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

Abstract

A novel bifidobacteria (designated S053-2T) was isolated from the gut of honeybee (Apis mellifera). Strain S053-2T was characterized using a polyphasic taxonomic approach. The result of 16S rRNA gene sequence analysis indicated that strain S053-2T was phylogenetically related to the type strains of Bifidobacterium asteroides , Bifidobacterium indicum , Bifidobacterium actinocoloniiforme , Bifidobacterium xylocopae , Bifidobacterium coryneforme , Bifidobacterium apousia , Bifidobacterium choladohabitans and Bifidobacterium polysaccharolyticum , and had 95.5–99.7 % 16S rRNA gene sequence similarities. Based on the 16S rRNA gene sequence analysis, strain S053-2T was most closely related to the type strain of B. asteroides , having 99.7 % 16S rRNA gene sequence similarity. Strain S053-2T had relatively low (91.6–95.7 %) pheS, atpA, clpC, dnaG, fusA, glnA, glyS, hsp60, argS, pyrG and recA sequence similarities to the type strain of B. asteroides . Strain S053-2T had 94.5–95.3% atpA, clpC, dnaG, dnaK and pyrG sequence similarities to the type strain of B. apousia . The phylogenomic tree indicated that strain S053-2T belonged to the B. asteroides group, and was most closely related to the type strains of B. asteroides , B. apousia , B. choladohabitans and B. polysaccharolyticum , and distantly related to type strains of other phylogenetically related species in the B. asteroides group. Strain S053-2T shared the highest average nucleotide identity (ANI, 93.8 %), digital DNA–DNA hybridization (dDDH, 52.4 %) and average amino acid identity (AAI, 95.6%) values with B. apousia W8102T. Strain S053-2T shared 91.1 % ANI, 41.9 % dDDH and 92.5 % AAI values with B. asteroides DSM 20089T. Acid production from l-arabinose, d-xylose, d-mannose, amygdalin, cellobiose, maltose, melibiose, sucrose, raffinose, gentiobiose and l-fucose, and activity of esterase lipase (C8) and α-fucosidase could differentiate strain S053-2T from B. asteroides DSM 20089T. Acid production from d-mannose, maltose, sucrose, melezitose and gentiobiose, and activity of α-fucosidase could differentiate strain S053-2T from B. apousia W8102T. Based upon the data obtained in the present study, a novel species, Bifidobacterium mizhiense sp. nov., is proposed, and the type strain is S053-2T (=JCM 34710T=CCTCC AB 2021129T).

Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes

“…nov. CL7 was excluded from the analysis. Altogether a consistent GH core was identified between all B. asteroides ‐related strains, encompassing GH43, GH3, GH31, GH2, GH42, GH30, GH13, GH32 and GH36 (Figure 6 ), reflecting metabolic activities towards a broad range of simple carbohydrates such as sucrose, glucose, fructose, galactose, ribose, mannose, melibiose, raffinose, xylose and cellobiose (Bottacini et al, 2012 ;Chen et al, 2021 ; Li et al, 2022 ). Recently, it has been demonstrated that an increase of sugars in flower nectar, the honey bee food, resulted in an increase in the relative abundance of bifidobacteria within the microbiome driven by their high‐grown performance on simple carbohydrates (Wang et al, 2020 ).…”

“…Among the identified clusters, four of them were represented by Bifidobacterium taxa recently characterized, that is, B. choladohabitans JCM 34586 (CL3), B. mizhiense JCM 34710 (CL4), B. apousia JCM 34587 (CL5) and B. polysaccharolyticum JCM 34588 (CL8) (Chen et al, 2021 ; Li et al, 2022 ) (Figure 2 ). Thus, thanks to isolation attempts and genomic characterization of the isolates, the large part of the identified clusters were reclassified and a representative type strain defined.…”

“…Here, we characterize the existence of eight species among the so‐called B. asteroides taxon by using genomics, metagenomics, and phylogenetics analyses. While five of them were validated by the characterization of isolates (Chen et al, 2021 ; Li et al, 2022 ), three are still missing a conventional classification. Interestingly, investigating their distribution among honey bee microbiomes, one unclassified species was found predominant in the gut of A. cerana and utterly absent in A. mellifera , opening a new insights regarding bifidobacterial species distribution among honey bees and their coevolution with the host.…”

“…More recently, four novel Bifidobacterium species were isolated from honey bees, named after Bifidobacterium apousia , Bifidobacterium choladohabitans , Bifidobacterium mizhiense and Bifidobacterium polysaccharolyticum , whose genomic investigation revealed a close genetic relatedness towards B. asteroides type strain DSM 20089 (Chen et al, 2021 ; Li et al, 2022 ). Furthermore, based on genomic investigation aiming at exploring the intraspecies genetic diversity of members of the genus Bifidobacterium , B. asteroides was fragmented into four putative distinct bifidobacterial species (Lugli et al, 2018 ), resulting in the most complex Bifidobacterium taxon identified to date.…”

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

“…Members of the genus Bifidobacterium are abundant symbiotic microorganisms inhabiting the gastrointestinal tract of mammals ( Alessandri et al, 2021 ). This bacterial genus currently counts more than 100 species ( Lugli et al, 2021 ; Li et al, 2022 ), and in recent decades particular scientific focus has been addressed on Bifidobacterium longum subsp. longum , due to its purported health benefits and because it is the most prevalent and abundant bifidobacterial species colonizing the human intestine throughout the entire lifespan ( Santos et al, 2021 ; Kim et al, 2022 ; Quintanilha et al, 2022 ).…”