Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine
- Published
- Accepted
- Subject Areas
- Genomics, Microbiology
- Keywords
- Romboutsia, functional genomics, rnaseq, gut, microbiome, small intestine, probiotics, prebiotics
- Copyright
- © 2017 Gerritsen et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, 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 Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Genomic and functional analysis of Romboutsia ilealis CRIBT reveals adaptation to the small intestine. PeerJ Preprints 5:e2918v1 https://doi.org/10.7287/peerj.preprints.2918v1
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) while growing on three different carbohydrate sources and short chain fatty acids were measured via HPLC.
Results. Hence, 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 pinpointing 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 and uncovered potential mechanisms for competition with mucus-degrading microbes.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Supplementary materials and methods
Additional information from the materials and methods, which were shortened in the main manuscript.
Distribution of COG categories in R. ilealis CRIBT.
Organization of the L-fucose degradation gene cluster of R. ilealis CRIBT compared to similar gene clusters found in C. perfringens (strain ATCCT) and C. sordellii (strains VPI 9048 and ATCC 9714T)
In the current annotation of C. sordellii ATCC 9714T open reading frame prediction seems to be suboptimal, with a considerable amount of potentially wrong stop codons. Genes are color-coded by predicted function: transporter (green), metabolic enzyme with EC number (blue), metabolic enzyme with preliminary EC number/without assigned EC number (dark blue), transcriptional regulator (yellow), hypothetical/unknown protein (grey), protein involved in DNA processing (brown), protein involved in vitamin metabolism (light blue).
Organization of the urease gene cluster of R. ilealis CRIBT compared to similar gene clusters found in H. pylori (strain 26695) and close-relative C. sordellii (strains VPI 9048 and ATCC 9714T)
In the current annotation of C. sordellii ATCC 9714T open reading frame prediction seems to be suboptimal, with a considerable amount of potentially wrong stop codons. Genes are color-coded by predicted function: urease accessory proteins (red), transporter (green), metabolic enzyme with EC number (blue), metabolic enzyme with preliminary EC number/without assigned EC number (dark blue), transcriptional regulator (yellow), hypothetical/unknown protein (grey), protein involved in vitamin metabolism (light blue), ribosomal proteins (green).
Growth characteristics of the individual cultures used for whole-genome transcriptome analysis of R. ilealis CRIBT grown in four experimental conditions
Summary of the RNA-seq raw data analysis for whole-genome transcriptome analysis of R. ilealis CRIBT grown in four experimental conditions
Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of glucose in comparison to at least one of the other three conditions
These three conditions included L-fucose, control (absence of additional carbon source) and FOS. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.
Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of FOS in comparison to at least one of the other three conditions
These conditions included glucose, L-fucose and control (absence of additional carbon source)]. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.
Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in the presence of L-fucose in comparison to at least one of the other three conditions
These conditions included glucose, FOS and control (absence of additional carbon source). Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.
Overview of the genes that were significantly upregulated during growth of R. ilealis CRIBT in absence of a carbon source (control condition) in comparison to at least one of the other conditions
These conditions included glucose, FOS and L-fucose. Differential gene expression values that did not meet the criteria for significance (≥1.5 log2(fold change) and q value ≤0.05) are color-coded in dark-grey.