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Deep Metagenomic Sequencing of Multiple Ruminant Guts Reveals Species-specific Microbiomes
University of Edinburgh

Deep metagenomic sequencing of multiple ruminant guts reveals species-specific microbiomes. Ruminant species such as cattle, sheep, deer, goats and reindeer represent a fascinating opportunity to study gut function and metagenomics. With a solely vegetarian diet, the gut microbiome of ruminants is perfectly adapted to digest and gain energy from plant material. However, different animals have different diets (e.g. grass vs lichen) which require different microbes to digest. We have deep-sequenced the rumen gut microbiome of several ruminant species using the Illumina HiSeq 2000 system, generation several hundred gigabases of sequence data in the process. Here we describe bioinformatic investigations into these data, including assembly into large contigs, prediction and annotation of genes and taxon assignment. We show that the vast majority of sequence data comes from as-yet uncharacterized bacterial species, representing huge potential for discovery of novel enzymes. Finally, we show that ruminants can be clustered together according to their gut microbiome structure and species abundance.

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