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    Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans

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    Author
    Neville, B. Anne
    Sheridan, Paul O.
    Harris, Hugh
    Coughlan, Simone
    Flint, Harry J.
    Duncan, Sylvia H.
    Jeffery, Ian B
    Claesson, Marcus J.
    Ross, R Paul
    Scott, Karen P.
    O'Toole, Paul W.
    Show allShow less
    Keyword
    Flagellin
    Genomic databases
    Pathogen motility
    Genetic loci
    Date
    23/07/2013
    
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    URI
    http://hdl.handle.net/11019/814
    Citation
    Neville BA, Sheridan PO, Harris HMB, Coughlan S, Flint HJ, Duncan SH, et al. (2013) Pro-Inflammatory Flagellin Proteins of Prevalent Motile Commensal Bacteria Are Variably Abundant in the Intestinal Microbiome of Elderly Humans. PLoS ONE 8(7): e68919. doi:10.1371/journal.pone.0068919
    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 σ28. 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.
    Funder
    Science Foundation Ireland; Department of Agriculture, Food and the Marine; Health Research Board; Scottish Government Rural and Environment Science and Analytical Service Division; Irish Research Council for Science, Engineering and Technology
    Grant Number
    07/IN.1/B1780
    ae974a485f413a2113503eed53cd6c53
    http://dx.doi.org/10.1371/journal.pone.0068919
    Scopus Count
    Collections
    Food Biosciences
    Food Biosciences
    Food Biosciences
    Food Biosciences

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