Management factors influence microbial ecology in commercial poultry

Background/Question/Methods

Housing of laying hens for commercial egg production may be configured as caged or cage-free systems, and further classified according to the manure collection methods. The consequences of alternative housing schemes for food safety and human and animal health are unclear. Management strategy and environmental factors may impact the diversity and composition of microorganisms within different housing operations, and the ecology of microbial communities in poultry housing may influence the probability of contamination of eggs by environmental bacteria and pathogens such as Salmonella and Campylobacter.  Samples of air, water, surfaces, eggs, dust, and feces were collected in three different types of laying-hen facilities (caged manure-belt, caged high-rise, and cage-free high-rise) in a large commercial midwest US poultry farm. Environmental variables including temperature, relative humidity, carbon dioxide, and aerial ammonia concentration were measured simultaneously. Automated ribosomal intergenic spacer analysis (ARISA) was used to compare microbial community composition within and among the housing units. Enrichment cultures were used to detect pathogens of interest, Salmonella and Campylobacter, in select samples.

Results/Conclusions

Bacterial community composition from most sample types was significantly different among distinct housing systems, suggesting the influence of management strategy and house environment on microbial community structure. In particular, manure management system (high rise vs. manure belt) was more strongly correlated with differences in microbial assemblages than caged/cage-free configuration for microbial communities observed in dust, on surfaces, and in fresh fecal samples. Humidity, aerial ammonia concentration and temperature) corresponded to the distinct microbial assemblages observed among houses with manure-management configurations. Flock size and space allowance were management variables that corresponded to the differences in microbial assemblages among the different housing configurations.

Salmonella and Campylobacter were detected in caged manure-belt (33% and 84% positive samples, respectively), caged high-rise (50% and 17%), and floor raised (17% and 100%) facilities via selective enrichment of fecal samples. Differences in pathogen prevalence among the housing systems suggest that management may be able to influence the poultry housing microbiome and niches available for pathogens. Characterization of microbial community structure in laying-hen housing and identification of those factors that influence microbial community structure may provide key insights into the control and prevention of the contamination of poultry eggs.