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...