Abstract
Some Eubacterium and Roseburia species are among the most prevalent motile bacteria present in the intestinal microbiota of healthy adults. These flagellate species contribute "cell motility" category genes to the intestinal microbiome and flagellin proteins to the intestinal proteome. We reviewed and revised the annotation of motility genes in the genomes of six Eubacterium and Roseburia species that occur in the human intestinal microbiota and examined their respective locus organization by comparative genomics. Motility gene order was generally conserved across these loci. Five of these species harbored multiple genes for predicted flagellins. Flagellin proteins were isolated from R. inulinivorans strain A2-194 and from E. rectale strains A1-86 and M104/1. The amino-termini sequences of the R. inulinivorans and E. rectale A1-86 proteins were almost identical. These protein preparations stimulated secretion of interleukin-8 (IL-8) from human intestinal epithelial cell lines, suggesting that these flagellins were pro-inflammatory. Flagellins from the other four species were predicted to be pro-inflammatory on the basis of alignment to the consensus sequence of pro-inflammatory flagellins from the β- and γ- proteobacteria. Many fliC genes were deduced to be under the control of σ. The relative abundance of the target Eubacterium and Roseburia species varied across shotgun metagenomes from 27 elderly individuals. Genes involved in the flagellum biogenesis pathways of these species were variably abundant in these metagenomes, suggesting that the current depth of coverage used for metagenomic sequencing (3.13-4.79 Gb total sequence in our study) insufficiently captures the functional diversity of genomes present at low (≤1%) relative abundance. E. rectale and R. inulinivorans thus appear to synthesize complex flagella composed of flagellin proteins that stimulate IL-8 production. A greater depth of sequencing, improved evenness of sequencing and improved metagenome assembly from short reads will be required to facilitate in silico analyses of complete complex biochemical pathways for low-abundance target species from shotgun metagenomes.
| Original language | English |
|---|---|
| Article number | e68919 |
| Number of pages | 15 |
| Journal | PloS ONE |
| Volume | 8 |
| Issue number | 7 |
| DOIs | |
| Publication status | Published - 23 Jul 2013 |
Bibliographical note
Funding: This work was supported by a Principal Investigator Award (07/IN.1/B1780) from Science Foundation Ireland to PWOT. BAN was the recipient of an Embark studentship from the Irish Research Council for Science Engineering and Technology. HMBH and IBJ were supported by the Government of Ireland National Development Plan by way of a Department of Agriculture Food and Marine, and Health Research Board FHRI award to the ELDERMET project, as well as by a Science Foundation Ireland award to the Alimentary Pharmabiotic Centre (APC). The RINH, UoA receives funding from the Scottish Government Rural and Environment Science and Analytical Service Division (RESAS). POS's studentship is jointly funded by RESAS and the APC, UCC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
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- Pro-inflammatory flagellin
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