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).
Highlights
Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut
At the same time, decreased F. prausnitzii levels were observed in various forms of inflammatory bowel disease (IBD) such as Crohn’s disease (CD) and ulcerative colitis (UC), as well as in colorectal cancer (CRC) and type 2 diabetes [8,9,10,11]
General characteristics of F. prausnitzii genome structure In total, draft genome assemblies were generated for 11 F. prausnitzii strains
Summary
Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Two decades later with the aid of 16S rRNA sequence information it was re-assigned to the Clostridium leptum group (clostridial cluster IV [2]). It was classified as a separate genus named Faecalibacterium (family Ruminococcaceae) in 2002 by Duncan et al [3]. The importance of the species to human health was not fully realized until the mid-2000’s when high throughput sequencing of 16S rRNA libraries and metagenomic analysis of faecal DNA revealed that F. prausnitzii is one of the most abundant bacteria in the human gut, accounting for 5–15% of the total bacterial population [4,5,6,7,8]. At the same time, decreased F. prausnitzii levels were observed in various forms of inflammatory bowel disease (IBD) such as Crohn’s disease (CD) and ulcerative colitis (UC), as well as in colorectal cancer (CRC) and type 2 diabetes [8,9,10,11]
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