Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

Abstract Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monit...

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Autores principales:	Aoife J. McHugh, Min Yap, Fiona Crispie, Conor Feehily, Colin Hill, Paul D. Cotter
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Nutrition. Foods and food supply TX341-641 Food processing and manufacture TP368-456
Acceso en línea:	https://doaj.org/article/bd599ca5d2f04504824bdb107983495e
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spelling	oai:doaj.org-article:bd599ca5d2f04504824bdb107983495e2021-12-02T14:21:42ZMicrobiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples10.1038/s41538-021-00087-22396-8370https://doaj.org/article/bd599ca5d2f04504824bdb107983495e2021-02-01T00:00:00Zhttps://doi.org/10.1038/s41538-021-00087-2https://doaj.org/toc/2396-8370Abstract Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.Aoife J. McHughMin YapFiona CrispieConor FeehilyColin HillPaul D. CotterNature PortfolioarticleNutrition. Foods and food supplyTX341-641Food processing and manufactureTP368-456ENnpj Science of Food, Vol 5, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Nutrition. Foods and food supply TX341-641 Food processing and manufacture TP368-456
spellingShingle	Nutrition. Foods and food supply TX341-641 Food processing and manufacture TP368-456 Aoife J. McHugh Min Yap Fiona Crispie Conor Feehily Colin Hill Paul D. Cotter Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
description	Abstract Efficient and accurate identification of microorganisms throughout the food chain can potentially allow the identification of sources of contamination and the timely implementation of control measures. High throughput DNA sequencing represents a potential means through which microbial monitoring can be enhanced. While Illumina sequencing platforms are most typically used, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. Initial assessment of the ability of rapid MinION-based sequencing to identify microbes within a simple mock metagenomic mixture is performed. Subsequently, we compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility. Overall, ONT MinION sequencing provides accurate classification to species level, comparable to Illumina-derived outputs. However, while the MinION-based approach provides a means of easy library preparations and portability, the high concentrations of DNA needed is a limiting factor.
format	article
author	Aoife J. McHugh Min Yap Fiona Crispie Conor Feehily Colin Hill Paul D. Cotter
author_facet	Aoife J. McHugh Min Yap Fiona Crispie Conor Feehily Colin Hill Paul D. Cotter
author_sort	Aoife J. McHugh
title	Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title_short	Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title_full	Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title_fullStr	Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title_full_unstemmed	Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title_sort	microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/bd599ca5d2f04504824bdb107983495e
work_keys_str_mv	AT aoifejmchugh microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples AT minyap microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples AT fionacrispie microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples AT conorfeehily microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples AT colinhill microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples AT pauldcotter microbiomebasedenvironmentalmonitoringofadairyprocessingfacilityhighlightsthechallengesassociatedwithlowmicrobialloadsamples
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Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples

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