Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

ABSTRACT The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obe...

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Autores principales:	Guojun Wu, Chenhong Zhang, Huan Wu, Ruirui Wang, Jian Shen, Linghua Wang, Yufeng Zhao, Xiaoyan Pang, Xiaojun Zhang, Liping Zhao, Menghui Zhang
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2017
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/c974703162d54c67b3ca53bb690a5afa
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spelling	oai:doaj.org-article:c974703162d54c67b3ca53bb690a5afa2021-11-15T15:51:07ZGenomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention10.1128/mBio.02348-162150-7511https://doaj.org/article/c974703162d54c67b3ca53bb690a5afa2017-03-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.02348-16https://doaj.org/toc/2150-7511ABSTRACT The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized. IMPORTANCE The manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multiple B. pseudocatenulatum strains isolated from the same habitat to the dietary intervention, as well as strain-specific correlations with bioclinical parameters of the host. The comparative genomics revealed a genome-level microdiversity of related functional genes, which may have contributed to these differences. These results highlight the necessity of understanding strain-level differences if precise manipulation of gut microbiota through dietary approaches is to be realized.Guojun WuChenhong ZhangHuan WuRuirui WangJian ShenLinghua WangYufeng ZhaoXiaoyan PangXiaojun ZhangLiping ZhaoMenghui ZhangAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 8, Iss 1 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Guojun Wu Chenhong Zhang Huan Wu Ruirui Wang Jian Shen Linghua Wang Yufeng Zhao Xiaoyan Pang Xiaojun Zhang Liping Zhao Menghui Zhang Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
description	ABSTRACT The genomic basis of the response to dietary intervention of human gut beneficial bacteria remains elusive, which hinders precise manipulation of the microbiota for human health. After receiving a dietary intervention enriched with nondigestible carbohydrates for 105 days, a genetically obese child with Prader-Willi syndrome lost 18.4% of his body weight and showed significant improvement in his bioclinical parameters. We obtained five isolates (C1, C15, C55, C62, and C95) of one of the most abundantly promoted beneficial species, Bifidobacterium pseudocatenulatum, from a postintervention fecal sample. Intriguingly, these five B. pseudocatenulatum strains showed differential responses during the dietary intervention. Two strains were largely unaffected, while the other three were promoted to different extents by the changes in dietary carbohydrate resources. The differential responses of these strains were consistent with their functional clustering based on the COGs (Clusters of Orthologous Groups), including those involved with the ABC-type sugar transport systems, suggesting that the strain-specific genomic variations may have contributed to the niche adaption. Particularly, B. pseudocatenulatum C15, which had the most diverse types and highest gene copy numbers of carbohydrate-active enzymes targeting plant polysaccharides, had the highest abundance after the dietary intervention. These studies show the importance of understanding genomic diversity of specific members of the gut microbiota if precise nutrition approaches are to be realized. IMPORTANCE The manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multiple B. pseudocatenulatum strains isolated from the same habitat to the dietary intervention, as well as strain-specific correlations with bioclinical parameters of the host. The comparative genomics revealed a genome-level microdiversity of related functional genes, which may have contributed to these differences. These results highlight the necessity of understanding strain-level differences if precise manipulation of gut microbiota through dietary approaches is to be realized.
format	article
author	Guojun Wu Chenhong Zhang Huan Wu Ruirui Wang Jian Shen Linghua Wang Yufeng Zhao Xiaoyan Pang Xiaojun Zhang Liping Zhao Menghui Zhang
author_facet	Guojun Wu Chenhong Zhang Huan Wu Ruirui Wang Jian Shen Linghua Wang Yufeng Zhao Xiaoyan Pang Xiaojun Zhang Liping Zhao Menghui Zhang
author_sort	Guojun Wu
title	Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
title_short	Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
title_full	Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
title_fullStr	Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
title_full_unstemmed	Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention
title_sort	genomic microdiversity of <italic toggle="yes">bifidobacterium pseudocatenulatum</italic> underlying differential strain-level responses to dietary carbohydrate intervention
publisher	American Society for Microbiology
publishDate	2017
url	https://doaj.org/article/c974703162d54c67b3ca53bb690a5afa
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Genomic Microdiversity of <italic toggle="yes">Bifidobacterium pseudocatenulatum</italic> Underlying Differential Strain-Level Responses to Dietary Carbohydrate Intervention

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