title: Genomic Microdiversity ofBifidobacterium pseudocatenulatumUnderlying 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 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 fiveB. pseudocatenulatumstrains 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. pseudocatenulatumC15, 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.IMPORTANCEThe manipulation of the gut microbiota via dietary approaches is a promising option for improving human health. Our findings showed differential responses of multipleB. pseudocatenulatumstrains 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.
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Guojun
authors.initials: G
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Chenhong
authors.initials: C
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Huan
authors.initials: H
authors.lastname: Wu
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Ruirui
authors.initials: R
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Jian
authors.initials: J
authors.lastname: Shen
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Linghua
authors.initials: L
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Yufeng
authors.initials: Y
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Pang
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Xiaojun
authors.initials: X
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China.
authors.forename: Liping
authors.initials: L
authors.lastname: Zhao
authors.affiliation: State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, People's Republic of China mhzhang@sjtu.edu.cn.
authors.forename: Menghui
authors.initials: M
authors.lastname: Zhang
mesh_terms: D000070257:Bifidobacterium pseudocatenulatum / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification / Q000378:metabolism; D001835:Body Weight; D002648:Child; D004040:Dietary Carbohydrates; D019422:Dietary Sucrose / Q000378:metabolism; D005243:Feces / Q000382:microbiology; D000069196:Gastrointestinal Microbiome; D014644:Genetic Variation; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D009765:Obesity / Q000382:microbiology; D011134:Polysaccharides; D011218:Prader-Willi Syndrome
chemical_list: D004040:Dietary Carbohydrates; D019422:Dietary Sucrose; D011134:Polysaccharides