Secondary analysis of the intestinal microbiota of healthy chickens

The intestinal microbiota plays a key role in poultry health and performance. Its composition is influenced by multiple factors such as diet, age, bird type, and housing. The aim of this secondary analysis was to summarize existing data and outline a baseline reference intestinal microbiota that could serve as a reference for future research and industry applications. For this, the intestinal microbiota of chickens across all intestinal segments and feces under standard conditions, without feed additives or infections were compiled and analyzed. A total of 3,562 samples from 79 BioProjects were retrieved from the National Center for Biotechnology Information database, together with their metadata including intestinal segment, bird type, age, housing system, continent, and sequenced hypervariable region. Across all samples, 2,603 unique bacterial genera in 73 phyla were identified, with Firmicutes being the most abundant phylum in all segments. The number of core genera was highest in the ceca, followed by the duodenum. Alpha diversity was highest in the ceca and lowest in feces, as well as highest in Africa and lowest in North America. For beta diversity, Principal Component Analysis revealed a minor overlap among intestinal segments and a major overlap for the other investigated factors. Metabolic pathway predictions revealed 8,674 unique functional orthologs (FOs), with the relative abundance of about 40 to 60% of the FOs constant across intestinal segments and other investigated factors. In conclusion, while microbial community composition may vary substantially between different flocks or production systems, core metabolic functions are often consistent. These findings provide a baseline framework for evaluating how treatments, infections, or management practices may impact the chicken intestinal microbiota.