Rumen microbial (meta)genomics and its application to ruminant production

Morgavi, Diego; Kelly, William J.; Janssen, Peter H.; Attwood, Graeme T.

doi:10.1017/s1751731112000419

Cited by 202 publications

(179 citation statements)

References 161 publications

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“…Depuis quelques années, les progrès de la métagénomique et de la métabolomique ont commencé à faire connaitre le microbiote ruminal sous un autre angle et à ouvrir une nouvelle aire de recherches sur le rumen (voir les définitions de Morgavi et al 2013). Il est clair que microbiote et hôte ont eu une co-évolution adaptative qui les rend dépendant mutuellement à un niveau encore plus étroit que ce que l'on pensait (Morgavi et al 2013). Il est clair également que les rations intensives ont remis en cause les résultats de cette co-évolution et qu'il est nécessaire d'étudier la variabilité individuelle, par le phénotypage, permettant d'identifier des individus et des microbiotes les mieux adaptés et les plus robustes vis-à-vis des régimes alimentaires modernes.…”

Section: Les Facteurs « Microbiens » Liés à L'acidose Du Rumenunclassified

Approche quantitative de l’aidose chez les ruminants

Sauvant¹,

Giger-Reverdin²

2015

bavf

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Section: Les Facteurs « Microbiens » Liés à L'acidose Du Rumenunclassified

Approche quantitative de l’aidose chez les ruminants

Sauvant¹,

Giger-Reverdin²

2015

bavf

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“…feeding, weaning and probiotics) and/ or selection. Metagenomics, which is the description of the combined genomes of the microorganisms present in the gut (or other ecosystem), will be a powerful tool for these studies (Morgavi et al, 2013).…”

Section: Exploiting Animal Adaptive Capacitiesmentioning

confidence: 99%

Forty research issues for the redesign of animal production systems in the 21st century

Dumont

García

Thomas

et al. 2014

Animal

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Agroecology offers a scientific and operational framework for redesigning animal production systems (APS) so that they better cope with the coming challenges. Grounded in the stimulation and valorization of natural processes to reduce inputs and pollutions in agroecosystems, it opens a challenging research agenda for the animal science community. In this paper, we identify key research issues that define this agenda. We first stress the need to assess animal robustness by measurable traits, to analyze trade-offs between production and adaptation traits at within-breed and between-breed level, and to better understand how group selection, epigenetics and animal learning shape performance. Second, we propose research on the nutritive value of alternative feed resources, including the environmental impacts of producing these resources and their associated non-provisioning services. Third, we look at how the design of APS based on agroecological principles valorizes interactions between system components and promotes biological diversity at multiple scales to increase system resilience. Addressing such challenges requires a collection of theories and models (concept-knowledge theory, viability theory, companion modeling, etc.). Acknowledging the ecology of contexts and analyzing the rationales behind traditional small-scale systems will increase our understanding of mechanisms contributing to the success or failure of agroecological practices and systems. Fourth, the large-scale development of agroecological products will require analysis of resistance to change among farmers and other actors in the food chain. Certifications and market-based incentives could be an important lever for the expansion of agroecological alternatives in APS. Finally, we question the suitability of current agriculture extension services and public funding mechanisms for scaling-up agroecological practices and systems.

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“…Furthermore, complete genomes will assist in the taxonomic and functional assignments of data from DNA and protein-sequencing studies. Progress in rumen metagenomics has been the subject of a recent review (Morgavi et al, 2013), and particular questions of interest are whether the presence of individual microbial species or particular microbial groups correlates with animal genotype, with high or low feed conversion-efficiency animals, or with high or low CH 4 -producing animals. Reference genome data sets will be crucial for the analysis of any 'omics' style research.…”

Section: Future Prospectsmentioning

confidence: 99%

Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies

Leahy

Kelly

Ronimus

et al. 2013

Animal

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Ruminant-derived methane (CH 4 ), a potent greenhouse gas, is a consequence of microbial fermentation in the digestive tract of livestock. Development of mitigation strategies to reduce CH 4 emissions from farmed animals is currently the subject of both scientific and environmental interest. Methanogens are the sole producers of ruminant CH 4 , and therefore CH 4 abatement strategies can either target the methanogens themselves or target the other members of the rumen microbial community that produce substrates necessary for methanogenesis. Understanding the relationship that methanogens have with other rumen microbes is crucial when considering CH 4 mitigation strategies for ruminant livestock. Genome sequencing of rumen microbes is an important tool to improve our knowledge of the processes that underpin those relationships. Currently, several rumen bacterial and archaeal genome projects are either complete or underway. Genome sequencing is providing information directly applicable to CH 4 mitigation strategies based on vaccine and small molecule inhibitor approaches. In addition, genome sequencing is contributing information relevant to other CH 4 mitigation strategies. These include the selection and breeding of low CH 4 -emitting animals through the interpretation of large-scale DNA and RNA sequencing studies and the modification of other microbial groups within the rumen, thereby changing the dynamics of microbial fermentation.Keywords: genome sequencing, methane mitigation, methanogens, rumen bacteria Implications Development of CH 4 mitigation strategies for ruminants without disrupting normal digestive function and reducing productivity is a major challenge. Genome sequencing is an effective way of gaining information on how rumen methanogens and bacteria interact and contribute to rumen function. This knowledge will be important when considering the design and implementation of ruminant CH 4 abatement strategies. Genomic information is already contributing to vaccine and small molecule inhibitor programmes that are aimed at reducing ruminant CH 4 emissions, but it will also underpin the analysis and comprehension of metagenomic sequence data sets, allowing the generation of testable hypotheses to gain a better understanding of rumen biology. IntroductionRuminants are foregut fermenters and have evolved an efficient digestive system in which microbes ferment plant fibre and provide fermentation end-products and other nutrients for growth of the animal (Clauss et al., 2010). Feed ingested by ruminants is fermented by a complex microbial community, which includes bacteria, ciliate protozoa, anaerobic fungi, archaea and viruses. The rumen is the first and largest foregut compartment and is the main site for microbial fermentation. The microbial ecology of the rumen has been the focus of numerous studies (reviewed by McSweeney and Mackie, 2012), but very little information is available regarding the microflora of the ruminant oral cavity and lower gastrointestinal tract. The rumen provides optimal conditio...

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Rumen microbial (meta)genomics and its application to ruminant production

Cited by 202 publications

References 161 publications

Approche quantitative de l’aidose chez les ruminants

Approche quantitative de l’aidose chez les ruminants

Forty research issues for the redesign of animal production systems in the 21st century

Genome sequencing of rumen bacteria and archaea and its application to methane mitigation strategies

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