Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine

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http://hdl.handle.net/10138/225109

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Gerritsen , J , Hornung , B , Renckens , B , van Hijum , S A F T , dos Santos , V A P M , Rijkers , G T , Schaap , P J , de Vos , W M & Smidt , H 2017 , ' Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine ' , PeerJ , vol. 5 , 3698 . https://doi.org/10.7717/peerj.3698

Title: Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Author: Gerritsen, Jacoline; Hornung, Bastian; Renckens, Bernadette; van Hijum, Sacha A. F. T.; dos Santos, Vitor A. P. Martins; Rijkers, Ger T.; Schaap, Peter J.; de Vos, Willem M.; Smidt, Hauke
Contributor: University of Helsinki, University of Helsinki
Date: 2017-09-11
Language: eng
Number of pages: 28
Belongs to series: PeerJ
ISSN: 2167-8359
URI: http://hdl.handle.net/10138/225109
Abstract: Background. 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. Methods. The 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. Results. We 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. Discussion. This revealed that R. ilealis CRIBT is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
Subject: Romboutsia
Functional genomics
RNAseq
Gut
Microbiome
Small intestine
Probiotics
Prebiotics
RIBOSOMAL-RNA OPERON
ESCHERICHIA-COLI
GASTROINTESTINAL-TRACT
BACILLUS-SUBTILIS
GUT MICROBIOTA
GEN. NOV
L-FUCOSE
BACTERIA
DIVERSITY
CLOSTRIDIUM
1183 Plant biology, microbiology, virology
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