ArticleNPJ science of food2021
Microbiome-based environmental monitoring of a dairy processing facility highlights the challenges associated with low microbial-load samples.
Article in NPJ science of food, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Emerging Microbiological and Sensor-Based Approaches for Biofilm Detection in Meat and Poultry Processing Environments.Foods (Basel, Switzerland) · 2026Review
- The food-associated resistome is shaped by processing and production environments.Nature microbiology · 2025Article
- Microbiome mapping in dairy industry reveals new species and genes for probiotic and bioprotective activities.NPJ biofilms and microbiomes · 2024Article
- Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake.Microbiome · 2024Article
- Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.Nature protocols · 2024Article
- Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome.mSphere · 2024Article
- Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment.Applied and environmental microbiology · 2023Article
- Microbial Dynamics during labneh Ambaris Production in Earthenware Jars.Foods (Basel, Switzerland) · 2023Article
- Artisanal Household Milk Pasteurization Is Not a Determining Factor in Structuring the Microbial Communities of Labneh Ambaris: A Pilot Study.Foods (Basel, Switzerland) · 2022Article
- Review
- Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study.Frontiers in microbiology · 2022Article
- Novel methods of microbiome analysis in the food industry.International microbiology : the official journal of the Spanish Society for Microbiology · 2021Review
- Full-Length SSU rRNA Gene Sequencing Allows Species-Level Detection of Bacteria, Archaea, and Yeasts Present in Milk.Microorganisms · 2021Article
- A Round Trip to the Desert:Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
6 authors.
Funding
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.
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Registered trials
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