Sequencing the starters

 Sequencing the starters

What are we sequencing? 

We are sequencing the starters to find what nucleotide sequences and microorganisms are present. Specifically we are sequencing the 16S rRNA gene which is bacterial and the ITS region which is fungal. https://ncsu.hosted.panopto.com/Panopto/Pages/Viewer.aspx?id=2288bbf2-6cd8-4faf-885b-acd8010517c2&start=15.579365  

Amplicon-based metagenomic sequencing

This type of DNA sequencing has pros and cons. When looking at the pros, this type of sequencing is frequently used for exactly what we are looking for, identifying microbial species. Cons to this type of sequencing is that it can be very time consuming with all the different tubes and containers and markers that are put in the samples to be able to tell which is which. It seems to me that the shotgun metagenomic sequencing would be easier because you don’t have to worry about doing everything that you do with amplicons before sequencing, you can just look at all the DNA without having to take the steps to separate amplicons. When it comes to analyzing the data, looking at specific amplicons seems much easier than having to look and interpret an entire genome. You can learn more from the shotgun metagenomic sequencing when dealing with more complex organisms because there are many more regions of DNA that can give useful information, rather than just two like with our sourdough starters.

Questions

Were there any microbes that were only present in the starters with a certain type of fruit?

What types of fruit make the more variety of microbes grow?

When comparing all the control starters to one another, why do they not all have the same amount and type of microbes present? What other factors can contribute to these differences?

QIIME practice analysis

ITS Data

From looking at this graph I took away that there could be an outside factor to what grows in the starters. I believe this to be true because starters in the same category have large variances in the types of fungi in them. For example the 2 applesauce starters have many different varieties of fungi relative to the other, the same is true for the 2 blueberry and 2 kiwi starters.

16S Data

From this data I took away that the microbes present in the starters at level 3 don’t have a lot to do with the fruit in the starter. There were a couple starters what had much different amounts bacterias present, but for the most part the amount and types of bacteria in the starters were consistent over all the starters, regardless of what fruit they contained.

Analyzing this data in QIIME was not too difficult. I like how we could change the categories of the axes and the colors of the bars. This made it much easier to read and interpret the graphs. The website let me do everything that I needed to in order to organize the data except for pick specific colors for the bars. All the color schemes on there were pre picked, which was still okay because there were multiple options.