Comparative metagenomic along the gut biogeography of indigenous chicken.

Gut microbiome modulates host immune system, metabolism, adaptability and affects food safety. Unfortunately, information on the gut microbiome of African indigenous chicken remains scanty despite the contribution of this genetic resource to food and nutrition security in Africa. Therefore, our capacity to accurately quantify gut microbiome diversity is extremely relevant to formulate host specific nutrition requirement, novel veterinary therapy, adaptability and productivity strategies. In the current study, 16S rRNA gene high-throughput illumina sequencing was used to explore the metagenomic diversity of four gastrointestinal tract regions (crop, gizzard, jejunum, cecum) and liver in chicken. 80 biopsies were collected from sixteen individuals chicken fed on the same diet and reared under intensive farming system for 14-weeks period. The alpha diversity indexes exhibited similar pattern distribution within-sample and tend to increase along the GIT, with a pic noted in the jejunum. The beta diversity showed that cecum microbiota forms a distinct clustered from other GIT microbiota. Analysis of the GIT content and liver revealed heterogenous microbiota taxonomy dynamic along GIT organ and liver. Venn diagram and heatmap also demonstrate that each organ sections form a unique ecosystem on his own, each associated to a particular physiological function. These results confirm the suitability of using the 16S rRNA gene high-throughput illumina sequencing pipeline to accurately quantify gut metagenome. Further, the non-invasive sampling strategies from a single gut biogeography cannot give a clear map of the gut microbiome diversity because each organ section forms a particular ecosystem on his own.
Keys words: Gut biogeography, Comparative metagenomic, Indigenous chicken, 16S rRNA gene, illumina Miseq.