The Use of Pyrosequencing to Analyze the Treatments in Poultry Management Designed to Minimize Downstream Contamination

The use of antibiotic growth promoters in animals grown for human consumption has been banned in many parts of the world and is becoming less favorable in the US. With less or no antibiotics fed at subtherapeutic level, the risk of microbial contamination of food is higher when processed. In the current study, the objective was to identify and compare the effect of both ceca and litter microbial communities present before and after treatment. The treatments consisted of 1) challenging newborn chicks at 7th day and then again at 39th day of age with either Salmonella enteritidis or Campylobacter jejuni or no bacteria in the presence of or without probiotics added to the feed and 2) windrow composting or no composting of litter as part of poultry house management. Bacterial genomic DNA was isolated from both sets of samples using either the Promega SV Wizard Genomic DNA Purification kit (Ceca) or Zymo-spin soil microbe DNA midiprep kit (litter). The DNA from each sample was then amplified using 16S universal forward and reverse primers containing the specific Roche defined library-L specific sequences as well as Multiplex Identifiers (MID) to allow for automated software identification of the samples after pooling, multiplexing and sequencing. We report the bioinformatic pipeline and the microbial distributions at the genus and species level for each treatment.