Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg

Authors: BUCHER, MAITE - University Of Georgia; ZWIRZITZ, BENJAMIN - University Of Veterinary Medicine; Oladeinde, Adelumola - Ade; Cook, Kimberly - Kim; PLYMEL, CAROLINE - University Of Georgia; ZOCK, GREGORY - University Of Georgia; AGGREY, SAMUEL - University Of Georgia; RITZ, CASEY - University Of Georgia; Looft, Torey; LIPP, ERIN - University Of Georgia; Agga, Getahun; Sistani, Karamat

Submitted to: Journal of Environmental Quality
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/3/2020
Publication Date: 4/14/2020
Citation: Bucher, M., Zwirzitz, B., Oladeinde, A.A., Cook, K.L., Plymel, C., Zock, G., Aggrey, S., Ritz, C., Looft, T.P., Lipp, E., Agga, G.E., Sistani, K.R. 2020. Reused poultry litter microbiome with competitive exclusion potential against Salmonella Heidelberg. Journal of Environmental Quality. 49(4):869-881. https://doi.org/10.1002/jeq2.20081.
DOI: https://doi.org/10.1002/jeq2.20081

Interpretive Summary: The practice of reusing “built-up” litter to raise multiple flock of chickens is known to promote the competitive exclusion of food-borne pathogens including Salmonella, however the mechanism and bacteria associated with this process is poorly understood. To gain a better understanding of the interactions between reused litter bacteria and pathogens, we inoculated Salmonella enterica serovar Heidelberg (S. Heidelberg) into “built-up” litter (bedding material that is intended for reuse on subsequent flock). Our results show that “built-up” litter reused after an adequate downtime (greater than 2 weeks between consecutive flocks, during which the broiler house is empty) harbors a stable and predictable microbiome dominated by two groups of bacteria. These bacteria were associated with a reduction in S. Heidelberg survival in reused litter (up to a million-fold reduction). This study supports the notion that the practice of litter reuse promotes an “unfavorable” environment for S. Heidelberg and highlights the reused litter bacteria associated with this phenomenon.

Technical Abstract: The success of poultry litter reuse in US poultry production can be attributed to the efficient treatment methods used by producers during downtimes (the time lapse between consecutive flocks, during which the broiler house is empty). During this period, reused “built-up” litter may be decaked, tilled/windrowed or treated with acid-based amendments to reduce ammonia and bacteria levels. Competitive exclusion, pH and temperature are proposed factors that influence the level of pathogens and the overall litter microbiome during downtimes. We previously reported on the bacterial genetic factors associated with the fitness of two strains of Salmonella enterica serovar Heidelberg (S. Heidelberg) incubated for 14 days in “built-up” litter collected after birds were removed. Here, we investigated the physicochemical parameters and the microbiome of the litter associated with S. Heidelberg persistence. The ß-diversity of the litter microbiome was significantly affected by the duration of incubation, microcosm and microcosm - Heidelberg strain combinations. In addition, ß-diversity was significantly affected by litter parameters including NH4, pH, moisture, water activity and Aluminum. The major phyla observed present in the reused litter throughout the 14-day incubation experiment were Firmicutes and Actinobacteria, although their abundance differed by microcosm and time. Amplicon specific variants homologous to the members of the genera Nocardiopsis, Ruania, Lentibacillus, Virgibacillus and the family Bacillaceae_2 were identified to be associated with a reduction in Salmonella populations.