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ORIGINAL RESEARCH article

Front. Microbiol.
Sec. Microorganisms in Vertebrate Digestive Systems
Volume 15 - 2024 | doi: 10.3389/fmicb.2024.1487595
This article is part of the Research Topic Parasite, Host, and Microbiome Interactions in Natural Host Systems View all 8 articles

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

Provisionally accepted
Mxolisi Nene Mxolisi Nene 1,2*Nokuthula Winfred Kunene Nokuthula Winfred Kunene 2Rian Pierneef Rian Pierneef 3Khanyisile Hadebe Khanyisile Hadebe 1*
  • 1 Biotechnology Platform, Agricultural Research Council of South Africa (ARC-SA), Pretoria, South Africa
  • 2 University of Zululand, KwaDlangezwa, South Africa
  • 3 Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South Africa

The final, formatted version of the article will be published soon.

    The production environment of extensively raised chickens necessitates the adaptability of these animals, with the hypothesis that gut microbial populations are pivotal for their survival in lowresource production systems. This study aimed to elucidate the diversity and functional capacities of the faecal microbiome in village chickens from Limpopo and KwaZulu-Natal province of South Africa, utilizing two approaches: 16S rRNA gene and shotgun metagenomic sequencing technologies. A total of 98 16S rRNA gene and 72 metagenomic datasets were generated. The taxonomic analysis revealed that in Limpopo, the predominant phyla were Firmicutes, Bacteroidota, Proteobacteria, and Actinobacteria, while KwaZulu-Natal exhibited a similar trend with Firmicutes, Proteobacteria, Bacteroidota, and Actinobacteria. Notably, the genera Escherichia and Shigella were prevalent in both regions, with Escherichia coli and Shigella dysenteriae identified as significant contributors to the gut microbiome. Antibiotic resistance genes (ARGs) were detected, with MarA, PmrF, and AcrE identified in KwaZulu-Natal, and cpxA, mdtG, and TolA in Limpopo, indicating mechanisms of antibiotic efflux and alteration. The findings underscore the necessity for improved household hygiene practices to mitigate zoonotic transmission risks associated with these bacteria, particularly Escherichia coli and Streptococcus spp., which pose potential health threats to humans through the food chain. This underscores the need for targeted interventions and further research to mitigate risks associated with village chicken farming in South Africa. This study highlights the critical role of the gut microbiome in the health and adaptability of village chickens, linking microbial diversity to production efficiency in low-resource settings.

    Keywords: Next Generation Sequencing1, Microbiome 2, Communal production system 3, antimicrobial resistance4, Gallus domesticus 5

    Received: 02 Sep 2024; Accepted: 13 Nov 2024.

    Copyright: © 2024 Nene, Kunene, Pierneef and Hadebe. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence:
    Mxolisi Nene, Biotechnology Platform, Agricultural Research Council of South Africa (ARC-SA), Pretoria, South Africa
    Khanyisile Hadebe, Biotechnology Platform, Agricultural Research Council of South Africa (ARC-SA), Pretoria, South Africa

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