Microbiome-Driven Biosecurity in Poultry Processing Plants: A Case Study

Thesis Abstract

The industrial-scale poultry processing sector faces persistent microbial threats that compromise product safety, traceability, and overall biosecurity, necessitating a deeper understanding of how resident microbiomes influence contamination dynamics and pathogen transmission. This study investigates the role of product-zone and facility-wide microbiomes as drivers of biosecurity outcomes in a commercial poultry processing plant located in the Southeastern United States, with specific focus on Salmonella and Campylobacter prevalence, facility hygiene indicators, and microbial community structure. The aim is to elucidate how microbiome configurations relate to biosecurity performance and to identify leverage points for risk-reduction interventions. The research objectives are (i) to characterize baseline microbial community profiles across processing stages (scalding, evisceration, chilling, and packaging) and on environmental surfaces (roller conveyors, chill tank liners, and cutting tables) using 16S rRNA gene amplicon sequencing and shotgun metagenomics; (ii) to quantify associations between microbial diversity metrics (alpha and beta diversity) and pathogen prevalence using multilevel logistic regression and PERMANOVA; (iii) to evaluate the influence of operational variables (temperature, pH, sanitizer regimes, downtime, and line speed) on microbiome composition through mixed-effects models; (iv) to develop a context-specific conceptual model integrating microbiome-driven pathways with conventional biosecurity controls; and (v) to propose evidence-based, microbiome-aware interventions for preharvest-to-processing continuity. A mixed-methods design combines quantitative microbial surveillance with qualitative interviews of line supervisors and sanitation personnel to capture operational practices and perceived control measures. The population comprises three value-stream lines within a single modern poultry processing facility, including 60 environmental swab sites sampled monthly over six months (n = 360 swabs) and 30 consecutive carcass rinse samples per month (n = 180). Data collection instruments include standardized swabbing protocols, real-time PCR screening for Salmonella and Campylobacter, 16S rRNA gene sequencing on Illumina MiSeq, whole-genome sequencing of isolates where detected, sanitizer efficacy assays, and structured interview guides. Validity and reliability are addressed through triplicate sampling on 20% of sites, external positive controls for PCR assays, Z-score normalization for sequencing data, and inter-rater reliability checks for interview coding. Data analysis employs regression-based modeling to relate microbiome features to pathogen detection outcomes, differential abundance analyses to identify indicator taxa, and network analysis to infer microbe–microbe interactions relevant to biosecurity risk. A conceptual model will be developed to integrate microbiome data with established HACCP-based controls, drawing on ecological theory and the precautionary principle. Theoretical underpinnings reference the Bray-Curtis dissimilarity approach for community comparison, Lotka-Volterra–inspired interaction frameworks for microbial networks, and the socio-ecological systems theory to interpret human–microbiome interactions within plant operations. Expected findings include (i) distinct microbiome signatures associated with low versus high pathogen prevalence across processing stages, (ii) evidence that certain sanitizer regimes alter microbial community structure in ways that suppress reservoirs of opportunistic pathogens, (iii) identification of core indicator taxa predictive of contamination risk, and (iv) actionable recommendations for microbiome-informed adjustments to cleaning frequencies, sanitizer rotations, and line sanitation sequencing. The study contributes to knowledge by bridging microbiome science with practical biosecurity management in poultry processing, advancing ecological and systems-thinking perspectives in industrial hygiene, and providing a validated framework for incorporating microbiome dynamics into HACCP and preventive controls. The main conclusion anticipates that managing microbiome configurations, not only pathogen presence, yields robust biosecurity benefits, and recommendations include routine microbiome monitoring, targeted sanitation optimization, and the adoption of microbiome-aware risk assessment tools within standard operating procedures.