Fecal Microbiota Profiling in Indigenous Backyard and Commercial Chickens Reveals Distinct Taxonomic Signatures

Farm management conditions and feeding practices in free-range (backyard), semi-intensive, or intensive production systems significantly influence the poultry gut microbiome, thereby impacting their productive performance and overall health. Here, fecal samples from asymptomatic indigenous backyard chickens raised in a free-range production system, characterized by little to no biosecurity measures in place, and from commercial chickens raised in an intensive production system with enhanced biosecurity measures were subjected to 16S rRNA sequencing analysis. Taxonomic assignment identified 19 bacterial phyla, 137 families, and 238 genera. The most prevalent phyla in indigenous backyard and commercial chickens were Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Spirochaetes. Similarities were detected between bacterial families and genera in both indigenous backyard and commercial chickens; however, the bacterial family Bacillaceae and genus Anoxybacillus were only observed in commercial chickens. Statistical tests performed to evaluate the alpha-diversity and beta-diversity metrics showed no significant difference in the fecal bacterial microbiota of indigenous backyard and commercial chickens, as indicated by the Wilcoxon rank-sum (p = 0.94) and PERMANOVA tests (p = 0.26). This study highlights bacteria that may affect the growth, development, and health of indigenous and commercial poultry raised under various production systems, thereby providing vital insights for the development of effective poultry farm management practices.