The poultry-associated microbiome: network analysis and farm-to-fork characterizations

Area of Science:

• Microbiology
• Food Science
• Animal Science

Background:

• Microbial communities in agricultural animals impact animal health, food safety, and public health.
• Understanding the poultry microbiome across the production chain is crucial for monitoring and control.

Purpose of the Study:

• To profile the poultry-associated microbiome and key pathogens using high-throughput sequencing (HTS).
• To analyze microbial community dynamics from farm to consumer, including processing stages.
• To investigate interactions of foodborne pathogens like Campylobacter within the microbiome.

Main Methods:

• High-throughput sequencing (HTS) for microbiome profiling.
• Quantitative-PCR assays for pathogen quantification.
• Network analysis to study microbial interactions.
• Longitudinal sampling of poultry flocks from farm through processing.

Main Results:

• A core microbiome was identified, including potentially pathogenic genera (Campylobacter, Clostridium, Shigella).
• Poultry processing significantly reduced overall microbial richness and Campylobacter abundance.
• Carcasses post-processing harbored unique taxa, including anaerobes and Campylobacter strains.
• Retail products were dominated by Pseudomonas but contained other genera found on-farm.
• Network analysis showed limited interactions for most Campylobacter types, suggesting challenges in competitive exclusion.

Conclusions:

• HTS is valuable for monitoring the food supply chain and identifying zoonotic disease sources.
• Microbial communities in poultry undergo significant shifts during processing.
• Understanding microbial interactions is key to controlling pathogens like Campylobacter in poultry.