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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Insect Control and Cotton Disease Research » Research » Publications at this Location » Publication #339119

Title: Utilization of pyrosequencing to monitor the microbiome dynamics of probiotic treated poultry (Gallus gallus domesticus) during downstream poultry processing

item GUTTALA, V - Stephen F Austin State University
item Medrano, Enrique
item BRAY, J - Stephen F Austin State University
item CLACK, B - Stephen F Austin State University

Submitted to: Agricultural Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/25/2017
Publication Date: 7/28/2017
Citation: Guttala, V.P., Medrano, E.G., Bray, J., Clack, B. 2017. Utilization of pyrosequencing to monitor the microbiome dynamics of probiotic treated poultry (Gallus gallus domesticus) during downstream poultry processing. Agricultural Sciences. 8:675-691.

Interpretive Summary: Poultry production is an international industry that is of particular importance to U. S. producers and consumers. Bird rearing facilities have traditionally administered antibiotic growth promoters (AGP) to control bacterial infections. A major disadvantage of AGP utilization is that they are conducive to providing an environment that both promotes and has produced antibiotic resistant strains of human pathogens. Preliminary work indicates that probiotics could be inoculated into poultry as an alternative method control disease causing bacteria. Probiotics consist of beneficial non-pathogenic microorganisms that either eliminate or reduce pathogens. Currently, traditional microbiological culture and characterization protocols are employed to determine the efficacy of a probiotic. Unfortunately, the materials and methods are expensive and time consuming. This work used next-generation pyrosequencing to determine if the technology could be applied as a cost effective and efficient means to examine microbiome effects of subjecting birds to a probiotic. The probiotic used in this work was determined to negligibly reduce pathogens. Nonetheless, the state of the art pyrosequencing platform was found to indeed be a powerful and resourceful tool to quickly assess the effectiveness of probiotics. In conclusion, high-throughput sequencing was shown to have the capacity to streamline the probiotic screening process and ultimately will provide poultry producers a cost savings means to decrease pathogens during production.

Technical Abstract: Antibiotic growth promoters that have been historically employed to control pathogens and increase the rate of animal development for human consumption are currently banned in many countries. Probiotics have been proposed as an alternative to control pathogenic bacteria. Traditional culture methods typically used to monitor probiotic effects on pathogens possess significant limitations such as a lack in sensitivity to detect fastidious and non-culturable bacteria, and are both time consuming and costly. Here, we tested next-generation pyrosequencing technology as a streamline and economical method to monitor the effects of a probiotic on microbial communities in juvenile poultry (Gallus gallus domesticus) after exposure to several microbiological challenges and litter conditions. Seven days and repeated again at 39 days following hatching, chicks were challenged with either Salmonella enterica serovar Enteritidis, Campylobacter jejuni, or no bacteria in the presence of, or without a probiotic (i.e., Bacillus subtilis) added to the feed. Three days following each of two challenges (i.e., days 10 and 42, respectively) the microbiome distribution of the poultry caecum were characterized based on 16S rDNA analysis. Generated PCR products were analyzed by automated identification of the samples after pooling, multiplexing and sequencing. A bioinformatics pipeline was then employed to identify microbial distributions at the phylum and genus level for the treatments. In conclusion, our results demonstrated that pyrosequencing technology is a rapid, efficient and cost-effective method to monitor the effects of probiotics on the microbiome of poultry propagated in an agricultural setting.