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

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...

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Autores principales: McHugh, Aoife J., Yap, Min, Crispie, Fiona, Feehily, Conor, Hill, Colin, Cotter, Paul D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884712/
https://www.ncbi.nlm.nih.gov/pubmed/33589631
http://dx.doi.org/10.1038/s41538-021-00087-2
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author McHugh, Aoife J.
Yap, Min
Crispie, Fiona
Feehily, Conor
Hill, Colin
Cotter, Paul D.
author_facet McHugh, Aoife J.
Yap, Min
Crispie, Fiona
Feehily, Conor
Hill, Colin
Cotter, Paul D.
author_sort McHugh, Aoife J.
collection PubMed
description 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.
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spelling pubmed-78847122021-02-25 Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples McHugh, Aoife J. Yap, Min Crispie, Fiona Feehily, Conor Hill, Colin Cotter, Paul D. NPJ Sci Food Article 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. Nature Publishing Group UK 2021-02-15 /pmc/articles/PMC7884712/ /pubmed/33589631 http://dx.doi.org/10.1038/s41538-021-00087-2 Text en © The Author(s) 2021 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
McHugh, Aoife J.
Yap, Min
Crispie, Fiona
Feehily, Conor
Hill, Colin
Cotter, Paul D.
Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples
title 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_short 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
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7884712/
https://www.ncbi.nlm.nih.gov/pubmed/33589631
http://dx.doi.org/10.1038/s41538-021-00087-2
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