Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa View Full Text


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Article Info

DATE

2018-12-14

AUTHORS

Cormac Brian Fitzgerald, Andrey N. Shkoporov, Thomas D. S. Sutton, Andrei V. Chaplin, Vimalkumar Velayudhan, R. Paul Ross, Colin Hill

ABSTRACT

BackgroundFaecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.ResultsIn this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.ConclusionsBased on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T). More... »

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931

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    PUBMED

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    36 schema:description BackgroundFaecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.ResultsIn this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.ConclusionsBased on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F. prausnitzii sensu stricto (neotype strain A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).
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    44 Faecalibacterium prausnitzii
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    46 acid
    47 amino acids
    48 analysis
    49 ani
    50 anti-inflammatory potential
    51 average nucleotide identity
    52 bacteria
    53 bowel disease
    54 carbohydrates
    55 catabolism
    56 catabolism of carbohydrates
    57 certain forms
    58 combination
    59 comparative analysis
    60 comparative genomics
    61 complement
    62 complement of genes
    63 complete genome
    64 connects
    65 core proteome
    66 data
    67 date
    68 decrease
    69 defense mechanisms
    70 differences
    71 disease
    72 diversity
    73 division
    74 draft
    75 form
    76 functional differences
    77 gene complement
    78 gene phylogeny
    79 gene transfer
    80 genes
    81 genetic differences
    82 genome
    83 genome plasticity
    84 genomic sequences
    85 genomics
    86 gut
    87 gut microbiome
    88 high levels
    89 high-quality draft
    90 horizontal gene transfer
    91 human gut
    92 human gut microbiome
    93 identity
    94 importance
    95 inflammation
    96 inflammatory bowel disease
    97 intestinal inflammation
    98 intraspecies diversity
    99 level taxa
    100 levels
    101 little analysis
    102 low levels
    103 markers
    104 mechanism
    105 members
    106 microbiome
    107 mobilome
    108 nucleotide identity
    109 onset
    110 phylogenetic analysis
    111 phylogeny
    112 phylogroup I
    113 phylogroups
    114 physiological data
    115 plasticity
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    117 prausnitzii
    118 progression
    119 proteome
    120 sensitive marker
    121 sensu stricto
    122 separation
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    133 schema:name Comparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa
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