Differences in microbial composition of litter and water line biofilm of broiler farms as influenced by water quality history

Abstract

Microbiome profiling of litter and drinking water lines of poultry environments is essential to understanding their role in the persistence and transmission of opportunistic and pathogenic microorganisms. While the litter environment is well characterized, the drinking water system has received less attention, despite its potential as a control point for Salmonella. In this study, we identified two groups of five farms based on historic water quality issues: normal sulfur-iron (NSIF) and high sulfur-iron (HSIF) content with the aim of assessing the incidence/quantity of Salmonella and characterize the microbiota of the litter and water line biofilms within the two farm groups. Our findings showed no differences in Salmonella incidence and quantity between the litter of both groups, while the biofilm of one of the HSIF farms had Salmonella. Common serotypes, such as Enteritidis, Infantis, Kentucky, and Typhimurium, were identified in the litter of both groups, while Agona, Alachua, and Schwarzengrund were unique to the NSIF group and Ouakam and Worthington to the HSIF group. Generally, the litter exhibited high microbial diversity compared to the biofilm. The litter of the NSIF group had lower alpha diversity than the HSIF group. Conversely, NSIF biofilms had higher alpha diversity than the HSIF biofilms. Distinct differences in microbial community composition were observed in the litter and biofilm of the two farm groups. Aerococcus, Lactobacillus, and Staphylococcus dominated the litter of the two groups, whereas probiotic (NSIF) and pathogenic (HSIF) Bacillus was the most prevalent in the biofilms. These results suggest that water quality issues could influence the microbiota of poultry house environments, particularly in water line biofilms. Effective removal of these biofilms is crucial for controlling Salmonella at pre-harvest poultry production.