Exploring the genomic diversity and antimicrobial susceptibility of<i>Bifidobacterium pseudocatenulatum</i>in the Vietnamese population to aid probiotic design
Abstract Bifidobacterium pseudocatenulatumis a member of the human gut microbiota, and has previously been used as a probiotic to improve gut integrity and reduce inflammatory responses. We showed previously thatB. pseudocatenulatumwas significantly depleted during dysenteric diarrhea, suggesting the organism may aid in recovery from diarrhea. Here, in order to investigate its probiotic potential, we aimed to assess the genomic diversity and predicted metabolic profiles ofB. pseudocatenulatumfound colonizing the gut of healthy Vietnamese adults and children. We found that the population ofB. pseudocatenulatumfrom each individual was distinct and highly diverse, with intra-clonal variation attributed to gain or loss of carbohydrate utilizing enzymes. TheB. pseudocatenulatumgenomes were enriched with glycosyl hydrolases that target plant-based non-digestible carbohydrates (GH13, GH43), but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed greater genetic diversity, and was subject to a high degree of genetic modification. Antimicrobial susceptibility testing revealed that the VietnameseB. pseudocatenulatumwere uniformly susceptible to beta-lactams, but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin and metronidazole. The genomic presence ofermXandtetvariants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with mutation(s) in the quinolone resistance determining region (GyrA, S115 and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization ofB. pseudocatenulatumfound in the Vietnamese population, which could inform the next phase of rational probiotic design.Importance Bifidobacterium pseudocatenulatumis a probiotic candidate with potential applications in several health conditions, but its efficacy is largely strain-dependent and associated with distinct genomic and biochemical features. However, most commercial probiotics have been developed by Western institutions, which may not have ideal efficacy when administered in developing countries. This study taps into the underexplored diversity of the organism in Vietnam, and provides more understanding to its lifestyles and antimicrobial susceptibility. These data are key for selecting an optimal probiotic candidate, from our established collection, for downstream investigations and validation. Thus, our work represents a model in identifying and characterizing bespoke probiotics from an indigenous population in a developing setting..
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Preprint| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
bioRxiv.org - (2023) vom: 02. Nov. Zur Gesamtaufnahme - year:2023 |
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| Sprache: |
Englisch |
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| Beteiligte Personen: |
The, Hao Chung [VerfasserIn] |
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| doi: |
10.1101/2021.04.22.441051 |
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| PPN (Katalog-ID): |
XBI020455135 |
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| 245 | 1 | 0 | |a Exploring the genomic diversity and antimicrobial susceptibility of<i>Bifidobacterium pseudocatenulatum</i>in the Vietnamese population to aid probiotic design |
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| 520 | |a Abstract Bifidobacterium pseudocatenulatumis a member of the human gut microbiota, and has previously been used as a probiotic to improve gut integrity and reduce inflammatory responses. We showed previously thatB. pseudocatenulatumwas significantly depleted during dysenteric diarrhea, suggesting the organism may aid in recovery from diarrhea. Here, in order to investigate its probiotic potential, we aimed to assess the genomic diversity and predicted metabolic profiles ofB. pseudocatenulatumfound colonizing the gut of healthy Vietnamese adults and children. We found that the population ofB. pseudocatenulatumfrom each individual was distinct and highly diverse, with intra-clonal variation attributed to gain or loss of carbohydrate utilizing enzymes. TheB. pseudocatenulatumgenomes were enriched with glycosyl hydrolases that target plant-based non-digestible carbohydrates (GH13, GH43), but not host-derived glycans. Notably, the exopolysaccharide biosynthesis region from organisms isolated from healthy children showed greater genetic diversity, and was subject to a high degree of genetic modification. Antimicrobial susceptibility testing revealed that the VietnameseB. pseudocatenulatumwere uniformly susceptible to beta-lactams, but exhibited variable resistance to azithromycin, tetracycline, ciprofloxacin and metronidazole. The genomic presence ofermXandtetvariants conferred resistance against azithromycin and tetracycline, respectively; ciprofloxacin resistance was associated with mutation(s) in the quinolone resistance determining region (GyrA, S115 and/or D119). Our work provides the first detailed genomic and antimicrobial resistance characterization ofB. pseudocatenulatumfound in the Vietnamese population, which could inform the next phase of rational probiotic design.Importance Bifidobacterium pseudocatenulatumis a probiotic candidate with potential applications in several health conditions, but its efficacy is largely strain-dependent and associated with distinct genomic and biochemical features. However, most commercial probiotics have been developed by Western institutions, which may not have ideal efficacy when administered in developing countries. This study taps into the underexplored diversity of the organism in Vietnam, and provides more understanding to its lifestyles and antimicrobial susceptibility. These data are key for selecting an optimal probiotic candidate, from our established collection, for downstream investigations and validation. Thus, our work represents a model in identifying and characterizing bespoke probiotics from an indigenous population in a developing setting. | ||
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| 700 | 1 | |a Thi Hong, Chau Tran |4 aut | |
| 700 | 1 | |a Thi Nguyen, To Nguyen |4 aut | |
| 700 | 1 | |a Pike, Lindsay J. |4 aut | |
| 700 | 1 | |a Zellmer, Caroline |4 aut | |
| 700 | 1 | |a Duc, Trung Pham |4 aut | |
| 700 | 1 | |a Tran, Tuan-Anh |4 aut | |
| 700 | 1 | |a Thanh, Tuyen Ha |4 aut | |
| 700 | 1 | |a Van, Minh Pham |4 aut | |
| 700 | 1 | |a Thwaites, Guy E. |4 aut | |
| 700 | 1 | |a Rabaa, Maia A. |4 aut | |
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| 700 | 1 | |a Baker, Stephen |0 (orcid)0000-0003-1308-5755 |4 aut | |
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