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Microbial metagenomics

Microbial metagenomics and the food industry

Imagine a world in which microbial populations are determined without needing to grow them on agar. Imagine being able to find organisms that we cannot culture in the lab. Imagine being able to pick up not just the healthy members of a community, but those that are injured as well. This is now a reality through a new technique known as 'Metagenomics'. The potential applications for this technique are limited only by the populations we can find, making it ideal for spoilage investigations, shelf life analyses and environmental monitoring (to name but a few!). It will also provide more information to the food manufacturer as the metagenomic “count” will be much more closely related to the mixture of species in the product. The following article aims to introduce the reader to this exciting new field of microbial analysis.

Technology and applications

Metagenomics is a technique that takes advantage of recent advances in DNA sequencing technology allowing huge numbers of different individual DNA sequences to be read at any one time. This means that the individual DNA sequences of a mixed bacterial population can be read directly from a single DNA extract of a food sample. The advantages of this are that previously uncultured organisms can be identified and little manipulation of is needed in order to produce data regarding the bacterial composition of that sample.

Currently if we wish to establish the bacterial types in a population present in a food (the microbiome), we would place dilutions of the food sample on different selective agar plates. The types of agar would be chosen by the microbiologist, according to what organisms they expected to be in the sample. This approach is very unstandardised and will introduce a bias into the results. Basically if an organism, however numerous in the sample, cannot grow on the agars chosen, they will never appear to the analyst and never be considered in any issue related to the food. This could result in an apparent invisibility of injured organisms, organisms that may affect quality or shelf life of products, or major spoilage groups simply because they cannot grow on the chosen agars.

The metagenomics approach reduces experimental biases that occur using the selective agar based approaches. Metagenomics worksbest for food samples which are expected to contain a mixed population of bacteria.