Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota
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Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota. / Li, Wenxi; Liang, Hewei; He, Wenxin; Gao, Xiaowei; Wu, Zhinan; Hu, Tongyuan; Lin, Xiaoqian; Wang, Mengmeng; Zhong, Yiyi; Zhang, Haifeng; Ge, Lan; Jin, Xin; Xiao, Liang; Zou, Yuanqiang.
In: Heliyon, Vol. 10, No. 5, e27270, 2024.Research output: Contribution to journal › Journal article › Research › peer-review
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TY - JOUR
T1 - Genomic and functional diversity of cultivated Bifidobacterium from human gut microbiota
AU - Li, Wenxi
AU - Liang, Hewei
AU - He, Wenxin
AU - Gao, Xiaowei
AU - Wu, Zhinan
AU - Hu, Tongyuan
AU - Lin, Xiaoqian
AU - Wang, Mengmeng
AU - Zhong, Yiyi
AU - Zhang, Haifeng
AU - Ge, Lan
AU - Jin, Xin
AU - Xiao, Liang
AU - Zou, Yuanqiang
N1 - Publisher Copyright: © 2024 The Authors
PY - 2024
Y1 - 2024
N2 - The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.
AB - The genus Bifidobacterium widely exists in human gut and has been increasingly used as the adjuvant probiotics for the prevention and treatment of diseases. However, the functional differences of Bifidobacterium genomes from different regions of the world remain unclear. We here describe an extensive study on the genomic characteristics and function annotations of 1512 genomes (clustered to 849 non-redundant genomes) of Bifidobacterium cultured from human gut. The distribution of some carbohydrate-active enzymes varied among different Bifidobacterium species and continents. More than 36% of the genomes of B. pseudocatenulatum harbored biosynthetic gene clusters of lanthipeptide-class-iv. 99.76% of the cultivated genomes of Bifidobacterium harbored genes of bile salt hydrolase. Most genomes of B. adolescentis, and all genomes of B. dentium harbored genes involved in gamma-aminobutyric acid synthesis. B. longum subsp. infantis were characterized harboring most genes related to human milk oligosaccharide utilization. Significant differences between the distribution of antibiotic resistance genes among different species and continents revealed the importance to use antibiotics precisely in the clinical treatment. Phages infecting Bifidobacterium and horizontal gene transfers occurring in genomes of Bifidobacterium were dependent on species and region sources, and might help Bifidobacterium adapt to the environment. In addition, the distribution of Bifidobacterium in human gut was found varied from different regions of the world. This study represents a comprehensive view of characteristics and functions of genomes of cultivated Bifidobacterium from human gut, and enables clinical advances in the future.
KW - Bifidobacterium
KW - Bile salt hydrolase
KW - Gut microbiome
KW - Horizontal gene transfers
KW - Phages
U2 - 10.1016/j.heliyon.2024.e27270
DO - 10.1016/j.heliyon.2024.e27270
M3 - Journal article
C2 - 38463766
AN - SCOPUS:85186716167
VL - 10
JO - Heliyon
JF - Heliyon
SN - 2405-8440
IS - 5
M1 - e27270
ER -
ID: 385123679