Abstract
Microbial communities associated with agricultural animals are important for animal health, food safety, and public health. Here we combine high-throughput sequencing (HTS), quantitative-PCR assays, and network analysis to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2–4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were potentially metabolically active and encountered in on-farm samples. Network analysis was focused on the foodborne pathogen Campylobacter and revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. These data represent the first use of HTS to characterize the poultry microbiome across a series of farm-to-fork samples and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.
Highlights
As the source of a majority of emerging infectious diseases, animal-associated microbiomes represent a nexus of food safety, animal health, and public health [1,2,3]
Current dogma generally holds that poultry-associated Campylobacters are C. jejuni or C. coli, but our results show multiple sequence types present at low relative abundance more closelyrelated to C. consisus and C. showae than any known C. jejuni sequence
High-throughput sequencing of 16S rRNA gene amplicons has become a common method to investigate microbial communities in complex samples [26,82,83], but to our knowledge, this study demonstrates the first use of high-throughput sequencing (HTS) to characterize the poultry microbiome across a series of farm-to-fork samples
Summary
As the source of a majority of emerging infectious diseases, animal-associated microbiomes represent a nexus of food safety, animal health, and public health [1,2,3]. Colonization of poultry by microbes from environmental sources associated with commercial poultry production may have important biosecurity and management implications if human pathogens are transferred from environmental reservoirs through the poultry supply chain to consumers. This potential is recognized in the recently implemented Food Safety Modernization Act which emphasizes prevention of foodborne illness via monitoring of the entire food supply chain [16], and serves as a compelling mandate for a microbial census along what has been termed the ‘farm-to-fork’ continuum
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