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Metagenomics for determination of origin part 2 (full study) - FA0141

Description
The project will develop a model for inferring origin based on the microbial component of a product, in this case shellfish. The composition of microbial communities associated with a food/commodity is a product of the commodity itself, its geographical origin and its method of production. A previous scoping study has identified sufficient evidence to indicate that microbial community profiles can be used to indicate the origin of a food. We propose to further this community analysis work using next-generation DNA sequencing methods, which are able to generate many thousands to millions of DNA sequences in a single analysis and hence characterise microbial communities in minute detail.

We will assess variation in total bacterial communities associated with a model commodity (shellfish), analysing multiple samples from within a single geographical source as well as from multiple sources. Data analysis methods will be developed to take raw sequence output and present this as a comparison of whole microbial communities, indicating the extent of intra- and inter-site variation. Results will allow us to demonstrate the effectiveness of using microbial community analysis to determine the origin of shellfish samples. Moreover the project will present a worked example of how microbial community data can be used to test provenance. This work begun in project SD0468.
Objective
The primary outcome of the work will be the development and demonstration of a model for origin determination of a defined shellfish species based on microbial metagenome data. This will initially be accomplished for samples mainly from UK sources but the model will be scalable to incorporate samples from other sources in the future by wider sampling. The work will accumulate libraries of microbial community data that are indicative of origin.
This work will constitute a proof of concept that is adaptable to other evidence requirements where origin is of significance. For example:
• Verification of production method (eg organic/conventional)
• Identification/verification of ingredients (by sequencing genes from the food itself rather than the microbial component)
• Ascertaining origins of endangered species, for example timber
• Determining age of a product and more accurate prediction of shelf life (for waste reduction)
• Indication of seasonality of production (of importance for products that have a closed season)

Specific objectives (linked to milestones) are:
• Develop a sampling plan for a given food (we propose oysters) to provide samples suitable for subsequent sequence analysis to assess variation within and between geographical sources.
• Produce libraries of bacterial 16S DNA sequence from all samples, constituting a resource with which to assess variation
• Develop bioinformatic pipelines for analysis of bacterial community sequence data and comparison between communities
• Present a model for using microbial metagenomic data to indicate origin and assessment of timeline for implementation
Project Documents
• EVID4 - Final project report : FA0141 EVID4   (956k)
Time-Scale and Cost
From: 2013

To: 2014

Cost: £85,400
Contractor / Funded Organisations
F E R A (FERA)
Keywords
Food              
Food Chain