Microbiome-informed food safety and quality: Longitudinal consistency and cross-sectional distinctiveness of retail chicken breast microbiomes

Authors: LI, SHAOTING - University Of Georgia; MANN, DAVID - University Of Georgia; ZHANG, SHAOKANG - University Of Georgia; QI, YAN - University Of Georgia; ZHAO, SHAOHUA - Us Food & Drug Administration (FDA); Meinersmann, Richard - Rick; DENG, XIANGYU - University Of Georgia

Submitted to: mSystems
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/20/2020
Publication Date: 9/8/2020
Citation: Li, S., Mann, D.A., Zhang, S., Qi, Y., Zhao, S., Meinersmann, R.J., Deng, X. 2020. Microbiome-informed food safety and quality: A longitudinal and cross-sectional survey of retail chicken breast microbiomes. mSystems. 5(5): e00589-20. https://doi.org/10.1128/mSystems.00589-20.
DOI: https://doi.org/10.1128/mSystems.00589-20

Interpretive Summary: The microbiome is the sum total of all the microorganisms that live in a given habitat. The cross section of what species these are can influence the presence of other species. Knowing this can be useful as predictive surrogates and may be manipulated to control presence of certain pathogens. For this study, chicken breasts were sampled from 4 processing establishments under 5 brands over 7 months and the microbiomes were characterized by metagenomic DNA sequencing. The character of the microbiomes correlated with the processing establishment and even more with whether the product was vacuum packed or not. Birds from three establishments were raised "No Antibiotic Ever" (ABF); one of those establishments had a substantially elevated presence of antibiotic resistance genes compared to all the other establishments. The chicken microbiome is a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information with a fraction of sequencing capacity on a common DNA sequencing platform.

Technical Abstract: Background: Microorganisms and their communities on foods are important determinants and indicators of food safety and quality. Despite growing interests in studying food and food-related microbiomes, how effective and practical it is to glean various food safety and quality information from food commodity microbiomes remains under-investigated. Results: Chicken breast microbiomes of retail products from 4 processing establishments in 3 major US broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with processing environments. Packaging type and processing environment other than antibiotic usage and seasonality affected composition and diversity of the microbiomes. Low abundances of antimicrobial resistance genes were found on chicken breasts and no significant resistome difference was observed between antibiotic free and conventional products. Benchmarked by culture enrichment, shotgun metagenomics sequencing delivered sensitive and specific detection of Salmonella enterica from chicken breasts. Conclusion: Our study represents a proof-of-concept investigation into the possibility and practicality of leveraging microbiome-informed food safety and quality. Through a longitudinal and cross-sectional survey of a household item, we established chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information with a fraction of sequencing capacity on a common sequencing platform.