Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures
IntroductionThe 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 fu...
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Frontiers Media S.A.
2025-02-01
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| author | Mxolisi Nene Mxolisi Nene Nokuthula Winfred Kunene Rian Pierneef Rian Pierneef Rian Pierneef Khanyisile Hadebe |
| author_facet | Mxolisi Nene Mxolisi Nene Nokuthula Winfred Kunene Rian Pierneef Rian Pierneef Rian Pierneef Khanyisile Hadebe |
| author_sort | Mxolisi Nene |
| collection | DOAJ |
| description | IntroductionThe 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.MethodsUsing 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.ResultsTaxonomic 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.DiscussionThe 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 low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming. |
| format | Article |
| id | doaj-art-8ca039a773f14757bbb3bec76929754b |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-02-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj-art-8ca039a773f14757bbb3bec76929754b2025-02-04T06:32:03ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-02-011510.3389/fmicb.2024.14875951487595Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signaturesMxolisi Nene0Mxolisi Nene1Nokuthula Winfred Kunene2Rian Pierneef3Rian Pierneef4Rian Pierneef5Khanyisile Hadebe6Department of Agriculture, University of Zululand, Kwa Dlangezwa, South AfricaBiotechnology Platform, Agricultural Research Council, Ondersterpoort, South AfricaDepartment of Agriculture, University of Zululand, Kwa Dlangezwa, South AfricaDepartment of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South AfricaCentre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, South AfricaDSI/NRF SARChI in Marine Microbiomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South AfricaBiotechnology Platform, Agricultural Research Council, Ondersterpoort, South AfricaIntroductionThe 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.MethodsUsing 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.ResultsTaxonomic 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.DiscussionThe 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 low-resource settings. Targeted interventions and further research are crucial for mitigating zoonotic risks and enhancing sustainability in village chicken farming.https://www.frontiersin.org/articles/10.3389/fmicb.2024.1487595/fullnext generation sequencingmicrobiomecommunal production systemantimicrobial Resistancegallus domesticus |
| spellingShingle | Mxolisi Nene Mxolisi Nene Nokuthula Winfred Kunene Rian Pierneef Rian Pierneef Rian Pierneef Khanyisile Hadebe 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 next generation sequencing microbiome communal production system antimicrobial Resistance gallus domesticus |
| title | Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| title_full | Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| title_fullStr | Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| title_full_unstemmed | Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| title_short | Profiling the diversity of the village chicken faecal microbiota using 16S rRNA gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| title_sort | profiling the diversity of the village chicken faecal microbiota using 16s rrna gene and metagenomic sequencing data to reveal patterns of gut microbiome signatures |
| topic | next generation sequencing microbiome communal production system antimicrobial Resistance gallus domesticus |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2024.1487595/full |
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