Abstract
BackgroundThe microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host.MethodsThe genome of the gut bacterium Romboutsia ilealis CRIBT was sequenced with multiple technologies (Illumina paired-end, mate-pair and PacBio). The transcriptome was sequenced (Illumina HiSeq) after growth on three different carbohydrate sources, and short chain fatty acids were measured via HPLC.ResultsWe present the complete genome of Romboutsia ilealis CRIBT, a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIBT possesses a circular chromosome of 2,581,778 bp and a plasmid of 6,145 bp, carrying 2,351 and eight predicted protein coding sequences, respectively. Analysis of the genome revealed limited capacity to synthesize amino acids and vitamins, whereas multiple and partially redundant pathways for the utilization of different relatively simple carbohydrates are present. Transcriptome analysis allowed identification of the key components in the degradation of glucose, L-fucose and fructo-oligosaccharides.DiscussionThis revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
Highlights
Intestinal microbes live in a complex and dynamic ecosystem, and to survive in this highly competitive environment, they have developed close associations with a diverse array of other intestinal microbes and with their host
An overview of the metabolic capabilities and nutritional potential of the type strain of R. ilealis CRIBT is provided here to identify potential mechanisms that enable this organism to survive in the competitive small intestinal environment
The overall G + C content of the genome is 27.9%, which is in good agreement with a G + C content of 28.1 mol% previously determined for R. ilealis CRIBT by HPLC methods (Gerritsen et al, 2014)
Summary
Intestinal microbes live in a complex and dynamic ecosystem, and to survive in this highly competitive environment, they have developed close (symbiotic) associations with a diverse array of other intestinal microbes and with their host. The microbiota in the small intestine relies on their capacity to rapidly import and ferment available carbohydrates to survive in a complex and highly competitive ecosystem. Understanding how these communities function requires elucidating the role of its key players, the interactions among them and with their environment/host. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available
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