Analysis of the Difference of Intestinal Microbes in Muchuan Black-bone Chickens with Two Skin Colors

Background: Skin color is an important economic trait in black-bone chicken production and it has been identified that the gut microbiota is an important factor in animal health and physiology. However, it is unknown about whether the gut microbiota in black-bone chickens is connected to the coloration of chicken skin. Methods: To investigate the relationship between the gut microbiota and skin coloration, comparing the differentiation of the gut microbiota structure and abundances in black- (B group) and white-skinned (W group) Muchuan black-bone chicken. Here, we characterized the microbiota in the jejunal contents of both the B and W groups using the Illumina MiSeq platform, targeting the genomic V4 region of the 16S rRNA gene. Result: In terms of community richness, the ACE community richness index of the B group was significantly higher than that of the W group (p less than 0.05) and the proportion of unique OTUs was higher in group B than in group W. According to the species annotation and abundance information of all samples at the genus level, Parabacteroides, Faecalicoccus and Alistipes were enriched in group B, whereas Actinomyces, Elstera and Nosocomiicoccus were enriched in group W. In the evolutionary branch diagram, the relative abundances of Enterobacteriaceae (Gammaproteobacteria, Enterobacteriales) were significantly higher in group B than in group W (LDA Score greater than 4). Our data provide a basis for the hypothesis that the discriminating bacterial taxa in gut is associated with the feature variants for skin coloration of Muchuan black-bone chickens, which were fed in the same feed and stocking niches.