This week we are sequencing the sourdough samples that we have grown over the last few weeks. Unfortunately, my sourdough samples could not be used as they were not thick enough to be sequenced. This being said though, I can use the groups sequencing data so not all is lost!
For the sequencing itself, specific genes and regions of the genome from microorganisms found within the starter will be sequenced in order to identify what these species of microorganisms are. For bacteria, we will be looking at the 16S rRNA gene and for fungi, we will be looking at the ITS region of the genome to determine the specific species of bacteria or fungi found within each sourdough starter.
Sequencing data by just looking at specific genes instead of sequencing the entire genome comes with various pros and cons.
Pros: Becuase this type of sequencing can identify what kind of organism is present within the sample by using just a small sample of the DNA, this method is more efficient and easier to analyze because there is less data overall.
Cons: This type of sequencing requires extra steps such as copying the gene multiple times and using PCR whild sequencing the genome does not. Thus this process is more complicated and harder to complete. Also if some species of bacteria, for example, were very closely related, the genes and gene regions chosen may be identical in each species and we would need the entire genome to correctly identify these bacteria species. So with this type of sequencing we may not get an entirely complete result.
Once we have the sequenced data, I have a few research questions I want to ask.
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- How did the microorganisms found in the control samples compare to the fruit samples for each person?
- For this question, I want to understand if starters grown in the same area have the same microbial composition or if the composition depends more on the fruit used or the presence of fruit.
- Did the number of bacteria versus fungi and yeast affect the rising rate of each sample?
- For the question, I want to analyze whether the microbial composition of each sample affected how it performed on the rising rate experiment we performed a couple of weeks ago. I would also like to understand if there is a specific organism or species responsible for making the starters rise.
- How does the location the fruit came from, affect the microbe composition between all of the sequenced fruit samples?
- In this experiment, each person tried to use different fruit and each of these fruits came from different locations. Whether that be a local farmers market or a grocery store. I wonder if the location the fruit was grown affects the organisms living on the fruit and thus present in the sourdough starter.
- How did the microorganisms found in the control samples compare to the fruit samples for each person?