2020 Yeast Sequencing

This week I decided it was probably time to toss my sourdough starters out. They had served their experimental purpose, but I was definitely saddened to be finished with them.

The DNA of our starters are being sequenced this week because we are trying to determine exactly what types of microbes are growing in the starters. We want to know if there’s yeast, bacteria, or both and what species of microbes they are. The end goal of the class project is to see if different fruits have different microbes on them and if they alter the starters, which would help to explain the cultural variations of bread in whatever region these fruits are grown in.

Before this class I knew a bit about DNA sequencing from prior work in a plant genetics lab. I have actually used PCR, Gel Electrophoresis and Sanger in the lab to isolate DNA. However, I don’t believe I’ve ever heard of NGS before.

The fundamental principles of Sanger and NGS are very similar, but the primary difference in the two methods is the volume of sequencing data during one run. NGS can sequence so much data because a “library” of DNA data must be created before so that it can be referenced.

The technology used for NGS is Illumina. From what I briefly gathered this technology appears to work by having sequences attach to other complimentary sequences as they move through a flow cell. Once a sequence binds it is amplified over and over again. Nucleotide bases are added one at a time and have fluorescent tags so each base pair emits a fluorescence which can be read by a computer program to determine the DNA sequence.

https://www.thermofisher.com/us/en/home/life-science/sequencing/sequencing-learning-center/next-generation-sequencing-information/ngs-basics/what-is-next-generation-sequencing.html

09/12-09/18/2020 Rising To The Top!

This week was the final week for growing my sourdough starter babies. 🙁

It’s strange how attached you can get to a cup of flour, water and microorganisms!

This past week my starters did not really change much at all. I continued to feed them on a 12 hour schedule. They never had a noticeable change in smell and the texture never changed that much. I believe they got a little bit thicker by the end of this week, but overall, they were still like a soupy consistency. The starters would rise and then fall pretty consistently, but not a lot, (as seen by the results below).

Quantifying Starter Rising

Top Left: Absolute Starter Height Bottom Right: Starter Height Percent Increase

In Central/South America where bananas are often cultivated and grown there are many types of bread eaten by the people that live in the region. Just a few examples of breads include: Pupusa, Hojaldres, Pan de Coco, and Quesadilla Salvadorena. Many of these types of bread are savory and buttery, often a street food or a treat. Many don’t seem to be very similar to sourdough because they are very dense, more like a pita bread.

https://www.tasteatlas.com/central-america/breads

09/04/20-09/11/20 Smells like … Alcohol?

On 09/04 both starters have some bubbles on top of a thin layer of hooch. They both smelled primarily of alcohol.

From 09/05 to 09/09 both of the starters had no visible change in appearance or smell. I followed a consistent 12 hour feeding schedule for these four days.

On 09/10 I was not able to feed either starters for the whole 24 hour period.

The next day, 09/11, there was a very large hooch that had formed on both the starters. Also, there were very few visible bubbles which did have me concerned a little bit.

During this whole week both starters have maintained the same consistency. They are still a little soupy, neither are very thick and sticky yet.

In my fruit starter I used a banana slice/peel. Banana’s originate from South East Asia, specifically in regions of India. Arabic people brought them from SE Asia to Africa and from there they spread to the Caribbean and South/Central America. In the Americas bananas are very culturally important and are eaten in many forms. Banana’s are also eaten a lot in African countries. For example, in Somali bananas are served with almost every meal to be cut up and put into the food.

https://community.plu.edu/~bananas/brief-history/#:~:text=Bananas%20were%20originally%20found%20in,and%20missionaries%20to%20the%20Caribbean.

https://www.huffpost.com/entry/somalian-food-banana_n_589b4c18e4b09bd304bf2c1b?guccounter=1&guce_referrer=aHR0cHM6Ly93d3cuZ29vZ2xlLmNvbS8&guce_referrer_sig=AQAAAFp28mpc5UCcOIjVHcgy6WaAVTO9krToZMr98Zbr5Gcr0zz9DDUH4DQMI_asQfcHIcaQxuZwPF0oIzSnNCLKEpZBDUUC7qaH2_6sANh5_XUWq-RwB95Nuz0Fu7yOgPBCHTko4e1NsU4KQVZd2sEoA4S35AM7F7sinkwxdMoQA-G_

New Smells and Bubbles! 08/29-09/03/2020

Beginning on 08/30 both the control and banana starters began to smell less like trash and more like yeast. You know, that “yeasty bready” smell I’m talking about. It smells kinda good, but still not great? Yeah, that’s the smell I’m talking about. Both of the mixtures also started to lose their air bubbles, which did have me slightly concerned.

On 08/31 I discovered that both starters had developed very large amounts of liquid on top of the flour/water mixtures. This layer of liquid is called a “hooch” and it is the byproduct of yeast fermentation occurring in the starter. As the yeast consume the flour they produce an alcoholic byproduct. This development of a large hooch meant that my starters were getting hungry! I adjusted to a 12 hour feeding schedule afterwards. By that night both of the starters began to develop that classic sourdough “sour” smell that is so easily distinguishable.

By 09/02 the control starter had started to rise! It was filled with air bubbles and had a foam like appearance. However, the banana starter had not started to rise yet.

The next day (09/03) the control had risen again, and this time it no longer smelled of sourdough. It smelled like ethanol. This was a very interesting development. I wonder what will happen next….