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Background   Faecalibacterium 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.    Results  In 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.    Conclusions  Based 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 A2–165 T  = DSM 17677 T  = JCM 31915 T ) and  F. moorei  sp. nov. (type strain ATCC 27768 T  = NCIMB 13872 T ).    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5313-6) contains supplementary material, which is available to authorized users.

bmc genomics

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