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16 Apr 2021
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Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production

Understanding the mechanisms behind natural bioactive compounds that can potentially reduce methane production in anaerobic conditions. A case study of Asparagopsis taxiformis

Recommended by ORCID_LOGO based on reviews by Alberto Atzori, Henk van Lingen and 2 anonymous reviewers

Naturally occurring compounds that can reduce methane production in anaerobic conditions have been studied for quite some time as feasible approaches to mitigate methane production in ruminant animals, especially those of commercial importance. Asparagopsis taxiformis (red algae) and Dictyota bartayresii (brown algae) are effective inhibitors of methane synthesis under in vitro anaerobic fermentation systems (Machado et al., 2014) likely because of their high concentration of secondary metabolites that are toxic to the typical rumen microbiota, including protozoa. In addition to phytoplankton (Palmer and Reason, 2009), Asparagopsis contains a high concentration of haloform compounds (e.g., bromoform, chloroform) while Dictyota has a high concentration of isoprenoid terpenes. Despite the economic and biological impact of diverse phytochemicals on reducing methane production in ruminant animals (Tedeschi et al., 2021), haloform compounds’ environmental impact and safety, in particular, are still unclear. In the present study, Munõz-Tamayo and collaborators (2021) listed relevant literature about the impact of A. taxiformis on ruminal methane production.

Concurrent to the understanding of mechanisms and biology behind the reduction of ruminal methane, mathematical models can lead the way to enhance the effectiveness of feeding A. taxiformis under commercial applications. Thus, in the present study, Munõz-Tamayo and collaborators (2021) sought to develop a mathematical model to understand the rumen fermentation changes in vitro experimentation containing extract of A. taxiformis by adapting a previously documented model by Muñoz-Tamayo et al. (2016).

Modeling development, calibration, and evaluation steps should be independent of each other, requiring complete, distinct, and separate databases (Tedeschi, 2006). However, in rare circumstances where such requirements cannot be met because data availability is scarce, the cross-validation technique, when possible, should be considered to assess data dispersion’s effects on model adequacy. In other situations, clear reasoning for failing to do so must be addressed in the paper. In the present paper, Munõz-Tamayo and collaborators (2021) explained the limitations in their modeling efforts were primarily due to the lack of ideal data: “experiments with simultaneous dynamic data of bromoform, volatile fatty acids, hydrogen, and methane.” Regardless of the availability of ideal data, improvements in the conceptual model are warranted to include amino acids and branched-chain fatty acids fermentation dynamics in the rumen and the fluctuations in ruminal pH.

References

Machado L, Magnusson M, Paul NA, Nys R de, Tomkins N (2014) Effects of Marine and Freshwater Macroalgae on In Vitro Total Gas and Methane Production. PLOS ONE, 9, e85289. https://doi.org/10.1371/journal.pone.0085289

Muñoz-Tamayo R, Chagas JC, Ramin M, Krizsan SJ (2021) Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane production. bioRxiv, 2020.11.09.374330, ver. 4 peer-reviewed and recommended by PCI Animal Science. https://doi.org/10.1101/2020.11.09.374330

Muñoz-Tamayo R, Giger-Reverdin S, Sauvant D (2016) Mechanistic modelling of in vitro fermentation and methane production by rumen microbiota. Animal Feed Science and Technology, 220, 1–21. https://doi.org/10.1016/j.anifeedsci.2016.07.005

Palmer CJ, Reason CJ (2009) Relationships of surface bromoform concentrations with mixed layer depth and salinity in the tropical oceans. Global Biogeochemical Cycles, 23. https://doi.org/10.1029/2008GB003338

Tedeschi LO (2006) Assessment of the adequacy of mathematical models. Agricultural Systems, 89, 225–247. https://doi.org/10.1016/j.agsy.2005.11.004

Tedeschi LO, Muir JP, Naumann HD, Norris AB, Ramírez-Restrepo CA, Mertens-Talcott SU (2021) Nutritional Aspects of Ecologically Relevant Phytochemicals in Ruminant Production. Frontiers in Veterinary Science, 8. https://doi.org/10.3389/fvets.2021.628445

Modelling the impact of the macroalgae Asparagopsis taxiformis on rumen microbial fermentation and methane productionRafael Muñoz-Tamayo , Juana C. Chagas, Mohammad Ramin, Sophie J. Krizsan<p>Background: The red macroalgae Asparagopsis taxiformis is a potent natural supplement for reducing methane production from cattle. A. taxiformis contains several anti-methanogenic compounds including bromoform that inhibits directly methanogene...Agricultural sustainability, Animal nutrition modelling, Emissions , Mathematical modelling, Microbial fermentation, Rumen microbiology, Rumen microbiome Luis Tedeschi2020-11-17 06:28:29 View
31 Jan 2020
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OneARK: Strengthening the links between animal production science and animal ecology

When scientific communities intertwine

Recommended by based on reviews by Rowland Raymond Kao, Arata Hidano and 1 anonymous reviewer

Scientific research can be seen by some as a competitive territory: competition of opinions, concepts, publications, competition for funding. Fortunately, it is above all a territory of sharing and cross-fertilization of ideas. It is gradually becoming a territory of productive interdisciplinary collaborations, despite persistent resistance to making borders more permeable [1]. At the crossroads of worlds, many challenges must be met for communities to understand each other, to be able to communicate with one another, and to benefit mutually from scientific interactions [2].

Delphine Destoumieux-Garzon and co-authors [3] propose to stimulate a single Animal Research Kinship (OneARK) to promote the crossing of the scientific communities in animal production and animal ecology. These two communities share many concepts and methods, which, while they are based on marked specificities (natural versus artificial systems), also and above all have common points that need to be explored more closely. Seven concepts of shared interest to improve the resilience and sustainability of animal population systems were explored by the authors: selection, system viability, system management, animal adaptability, inter-individual diversity in systems, agroecology, and animal monitoring.

This foundation stone paves the way for a finer integration between these two communities, which are close and yet distant, and which are slowly getting to know, understand, and recognize each other.

References

[1] Ledford, H. (2015). How to solve the world’s biggest problems. Nature, 525, 308–311. doi: 10.1038/525308a
[2] Knapp, B., Bardenet, R., Bernabeu, M. O., Bordas, R., Bruna, M., Calderhead, B., … Deane, C. M. (2015). Ten simple rules for a successful cross-disciplinary collaboration. PLoS Computational Biology, 11(4), e1004214. doi: 10.1371/journal.pcbi.1004214
[3] Destoumieux-Garzón, D., Bonnet, P., Teplitsky, C., Criscuolo, F., Henry, P.-Y., Mazurais, D., … Friggens, N. (2020). OneARK: Strengthening the links between animal production science and animal ecology. Ver 6 Peer-Reviewed and Recommended by PCI Animal Science. doi: 10.5281/zenodo.3632731

OneARK: Strengthening the links between animal production science and animal ecologyDelphine Destoumieux-Garzón, Pascal Bonnet, Céline Teplitsky, François Criscuolo, Pierre-Yves Henry, David Mazurais, Patrick Prunet, Gilles Salvat, Philippe Usseglio-Polatera, Etienne Verrier and Nicolas Friggens<p>1. Wild and farmed animals are key elements of natural and managed ecosystems that deliver functions such as pollination, pest control and nutrient cycling within the broader roles they play in contributing to biodiversity and to every category...Agricultural sustainability, Animal genetics, Animal welfare, Ecology, Precision livestock farming, Veterinary epidemiology Pauline Ezanno2019-07-05 15:33:21 View
15 Feb 2024
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On-farm hatching and contact with adult hen post hatch induce sex-dependent effects on performance, health and robustness in broiler chickens

The hen, the egg and the chick in conventional and on-farm hatching systems

Recommended by based on reviews by Nicolas Bedere and Anna Olsson

To limit the use of antibiotics in the few days after hatching, it is necessary to improve the robustness of chicks during the early post-hatch period. This can be achieved by ensuring immediate access to feeds, optimizing the implantation and maturation of the microbiota and immune system of each chick, and minimizing exposure of stressors such as transportation. The study conducted by Guilloteau and colleagues (2024) compared the performance and health of chicks raised in conventional hatching systems with those raised in on-farm hatching systems. The authors showed that both systems yielded similar hatching percentage of eggs. Chicks from on-farm hatching systems exhibited higher body weights during the post-hatch period compared to those from conventional hatching, whereas health parameters were not affected by the system. An originality of the study was the examination of the benefits of the presence of an adult hen in hatching systems. The effects on chick traits were interpreted in relation to the hen behavior at hatching and a classification according to maternal or agonistic activities towards the chicks. However, the experimental design did not allow to make statistical correlations between hen behavior pattern and chick traits. Importantly, the presence of a hen decreased the hatching percentage, and this was likely associated with hen aggressiveness in the pen. The presence of the hen deteriorated the quality scores of the chicks in the on-farm hatching system, and increased mortality of chicks at hatching, negatively impacting chick weight gain and feed efficiency during the few days after hatching in both conventional and on-farm hatching systems. Thereafter, the effect of the presence of a hen on chick body weight was different according to the sex of the chicks and the type of hatching system. The presence of a hen did not reduce the parasitic load of the chicks nor improved clinical signs. No specific characterization of the fecal microbiota of the chicks was conducted, preventing the testing whether or not the presence of the hen affected the early implantation and maturation of the chick microbiome. Altogether, the data indicate that on-farm hatching systems are at least equivalent (in terms of health traits, feed efficiency) or even favorable (for faster growth in the early period after hatching) for chicks. Training the hens (considered as foster adults) to the presence of eggs and chicks or selecting hens according to specific activity behavioral patterns could be ways to establish better interactions between hens and chicks. Although the number and type of environmental stressors tested in the experiment differ from those in commercial farms, the article opens new perspectives for alternative hatching and farming practices.

Reference

Guilloteau LA, Bertin A, Crochet S, Bagnard C, Hondelatte A, Ravon L, Schouler C, Germain K, Collin A (2024) On-farm hatching and contact with adult hen post hatch induce sex-dependent effects on performance, health and robustness in broiler chickens. bioRxiv, 2023.05.17.541117. ver. 3 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2023.05.17.541117

 

On-farm hatching and contact with adult hen post hatch induce sex-dependent effects on performance, health and robustness in broiler chickensL. A. Guilloteau, A. Bertin, S. Crochet, C. Bagnard, A. Hondelatte, L. Ravon, C. Schouler, K. Germain, A. Collin<p>To improve the early perinatal conditions of broiler chicks, alternative hatching systems have been developed. On-farm hatching (OFH) with an enriched microbial and stimulating environment by the presence of an adult hen is a promising solution...Animal welfare, Farming systems, Poultry, Veterinary scienceFlorence Gondret2023-05-31 12:56:47 View
09 Feb 2024
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Pig herd management and infection transmission dynamics: a challenge for modellers.

Towards models of infection transmission dynamics

Recommended by based on reviews by Gustavo Machado and 1 anonymous reviewer

Epidemics such as PRRSv-like virus in pig farms has tremendous impact on the competitiveness of swine production. However, its control requires an understanding of the complex interaction between pathogen transmission, disease impact, population dynamics and management. By using mechanistic epidemiological modelling, Sicard et al. (2023) open up a very interesting field of possibilities. This article describes work aimed at assessing the consequences of infections, taking into account the interaction between clinical outcomes and population dynamics. This study shows how this interaction can influence transmission dynamics at the herd level. It highlights the need to further explore this direction, integrating both disease impacts in breeding practices and structural changes in population dynamics, such as pig crossbreeding and grouping methodologies.
The provision of a new tool making it possible to model herd management practices and the transmission of a virus, such as PRRS, in time and space is a major contribution to understanding the dynamics of this category of diseases. It opens up the possibility of being able to represent specific herd structures and evaluate transmission dynamics using real data. This work improves our understanding of disease spread across herds, taking into account herd management.

Reference

Sicard V, Picault S, Andraud M (2023) Pig herd management and infection transmission dynamics: a challenge for modellers. bioRxiv, 2023.05.17.541128. ver. 2 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2023.05.17.541128

 

 

 

 

 

Pig herd management and infection transmission dynamics: a challenge for modellers.Vianney Sicard, Sébastien Picault, Mathieu Andraud<p>The control of epidemics requires a thorough understanding of the complex interactions between pathogen transmission, disease impact, and population dynamics and management. Mechanistic epidemiological modelling is an effective way to address t...Animal epidemiology modelling, Animal health, Bioinformatics, Farming systems, Infectious diseases, Mathematical modelling, Open science, Population dynamics, Veterinary epidemiology Marie-Pierre Letourneau Montminy2023-05-22 15:07:37 View
06 Feb 2025
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Preferred livestock interventions for small-scale farmers in the Great Limpopo Transfrontier Conservation Area: a demand-driven and participatory approach

What kind of livestock interventions are relevant for small-scale farmers in Great Limpopo Transfrontier Conservation Area?

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The predominant form of agriculture in sub-Saharan Africa is mixed crop and livestock production, typically in extensive systems characterised by low productivity and little input (Tui et al., 2021). Such extensive systems experience many challenges, including access to rangeland and other sources of livestock feed, loss of soil quality, increasingly unpredictable climate but also operational constraints such as access to markets and veterinary care.

The work by Gobvu and collaborators (2025) addresses livestock farming sustainability specifically in the context of a Transfrontier Conservation Area (TFCA). A TFCA is defined as part of an ecological region reaching across boundaries of two or more countries and in which there are protected areas as well as resource use areas. TFCAs are founded to facilitate collective management of resources for the benefit of biodiversity as well as socio-economic development (SADC, 2025).

Livestock farming in TFCAs face additional challenges arising from the tension between biodiversity protection and resource use, such as wildlife predation on livestock, competition between livestock and wildlife for feed and water as well as spread of infections between livestock and wild animals (Matseketsa et al., 2019; Caron et al., 2013; Cumming, 2011).

The paper reports a study that was part of a larger project (EU-ProSuLi project, Caron et al.,  2022) aiming at promoting local development and well-being of residents in the Great Limpopo TFCA, with focus on the Sengwe Communal Area in Zimbabwe. The specific aim was to test a methodology for identifying interventions that are aligned with the needs of the local stakeholders (demand-driven interventions. Anticipatory scenario building in the context of workshops was used in combination with individual questionnaires.

Community representatives (n=31) were purposefully selected for their expected ability to act as knowledge brokers. A team of 10 facilitators supported the discussion through plenary and group work sessions. The participants were asked to identify factors of change with impact on local community livelihood, and subsequently to vote to select the most influential factors. Different future states for the year 2038, resulting from the impact of the factors of change, were discussed. In a follow-up workshop, participants were asked to propose activities that would support the development towards the most desirable scenario. In addition, a questionnaire was distributed through semi-structured/structured interviews to 126 households in nine villages.

Results were largely similar and complementary between the two approaches. Preferred interventions were: restocking herds with locally adapted breeds, training in livestock management, marketing support, feed development and value addition, loan schemes for investment in livestock production and support for animal health interventions to reduce the heavy disease burden. Whereas the participatory process is time consuming and requires considerable human resources, it is important to ensure locally relevant interventions are chosen, and it is in itself part of the process towards successful implementation of these interventions.

The study is thoughtfully designed based on previous work by the authors. The paper is well written and has been further improved through the reviewer feedback and revision process.

References

Caron, A., Miguel, E., Gomo, C., Makaya, P., Pfukenyi, D.M., Foggin, C., Hove, T. and de Garine-Wichatitsky, M., 2013. Relationship between burden of infection in ungulate populations and wildlife/livestock interfaces. Epidemiology & Infection, 141 (7), pp.1522-1535. https://doi.org/10.1017/S0950268813000204

Caron, A., Mugabe, P., Bourgeois, R., Delay, E., Bitu, F., Ducrot, R., Fafetine, J., Fynn, R., Guerbois, C., Motsholapheko, M. and Daré, W., 2022. Social-ecological System Health in  Transfrontier Conservation Areas to Promote the Coexistence Between People and Nature. One Health Cases. https://doi.org/10.1079/onehealthcases.2022.0005 

Cumming, D. H. M. 2011. Constraints to conservation and development success at the wildlife-livestock-human interface in southern African transfrontier conservation areas: a preliminary review. Wildlife Conservation Society, New York.  http://www.wcs-ahead.org/workinggrps_kaza.html

Gobvu, V. Ncube, S. Imbayarwo-Chikosi, V.E., Bourgeois, R. Mugabe, P.H. and Caron A. 2025. Preferred livestock interventions for small-scale farmers in the Great Limpopo Transfrontier Conservation Area: a demand-driven and participatory approach. HAL, ver.5 peer-reviewed and recommended by PCI Animal Science. https://hal.science/hal-04060712

Matseketsa, G., Muboko, N., Gandiwa, E., Kombora, D.M. and Chibememe, G., 2019. An assessment of human-wildlife conflicts in local communities bordering the western part of Save Valley Conservancy, Zimbabwe. Global Ecology and Conservation, 20, p.e00737. https://doi.org/10.1016/j.gecco.2019.e00737 

Tui, S.H.K., Descheemaeker, K., Valdivia, R.O., Masikati, P., Sisito, G., Moyo, E.N., Crespo, O., Ruane, A.C. and Rosenzweig, C., 2021. Climate change impacts and adaptation for dryland farming systems in Zimbabwe: a stakeholder-driven integrated multi-model assessment. Climatic Change, 168 (1-2), p.10. https://doi.org/10.1007/s10584-021-03151-8 

South African Development Community. 2025. Transfrontier Conservation Areas.  . Consulted 7 January 2025. https://www.sadc.int/pillars/transfrontier-conservation-areas

 

Preferred livestock interventions for small-scale farmers in the Great Limpopo Transfrontier Conservation Area: a demand-driven and participatory approachVimbai Gobvu, Sharai Ncube, Venancio E. Imbayarwo-Chikosi, Robin Bourgeois, Prisca H. Mugabe, Alexandre Caron<p>In southern Africa, residents of Transfrontier Conservation Areas (TFCAs), devoted to biodiversity &nbsp;conservation and local development and well-being, practice small-scale farming in semi-arid environments constrained by the presence of pr...Agricultural sustainability, Cattle productionAnna Olsson2023-04-06 12:54:58 View
20 Dec 2021
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Quantifying growth perturbations over the fattening period in swine via mathematical modelling

An innovative modelling approach to enhance the quality of the quantification of pig resilience during the entire fattening period: Towards an individual pig resilience index

Recommended by ORCID_LOGO based on reviews by Arata Hidano, Ludovic Brossard and 2 anonymous reviewers

The identification of reliable estimates of growth potential and resilience over the fattening period in large populations is a challenge in actual swine breeding conditions. To overcome this drawback, the study by Revilla et al. 2021 in the frame of precision livestock farming aimed to propose an innovative modelling approach, in addition to previous studies from the same group (Revilla et al. 2019), to enhance the quality of the quantification of pig resilience during the entire fattening period. 

The authors developed a model that quantifies an “individual pig resilience indicator” based on longitudinal data, for instance body weight, recorded routinely by a commercially available automatic feeding system. Revilla and co-workers considered in their study two mainly commercialised pure pig breeds these being Piétrain including Piétrain Français NN Axiom line (Pie NN) free from halothane-sensitivity (ryanodine receptor gene, RYR1) and Piétrain Français Axiom line positive to this gene and Duroc. Therefore, the authors investigated the potential of improving resilience of swine livestock through inclusion for the first time of an “individual pig resilience indicator” in breeding objectives. A database of 13 093 boars (approximately 11.1 million of weightings) belonging to Pie (n= 5 841), Pie NN (n = 5 032) and Duroc (n= 2 220) finished under ad libitum feeding, high sanitary level and controlled temperature was used to develop robust models.

The authors checked the three datasets (for each pig breed)​ independently to explore the variation and gaps (a data pre-treatment procedure) to ensure high quality data for the modelling approach. Then, they applied the Gompertz model and linear interpolation on body weight data to quantify individual deviations from the expected production, allowing the creation of the ABC index. For the modelling, the authors applied a two-step mathematical model approach by first establishing a theoretical growth curve of each animal, while the second step aimed to build the actual perturbed growth curve. The heritability of the index ranged from 0.03 to 0.04, with similar heritability between Piétrain and Duroc breeds. Moreover, moderate genetic relationships were computed between the proposed index and important phenotypic traits in swine production likely BF100: backfat thickness at 100kg; LD100: longissimus dorsi thickness at 100kg; ADG: average daily gain during control and FCR: feed conversion ratio.

Developing models able to capture perturbations during the fattening period is a challenge in swine breeding industry. The model and methodology proposed by the authors in this innovative work (although preliminary and with low heritabilities) would help overcome such limit and facilitate a real implementation at large scale in pig breeding system. The modelling approach further offers an opportunity to develop a selection criterion to improve resilience in swine breeding conditions. 

To explore the full potential of this modelling approach, a larger database and other factors such as breed, behaviour and feeding behaviour of the animals, rearing practices, management and environment conditions, age… etc. are worthy to consider. In the future, more in depth measurements of behaviour that can be computed for example using computer vision should be desirable to increase the robustness of the proposed model.

References

Revilla, M., Friggens, N.C., Broudiscou, L.P., Lemonnier, G., Blanc, F., Ravon, L., Mercat, M.J., Billon, Y., Rogel-Gaillard, C., Le Floch, N. and Estellé, J. (2019). Towards the quantitative characterisation of piglets’ robustness to weaning: a modelling approach. Animal, 13(11), 2536-2546. https://doi.org/10.1017/S1751731119000843 

Revilla M, Lenoir G, Flatres-Grall L, Muñoz-Tamayo R, Friggens NC (2021). Quantifying growth perturbations over the fattening period in swine via mathematical modelling. bioRxiv, 2020.10.22.349985, ver. 5 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.1101/2020.10.22.349985 

Quantifying growth perturbations over the fattening period in swine via mathematical modellingManuel Revilla, Guillaume Lenoir, Loïc Flatres-Grall, Rafael Muñoz-Tamayo, Nicolas C Friggens<p>Background: Resilience can be defined as the capacity of animals to cope with short-term perturbations in their environment and return rapidly to their pre-challenge status. In a perspective of precision livestock farming, it is key to create i...Animal genetics, Animal health, Farming systems, Mathematical modelling, Precision livestock farmingMohammed Gagaoua 2020-10-26 11:47:08 View
07 Feb 2022
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Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait

Measuring resilience in farm animals: theoretical considerations and application to dairy cows

Recommended by ORCID_LOGO based on reviews by Ian Colditz and 2 anonymous reviewers

Farm animals differ in their ability to respond to the many environmental challenges they face. Such challenges include infectious diseases, metabolic diseases resulting from inadequate coverage of dietary needs, as well as the diverse consequences of climate change. Various concepts exist to characterise the responses of animals to different types of challenges. This article by Friggens et al. (2022) focuses on resilience, providing a conceptual definition and proposing a method to quantify resilience in dairy cows.

The first part of the paper provides a definition of resilience and highlights its differences and relations with the related concepts of robustness, and, to a lesser extent, resistance and tolerance. In essence, resilience is the ability of an animal to bounce back quickly after a challenge of limited duration. On the other hand, robustness is the ability of an animal to cope with conditions that are overall unfavourable. From these conceptual and intuitive definitions, there are several difficulties precluding the design of concrete methods to measure resilience. First, there is some degree of overlap between the concepts of resilience, robustness, resistance and tolerance. Secondly, resilience is a multidimensional concept whereby resilience to a given perturbation does not imply resilience to other types of perturbation, e.g. resilience to a challenge by a specific pathogen does not imply resilience to a nutritional challenge. A further difficulty in the measure of resilience is the fact that different animals may be exposed to challenges that are different in nature and in number. The authors argue that although resilience cannot be measured directly (it should be seen as a latent construct), it is possible to quantify it indirectly through its consequences.

In the second part of the paper, the authors propose a method to quantify resilience of individual dairy cows. The method is based on the premise that resilient animals should be kept longer in their herd than non-resilient animals. The main criterion in the evaluation is therefore the ability of cows to re-calve. Each cow that is calving receives a certain number of points, to  which, in each lactation, bonus points are added for higher milk production and penalty points are removed for each insemination after the first one, for each disease event and for each day of calving interval above some herd specific value. Therefore, cows have a resilience score in each lactation. They also have a lifetime resilience score obtained by summing the scores for all the lactations, that gets bigger as the cow has more calves, and that also takes the age at first calving into account. In a previous study, Adriaens et al. (2020) showed that higher resilience scores were associated with fewer drops in milk yield and more stable activity dynamics.

Starting from theoretical considerations on the notion of resilience, this paper describes a concrete method to quantify animal-level resilience on farm. Such quantification will be useful for breeding and culling decisions. Finally, the general framework to design resilience measures that is presented will be useful to researchers working on the quantification of farm animal resilience using new methods and data sources.

 

References

Adriaens I, Friggens NC, Ouweltjes W, Scott H, Aernouts B and Statham J 2020. Productive life span and resilience rank can be predicted from on-farm first-parity sensor time series but not using a common equation,  across farms. Journal of Dairy Science 103, 7155-7171.https://doi.org/10.3168/jds.2019-17826

Friggens, N.C. , Adriaens, I., Boré, R., Cozzi, G., Jurquet, J., Kamphuis, C., Leiber, F., Lora, I., Sakowski, T., Statham, J., De Haas, Y. (2022). Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this trait. Zenodo, 5215797, ver. 5 peer-reviewed and recommended by Peer community in Animal Science. https://dx.doi.org/10.5281/zenodo.5215797

Resilience: reference measures based on longer-term consequences are needed to unlock the potential of precision livestock farming technologies for quantifying this traitFriggens, N. C., Adriaens, I., Boré, R., Cozzi, G., Jurquet, J., Kamphuis, C., Leiber, F., Lora, I., Sakowski, T., Statham, J. and De Haas, Y.<p style="text-align: justify;">Climate change, with its increasing frequency of environmental disturbances puts pressures on the livestock sector. To deal with these pressures, more complex traits such as resilience must be considered in our mana...Precision livestock farmingAurélien Madouasse2021-08-20 15:34:13 View
04 Apr 2025
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Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic lines

Advancing sustainable aquaculture: behavioral insights for climate-change resilient fishes

Recommended by ORCID_LOGO based on reviews by 2 anonymous reviewers

The study by Lagarde et al. (2025) is part of efforts aiming to meet the challenges of adapting livestock farming, and more specifically of aquaculture, to the effects of climate change. In fact, during heat waves, water temperatures rise and oxygen becomes scarce. Fish have to adapt to these conditions of hyperthermia and hypoxia. Studies have already shown that it is possible to genetically improve these resistances in salmonids (e.g. Debes et al., 2021). However, current methods for phenotyping these resistances rely on exposing fish to extreme conditions until they lose equilibrium, which indicates that the animal experiences severe conditions and raises ethical and animal welfare concerns.

From the aforementioned, there is then a strong interest in using and identifying less invasive phenotypes, such as behavioural changes, that could serve as indicators of fish responses to hyperthermia and hypoxia. Some behaviours show promise in both wild (Campos et al., 2018) and farmed fish (Van Raaij et al., 1996). A former study by the authors of this manuscript suggests that some of these behaviours are sufficiently heritable to consider applying selection on them (Lagarde et al., 2023). Therefore, the main aim of the present study was to test whether behaviour can be used as an indirect selection criterion to improve the adaptation of rainbow trout to heat waves. To achieve this lofty goal, the responses of different isogenic lines of trout to hyperthermia and hypoxia were investigated using new criteria based on behavioural responses and the reference measure of loss of equilibrium.

The results suggest that certain behavioural traits, such as distance travelled and frequency of zone changes, are associated with resistance to these stresses. Moreover, moderate correlations were observed between certain behavioural variables and resistance to hyperthermia. Indeed, lines that were more resistant to hyperthermia had lower distance travelled and frequency of zone changes during the behavioural test. Other significant and positive correlations were observed between acute hypoxia resistance and certain behavioural variables, likely distance travelled, frequency of zone change and percentage of time spent moving.

These results pave the way for less invasive methods in assessing hyperthermia and hypoxia resistance based on behavioural observations, which could improve the resistance of farmed fish in response to climate change. The study further allows refining the measurements carried out on candidates for selection in order to improve their welfare during evaluation tests.

In conclusion, this study is commendable for its thematic relevance, originality and the potential application of its results to genetic selection of farmed fish.

 

References

Campos DF, Val AL, Almeida-Val VMF. 2018. The influence of lifestyle and swimming behavior on metabolic rate and thermal tolerance of twelve Amazon forest stream fish species. Journal of Thermal Biology 72:148–154. https://doi.org/10.1016/j.jtherbio.2018.02.002

Debes P V., Solberg MF, Matre IH, Dyrhovden L, Glover KA. 2021. Genetic variation for upper thermal tolerance diminishes within and between populations with increasing acclimation temperature in Atlantic salmon. Heredity 127:455–466. https://doi.org/10.1038/s41437-021-00469-y

Lagarde H, Phocas F, Pouil S, Goardon L, Bideau M, Guyvarc’h F, Labbé L, Dechamp N, Prchal M, Dupont-Nivet M, Lallias D. 2023. Are resistances to acute hyperthermia or hypoxia stress similar and consistent between early and late ages in rainbow trout using isogenic lines? Aquaculture 562:738800. https://doi.org/10.1016/j.aquaculture.2022.738800

Lagarde H, Lallias D, Phocas F, Goardon L, Bideau M, Guyvarc'h F, Labbé L, Dupont-Nivet M, Cousin X. 2025. Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic lines. bioRxiv, ver.4 peer-reviewed and recommended by PCI Animal Science https://doi.org/10.1101/2023.10.19.563047

Van Raaij MTM, Pit DSS, Balm PHM, Steffens AB, Van Den Thillart GEEJM. 1996. Behavioral strategy and the physiological stress response in rainbow trout exposed to severe hypoxia. Hormones and Behavior 30:85–92. https://doi.org/10.1006/hbeh.1996.0012

Screening for links between behaviour and acute hyperthermia and hypoxia resistance in rainbow trout using isogenic linesHenri Lagarde, Delphine Lallias, Florence Phocas, Lionel Goardon, Marjorie Bideau, Fanch' Guyvarc'h, Laurent Labbé, Mathilde Dupont-Nivet, Xavier Cousin<p style="text-align: justify;">In the context of adaptation to climate change, acute hyperthermia and hypoxia resistance are traits of growing interest in aquaculture. The feasibility of genetic improvement of these resistance traits through sele...Animal behaviour , Animal geneticsNicolas Bedere2024-07-12 15:37:31 View
13 Mar 2025
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Shade use, welfare and performance of ewes grazing in temperate silvopastures differing in tree density

Provision of optimal shade for ewes: a question of choice

Recommended by ORCID_LOGO based on reviews by Matteo Chincarini and Pol Llonch

As the world slowly (or not so slowly) warms, the ability to regulate heat becomes even more pertinent for livestock kept in enclosed areas. Trees are not always present on land grazed by sheep, and when the pasture has some forestation, the coverage will provide varying degrees of shade. In this study by Ginane et al. (2025), ewes kept in enclosures with different levels of tree cover were observed at different times over a period of three years to investigate the extent to which the animals chose to spend time in the shade. By using fields with very different provision of shade (approximately 1, 40, and 81% shade, respectively), the authors wanted to test the hypothesis that ewes would actively seek out tree shade when the combined temperature and humidity increased – especially if the conditions reached levels associated with heat stress. Even at the lowest provision of shade, which consisted of a single tree in the paddock, all ewes could fit within the shade cast by the tree; but if the distribution of ewes or groups of ewes were random, i.e. independent of shade, the likelihood of these ewes being in the shade by chance was effectively 1%. By factoring in the element of chance, the authors found that mean shade use was greater than the tree canopy cover for the low and medium shade treatments, whereas it didn’t differ from chance for the densely forested treatment. Across treatments, all ewes spent just under 60% of the observation time grazing, and the ewes with the low and medium level of shade actively selected shade for foraging activity, whereas the ewes with over 80% canopy cover avoided it. Across treatments, shade was used primarily for resting and ruminating.

Tree cover affected the availability of forage in a negative manner, with more biomass available for ewes in the low shade treatment and significantly less in the high treatment, although this did not translate into significant differences in live weight or body condition score. Using this information, Ginane et al. (2025) calculated the optimal level of tree cover to be somewhere between the low and medium cover, at roughly 30 trees per hectare – preferably spread out over the area to offer different locations of shade and to encourage a natural spread of manure.

This longitudinal study of shade use by ewes provides novel and useful information on the positive and negative effects of tree cover in paddocks used to rear ewes with lambs. The authors raise the limitation of the study themselves, and they would have liked to also include observations on non-sunny days, to be able to eliminate place preferences independently of shade availability. But the clever calculation of active shade-selection makes this study easily applicable for use in the assessment of paddock suitability for pregnant ewes.

References

Cécile Ginane, Mickaël Bernard, Véronique Deiss, Donato Andueza, Camille Béral (2025) Shade use, welfare and performance of ewes grazing in temperate silvopastures differing in tree density. Zenodo, ver.4 peer-reviewed and recommended by PCI Animal Science https://doi.org/10.5281/zenodo.15001481

Shade use, welfare and performance of ewes grazing in temperate silvopastures differing in tree densityCécile Ginane, Mickaël Bernard, Véronique Deiss, Donato Andueza, Camille Béral<p>The study aimed to objectify the importance of trees for sheep welfare by characterising how productive ewes, grazing in temperate mid-mountain pastures, use shade depending on climatic conditions and tree density. The impact of trees on sheep ...Animal behaviour , Animal welfare, Grazing management , Small ruminantsBirte L Nielsen2024-04-03 11:39:54 View
31 Jul 2023
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The big challenge for livestock genomics is to make sequence data pay

The price of sequencing the livestock genomics

Recommended by based on reviews by Mario Calus and 1 anonymous reviewer

Using sequence data in livestock genomics has often been regarded as a solution to revolutionize livestock breeding (Meuwissen & Goddard, 2010). The main expected benefits were to enhance the accuracy of breeding values, achieve better persistence of the accuracy over generations, and enable across populations or breed predictions (Hickey, 2013). Despite the promised benefits, whole-genome sequencing has not yet been implemented in livestock breeding programs, replacing SNP arrays for routine evaluation.

In this work, Johnsson (2023) thoroughly reviewed the literature regarding the implications of whole-genome sequencing and functional genomics for livestock breeding practice. The author discusses the potential applications and reasons for difficulties in their implementation. The author speculates that the main challenge for making using the sequence data profitable is to overcome the problem of the small dimensionality of the genetic data and proposes three potential ways to achieve this goal. The first approach is better modeling of genomic segments, the second inclusion of undetected genetic variation, and the third use of functional genomic information.  

The paper presents an original and interesting perspective on the current status of the use of sequence data in livestock breeding programs and perspectives for the future. 

References

Hickey,J.M.,2013.Sequencing millions of animals for genomic selection 2.0. Journal of Animal Breeding and Genetics 130:331–332. https://doi.org/10.1111/jbg.12054 

Johnsson, M., 2023. The big challenge for livestock genomics is to make sequence data pay. arXiv, 2302.01140, ver. 4 peer-reviewed and recommended by Peer Community in Animal Science. https://doi.org/10.48550/arXiv.2302.01140 

Meuwissen, T., Goddard, M.,2010. Accurate prediction of genetic values for complex traits by whole-genome resequencing. Genetics 185:623–631. https://doi.org/10.1534/genetics.110.116590 

 

The big challenge for livestock genomics is to make sequence data payMartin Johnsson<p>This paper will argue that one of the biggest challenges for livestock genomics is to make whole-genome sequencing and functional genomics applicable to breeding practice. It discusses potential explanations for why it is so difficult to consis...Genomics, Genomic selectionMarcin Pszczoła2023-02-03 08:08:39 View