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Characterization of the cecal microbiome composition of Nigerian indigenous chickens

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Poultry cecum microbes are dynamic and complex. They play important roles in disease prevention, detoxification of harmful substances, nutrient processing, and ingestion harvesting. It may be possible to increase poultry productivity by better understanding and controlling the microbial population. We analyzed the composition and function of Nigerian hens’ cecal microbiota using high-throughput sequencing methods. Using high-throughput sequencing of the 16S rRNA genes (V1-V9) hypervariable regions, the cecal microbiota of three Nigerian indigenous chicken genotypes (Naked neck, Frizzle, and Normal feather) was described and compared. A total of two phyla were represented among the three genotypes (Firmicutes and Proteobacteria). Microbiological diversity was found in the community, with naked neck having the most evenness, followed by normal feather, which had the least. There were a lot of similarities between the naked neck and frizzle feather chicken groups when it came to genetic diversity between them. For example, the bacterial cecal microbiota of the naked neck chickens was more diverse, with a higher concentration of motility proteins, two-component systems, bacterial secretion systems, and the formation and breakdown of secondary metabolites. More understanding on gut microbiota roles and interactions will help Nigerian poultry farmers improve their methods and give valuable data for the study of bacteria in the chicken gut.

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Data availability

Raw sequence data is available in Sequence Read Archive (SRA) division of GenBank database. Weblink:

Code availability

The codes used are available on request from main author.


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AAS, AU, and ICON designed the work. AAS, AOO, and OO did the statistical analysis. AAS, AU, AOO, OO, AAO, AM, and ICON were involved in writing the manuscript. All the authors read and approved the final manuscript.

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Correspondence to A. S. Adenaike.

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Adenaike, A.S., Akpan, U., Awopejo, O.O. et al. Characterization of the cecal microbiome composition of Nigerian indigenous chickens. Trop Anim Health Prod 54, 211 (2022).

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