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Mudhluli, Taona Emmah, Kujawska, Magdalena, Mueller, Julia, Felsl, Angela, Truppel, Bastian-Alexander, Hall, Lindsay J. 
ORCID: https://orcid.org/0000-0001-8938-5709, Chitsike, Inam, Gomo, Exnevia and Zhou, Danai Tavonga
(2024)
Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort.
BMC Genomics, 25.
ISSN 1471-2164
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Abstract
Introduction: Our understanding of particular gut microbiota members such as Bifidobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level beneficial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; comparing their genomic characteristics with strains isolated from infants across North America, Europe, and other regions of Africa. Materials and method: From 110 infant stool samples collected in Harare, Zimbabwe, 20 randomly selected samples were used to isolate dominant early-life gut microbiota members Bifidobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbohydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibiotic resistance genes (ARGs). Results: The study observed some location-based clustering within the main five identified taxonomic groups. Furthermore, there were varying and overall species-specific numbers of genes belonging to different GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specific variances were identified in the potential of Bifidobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifidobacterium, while Enterococcus genomes exhibited a high abundance of aspartyl peptidases. Both genera harboured resistance genes against multiple classes of antimicrobial drugs, with Enterococcus genomes containing a higher number of ARGs compared to Bifidobacterium, on average. Conclusion: This study identified promising probiotic strains within Zimbabwean isolates, offering the potential for early-life diet and microbial therapies. However, the presence of antibiotic resistance genes in infant-associated microbes raises concerns for infection risk and next-stage probiotic development. Further investigation in larger cohorts, particularly in regions with limited existing data on antibiotic and probiotic use, is crucial to validate these initial insights. Impact statement: This research represents the first investigation of its kind in the Zimbabwean context, focusing on potential probiotic strains within the early-life gut microbiota. By identifying local probiotic strains, this research can contribute to the development of probiotic interventions that are tailored to the Zimbabwean population, which can help address local health challenges and promote better health outcomes for infants. Another essential aspect of the study is the investigation of antimicrobial resistance genes present in Zimbabwean bacterial strains. Antimicrobial resistance is a significant global health concern, and understanding the prevalence and distribution of resistance genes in different regions can help inform public health policies and interventions.
| Item Type: | Article |
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| Additional Information: | Availability of data and materials: The draft genomes of 15 infant-associated Zimbabwean isolates sequenced here have been deposited to the NCBI database under the BioProject number PRJNA1036581. Funding Information: DTZ. is supported by the Africa Research Excellence Fund (AREF) DDI.02073952402, and NIH Fogarty International Center Grant # 1D43TW011326, awarded to the Biomedical Research Training Institute (BRTI), Zimbabwe\u2019s D43 ATCHIVR Program. TEM. is supported by NIH Fogarty International Center Grant # D43TW010313, awarded to the University of Buffalo, SUNY, USA and the University of Zimbabwe\u2019s HIV Research Training Program. LJH. is supported by Wellcome Trust Investigator Award 220876/Z/20/Z; and a BBSRC Institute Strategic Programme, Gut Microbes and Health BB/R012490/1, and its constituent projects BBS/E/F/000PR10353 and BBS/E/F/ 000PR10356. |
| Uncontrolled Keywords: | biotechnology,genetics,sdg 3 - good health and well-being ,/dk/atira/pure/subjectarea/asjc/1300/1305 |
| Faculty \ School: | Faculty of Medicine and Health Sciences > Norwich Medical School |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 22 Oct 2024 14:30 |
| Last Modified: | 04 Nov 2024 11:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/97116 |
| DOI: | 10.1186/s12864-024-10618-2 |
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