Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures

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Authors

Nene, Mxolisi
Kunene, Nokuthula W.
Pierneef, Rian
Hadebe, Khanyisile

Journal Title

Journal ISSN

Volume Title

Publisher

Frontiers Media

Abstract

INTRODUCTION: 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. METHODS: 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. RESULTS: Taxonomic analysis showed that the predominant phyla in both provinces were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria. At the genus level, Escherichia and Shigella were prevalent, with Escherichia coli and Shigella dysenteriae identified as major contributors to the gut microbiome. ARGs were identified, with MarA, PmrF, and AcrE detected in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo. These genes primarily mediate antibiotic efflux and alteration. DISCUSSION: The detection of zoonotic bacteria such as Escherichia coli and Streptococcus 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 lowresource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.

Description

DATA AVAILABILITY STATEMENT: The sequencing data supporting this study have been deposited in the NCBI Sequence Read Archive (SRA) under the BioProject ID PRJNA1180228. The data are publicly accessible and include all raw sequence files used in the analysis.

Keywords

Microbiome, Communal production system, Gallus domesticus, SDG-02: Zero hunger, SDG-03: Good health and well-being, Next generation sequencing (NGS), Antimicrobial resistance (AMR)

Sustainable Development Goals

SDG-02:Zero Hunger
SDG-03:Good heatlh and well-being

Citation

Nene, M., Kunene, N.W., Pierneef, R. & Hadebe, K. (2025) Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures. Frontiers in Microbiology 15:1487595. doi: 10.3389/fmicb.2024.1487595.