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

Area of Science:

• Animal Science
• Microbiology
• Agricultural Science

Background:

• Poultry production systems, including free-range (backyard) and intensive, significantly influence gut microbiome composition.
• Gut health is crucial for poultry performance and disease resistance.
• Biosecurity measures vary greatly between production systems.

Purpose of the Study:

• To compare the fecal bacterial microbiota of indigenous backyard chickens and commercial chickens raised under different production systems.
• To identify key bacterial taxa associated with different poultry farming environments.
• To assess the impact of production systems and biosecurity on poultry gut diversity.

Main Methods:

• Fecal samples were collected from indigenous backyard and commercial chickens.
• 16S rRNA sequencing was used for taxonomic analysis of the gut microbiota.
• Statistical tests (Wilcoxon rank-sum, PERMANOVA) were employed to compare alpha- and beta-diversity.

Main Results:

• Nineteen bacterial phyla, 137 families, and 238 genera were identified.
• Firmicutes, Proteobacteria, Bacteroidetes, Fusobacteria, and Spirochaetes were prevalent in both groups.
• No significant differences in alpha- or beta-diversity were found between the two chicken groups (p > 0.05).
• The family Bacillaceae and genus Anoxybacillus were exclusively found in commercial chickens.

Conclusions:

• Despite differences in farm management and biosecurity, the overall fecal bacterial microbiota composition showed no significant divergence between indigenous backyard and commercial chickens.
• Specific bacterial taxa, such as Bacillaceae and Anoxybacillus, may be associated with intensive commercial poultry farming.
• Findings provide insights for optimizing poultry farm management practices to enhance gut health and productivity.