Exploring the genomic diversity and antimicrobial susceptibility of bifidobacterium pseudocatenulatum in a Vietnamese population

The, Hao Chung, Minh, Chau Nguyen Ngoc, Hong, Chau Tran Thi, Nguyen, To Nguyen Thi, Pike, Lindsay J., Zellmer, Caroline, Duc, Trung Pham, Tran, Tuan Anh, Thanh, Tuyen Ha, Van, Minh Pham, Thwaites, Guy E., Rabaa, Maia A., Hall, Lindsay J. and Baker, Stephen (2021) Exploring the genomic diversity and antimicrobial susceptibility of bifidobacterium pseudocatenulatum in a Vietnamese population. Microbiology Spectrum, 9 (2). ISSN 2165-0497

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Abstract

Bifidobacterium pseudocatenulatum is a member of the human gut microbiota, and specific variants of B. pseudocatenulatum have been associated with health benefits such as improving gut integrity and reducing inflammatory responses. Here, we aimed to assess the genomic diversity and predicted metabolic profiles of B. pseudocatenulatum cells found colonizing the gut of healthy Vietnamese adults and children. We found that the population of B. pseudocatenulatum from each individual was distinct and highly diverse, with intraclonal variation attributed largely to a gain or loss of carbohydrate-utilizing enzymes. The B. pseudocatenulatum genomes were enriched with glycosyl hydrolases predicted to target plant-based nondigestible carbohydrates (GH13, GH43) but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed extensive genetic diversity and was subject to a high degree of genetic modification. Antimicrobial susceptibility profiling revealed that the Vietnamese B. pseudocatenulatum cells were uniformly susceptible to beta-lactams but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin, and metronidazole. The genomic presence of ermX and tet variants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with a mutation(s) in the quinolone resistance-determining region (GyrA, S115, and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization of B. pseudocatenulatum found in the Vietnamese population, which can be exploited for the rational design of probiotics. IMPORTANCE Bifidobacterium pseudocatenulatum is a beneficial member of the human gut microbiota. The organism can modulate inflammation and has probiotic potential, but its characteristics are largely strain dependent and associated with distinct genomic and biochemical features. Population-specific beneficial microbes represent a promising avenue for the development of potential probiotics, as they may exhibit a more suitable profile in the target population. This study investigates the underexplored diversity of B. pseudocatenulatum in Vietnam and provides more understanding of its genomic diversity, metabolic potential, and antimicrobial susceptibility. Such data from indigenous populations are essential for selecting probiotic candidates that can be accelerated into further preclinical and clinical investigations.

Item Type: Article
Additional Information: Funding Information: We thank all participants and their parents/guardians for their participation in the study and Magdalena Kujawska for her advice in Bifidobacterium culturing. H.C.T. is a Wellcome International Training Fellow (218726/Z/19/Z). L.J.H. is supported by Wellcome Trust Investigator Awards (100974/C/13/Z and 220876/Z/20/Z), the Biotechnology and Biological Sciences Research Council (BBSRC), Institute Strategic Program Gut Microbes and Health (BB/R012490/1), and its constituent projects BBS/ E/F/000PR10353 and BBS/E/F/000PR10356. S.B. is a Wellcome Senior Research Fellow (215515/Z/19/Z). We declare no conflicts of interest. Publisher Copyright: © 2021 American Society for Microbiology. All rights reserved.
Uncontrolled Keywords: physiology,ecology,immunology and microbiology(all),genetics,microbiology (medical),cell biology,infectious diseases,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1314
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
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Depositing User: LivePure Connector
Date Deposited: 26 Nov 2021 01:39
Last Modified: 29 Nov 2021 01:41
URI: https://ueaeprints.uea.ac.uk/id/eprint/82335
DOI: 10.1128/Spectrum.00526-21

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