Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort

Abstract

Introduction Our understanding of particular gut microbiota members such as Bifdobacterium and Enterococcus in low-middle-income countries remains very limited, particularly early life strain-level benefcial traits. This study addresses this gap by exploring a collection of bacterial strains isolated from the gut of Zimbabwean infants; compar‑ ing 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 Bifdobacterium and Enterococcus. Isolated strains were subjected to whole genome sequencing and bioinformatics analysis including functional annotation of carbo‑ hydrates, human milk oligosaccharide (HMO) and protein degradation genes and clusters, and the presence of antibi‑ otic resistance genes (ARGs). Results The study observed some location-based clustering within the main fve identifed taxonomic groups. Furthermore, there were varying and overall species-specifc numbers of genes belonging to diferent GH families encoded within the analysed dataset. Additionally, distinct strain- and species-specifc variances were identifed in the potential of Bifdobacterium for metabolizing HMOs. Analysis of putative protease activity indicated a consistent presence of gamma-glutamyl hydrolases in Bifdobacterium, while Enterococcus genomes exhibited a high abun‑ dance 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 Bifdobacterium, on average. Conclusion This study identifed promising probiotic strains within Zimbabwean isolates, ofering 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.