Bifidobacterium favimelis sp. nov., isolated from black comb honey.

Abstract

A strain of the bacterial genus Bifidobacterium, IMAU50987^T, that was isolated from black comb honey from Lianghe County, Dehong Autonomous Prefecture, Yunnan Province, China, could not be accurately identified as a known species using 16S rRNA gene sequencing. In this study, the taxonomic status of strain IMAU50987^T was evaluated using whole-genome sequencing combined with phenotypic analyses. Strain IMAU50987^T was Gram-positive, non-motile and non-spore-forming. Comparative of 16S rRNA gene sequence similarity analysis indicated that strain IMAU50987^T could be attributed to the genus Bifidobacterium and most closely related to the B. mellis Bin7N^T (98.5% identity). Comparative sequence analysis of eight housekeeping genes (pyrG, thrS, glnA1, recA, tuf, dnaB, rpoC and xfp) showed that strain IMAU50987^T was different from closely related species. Phylogenomic analysis based on the 88 single-copy genes in the phylogenetic tree showed that strain IMAU50987^T belonged to the B. asteroides group. The highest average nucleotide identity value for strain IMAU50987^T was 77.0% in comparison with B. choladohabitans B14384H11^T and B. apis F753-1^T. However, the highest digital DNA-DNA hybridization value was 23.1% compared with B. apis F753-1^T and B. xylocopae XV2^T; the highest average amino acid identity value was 73.2% compared with B. polysaccharolyticum W8117^T. These values are below the accepted threshold for novel species boundaries. The draft genome size of strain IMAU50987^T was 1.9 Mb, and the DNA G+C content was 63.5%. The major cellular fatty acids of strain IMAU50987^T were C_16 : 0, C_18 : 1  ω9c and Sum in Feature 7 (C_19 : 1  ω7c/C_19 : 1  ω6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, Bifidobacterium favimelis sp. nov., is proposed with the type strain IMAU50987^T (= GDMCC 1.4189^T = JCM 36315^T).