Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

    Full text documents are added when available. The database is updated daily and currently holds about 240,000 items, of which 72,000 in open access.

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Record number 527387
Title Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
Author(s) Gerritsen, Jacoline; Hornung, Bastian; Renckens, Bernadette; Hijum, Sacha A.F.T. van; Martins dos Santos, Vitor A.P.; Rijkers, Ger T.; Schaap, Peter J.; Vos, Willem M. de; Smidt, Hauke
Source PeerJ 2017 (2017)9. - ISSN 2167-8359
DOI https://doi.org/10.7717/peerj.3698
Department(s) Systems and Synthetic Biology
VLAG
Microbiology
WIMEK
Publication type Refereed Article in a scientific journal
Publication year 2017
Keyword(s) Functional genomics - Gut - Microbiome - Prebiotics - Probiotics - RNAseq - Romboutsia - Small intestine
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.
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