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

A strain of the bacterial genus <i>Bifidobacterium</i>, 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 <i>Bifidobacterium</i> and most closely related to the <i>B. mellis</i> Bin7N^T (98.5% identity). Comparative sequence analysis of eight housekeeping genes (<i>pyrG</i>, <i>thrS</i>, <i>glnA1</i>, <i>recA</i>, <i>tuf</i>, <i>dnaB</i>, <i>rpoC</i> and <i>xfp</i>) 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 <i>B. asteroides</i> group. The highest average nucleotide identity value for strain IMAU50987^T was 77.0% in comparison with <i>B. choladohabitans</i> B14384H11^T and <i>B. apis</i> F753-1^T. However, the highest digital DNA-DNA hybridization value was 23.1% compared with <i>B. apis</i> F753-1^T and <i>B. xylocopae</i> XV2^T; the highest average amino acid identity value was 73.2% compared with <i>B. polysaccharolyticum</i> 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} <i> ω</i>9c and Sum in Feature 7 (C_{19 : 1} <i> ω</i>7c/C_{19 : 1} <i> ω</i>6c). The cell-wall peptidoglycan was of the A3α l-Lys-Gly type. Based on data from this study, a novel species, <i>Bifidobacterium favimelis</i> sp. nov., is proposed with the type strain IMAU50987^T (= GDMCC 1.4189^T = JCM 36315^T).