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Study

Study Name: Surface microbial communities from dairy processing plant in Ireland

Projects

Biosamples

Organisms

Biosamples: 5 Seq. Projects: 5
STUDY INFORMATION
GOLD Study ID Gs0153900
Study Name Surface microbial communities from dairy processing plant in Ireland
Other Names
NCBI Umbrella Bioproject Name
NCBI Umbrella Bioproject ID
SRA Studies
SRA Study Id ERP122763  (Link to NCBI )
Study Title Microbiome-based environmental monitoring of a dairy processing facility using Oxford Nanopore Technologies rapid MinION sequencing as well as Illumina based sequencing
Study Abstract Food processing environments can harbor microorganisms responsible for food spoilage or foodborne disease. Efficient and accurate identification of microorganisms throughout the food chain can allow the identification of sources of contamination and the implementation of control measures. Currently, microbial monitoring of the food chain relies heavily on culture-based techniques. These assays are selected on the basis of the microbes expected to be present in the environment, and thus do not cater for unexpected contaminants. Many culture-based assays are also unable to distinguish between undesirable taxa and closely related harmless species. Furthermore, even when multiple culture-based approaches are used in parallel, it is still not possible a comprehensively characterize the entire microbiology of a food-chain sample. High throughput DNA sequencing represents a potential means through which microbial monitoring of the food chain can be enhanced. While sequencing platforms, such as the Illumina MiSeq, NextSeq and NovaSeq, are most typically found in research or commercial sequencing laboratories, newer portable platforms, such as the Oxford Nanopore Technologies (ONT) MinION, offer the potential for rapid analysis of food chain microbiomes. In this study, having initially assessed the ability of rapid MinION-based sequencing to discriminate between different components of a simple mock metagenomic mixture of related food spoilage, spore-forming microorganisms, we proceeded to compare outcomes from ONT and Illumina sequencing of metagenomic DNA obtained from environmental monitoring in an active food processing facility. Overall, ONT MinION sequencing provided accurate classification to species level, which was comparable to Illumina-derived outputs. However, while the MinION-based approach provided a means of easy library preparations and portability, the high concentrations of DNA needed to run the rapid sequencing protocols can be a limiting factor, requiring the random amplification of template DNA in order to generate sufficient material for analysis.
  
Legacy ER Study ID
Legacy GOLD ID
Added By JGI automated process on 2021-03-18
Last Modified By
PI
Description The goal of this study is to compare the performance of both ONT and Illumina sequencing for environmental monitoring of an active food processing facility
Relevance
Study Information Link
Study Information Visibility Public
Metagenomic Study Yes
Publication
Is GEBA
Is HMP
ECOSYSTEM CLASSIFICATION
Ecosystem Engineered
Ecosystem Category Built environment
Ecosystem Type Dairy processing facility
Ecosystem Subtype Unclassified
Specific Ecosystem Unclassified
STUDY COMPOSITION
Number of Biosamples 5
Number of Organisms 0
Number of Seq Projects 5
Number of Analysis Projects 0
Number of Related Studies 0

 

 

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