Association of Broiler Litter Microbiome Composition and Isolation

Infection with species is one of the leading causes of bacterial diarrhea in humans in the US. Chickens, which become colonized on the farm, are important reservoirs of this bacterium. can establish itself in the broiler house via a variety of sources, can survive in the litter of the house, and possibly persist over successive flock cycles. However, the role of the broiler litter microbiome on persistence is not clear. A matched case-control study was conducted to determine whether the broiler litter microbiome composition was associated with isolation within the broiler house. Flocks were classified as cases when either or was isolated in boot sock samples, or as controls otherwise. Case and control flocks were matched at the broiler house level. Composite broiler litter samples were collected and used for DNA extraction and 16S rRNA gene V4 region sequencing. Reads were processed using the DADA2 pipeline to obtain a table of amplicon sequence variants. Alpha diversity and differential bacterial relative abundance were used as predictors of isolation status in conditional logistic regression models adjusting for flock age and sampling season. Beta diversity distances were used as regressors in stratified PERMANOVA with isolation status as predictor, and broiler house as stratum. When was isolated in boot socks, broiler litter microbiome richness and evenness were lower and higher, respectively, without reaching statistical significance. isolation status significantly explained a small proportion of the beta diversity (genus-level Aitchison dissimilarity distance). and were positively associated with isolation status, whereas , and were negatively associated. Our results suggest the presence of bacterial interactions between and the broiler litter microbiome. The negative association of with , and in litter could be potentially exploited as a pre-harvest control strategy.