production. One of the keys to delivering on this challenge is to improve the efficiency of how dairy cows utilize nitrogen. Thus, estimating the nitrogen utilization of lactating grazing dairy cows and exploring the association between animal factors and productivity with nitrogen utilization are the first steps to understanding the nitrogen utilization complex in dairy cows. Nitrogen utilization metrics were derived from milk and body weight records from 1,291 grazing dairy cows of multiple breeds and crossbreeds; all cows had sporadic information on nitrogen intake concurrent with information on nitrogen sinks (and other nitrogen sources such as body tissue mobilization). Several nitrogen utilization metrics were investigated, including nitrogen use efficiency (nitrogen output as products such as milk and/or meat divided by nitrogen intake) and nitrogen excreted (nitrogen intake less the nitrogen output as products such as milk and/or meat). In the present study, a primiparous Holstein-Friesian used, on average, 20.6% of the nitrogen it ate, excreting the surplus as feces and urine, representing 402 g N/day. Inter-cow variability existed, with a between cow standard deviation of 0.0094 for nitrogen use efficiency and 24 g N/ day for nitrogen excretion. As lactation progressed, nitrogen use efficiency declined while nitrogen excretion increased. Nevertheless, nitrogen use efficiency improved (i.e., decreased) from first to second parity, even though it did not improve from second to third parity or greater. Furthermore, nitrogen excretion continued to increase from first to third parity or greater. Nitrogen use efficiency and nitrogen excretion were negatively correlated (-0.56 to -0.40), signifying that dairy cows who partition more of the ingested nitrogen into products such as milk and/or meat, on average, also excrete less nitrogen. Milk urea nitrogen was, at best, weakly correlated with nitrogen use efficiency and nitrogen excretion; the correlation were between -0.01 and 0.06. In conclusion, several cow-level factors like parity, stage of lactation, and breed were associated with the range of different nitrogen efficiency metrics investigated; moreover, even after accounting for such effects, 4.8% to 6.3% of the remaining variation in the nitrogen use efficiency and nitrogen balance metrics were attributable to inter-cow differences. (E. Tavernier) 17 Nov 2023
  • [hal-04101365] Prediction of fatty acid composition in intact and minced fat of European autochthonous pigs breeds by near infrared spectroscopy

    The fatty acids profile has been playing a decisive role in recent years, thanks to technological, sensory and health demands from producers and consumers. The application of NIRS technique on fat tissues, could lead to more efficient, practical, and economical in the quality control. The study aim was to assess the accuracy of Fourier Transformed Near Infrared Spectroscopy technique to determine fatty acids composition in fat of 12 European local pig breeds. A total of 439 spectra of backfat were collected both in intact and minced tissue and then were analyzed using gas chromatographic analysis. Predictive equations were developed using the 80% of samples for the calibration, followed by full cross validation, and the remaining 20% for the external validation test. NIRS analysis of minced samples allowed a better response for fatty acid families, n6 PUFA, it is promising both for n3 PUFA quantification and for the screening (high, low value) of the major fatty acids. Intact fat prediction, although with a lower predictive ability, seems suitable for PUFA and n6 PUFA while for other families allows only a discrimination between high and low values. The proportions of fatty acids in pork fat took on a decisive role over the years, both due to the degree of fat unsaturation representing a key factor in the technological quality of processed meat and to the significant influence on qualitative parameters linked to sensory and nutritional profile 1. High quality meat demand of consumers and processing industry is increasing, in particular meat and meat-products derived from local breeds has been growing interest due to the positive perception of their quality products in terms of health and animal welfare 2 . (Silvia Parrini) 19 May 2023
  • [hal-03941229] Pre-weaning social behaviours and peripheral serotonin levels are associated with behavioural and physiological responses to weaning and social mixing in pigs

    In pig production systems, weaning is a major challenge that is usually paired with social mixing and may greatly affect health and welfare of piglets. Research efforts have been devoted to characterising early predictors of weaning adaptation, but have focused mainly on aggressive and harmful behaviours, whereas socio-positive behaviours have been poorly studied. Furthermore, serotonin (5-HT), a neurotransmitter regulating social behaviours, may also be a pertinent predictor of piglets’ adaptation to challenging situations. This study aimed to assess whether social behaviours and blood 5-HT concentration before weaning were associated with behavioural and physiological responses of piglets to weaning. Social interactions (social exploration, aggression, play-fight, locomotor play) of 72 focal piglets from 12 litters were scored continuously for 8 h at 42 days of age. At weaning (d48), focal piglets were allocated to four pens of 33 piglets from six litters. During the two days following weaning (d49-50), social interactions were scored continuously for 6 h per day, and behavioural activities were scored with 6-min instantaneous scan sampling. Blood was sampled one week before (d41) and 24 h after (d49) weaning to measure 5-HT concentrations and health-related variables. Exploration of pen mates represented 55% and 79% of all scored social interactions before and after weaning, respectively, and play was not observed after weaning. Using a multivariate analysis paired with clustering analysis on post-weaning behavioural and physiological responses, we identified three clusters of piglets with distinct profiles of adaption to weaning: unhealthy inactive animals, healthy inactive aggressors and healthy active affiliative animals. Compared to other clusters, unhealthy inactive animals at weaning were characterised by lower levels of social exploration and aggression before weaning (p < 0.05 for both). Furthermore, piglets that explored their pen mates more before weaning were more active (p = 0.03) after weaning, while piglets that were involved in greater number of locomotor play episodes (p = 0.009) or that were less aggressive (p = 0.04) before weaning walked more after weaning. Piglets with higher blood 5-HT concentrations before weaning were less aggressive (p = 0.01) and had greater growth (p = 0.009) after weaning. Pre-weaning aggression was also positively associated with post-weaning lymphocyte count (p = 0.04), and pre-weaning locomotor play with post-weaning hydroperoxide concentration (p = 0.05), a marker of oxidative stress. Our findings suggest that pre-weaning social behaviours and blood 5-HT concentration may be relevant predictors of piglets’ adaptive responses to social mixing at weaning and deserve more research attention. (Caroline Clouard) 17 Jan 2023
  • [hal-04093048] “Cellular agriculture”: current gaps between facts and claims regarding “cell-based meat”

    [...] (Paul Wood) 09 May 2023
  • [hal-04153699] Male reproductive organ weight: criteria for detection of androstenone-positive carcasses in immunocastrated and entire male pigs

    Immunocastration and rearing of entire males (EMs) are sustainable alternatives to surgical castration. However, these animal carcasses have variable risk of boar taint and should be identified at the slaughter line. We aimed to identify a simple and reliable indicator of androstenone-related boar taint by evaluating pelvic urogenital tract weight as a marker of boar-taint animals at the slaughter line. The pelvic urogenital tract, testes, and accessory sex glands of EMs and immunocastrates (ICs) were collected, dissected, and weighed, before colorimetric measurements of testicular tissue. Additionally, GnRH antibody titers and testosterone, androstenone, and skatole levels were determined. Our results showed that 81.8% of EMs had androstenone levels above the risk threshold (>0.5 µg/g fat; EM/Ahigh subgroup), whereas in ICs, the C/Ahigh subgroup with androstenone >0.5 µg/g fat accounted for only 4.3%. Androstenone levels correlated negatively with GnRH antibody titers and positively with testosterone levels and reproductive organ weights. Identification of ICs with androstenone levels above the threshold (IC/Ahigh subgroup) may be achieved via testes or pelvic urogenital tract weight measurements. However, in EMs, the latter is a more reliable parameter. A principal component analysis based on these variables and hierarchical clustering also distinguished the Ahigh from the Alow subgroup, irrespective of IC/EM. The findings highlight the possible use of pelvic urogenital tract weight along with testes weight as a simple, reliable, and efficient morphometric indicator for identifying androstenone-positive carcasses of different sex categories. (Gregor Fazarinc) 06 Jul 2023
  • [hal-04128372] Edito : Les prairies au cœur des systèmes alimentaires circulaires et durables

    La 29ème conférence EGF (European Grassland Federation) s'est tenue à Caen (en juin 2022), la Normandie étant une des grandes régions de prairies et d’élevage d’herbivores en France. Elle était organisée conjointement par INRAE et l'Université de Caen et a accueilli plus de 300 délégués, dont de nombreux jeunes chercheurs, venus de différentes parties de l'Europe et de Pays tiers. (Jean-Louis J.L. Peyraud) 14 Jun 2023
  • [hal-04232676] First comparison of early post-mortem proteomes in two goat muscle types: M. Longissimus thoracis and M. semitendinosus

    This study aimed to characterize and compare the muscle proteomes of goat Longissimus thoracis (LT) and Semitendinosus (ST) muscles taken early post-mortem from young crossbred males. Thanks to a quantitative proteomics approach, 129 differentially expressed proteins (DEPs) were identified. The proteins belong to five interconnected biological pathways: muscle contraction and structure (n = 47), catalytic, metabolism & ATP processes (n = 33), binding and transport (n = 23), oxidative stress and cell redox homeostasis (n = 10), response to stress and protein folding (n = 6). An additional group of miscellaneous proteins (n = 10) grouped proteins playing other functions. The chemometrics analyses allowed clear separations of the muscles and evidenced 14 common proteins (ACTB, ACTN3, TMOD4, TPM3, TNNT1, AK1, AKR1B1, ACAA2, GPI, AGL, DNPEP, RTN4, ATP2A1, and CAVIN4) that could be considered as potential biomarkers. Overall, the study provided the first insights on the differences between goat LT and ST muscles and the basis related to the regulation of the skeletal muscle. Moreover, it resulted that a better understanding of the muscle characteristics would help in developing practices/processes to monitor meat quality and reduce the variations in fresh quality of meat, aged meat, and/or processed goat meat products. (Antonella della Malva) 09 Oct 2023
  • [hal-03797425] A step towards sustainable aquaculture: Multiobjective feed formulation reduces environmental impacts at feed and farm levels for rainbow trout

    Aquaculture is growing to meet the increasing demand for aquaculture products but is not free of environmental impacts. One solution is to improve how feed are formulated, limiting the environmental impact of fish production. Multiobjective (MO) formulation, which aims for a compromise between lower cost and lower environmental impacts, appears to be a promising solution to reduce the environmental footprint of aquaculture production. The objectives of this study were to design an eco-friendly trout feed (ECO-diet) using MO formulation and to compare its zootechnical and environmental performances to those of a commercial feed (C-diet) containing 16% fishmeal and 6.5% fish oil. MO formulation changed the composition of the diet greatly, which decreased environmental impacts of the feed as well as its price. It increased the number of ingredients used but reduced the use of fishmeal and fish oil by half. MO formulation also led to the elimination of soy products, faba bean, and gluten in favour of processed animal co-products that have high protein contents and low climate change impact. Rapeseed oil also disappeared from the ECO-diet due to its major contribution to land use, eutrophication, and acidification and, to a lesser extent, climate change. Overall, the ECO-diet had high digestibility, which differed little from that of the C-diet. Mean fish body weight after 12 weeks of growth did not differ significantly from that obtained with the C-diet, but analysis of fish growth curves indicated that the ECOdiet could lead to lower growth in the long term. This observation was consistent with the significantly lower feed intake in fish fed the ECO-diet. The decrease in impacts observed at the feed level was also observed at the farm level, although less so for eutrophication, non-renewable energy use, and climate change calculated per kg of body weight gain. MO formulation is a useful tool to reduce the environmental footprint of aquaculture production without compromising animal performances or necessarily increasing production cost. (Aurélie Wilfart) 25 Jan 2023
  • [hal-04308364] Évaluer la contribution des élevages de ruminants laitiers français à la production de denrées alimentaires consommables par l’être humain

    Les systèmes laitiers français (vache, chèvre et brebis) présentent une diversité de systèmes alimentaires. Les aliments consommés peuvent être en concurrence avec l’alimentation humaine (céréales, légumineuses à graines, maïs ensilage) ou non (prairies, parcours). Les efficiences énergétiques et protéiques, en brut et en net ont été évaluées. L’approche nette permet de mieux prendre en compte la compétition « feed-food-fuel ». Les systèmes laitiers sont consommateurs nets d’énergie et producteurs nets de protéines pour l’homme, avec de meilleurs résultats en systèmes herbagers. A l’échelle nationale, l’efficience protéique nette est de 1,16 pour les brebis, 1,12 pour les chèvres et 1,88 pour les vaches. L’efficience énergétique nette est respectivement de 0,63, 0,54 et 1,00. Il existe des marges d’amélioration technique dans les trois filières, lesquelles connaissent une variabilité parfois importante. Afin de vulgariser ces résultats, des groupes d’innovation composés de membres des filières et d’éleveurs ont permis de mieux cibler les modalités de communication des principaux résultats du projet ERADAL. En complément, un ensemble de supports a été créé et mis à disposition de chacun tout au long du projet ERADAL. (Benoit Rouillé) 06 Dec 2023
  • [hal-04304335] Small networks of expressed genes in the whole blood and relationships to profiles in circulating metabolites provide insights in inter-individual variability of feed efficiency in growing pigs

    Background Feed efficiency is a research priority to support a sustainable meat production. It is recognized as a complex trait that integrates multiple biological pathways orchestrated in and by various tissues. This study aims to determine networks between biological entities to explain inter-individual variation of feed efficiency in growing pigs. Results The feed conversion ratio (FCR), a measure of feed efficiency, and its two component traits, average daily gain and average daily feed intake, were obtained from 47 growing pigs from a divergent selection for residual feed intake and fed high-starch or high-fat high-fiber diets during 58 days. Datasets of transcriptomics (60 k porcine microarray) in the whole blood and metabolomics (H-1-NMR analysis and target gas chromatography) in plasma were available for all pigs at the end of the trial. A weighted gene co- expression network was built from the transcriptomics dataset, resulting in 33 modules of co-expressed molecular probes. The eigengenes of eight of these modules were significantly (P <= 0.05) or tended to be (0.05 < P <= 0.10) correlated to FCR. Great homogeneity in the enriched biological pathways was observed in these modules, suggesting co-expressed and co-regulated constitutive genes. They were mainly enriched in genes participating to immune and defense-related processes, and to a lesser extent, to translation, cell development or learning. They were also generally associated with growth rate and percentage of lean mass. In the whole network, only one module composed of genes participating to the response to substances, was significantly associated with daily feed intake and body adiposity. The plasma profiles in circulating metabolites and in fatty acids were summarized by weighted linear combinations using a dimensionality reduction method. Close association was thus found between a module composed of co-expressed genes participating to T cell receptor signaling and cell development process in the whole blood and related to FCR, and the circulating concentrations of polyunsaturated fatty acids in plasma. Conclusion These systemic approaches have highlighted networks of entities driving key biological processes involved in the phenotypic difference in feed efficiency between animals. Connecting transcriptomics and metabolic levels together had some additional benefits. (Camille Juigné) 24 Nov 2023
  • [hal-04153227] Molecular mechanisms contributing to the development of beef sensory texture and flavour traits and related biomarkers: Insights from early post-mortem muscle using label-free proteomics

    Beef sensory quality comprises a suite of traits, each of which manifests its ultimate phenotype through interaction of muscle physiology with environment, both in vivo and post-mortem. Understanding variability in meat quality remains a persistent challenge, but omics studies to uncover biological connections between natural variability in proteome and phenotype could provide validation for exploratory studies and offer new insights. Multivariate analysis of proteome and meat quality data from Longissimus thoracis et lumborum muscle samples taken early post-mortem from 34 Limousin-sired bulls was conducted. Using for the first-time label-free shotgun proteomics combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS), 85 proteins were found to be related with tenderness, chewiness, stringiness and flavour sensory traits. The putative biomarkers were classified in five interconnected biological pathways; i) muscle contraction, ii) energy metabolism, iii) heat shock proteins, iv) oxidative stress, v) regulation of cellular processes and binding. Among the proteins, PHKA1 and STBD1 correlated with all four traits, as did the GO biological process ‘generation of precursor metabolites and energy’. Optimal regression models explained a high level (58–71%) of phenotypic variability with proteomic data for each quality trait. The results of this study propose several regression equations and biomarkers to explain the variability of multiple beef eating quality traits. Thanks to annotation and network analyses, they further suggest protein interactions and mechanisms underpinning the physiological processes regulating these key quality traits. (Yao Zhu) 04 Sep 2023
  • [hal-04529459] La contribution des protéines animales aux apports totaux recommandés en protéines. Republication de l'étude publiée dans "The Journal of Nutrition" le 11 juillet 2022, vol. 152 (11): 2514-2525.

    L'évolution vers une alimentation plus végétale, telle que préconisée dans les pays occidentaux, réduirait la contribution des protéines animales aux protéines totales. Une telle réduction pourrait compromettre l'adéquation nutritionnelle de l’alimentation, pas seulement pour les protéines, mais aussi pour les autres nutriments. Utilisant les données d'une enquête alimentaire transversale représentative de la population française, nous avons déterminé, pour 5 sous-populations adultes (i.e. : 1) femmes < 50 ans ; 2) femmes de 50 à 64 ans ; 3) femmes ≥ 65 ans ; 4) hommes < 65 ans ; 5) hommes ≥ 65 ans), le niveau minimal de protéines totales et la contribution minimale de protéines animales aux protéines totales compatibles avec le respect de toutes les recommandations d’apports en nutriments non protéiques. Pour chacune des 5 sous-populations, une optimisation (par programmation linéaire) de son régime moyen observé a été utilisée pour évaluer le niveau minimum de protéines (série de modèles # 1) et la contribution minimale des protéines animales aux protéines totales (série de modèles # 2) compatibles avec le respect de toutes les recommandations basées sur les nutriments (à l'exception des protéines, dont les niveaux ont été analysés a posteriori, en sortie des modèles. Les coûts totaux des régimes modélisés ne devaient pas augmenter par rapport aux régimes observés. Les habitudes alimentaires n'ont été prises en compte que dans l'ensemble de modèles # 2. La quantité minimale de protéines qui était théoriquement compatible avec le respect des recommandations nutritionnelles pour les autres nutriments (série de modèles #1) était inférieure à l'apport minimal recommandé en protéines pour toutes les sous-populations, à l'exception des femmes < 50 ans. Dans la série de modèles # 2, pour les femmes et les hommes de ≥ 65 ans, la diminution de la contribution des protéines animales aux protéines totales en dessous de 55% et 60%, respectivement, a conduit à des niveaux de protéines inférieurs aux niveaux recommandés. Pour les autres sous-populations (femmes < 50 ans, femmes de 50 à 64 ans et hommes < 65 ans), les contributions les plus faibles de protéines anim ales aux protéines totales compatibles avec une alimentation adéquate sur le plan nutritionnel (y compris l'adéquation protéique) étaient de 55%, 50% et 45%, respectivement. (Florent Vieux) 02 Apr 2024
  • [hal-04320566] Estimation of gestating sows’ welfare status based on machine learning methods and behavioral data

    Estimating the welfare status at an individual level on the farm is a current issue to improve livestock animal monitoring. New technologies showed opportunities to analyze livestock behavior with machine learning and sensors. The aim of the study was to estimate some components of the welfare status of gestating sows based on machine learning methods and behavioral data. The dataset used was a combination of individual and group measures of behavior (activity, social and feeding behaviors). A clustering method was used to estimate the welfare status of 69 sows (housed in four groups) during different periods (sum of 2 days per week) of gestation (between 6 and 10 periods, depending on the group). Three clusters were identified and labelled (scapegoat, gentle and aggressive). Environmental conditions and the sows’ health influenced the proportion of sows in each cluster, contrary to the characteristics of the sow (age, body weight or body condition). The results also confirmed the importance of group behavior on the welfare of each individual. A decision tree was learned and used to classify the sows into the three categories of welfare issued from the clustering step. This classification relied on data obtained from an automatic feeder and automated video analysis, achieving an accuracy rate exceeding 72%. This study showed the potential of an automatic decision support system to categorize welfare based on the behavior of each gestating sow and the group of sows. (Maëva Durand) 05 Dec 2023

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Modification date : 23 November 2023 | Publication date : 03 June 2020 | Redactor : Pegase