Genome reconstruction of a novel carbohydrate digesting bacterium from the chicken caecal microflora

Abstract The advent of metagenomics using Next-Generation Sequencing (NGS) has led to the acquisition of unprecedented quantities of bacterial sequence data. One use for these data is the recovery of complete genomes of uncultivable, and thus uncharacterised, organisms. The separation of genome from metagenomics data remains challenging, however genomes of several novel lineages and organisms have been reconstructed successfully. Here, we report the use of NGS to reconstruct the draft genome of a previously undescribed bacterium from the caecal microbiome of domestic chickens. This bacterium has a genome size of 2.38 Mb, a 52.13% GC content and 16S rRNA gene phylogenetic analysis indicates that it belongs to a recently recognised family of anaerobes, the Muribaculaceae belonging to Bacteroidetes phylum. Bacteroidetes is one of the major phyla in chicken caecum amounting to 12%–61%. The caecum is a major site of intestinal fermentation that harbours a diverse collection of anaerobic bacteria. From direct genome annotation, this newly identified bacterium is predicted to utilise starch as its primary carbon source, as evidenced by the large number of amylases encoded within its genome: we thus propose the name Candidatus Amulumruptor caecigallinarius . The importance of caecal carbohydrate metabolism and fermentation to the overall health, welfare and productivity of the chicken predicts an important role for this novel Candidatus bacterium in food security.