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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Date
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
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.