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. 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. 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 A2–165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).

Culture-based study of the faecal microbiome in two adult female subjects revealed the presence of two obligately anaerobic, non-spore-forming, rod-shaped, non-motile, Gram-negative bacterial strains that represent novel species. The first strain, designated 627^T, was a fastidious, slow-growing, indole-positive bacterium with a non-fermentative type of metabolism. The strain was characterized by the production of acetic and succinic acids as metabolic end products, the prevalence of iso-C_15 : 0fatty acid and the presence of menaquinones MK-10 and MK-11. The DNA G+C content was found to be 56.6 mol%. The second strain, designated 177^T, was capable of fermenting a rich collection of carbohydrate substrates, producing acetic acid as a terminal product. The strain was indole-negative and resistant to bile. The major cellular fatty acids were iso-C_15 : 0and anteiso-C_15 : 0(in a 1 : 1 ratio) and the predominant menaquinone was MK-11. The DNA G+C content was 37.8 mol%. A phylogenomic analysis of the draft genomes of strains 627^Tand 177^Tplaced these bacteria in the generaAlistipes(familyRikenellaceae) andCoprobacter(familyPorphyromonadaceae), respectively.On the basis of the phenotypic and genotypic properties of strains 627^Tand 177^T, we conclude that these strains from human faeces represent two novel bacterial species, for which the namesAlistipes inopssp. nov. (type strain 627^T = DSM 28863^T = VKM B-2859^T) andCoprobacter secundussp. nov. (type strain 177^T = DSM 28864^T = VKM B-2857^T) are proposed.

Two novel strains of Gram-negative staining, rod-shaped, obligately anaerobic, non-sporeforming, non-motile bacteria were isolated from the feces of healthy human subjects. The strains designated as 585-1T and 668 are characterized by mesophilic fermentative metabolism, production of D-lactic, succinic, and acetic acids as end products of D-glucose fermentation, prevalence of C18:1ω9, C18:1ω9a, C16:0, and C16:1ω7-сis fatty acids, presence of glycine, glutamic acid, lysine, alanine, and aspartic acid in petidoglycan peptide moiety and lack of respiratory quinones. Whole genome sequencing revealed the DNA G+C content was 56.4-56.6 mol%. Complete 16S rRNA gene sequences shared 91.7/91.6% identity with Anaerofilum pentosovorans FaeT, 91.3/91.2% with Gemmiger formicilis ATCC 27749T, and 88.9/88.8% with Faecalibacterium prausnitzii ATCC 27768T. On the basis of chemotaxonomic and genomic properties it was concluded that the strains represent a new species in a new genus within the family Ruminococcaceae, for which the name Ruthenibacterium lactatiformans gen. nov., sp. nov. is proposed. The type strain is 585-1T (= DSM 100348T, = VKM B-2901T).

A novel obligately anaerobic, non-spore-forming, rod-shaped, non-motile Gram-reaction-negative bacterium was isolated from infant faeces. The strain, designated NSB1^T, was able to grow on rich media at 30–37 °C, in the presence of up to 2 % (w/v) Oxgall and 2 % (w/v) NaCl. Cells of strain NSB1^T produced catalase, but not urease and indole. Aesculin was not hydrolysed. The strain was able to utilize d-glucose, lactose, maltose, mannose and raffinose as electron donors. When grown on d-glucose, the main metabolic end products were propionic and acetic acids, with a minor product being succinic acid. The major cellular fatty acids, iso-C_15 : 0 and anteiso-C_15 : 0, were present at a 1 : 1 molar ratio. The major menaquinone was MK-11. The DNA G+C content was found to be 38.5 mol%. According to 16S rRNA gene sequence analysis strain NSB1^T is a member of the family Porphyromonadaceae , phylum Bacteroidetes . The closest relatives of the strain were Barnesiella viscericola (88.2 % identity) and Barnesiella intestinihominis (87.4 % identity). On the basis of phenotypic and genotypic properties of strain NSB1^T we conclude that this strain represent a novel species in a new genus within the family of Porphyromonadaceae for which the name Coprobacter fastidiosus gen. nov., sp. nov. is proposed. The type strain of the species is NSB1^T ( = DSM 26242^T, = VKM B-2743^T).

Members of genus Bifidobacterium are Gram-positive bacteria, representing a large part of the human infant microbiota and moderately common in adults. However, our knowledge about their diversity, intraspecific phylogeny and long-term persistence in humans is still limited. Bifidobacterium longum is generally considered to be the most common and prevalent species in the intestinal microbiota. In this work we studied whole genome sequences of 28 strains of B. longum, including 8 sequences described in this paper. Part of these strains were isolated from healthy children during a long observation period (up to 10 years between isolation from the same patient). The three known subspecies (longum, infantis and suis) could be clearly divided using sequence-based phylogenetic methods, gene content and the average nucleotide identity. The profiles of glycoside hydrolase genes reflected the different ecological specializations of these three subspecies. The high impact of horizontal gene transfer on genomic diversity was observed, which is possibly due to a large number of prophages and rapidly spreading plasmids. The pan-genome characteristics of the subspecies longum corresponded to the open pan-genome model. While the major part of the strain-specific genetic loci represented transposons and phage-derived regions, a large number of cell envelope synthesis genes were also observed within this category, representing high variability of cell surface molecules. We observed the cases of isolation of high genetically similar strains of B. longum from the same patients after long periods of time, however, we didn’t succeed in the isolation of genetically identical bacteria: a fact, reflecting the high plasticity of microbiota in children.

A study of species distribution of numerically predominant Bacteroidales order isolates in feces of healthy people aged 1-33 years was accomplished using a combination of amplified ribosomal DNA restriction analysis (ARDRA) and 16S ribosomal DNA (rDNA) sequencing. It was found that the majority of isolates in all age groups belonged to species B. xylanisolvens, B. vulgatus, and B. uniformis. Members of genera Alistipes, Parabacteroides, Odoribacter, Barnesiella, and Prevotella were also detected frequently.