Competitive exclusion modulates broiler microbiota structure and microbial interaction networks

Competitive exclusion (CE) strategies represent a promising complementary approach to control foodborne pathogens in poultry production by modulating gut microbiota assembly. This field study evaluated the impact of a CE intervention applied at chick placement on cloacal microbiota temporal development, structure, and pathogen integration in commercial broiler chickens. Fifteen broiler farms with a history of Salmonella Infantis persistence were enrolled, including CE-treated farms and untreated controls. Cloacal samples were collected at 7, 18, 31, and 42 days of age and analyzed by 16S rRNA gene amplicon sequencing. Microbiota dynamics were evaluated through diversity metrics, differential abundance analysis, and microbial association network inference. CE treatment significantly altered microbiota composition and structure throughout the production cycle. Treated flocks showed a progressive increase in microbial richness and Shannon diversity from day 18 onward, while evenness remained largely unaffected. Beta-diversity analyses revealed persistent separation between treated and Un-Treated communities at all time points, indicating long-lasting treatment effects. Differential abundance analysis highlighted enrichment of beneficial genera, including Lactobacillus, Faecalicoccus, Roseburia, and Butyricimonas, in treated birds, whereas untreated flocks showed higher relative abundances of Campylobacter and other taxa associated with unstable community dynamics. Microbial network analysis revealed marked treatment-dependent differences in community organization. CE-treated networks exhibited higher modularity and edge density, suggesting increased structural complexity and potential resilience. Notably, Campylobacter showed strong early network integration and hub-like behaviour in untreated birds, while being completely disconnected in treated flocks at early life stages, indicating reduced ecological embedding. Overall, these findings demonstrate that competitive exclusion modulates broiler microbiota not only at the compositional level but also through restructuring microbial interaction networks. Early-life microbiota modulation appears to constrain pathogen ecological integration, providing a mechanistic framework for microbiota-driven control strategies under commercial poultry production conditions.