Now that the sourdough starters have started to be DNA sequenced its time to talk about what exactly is being sequenced. There are two specific genes/regions within genomes that are being sequenced.
16S rRNA gene: found in bacterial cells
ITS region: found in eukaryotic cells such as yeast
To accomplish this sequencing the cells must lysed and all the debris must be removed until only the DNA is left. Then, a specific primer that will only attach to these genes is mixed in with the DNA solution and PCR is performed to make lots of copies of the targeted gene. Next, a unique “barcode” is added to each gene so it can be later identified. Finally, all the DNA samples are added to one tube and are sequenced using a computer program to generate useful genomic data.
When comparing shotgun and amplicon sequencing I believe it would be easier to prepare DNA for shotgun sequencing because it is not necessary to worry about tagging specific genes and introducing the correct primers to only amply them. However, when it comes to actually analyzing the results it would be a lot more tedious using shotgun because it would require working with thousands and thousands of genes and trying to find a particular gene would be like trying to find a needle in a haystack.
Some questions I have that could be answered by our sourdough genomic data:
Does adding fruit, such as a banana, change the microbial composition of a starter?
What sorts of “outliers” will be discovered? What kind of unique or interesting microbes will be found in some classmates starter samples?
Will all of my classmates control cups be gnomically very similar? Or will they be different based on the environmental conditions they grew in while in our homes?