title: Comparative genomic analysis of 45 type strains of the genus Bifidobacterium: a snapshot of its genetic diversity and evolution.
abstract: Bifidobacteria are well known for their human health-promoting effects and are therefore widely applied in the food industry. Members of the Bifidobacterium genus were first identified from the human gastrointestinal tract and were then found to be widely distributed across various ecological niches. Although the genetic diversity of Bifidobacterium has been determined based on several marker genes or a few genomes, the global diversity and evolution scenario for the entire genus remain unresolved. The present study comparatively analyzed the genomes of 45 type strains. We built a robust genealogy for Bifidobacterium based on 402 core genes and defined its root according to the phylogeny of the tree of bacteria. Our results support that all human isolates are of younger lineages, and although species isolated from bees dominate the more ancient lineages, the bee was not necessarily the original host for bifidobacteria. Moreover, the species isolated from different hosts are enriched with specific gene sets, suggesting host-specific adaptation. Notably, bee-specific genes are strongly associated with respiratory metabolism and are potential in helping those bacteria adapt to the oxygen-rich gut environment in bees. This study provides a snapshot of the genetic diversity and evolution of Bifidobacterium, paving the way for future studies on the taxonomy and functional genomics of the genus.
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, China.
authors: Zhihong
authors: Z
authors: Sun
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
authors: Wenyi
authors: W
authors: Zhang
authors: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors: Chenyi
authors: C
authors: Guo
authors: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors: Xianwei
authors: X
authors: Yang
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, China.
authors: Wenjun
authors: W
authors: Liu
authors: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors: Yarong
authors: Y
authors: Wu
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
authors: Yuqin
authors: Y
authors: Song
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
authors: Lai Yu
authors: LY
authors: Kwok
authors: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors: Yujun
authors: Y
authors: Cui
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China.
authors: Bilige
authors: B
authors: Menghe
authors: State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China.
authors: Ruifu
authors: R
authors: Yang
authors: Consulting Centre of Biomedical Statistics, Beijing, 100850, China.
authors: Liangping
authors: L
authors: Hu
authors: Key Laboratory of Dairy Biotechnology and Engineering, Education Ministry of China, Inner Mongolia Agricultural University, Hohhot, Inner Mongolia, China; Synergetic Innovation Center of Food Safety and Nutrition, Northeast Agricultural University, Harbin, 150030, China.
authors: Heping
authors: H
authors: Zhang
mesh_terms: D000222:Adaptation, Physiological; D000818:Animals; D001516:Bees / Q000382:microbiology; D001644:Bifidobacterium / Q000235:genetics* / Q000502:physiology; D019143:Evolution, Molecular; D041981:Gastrointestinal Tract / Q000382:microbiology; D014644:Genetic Variation; D023281:Genomics; D054884:Host-Pathogen Interactions; D006801:Humans; D010802:Phylogeny