Feeder- and Drinker-Associated Microbiota Differ from Host-Associated Fecal Microbiota During a Commercial Broiler Production Cycle with Age-Associated Changes in Taxonomic Composition

Broiler chickens are continuously exposed to microorganisms in the production environment, but the relationship between microorganisms on bird-contact surfaces and fecal microbiota remains unclear. In this exploratory observational study, shotgun metagenomic sequencing was used to compare microbial communities in feeder- and drinker-associated surface samples and individual fecal samples during one production cycle in a single commercial system housing Ross 308 broilers. The dataset comprised 22 individual fecal samples collected on days 1, 7, 19, 27, and 39 and four composite feeder- or drinker-associated environmental surface samples collected on days 1, 19, 27, and 39. Taxonomic composition, alpha and beta diversity, differential taxonomic signatures, and genus-level co-abundance patterns were evaluated. Environmental samples had greater richness and were dominated by Proteobacteria and Bacteroidetes, whereas host-associated fecal samples were dominated by Firmicutes and lactobacilli. Sample type explained 20.0% of variation in Bray–Curtis distances and 15.5% in Binary Jaccard distances (both p = 0.001). Within host-associated samples, Firmicutes increased from 51.4% on day 1 to 93.6% on day 39, while Proteobacteria decreased from 26.5% to 1.4%. Despite these taxonomic changes, host-associated communities did not form statistically distinct clusters by sampling day. Within the investigated production system, host-associated fecal microbial communities differed from those detected on the sampled feeder and drinker surfaces, while the relative abundance of dominant fecal taxa varied across sampling days. These findings are specific to the investigated production system and production cycle.