Shotgun Metagenomics

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"Shotgun metagenomics, is the
untargeted (‘shotgun’) sequencing of all (‘meta-’) microbial genomes
‘genomics’ present in a sample. Shotgun sequencing can be used to
profile taxonomic composition and functional potential of microbial
communities and to recover whole genome sequences."

Shotgun metagenomics, from sampling
to analysis
Christopher Quince, Alan W Walker, Jared T Simpson, Nicholas J Loman & Nicola Segata

Sean Meaden, a research fellow at Exeter University, will be running ferment samples through a sequencing machine that allows us to process the dna population within a few days.  We hope to compare the make up of kimchi through its fermentation process as well as latent bacterial populations present on plants and leaves.  Here's a short description of the process written by Sean.

To monitor the microbes directly, we can use modern techniques that use the genetic blueprints of the bacteria to distinguish them. DNA is the substance that makes up this blueprint, much the same as humans and other animals and plants. All living things use DNA to encode their functions and we can ‘read’ the DNA using different technologies. Much like reading a book we can interpret what these strings of DNA letters mean for the biology of the bacteria.

To take this one step further, the genetic blueprints (or genomes) are all different. In a practical sense, we can use these differences to tell the bacteria apart and see which ones are thriving in the fermentation.

The way we look for these differences is to extract all the DNA in the sample- including all the vegetables and bacteria, then fish out a certain type of DNA. This piece of DNA is a gene that only the bacteria have and contains enough differences (i.e. a bunch of different letters scattered throughout the blueprint) to tell each species apart. The way we fish out this gene is to use bits of DNA that we design to stick onto the target gene we want. Once we have fished out these genes we can amplify them so we have enough to work with.

The next step is to read the DNA that we are interested in. To do this we take the pieces of DNA that we fished out of the sample and run it through a sequencing machine. This machine works by containing a membrane that has nano-sized holes in it. As the DNA passes through the hole, the membrane vibrates- and vibrates a little differently depending on the letter that passes through. We can then use computer algorithms to convert the signals from these vibrations into letters.

The last part of the process is to match up these strings of letters (or DNA sequences as they are known) to a dictionary that contains the sequences for thousands of bacterial species. From this we can get an idea about which bacteria are present in the ferment and how many of each one there are.

Ultimately, this allows us to see how the microbial community changes throughout the fermentation process. We can ask questions about where the microbes come from and how they interact with each other to create certain flavours