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Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine

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 a...

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Autores principales: Gerritsen, Jacoline, Hornung, Bastian, Renckens, Bernadette, van Hijum, Sacha A.F.T., Martins dos Santos, Vitor A.P., Rijkers, Ger T., Schaap, Peter J., de Vos, Willem M., Smidt, Hauke
Formato: Online Artículo Texto
Lenguaje:English
Publicado: PeerJ Inc. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598433/
https://www.ncbi.nlm.nih.gov/pubmed/28924494
http://dx.doi.org/10.7717/peerj.3698
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author Gerritsen, Jacoline
Hornung, Bastian
Renckens, Bernadette
van Hijum, Sacha A.F.T.
Martins dos Santos, Vitor A.P.
Rijkers, Ger T.
Schaap, Peter J.
de Vos, Willem M.
Smidt, Hauke
author_facet Gerritsen, Jacoline
Hornung, Bastian
Renckens, Bernadette
van Hijum, Sacha A.F.T.
Martins dos Santos, Vitor A.P.
Rijkers, Ger T.
Schaap, Peter J.
de Vos, Willem M.
Smidt, Hauke
author_sort Gerritsen, Jacoline
collection PubMed
description 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 CRIB(T) 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 CRIB(T), a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIB(T) 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 CRIB(T) is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available.
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spelling pubmed-55984332017-09-18 Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine Gerritsen, Jacoline Hornung, Bastian Renckens, Bernadette van Hijum, Sacha A.F.T. Martins dos Santos, Vitor A.P. Rijkers, Ger T. Schaap, Peter J. de Vos, Willem M. Smidt, Hauke PeerJ Genomics 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 CRIB(T) 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 CRIB(T), a natural inhabitant and key player of the small intestine of rats. R. ilealis CRIB(T) 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 CRIB(T) is adapted to a nutrient-rich environment where carbohydrates, amino acids and vitamins are abundantly available. PeerJ Inc. 2017-09-11 /pmc/articles/PMC5598433/ /pubmed/28924494 http://dx.doi.org/10.7717/peerj.3698 Text en ©2017 Gerritsen et al. http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
spellingShingle Genomics
Gerritsen, Jacoline
Hornung, Bastian
Renckens, Bernadette
van Hijum, Sacha A.F.T.
Martins dos Santos, Vitor A.P.
Rijkers, Ger T.
Schaap, Peter J.
de Vos, Willem M.
Smidt, Hauke
Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title_full Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title_fullStr Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title_full_unstemmed Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title_short Genomic and functional analysis of Romboutsia ilealis CRIB(T) reveals adaptation to the small intestine
title_sort genomic and functional analysis of romboutsia ilealis crib(t) reveals adaptation to the small intestine
topic Genomics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5598433/
https://www.ncbi.nlm.nih.gov/pubmed/28924494
http://dx.doi.org/10.7717/peerj.3698
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