Bifidobacterium apicola sp. nov., isolated from the gut of honeybee (Apis mellifera)

Two novel bifidobacteria (designated F806-1T and F814-1.1) isolated from the gut of honeybee (Apis mellifera) were characterized in the present study. 16S rRNA gene sequence analysis indicated that strains F806-1T and F814-1.1 belonged to the Bifidobacterium asteroides group and were most closely related to Bifidobacterium apousia W8102T and Bifidobacterium polysaccharolyticum W8117T, having 98.9-99.4% 16S rRNA gene sequence similarities. Strains F806-1T and F814-1.1 had the highest 16S rRNA gene sequence similarities (99.1 and 99.4 %) with B. polysaccharolyticum W8117T. Strains F806-1T and F814-1.1 had 73.2-90.5% average nucleotide identity, 21.5-40.8% digital DNA-DNA hybridization and 67.4-92.5% average amino acid identity values with type strains of all species in the B. asteroides group. Acid production from d-arabinose, l-arabinose, d-xylose, l-xylose, d-galactose, d-fructose, d-mannose and methyl-α-d-glucopyranoside; tolerance to 3% NaCl and activity of cystine arylamidase, N-acetyl-β-glucosaminidase, α-mannosidase and α-fucosidase could differentiate strains F806-1T and F814-1.1 from the type strain of B. polysaccharolyticum. Based on the data obtained in the present study, a novel species, Bifidobacterium apicola sp. nov., is proposed, and the type strain is F806-1T (=CCTCC AB 2024129T=JCM 37002T).

The Type Strain of Bifidobacterium indicum Scardovi and Trovatelli 1969 (Approved Lists 1980) is ATCC 25912, not DSM 20214, and Rejection to Reclassify Bifidobacterium coryneforme as Bifidobacterium indicum

In 2018, Nouioui et al. proposed that Bifidobacterium coryneforme was a later synonym of Bifidobacterium indicum on the basis of the digital DNA-DNA hybridization (dDDH) value (85.0%) between B. coryneforme LMG 18911T and B. indicum LMG 11587T. However, in the study of Scardovi et al. (1970), the type strains of B. indicum and B. coryneforme only exhibited 60% DNA-DNA hybridization value. In the present study, the genomes of B. coryneforme CGMCC 1.2279T, B. coryneforme JCM 5819T, B. indicum JCM 1302T, B. indicum CGMCC 1.2275T, B. indicum DSM 20214T, B. indicum LMG 27437T, B. indicum ATCC 25912T, B. indicum KCTC 3230T, B. indicum CCUG 34985T, were sequenced, and the taxonomic relationship between B. coryneforme and B. indicum was re-evaluated. On the basis of the results presented here, (i) ATCC 25912 and DSM 20214 deposited by Vittorio Scardovi are two different strains; (ii) the type strain of B. indicum is ATCC 25912T (= JCM 1302T = LMG 27437T = CGMCC 1.2275T = KCTC 3230T), and not DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587); (iii) B. coryneforme and B. indicum represent two different species of the genus Bifidobacterium; (iv) strain DSM 20214 (= BCRC 14674 = CCUG 34985 = LMG 11587) belongs to B. coryneforme.

Identification of a prototype human gut Bifidobacterium longum subsp. longum strain based on comparative and functional genomic approaches

Bifidobacteria are extensively exploited for the formulation of probiotic food supplements due to their claimed ability to exert health-beneficial effects upon their host. However, most commercialized probiotics are tested and selected for their safety features rather than for their effective abilities to interact with the host and/or other intestinal microbial players. In this study, we applied an ecological and phylogenomic-driven selection to identify novel B. longum subsp. longum strains with a presumed high fitness in the human gut. Such analyses allowed the identification of a prototype microorganism to investigate the genetic traits encompassed by the autochthonous bifidobacterial human gut communities. B. longum subsp. longum PRL2022 was selected due to its close genomic relationship with the calculated model representative of the adult human-gut associated B. longum subsp. longum taxon. The interactomic features of PRL2022 with the human host as well as with key representative intestinal microbial members were assayed using in vitro models, revealing how this bifidobacterial gut strain is able to establish extensive cross-talk with both the host and other microbial residents of the human intestine.