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Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients

The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile i...

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Autores principales: Yan, Qiulong, Zhang, Siyi, Li, Shenghui, Wang, Guangyang, Zhang, Aiqin, Jin, Taiyang, Zhang, Yue, Lv, Qingbo, Xiao, Manchun, Sun, Yuanyuan, Li, Xiang, Cui, Song, Li, Rui, Ma, Xiaochi, Wang, Chao, Tian, Xiangge, Duan, Xiaohui, Xin, Yi, Mao, Xianhai, Ma, Yufang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591784/
https://www.ncbi.nlm.nih.gov/pubmed/34790179
http://dx.doi.org/10.3389/fmicb.2021.739621
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author Yan, Qiulong
Zhang, Siyi
Li, Shenghui
Wang, Guangyang
Zhang, Aiqin
Jin, Taiyang
Zhang, Yue
Lv, Qingbo
Xiao, Manchun
Sun, Yuanyuan
Li, Xiang
Cui, Song
Li, Rui
Ma, Xiaochi
Wang, Chao
Tian, Xiangge
Duan, Xiaohui
Xin, Yi
Mao, Xianhai
Ma, Yufang
author_facet Yan, Qiulong
Zhang, Siyi
Li, Shenghui
Wang, Guangyang
Zhang, Aiqin
Jin, Taiyang
Zhang, Yue
Lv, Qingbo
Xiao, Manchun
Sun, Yuanyuan
Li, Xiang
Cui, Song
Li, Rui
Ma, Xiaochi
Wang, Chao
Tian, Xiangge
Duan, Xiaohui
Xin, Yi
Mao, Xianhai
Ma, Yufang
author_sort Yan, Qiulong
collection PubMed
description The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia–Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria.
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spelling pubmed-85917842021-11-16 Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients Yan, Qiulong Zhang, Siyi Li, Shenghui Wang, Guangyang Zhang, Aiqin Jin, Taiyang Zhang, Yue Lv, Qingbo Xiao, Manchun Sun, Yuanyuan Li, Xiang Cui, Song Li, Rui Ma, Xiaochi Wang, Chao Tian, Xiangge Duan, Xiaohui Xin, Yi Mao, Xianhai Ma, Yufang Front Microbiol Microbiology The microbes in human bile are closely related to gallbladder health and other potential disorders. Although the bile microbial community has been investigated by recent studies using amplicon or metagenomic sequencing technologies, the genomic information of the microbial species resident in bile is rarely reported. Herein, we isolated 138 bacterial colonies from the fresh bile specimens of four cholecystitis patients using a culturome approach and genomically characterized 35 non-redundant strains using whole-genome shotgun sequencing. The bile bacterial isolates spanned 3 classes, 6 orders, 10 families, and 14 genera, of which the members of Enterococcus, Escherichia–Shigella, Lysinibacillus, and Enterobacter frequently appeared. Genomic analysis identified three species, including Providencia sp. D135, Psychrobacter sp. D093, and Vibrio sp. D074, which are not represented in existing reference genome databases. Based on the genome data, the functional capacity between bile and gut isolates was compared. The bile strains encoded 5,488 KEGG orthologs, of which 4.9% were specific to the gut strains, including the enzymes involved in biofilm formation, two-component systems, and quorum-sensing pathways. A total of 472 antibiotic resistance genes (ARGs) were identified from the bile genomes including multidrug resistance proteins (42.6%), fluoroquinolone resistance proteins (12.3%), aminoglycoside resistance proteins (9.1%), and β-lactamase (7.2%). Moreover, in vitro experiments showed that some bile bacteria have the capabilities for bile salt deconjugation or biotransformation (of primary bile acids into secondary bile acids). Although the physiological or pathological significance of these bacteria needs further exploration, our works expanded knowledge about the genome, diversity, and function of human bile bacteria. Frontiers Media S.A. 2021-11-01 /pmc/articles/PMC8591784/ /pubmed/34790179 http://dx.doi.org/10.3389/fmicb.2021.739621 Text en Copyright © 2021 Yan, Zhang, Li, Wang, Zhang, Jin, Zhang, Lv, Xiao, Sun, Li, Cui, Li, Ma, Wang, Tian, Duan, Xin, Mao and Ma. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Microbiology
Yan, Qiulong
Zhang, Siyi
Li, Shenghui
Wang, Guangyang
Zhang, Aiqin
Jin, Taiyang
Zhang, Yue
Lv, Qingbo
Xiao, Manchun
Sun, Yuanyuan
Li, Xiang
Cui, Song
Li, Rui
Ma, Xiaochi
Wang, Chao
Tian, Xiangge
Duan, Xiaohui
Xin, Yi
Mao, Xianhai
Ma, Yufang
Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title_full Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title_fullStr Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title_full_unstemmed Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title_short Cultivation and Genomic Characterization of the Bile Bacterial Species From Cholecystitis Patients
title_sort cultivation and genomic characterization of the bile bacterial species from cholecystitis patients
topic Microbiology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8591784/
https://www.ncbi.nlm.nih.gov/pubmed/34790179
http://dx.doi.org/10.3389/fmicb.2021.739621
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