Improving Animal Production & Welfare
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Rumen microbiome is associated with important livestock traits

Rumen metagenomes as an intermediate phenotype in methane emission from cattle.

A cow eating grass

The microbiome is the population of microbes – bacteria, archaea, fungi, protozoa, viruses, etc – that live in a particular environment.  Ruminants include important farm animals such as cattle, sheep, goats and buffalo as well as more exotic animals such as giraffe.  They have a complex digestive system, including the rumen, which is a remarkable organ that is able to extract energy and nutrition from hard-to-digest plant matter. 

The rumen contains around 1000 microbial species, who together encode the genes responsible for the degradation of plant matter and the release of energy and nutrition for the host animal.  Unfortunately, ruminants also house methane-producing archaea, making them the major source of greenhouse gases emissions from anthropogenic activities. 

We have used deep Illumina sequencing of multiple cattle rumens to characterise the structure and function of the microbiome.  We have shown that cattle which produce more methane also house more archaea and more enzymes that are involved in methane production1.  Whilst this may appear obvious, such a link has proven elusive for many years. 

We also began to characterise the remarkable genomic diversity of the rumen, and found thousands of novel proteins related to important livestock traits, and investigated how it links with the microbiome structure and function2.  Our analyses suggested that the abundance of key parts of the rumen microbiome are under host genetic control. This provides a proof-of-principle for the use of microbial abundance as an intermediate phenotype for complex traits such as methane emissions and feed-conversion-ratio.

Original Publications

  1. R.J. Wallace et al. (2015) The rumen microbial metagenome associated with high methane production in cattle. BMC Genomics 16:839 DOI: 10.1186/s12864-015-2032-0
  2. R. Roehe et al. (2016) Bovine host genetic variation influences rumen microbial methane production with best selection criterion for low methane emitting and efficiently feed converting hosts based on metagenomic gene abundance. PLOS Genetics 12(2) DOI:10.1371/journal.pgen.1005846