The Poultry-Associated Microbiome: Network Analysis and Farm-to-Fork Characterizations

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.

Correlation detection strategies in microbial data sets vary widely in sensitivity and precision

“…This notion is supported by the observation that phylogenetically related microbes have a tendency to positively co-occur (Lozupone et al, 2012). Recent studies suggest that the microbial relationships shown in correlation interaction networks can be used to determine drivers in environmental ecology (Ruan et al, 2006;Steele et al, 2011;Zhou et al, 2011;Lima-Mendez et al, 2015) or contribution to habitat niches or disease (Chaffron et al, 2010;Arumugam et al, 2011;Greenblum et al, 2012;Oakley et al, 2013;Goodrich et al, 2014;Buffie et al, 2015). Correlation is also a powerful tool to help researchers with hypothesis generation, such as determining which interactions might be biologically relevant in their system, and should be given further study (for example, through co-culturing or whole-genome sequencing).…”

The chicken gastrointestinal microbiome

“…Data from Tillman et al . () and Wise & Siragusa () are re‐analyzed from data included in (Oakley et al ., ) representing 8 and 10 birds, respectively. Kogut et al .…”

Assessing the microbiomes of scalder and chiller tank waters throughout a typical commercial poultry processing day

“…In terms of commercial poultry production and processing, microbial community studies have focused on gastrointestinal tract (Sekelja et al, 2012;Yeoman et al, 2012;Stanley et al, 2013;Sergeant et al, 2014), fecal (Sekelja et al, 2012;Singh et al, 2012;Stanley et al, 2015), litter (Dumas et al, 2011;Smith et al, 2014), carcass (Oakley et al, 2013), and raw retail poultry meat (Nieminen et al, 2012) samples; however, no study has specifically characterized commercial scalder and chiller water tank microbiomes. Therefore, in this study, Illumina MiSeq-based 16S rRNA-based pyrosequencing was used to characterize final scalder and chiller water tank microbiomes and investigate their dynamics during a typical commercial processing d, not only in terms of general microbial populations, but also to specifically target poultryassociated bacterial pathogens and spoilage organisms.…”