Nene Mxolisi, Kunene Nokuthula Winfred, Pierneef Rian, Hadebe Khanyisile
Department of Agriculture, University of Zululand, Kwa Dlangezwa, South Africa.
Biotechnology Platform, Agricultural Research Council, Ondersterpoort, South Africa.
Front Microbiol. 2025 Feb 4;15:1487595. doi: 10.3389/fmicb.2024.1487595. eCollection 2024.
The production environment of extensively raised village chickens necessitates their adaptability to low-resource systems. The gut microbiome plays a critical role in supporting this adaptability by influencing health and productivity. This study aimed to investigate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal provinces of South Africa.
Using a combination of 16S rRNA gene sequencing and shotgun metagenomic sequencing technologies, we analysed 98 16S rRNA and 72 metagenomic datasets. Taxonomic profiles and functional gene annotations were derived, focusing on microbial diversity, antibiotic resistance genes (ARGs), and potential zoonotic pathogens.
Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, and were prevalent, with and identified as major contributors to the gut microbiome. ARGs were identified, with , , and detected in KwaZulu-Natal, and , and in Limpopo. These genes primarily mediate antibiotic efflux and alteration.
The detection of zoonotic bacteria such as and S spp. highlights potential health risks to humans through the food chain, emphasizing the importance of improved household hygiene practices. This study underscores the role of the gut microbiome in village chicken health and adaptability, linking microbial diversity to production efficiency in low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.
大规模养殖的乡村鸡的生产环境要求它们适应资源匮乏的系统。肠道微生物群通过影响健康和生产力，在支持这种适应性方面发挥着关键作用。本研究旨在调查南非林波波省和夸祖鲁-纳塔尔省乡村鸡粪便微生物群的多样性和功能能力。
我们结合使用16S rRNA基因测序和鸟枪法宏基因组测序技术，分析了98个16S rRNA和72个宏基因组数据集。得出了分类学概况和功能基因注释，重点关注微生物多样性、抗生素抗性基因（ARG）和潜在的人畜共患病原体。
分类学分析表明，两个省份中占主导地位的门是厚壁菌门、拟杆菌门、变形菌门和放线菌门。在属水平上，[此处原文缺失具体属名]普遍存在，[此处原文缺失具体属名]被确定为肠道微生物群的主要贡献者。鉴定出了抗生素抗性基因，在夸祖鲁-纳塔尔省检测到了[此处原文缺失具体基因名]、[此处原文缺失具体基因名]和[此处原文缺失具体基因名]，在林波波省检测到了[此处原文缺失具体基因名]、[此处原文缺失具体基因名]和[此处原文缺失具体基因名]。这些基因主要介导抗生素外排和改变。
检测到诸如[此处原文缺失具体细菌名]和沙门氏菌属等人畜共患病菌，凸显了通过食物链对人类造成的潜在健康风险，强调了改善家庭卫生习惯的重要性。本研究强调了肠道微生物群在乡村鸡健康和适应性中的作用，将微生物多样性与资源匮乏环境下的生产效率联系起来。有针对性的干预措施和进一步研究对于减轻人畜共患病风险和提高乡村养鸡业的可持续性至关重要。
