Microbiomic Investigation of the Poultry Production Chain: Using Next Generation Sequencing to Study General Microbial and Foodborne Pathogen Dynamics.

There has been a recent effort to look at production systems as an entire “farm to fork” continuum to better understand what is occurring physically, chemically, and biologically within our food chains.  These types of studies are especially applicable to human and environmental health issues, although to understand the microbial complexity inherent in these systems (and the interactions of specific microbial groups of interest with the entire microbial community), these communities need to be exhaustively surveyed.  Technological advances in next generation sequencing technologies allow for the depth of community coverage necessary to potentially observe some of these vitally important human and environmental health microbial interactions.  Two separate studies were performed using microbiomic approaches (using the Illumina MiSeq platform) to determine the microbial and foodborne pathogen diversity within the different sample types.  Additionally, each study also had their own specific goal.  In one study, litter and fecal samples representative of an entire house were collected, and the effect of DNA extraction method (DNA release from matrix by physical, chemical, or a combination means) on the recovered microbiomes for both sample types.  In a second study, processing water samples from the scalder and chiller tanks were temporally sampled (Prior to first line, mid-run, after the last line) to determine the changes in the microbiomes within these tanks throughout a typical production cycle.  Both of these studies allow for a better understanding of general microbial and foodborne pathogen diversity and dynamics within the poultry production chain, as well as elucidating correlations between the microbiomic data and the “gold standard” cultural techniques (targeting Salmonella spp., Campylobacter spp., E. coli 0157:H7, Clostridium perfringens, Listeria monocytogenes).  These combined datasets can act as a starting point towards directing interventions toward minimizing the environmental and human health impacts of the poultry industry.