Abstract
Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters—A, B, and C—composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains. Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.
Highlights
Members of genus Faecalibacterium are commensal bacteria, ubiquitous in the gastrointestinal tracts of animals and humans
The phylogenetic analysis of 16S rRNA sequences revealed that the genospecies of Faecalibacterium can be clustered into different groups
We used a variety of methods to analyze 16S rRNA and whole genome data, which together showed that: (i) the current application of phylogroups to differentiate among strains of F. prausnitzii should be revised; (ii) this genus contains at least three separate clusters, spanning both phylogroups I and II, which are all derived from a common recent ancestor; and (iii) some strains (e.g., F. prausnitzii AHMP-21, F. prausnitzii_L2-6, and F. prausnitzii_CNCM_I_4575) appear to represent a deeper, more divergent branch of “Faecalibacterium prausnitzii.”
Summary
Members of genus Faecalibacterium are commensal bacteria, ubiquitous in the gastrointestinal tracts of animals and humans. The relative abundance of F. prausnitzii in vertebrate animals other than humans, such as pigs (Castillo et al, 2007), mice (Nava and Stappenbeck, 2011), calves (Oikonomou et al, 2013), and chickens (Scupham, 2007), suggests that the species is a functionally important member of the microbiota and likely has an impact on the physiology and health of the host. Despite its relevance in the human gut ecosystem, little is known about the diversity of F. prausnitzii (Miquel et al, 2014) and only a few studies have examined isolated strains and used functional approaches (Duncan et al, 2002; Lopez-Siles et al, 2012). To better understand the biodiversity and beneficial effect of this species, it is essential to increase our knowledge of several cultured strains and their genomes
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