Cargando…

The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China

Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including a...

Descripción completa

Detalles Bibliográficos
Autores principales: Lin, Guopeng, Liu, Qian, Wang, Luyao, Li, Haitao, Zhao, Jianxin, Zhang, Hao, Wang, Gang, Chen, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9183100/
https://www.ncbi.nlm.nih.gov/pubmed/35684146
http://dx.doi.org/10.3390/nu14112347
_version_ 1784724206480523264
author Lin, Guopeng
Liu, Qian
Wang, Luyao
Li, Haitao
Zhao, Jianxin
Zhang, Hao
Wang, Gang
Chen, Wei
author_facet Lin, Guopeng
Liu, Qian
Wang, Luyao
Li, Haitao
Zhao, Jianxin
Zhang, Hao
Wang, Gang
Chen, Wei
author_sort Lin, Guopeng
collection PubMed
description Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase families of the carbohydrate active enzyme (CAZy). A total of 30 kinds of glycoside hydrolases (GHs), 14 kinds of glycosyl transferases (GTs), 13 kinds of carbohydrate-binding modules (CBMs), 6 kinds of carbohydrate-esterases (CEs), and 2 kinds of auxiliary activities (AAs) gene families were identified across the genomes of the 88 B. pseudocatenulatum strains. Specifically, this showed that significant differences were also present in the number of 10 carbohydrate-active enzyme gene families (GT51, GH13_32, GH26, GH42, GH121, GH3, AA3, CBM46, CE2, and CE6) among the strains derived from the hosts of different age groups, particularly between strains from infants and those from other human age groups. Twelve different individuals of B. pseudocatenulatum from four main clusters were selected for further study to reveal the genetic diversity of carbohydrate metabolism-related genes within the same phylogenetics. The animal experiment showed that 3 weeks of oral administration and 1 week after cessation of administration of these strains did not markedly alter the serum routine inflammatory indicators in mice. Furthermore, the administration of these strains did not significantly cause adverse changes in the gut microbiota, as indicated by the α- and β-diversity indexes, relative to the control group (normal diet). Beyond that, FAHBZ9L5 significantly increased the abundance of B. pseudocatenulatum after 3 weeks and significantly increased the abundance of acetic acid and butyric acid in the host’s intestinal tract 3 and 4 weeks after the first administration, respectively, compared with the control group. Corresponding to this, comparative genomic analyses of 12 B. pseudocatenulatum suggest that FAHBZ9L5-specific genes were rich in ABC transporters and carbohydrate esterase. Combining the results of comparative genomics analyses and animal experiment, it is suggested that the strains containing certain gene clusters contribute to another competitive growth advantage of B. pseudocatenulatum, which facilitates its intestinal carbohydrate metabolism in a host.
format Online
Article
Text
id pubmed-9183100
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-91831002022-06-10 The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China Lin, Guopeng Liu, Qian Wang, Luyao Li, Haitao Zhao, Jianxin Zhang, Hao Wang, Gang Chen, Wei Nutrients Article Eighty-eight Bifidobacterium pseudocatenulatum strains, which were isolated from human, chicken and cow fecal samples from different niches of China, were compared genomically in this study to evaluate their diversity. It was found that B. pseudocatenulatum displayed a closed pan-genome, including abundant glycoside hydrolase families of the carbohydrate active enzyme (CAZy). A total of 30 kinds of glycoside hydrolases (GHs), 14 kinds of glycosyl transferases (GTs), 13 kinds of carbohydrate-binding modules (CBMs), 6 kinds of carbohydrate-esterases (CEs), and 2 kinds of auxiliary activities (AAs) gene families were identified across the genomes of the 88 B. pseudocatenulatum strains. Specifically, this showed that significant differences were also present in the number of 10 carbohydrate-active enzyme gene families (GT51, GH13_32, GH26, GH42, GH121, GH3, AA3, CBM46, CE2, and CE6) among the strains derived from the hosts of different age groups, particularly between strains from infants and those from other human age groups. Twelve different individuals of B. pseudocatenulatum from four main clusters were selected for further study to reveal the genetic diversity of carbohydrate metabolism-related genes within the same phylogenetics. The animal experiment showed that 3 weeks of oral administration and 1 week after cessation of administration of these strains did not markedly alter the serum routine inflammatory indicators in mice. Furthermore, the administration of these strains did not significantly cause adverse changes in the gut microbiota, as indicated by the α- and β-diversity indexes, relative to the control group (normal diet). Beyond that, FAHBZ9L5 significantly increased the abundance of B. pseudocatenulatum after 3 weeks and significantly increased the abundance of acetic acid and butyric acid in the host’s intestinal tract 3 and 4 weeks after the first administration, respectively, compared with the control group. Corresponding to this, comparative genomic analyses of 12 B. pseudocatenulatum suggest that FAHBZ9L5-specific genes were rich in ABC transporters and carbohydrate esterase. Combining the results of comparative genomics analyses and animal experiment, it is suggested that the strains containing certain gene clusters contribute to another competitive growth advantage of B. pseudocatenulatum, which facilitates its intestinal carbohydrate metabolism in a host. MDPI 2022-06-04 /pmc/articles/PMC9183100/ /pubmed/35684146 http://dx.doi.org/10.3390/nu14112347 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Lin, Guopeng
Liu, Qian
Wang, Luyao
Li, Haitao
Zhao, Jianxin
Zhang, Hao
Wang, Gang
Chen, Wei
The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title_full The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title_fullStr The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title_full_unstemmed The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title_short The Comparative Analysis of Genomic Diversity and Genes Involved in Carbohydrate Metabolism of Eighty-Eight Bifidobacterium pseudocatenulatum Isolates from Different Niches of China
title_sort comparative analysis of genomic diversity and genes involved in carbohydrate metabolism of eighty-eight bifidobacterium pseudocatenulatum isolates from different niches of china
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9183100/
https://www.ncbi.nlm.nih.gov/pubmed/35684146
http://dx.doi.org/10.3390/nu14112347
work_keys_str_mv AT linguopeng thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT liuqian thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT wangluyao thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT lihaitao thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT zhaojianxin thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT zhanghao thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT wanggang thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT chenwei thecomparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT linguopeng comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT liuqian comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT wangluyao comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT lihaitao comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT zhaojianxin comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT zhanghao comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT wanggang comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina
AT chenwei comparativeanalysisofgenomicdiversityandgenesinvolvedincarbohydratemetabolismofeightyeightbifidobacteriumpseudocatenulatumisolatesfromdifferentnichesofchina