Faculty 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.
Faculty of Medicine and Health Science, Department of Biochemistry, Midlands State University, P. Bag 9055, Senga Road, Gweru, Zimbabwe.
BMC Genomics. 2024 Jul 25;25(1):718. doi: 10.1186/s12864-024-10618-2.
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.
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).
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.
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.
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.
我们对低中等收入国家（如津巴布韦）特定肠道微生物群成员（如双歧杆菌和肠球菌）的了解非常有限，尤其是在生命早期阶段，对其有益特性的了解更是如此。本研究通过探索从津巴布韦婴儿肠道中分离出的细菌菌株集合来填补这一空白，并将这些菌株的基因组特征与从北美、欧洲和非洲其他地区的婴儿中分离出的菌株进行比较。
从津巴布韦哈拉雷收集的 110 份婴儿粪便样本中，随机选择 20 份样本用于分离早期生命肠道微生物群的主要成员双歧杆菌和肠球菌。分离出的菌株进行全基因组测序和生物信息学分析，包括碳水化合物、人乳寡糖（HMO）和蛋白质降解基因和簇的功能注释，以及抗生素耐药基因（ARGs）的存在。
该研究观察到主要五个鉴定的分类群内存在一些基于位置的聚类。此外，在所分析的数据集内，属于不同 GH 家族的不同数量的基因在不同的物种中都有编码。此外，双歧杆菌代谢 HMO 的潜力存在明显的菌株和种特异性差异。蛋白酶活性分析表明，双歧杆菌中存在一致的γ-谷氨酰水解酶，而肠球菌基因组中则存在大量的天冬氨酰肽酶。两个属都携带针对多种类别的抗菌药物的耐药基因，肠球菌基因组中平均比双歧杆菌含有更多的 ARGs。
本研究在津巴布韦分离株中发现了有前景的益生菌株，为生命早期饮食和微生物治疗提供了可能。然而，婴儿相关微生物中存在抗生素耐药基因引起了对感染风险和下一阶段益生菌开发的关注。在更大的队列中进行进一步的研究，特别是在抗生素和益生菌使用数据有限的地区，对于验证这些初步发现至关重要。
本研究代表了在津巴布韦背景下首次进行的此类研究，重点关注生命早期肠道微生物群中的潜在益生菌株。通过鉴定当地的益生菌株，这项研究可以为针对津巴布韦人群的益生菌干预措施的发展做出贡献，这有助于解决当地的健康挑战，并为婴儿带来更好的健康结果。研究的另一个重要方面是调查津巴布韦细菌株中存在的抗生素耐药基因。抗生素耐药性是一个全球性的健康关注问题，了解不同地区耐药基因的流行和分布情况有助于为公共卫生政策和干预措施提供信息。
