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Published on: March 23, 2018
Exploring the genomic traits of infant-associated microbiota members from a Zimbabwean cohort
Taona Emmah Mudhluli1,2, Magdalena Kujawska3, Julia Mueller3
1Faculty of Medicine and Health Sciences, Department of Laboratory Diagnostic and Investigative Sciences, Medical Laboratory Sciences Unit, University of Zimbabwe, Box A 178, Avondale, Harare, Zimbabwe. mudhlulit@staff.msu.ac.zw.
Insights
This study identified potential probiotic Bifidobacterium and Enterococcus strains from Zimbabwean infants, highlighting their unique metabolic capabilities and antibiotic resistance genes. Findings inform targeted probiotic development and public health strategies in low-middle-income countries.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- Limited understanding of gut microbiota in low-middle-income countries, especially early-life beneficial traits of Bifidobacterium and Enterococcus.
- This study addresses the gap by analyzing strains from Zimbabwean infants and comparing them globally.
Purpose of the Study:
- To characterize genomic features of Bifidobacterium and Enterococcus strains from Zimbabwean infants.
- To assess their potential for metabolizing carbohydrates, human milk oligosaccharides (HMOs), and protein degradation.
- To identify antibiotic resistance genes (ARGs) within these infant-associated gut microbes.
Main Methods:
- Isolation of Bifidobacterium and Enterococcus from 110 infant stool samples in Harare, Zimbabwe.
- Whole genome sequencing and bioinformatics analysis of 20 selected strains.
- Functional annotation of carbohydrate, HMO, and protein degradation genes, and ARGs.
Main Results:
- Location-based clustering observed among identified taxonomic groups.
- Species-specific variations in genes for carbohydrate metabolism and HMO utilization.
- Consistent presence of gamma-glutamyl hydrolases in Bifidobacterium and aspartyl peptidases in Enterococcus.
- Both genera harbored ARGs, with Enterococcus showing a higher average number.
Conclusions:
- Identification of promising probiotic strains from Zimbabwean infants for early-life therapies.
- Concerns raised regarding ARGs in infant gut microbes, impacting infection risk and probiotic development.
- Need for further research in larger cohorts, especially in understudied regions, to validate findings.
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.
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