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

dc.contributor.authorNene, Mxolisi
dc.contributor.authorKunene, Nokuthula W.
dc.contributor.authorPierneef, Rian
dc.contributor.authorHadebe, Khanyisile
dc.date.accessioned2025-04-30T12:36:06Z
dc.date.available2025-04-30T12:36:06Z
dc.date.issued2025-02
dc.descriptionDATA 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.en_US
dc.description.abstractINTRODUCTION: 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.en_US
dc.description.departmentBiochemistry, Genetics and Microbiology (BGM)en_US
dc.description.sdgSDG-02:Zero Hungeren_US
dc.description.sdgSDG-03:Good heatlh and well-beingen_US
dc.description.sponsorshipThe Agricultural Research Council—Postgraduate Development Program, Department of Land Reform, Agriculture and Rural Development and Agri-SETA.en_US
dc.description.urihttps://www.frontiersin.org/journals/microbiologyen_US
dc.identifier.citationNene, 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.en_US
dc.identifier.issn1664-302X (online)
dc.identifier.other10.3389/fmicb.2024.1487595
dc.identifier.urihttp://hdl.handle.net/2263/102285
dc.language.isoenen_US
dc.publisherFrontiers Mediaen_US
dc.rights© 2025 Nene, Kunene, Pierneef and Hadebe. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (CC BY).en_US
dc.subjectMicrobiomeen_US
dc.subjectCommunal production systemen_US
dc.subjectGallus domesticusen_US
dc.subjectSDG-02: Zero hungeren_US
dc.subjectSDG-03: Good health and well-beingen_US
dc.subjectNext generation sequencing (NGS)en_US
dc.subjectAntimicrobial resistance (AMR)en_US
dc.titleProfiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signaturesen_US
dc.typeArticleen_US

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