Phylogenetic and phenotypic evidence for the transfer of Eubacterium aerofaciens to the genus Collinsella as Collinsella aerofaciens gen. nov., comb. nov.

Abstract

Three strains of Eubacterium aerofaciens, JCM 10188T, JCM 7790 and JCM 7791, and 178 freshly isolated strains of the Eubacterium aerofaciens group from human faeces were characterized by biochemical tests, cell wall peptidoglycan type and 165 rRNA analysis. The Eubacterium aerofaciens group was divided into four groups by fermentation patterns of sucrose and cellobiose, and were further divided into 16 sub-groups by fermentation patterns of aesculin, salicin and amygdalin. All of the strains of the Eubacterium aerofaciens group were shown to be phylogenetically distantly related to Eubacterium limosum, which is the type species of genus Eubacterium. Eubacterium aerofaciens was shown to have a specific phylogenetic association with Coriobacterium glomerans. All the strains belonging to Eubacterium aerofaciens resembled Coriobacterium glomerans in possessing a high G+C content (60 mol%). Cell wall analysis, however, revealed the presence of different A4P (L-Ala)-D-GIu-L-Orn-L-Asp peptidoglycan types. Based on a 165 rRNA sequence divergence of greater than 9 % with Coriobacterium glomerans and the presence of a unique peptidoglycan type, a new genus, Collinsella, is proposed for Eubacterium aerofaciens, with one species, Collinsella aerofaciens. The type strain of Collinsella aerofaciens is JCM 101 88T.

Dynamics and diversity of the ‘Atopobium cluster' in the human faecal microbiota, and phenotypic characterization of ‘Atopobium cluster' isolates

“…Eight of the groups classified in this study were distinct from the groups previously described (Kageyama et al, 1999a) based on demonstration of acid production from one or more of: L-arabinose, D-mannitol, D-melezitose, D-sorbitol and D-xylose or no acid produced from D-maltose. No Group IV fermentation profiles (Kageyama et al, 1999a) were seen from our faecal Col. aerofaciens isolates. However, isolates with biochemical profiles corresponding to Groups IA, IE/IF (amygdalin is not included in API 20 A), IIF/IIG (no amygdalin data) and III were observed.…”

“…Moore & Holdeman (1974) classified three groups of Col. aerofaciens based on acid production from sucrose and/or cellobiose fermentation. Kageyama et al (1999a) extended this, demonstrating four groups of Col. aerofaciens based on carbohydrate fermentation patterns of 181 faecal isolates. In addition, these four groups were further divided into 16 subgroups in relation to fermentation of aesculin, salicin and amygdalin.…”

“…Phenotypic characterization of Col. aerofaciens strains isolated from human faecal samples has revealed great diversity in the metabolic capabilities of different strains (Moore & Holdeman, 1974;Holdeman et al, 1976;Kageyama et al, 1999a). Moore & Holdeman (1974) classified three groups of Col. aerofaciens based on acid production from sucrose and/or cellobiose fermentation.…”

“…Kageyama et al (1999a) sequenced three strains of Col. aerofaciens (including the type strain) and found they shared 96.6-97.8 % sequence similarity. DNA-DNA hybridization data showed they had .72 % reassociation, indicating that the strains belonged to the same species.…”

Functional metagenomics reveals novel salt tolerance loci from the human gut microbiome

“…COLAER_01957 (murB) is located 226 nucleotides downstream of COLAER_01956. C. aerofaciens' galE may still be involved in galactose metabolism, as the organism can utilize galactose (Kageyama et al, 1999). The galE gene from SMG 25 is not found on the galactose operon and also exhibits a different genomic arrangement to SMG 3.…”