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

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).Electronic supplementary materialThe online version of this article (10.1186/s12864-018-5313-6) contains supplementary material, which is available to authorized users.

Metabolic Response of Faecalibacterium prausnitzii to Cell-Free Supernatants from Lactic Acid Bacteria

“…These phylogroups were shown to be independent of substrate use, pH tolerance, or bile sensitivity [ 15 ]. A recent analysis of 31 genomes identified two “genomogroups” differing in terms of their carbohydrate and amino-acid metabolism and their defense mechanisms [ 16 ].…”

Sorting and cultivation of Faecalibacterium prausnitzii from fecal samples using flow cytometry in anaerobic conditions

“…This is also the case for other important traits such as butyrate production or the production of various enzymes [2]. These differences could partly be explained by the complex phylogeny of the F. prausnitzii species that comprise at least 3 different phylogroups, and the probable existence of closely related species [1, 19, 20] that have not been described so far and that were mistakenly identified as ‘ F. prausnitzii ’ in 16S repertoire studies that provide only limited phylogenetic information at the species level. Relative proportions between the different phylogroups in one same individual seem to vary depending on specific disease condition, with phylogroup IIb strains being depleted in Crohn’s Disease patients [21, 22].…”

“…In addition, the EOS species F. prausnitzii sorted after various staining methods remained cultivable and the LIVE/DEAD staining was in good correlation with cultivability, with only very few colonies obtained from PI-stained bacteria. The WGA lectin bound very efficiently to a subset of strains that belong to the phylogroup IIb, whereas strains that belong to the phylogroup IIa and to the phylogroup I (recently proposed as ‘ Faecalibacterium moorei ’ [1]) were less efficiently stained. These differences likely correspond to differences in cell wall compositions, such as for instance the presence of an extracellular polymeric matrix as described for F. prausnitzii strain HTF-F [17].…”

“…Partial 16S-rRNA encoding genes were amplified and sequenced from these strains, resulting in a collection of 8 confirmed F. prausnitzii and 1 Gemmiger-related strains. The phylogenetic tree inferred from these sequences encompassed a variety of strains recovered from the fecal samples of healthy volunteers, with strains belonging to the 3 phylogroups (I, IIa and IIb) described for F. prausnitzii [1] (Fig. 7).…”

“…Branch values < 50% are not displayed. The tree was built using reference sequences and outgroups described by [1]. Colonies aspects (bar: 0.5 cm) as well as Gram-stains (100x objective lens) are reported for the strains used in this study.…”