Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

ABSTRACT 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 commo...

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Autores principales:	Shaoting Li, David Ames Mann, Shaokang Zhang, Yan Qi, Richard J. Meinersmann, Xiangyu Deng
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2020
Materias:	chicken microbiome shotgun metagenomics antimicrobial resistance Salmonella Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/b55408d4dfba405ba09d2461f90181f1
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spelling	oai:doaj.org-article:b55408d4dfba405ba09d2461f90181f12021-12-02T19:46:19ZMicrobiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes10.1128/mSystems.00589-202379-5077https://doaj.org/article/b55408d4dfba405ba09d2461f90181f12020-10-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSystems.00589-20https://doaj.org/toc/2379-5077ABSTRACT 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 underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not 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. IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. 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, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.Shaoting LiDavid Ames MannShaokang ZhangYan QiRichard J. MeinersmannXiangyu DengAmerican Society for Microbiologyarticlechickenmicrobiomeshotgun metagenomicsantimicrobial resistanceSalmonellaMicrobiologyQR1-502ENmSystems, Vol 5, Iss 5 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	chicken microbiome shotgun metagenomics antimicrobial resistance Salmonella Microbiology QR1-502
spellingShingle	chicken microbiome shotgun metagenomics antimicrobial resistance Salmonella Microbiology QR1-502 Shaoting Li David Ames Mann Shaokang Zhang Yan Qi Richard J. Meinersmann Xiangyu Deng Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
description	ABSTRACT 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 underinvestigated. Microbiomes of retail chicken breast from 4 processing establishments in 3 major U.S. broiler production states displayed longitudinal consistency over 7 months and cross-sectional distinctiveness associated with individual processing environments. Packaging type and processing environment but not 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. IMPORTANCE Chicken has recently overtaken beef as the most-consumed meat in the United States. The growing popularity of chicken is accompanied by frequent occurrences of foodborne pathogens and increasing concerns over antibiotic usage. 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, we established the chicken microbiome as a robust and multifaceted food microbiology attribute that could provide a variety of safety and quality information and retain systematic signals characteristic of overall processing environments.
format	article
author	Shaoting Li David Ames Mann Shaokang Zhang Yan Qi Richard J. Meinersmann Xiangyu Deng
author_facet	Shaoting Li David Ames Mann Shaokang Zhang Yan Qi Richard J. Meinersmann Xiangyu Deng
author_sort	Shaoting Li
title	Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
title_short	Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
title_full	Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
title_fullStr	Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
title_full_unstemmed	Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes
title_sort	microbiome-informed food safety and quality: longitudinal consistency and cross-sectional distinctiveness of retail chicken breast microbiomes
publisher	American Society for Microbiology
publishDate	2020
url	https://doaj.org/article/b55408d4dfba405ba09d2461f90181f1
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Microbiome-Informed Food Safety and Quality: Longitudinal Consistency and Cross-Sectional Distinctiveness of Retail Chicken Breast Microbiomes

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