Skip to main content

Research, Research, Research! (Week of 2/22)

 

This week, we'll be focusing on the research questions generated by our starters! Unfortunately, my starters are no longer alive and well (pauses for a moment of silence), but we are still scientists, and we must continue to work! 

So, the burning question on my reader's mind is probably "What should I have for lunch today?", but the question they should be asking is "What is he sequencing exactly?"! Well, my dear patrons, we are sequencing the 16S (a portion of the ribosome of the cell) rRNA gene and the ITS region, not the entire genome of the starters! The rRNA genes we sequence encode the RNA amount of the 16S location on the ribosomes of bacterial cells, while the ITS region works much in the same way as fungal cells. A benefit of only sequencing these specific regions of DNA is that it enables a researcher to have an easier time sorting through potential differences and similarities between DNA by limiting the amount that one has to sort through. One benefit of sequencing entire genomes will always be to progress academia, but when you limit the sample size of what is being sequenced, you also limit any new discoveries or advancements that could be made. 

There are some obstacles with the type of metagenomic sequencing we are performing (Amplicon-based sequencing), however. One such obstacle is the extra steps needed to analyze the samples and the then-added difficulty of preparing/completing the sequencing process. This is in comparison to shotgun metagenomic sequencing, which is just the academic term for sequencing all the DNA in a genome at once. With Amplicon sequencing, we can question how the composition of the starters is affected by different conditions such as temperature and age. Shotgun sequencing may be easier but wouldn't allow the specificity that we enjoy with Amplicon sequencing. 

Below I have the graph and legend for the data collected last semester for the 16S sequencing set. I can only paste the 16S below mainly due to file size of both the graphs and legends. There were several trends, the most notable of which was that the majority of the starters mostly comprised themselves of Firmicutes, the scientific name for the Phylum in which they reside. There were other smaller trends but I could not make much sense of them, unfortunately. This could possibly be due to lurking variables in the environment. I did not have a super difficult time analyzing this data, thankfully, but I did have a short period where I was unsure of the process of uploading the data sets to the system... I am not terribly tech-savvy! In order to progress and think critically, we must create and ask questions! A few examples of which include whether or not younger starters have more or less variation in composition, if the comparison of microbial composition changes between older and new starters, and if different fruits have trends as to which microbes are exhibited when sequencing! Thanks so much for following along this week!!!




Citations:

 https://view.qiime2.org/visualization/?type=html&src=ee51343a-3068-49d3-b1fe-9ee1230596e9

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927574/


Comments

Post a Comment

Popular posts from this blog

Unique Microbes Analysis Blogpost (Week of 4/5)

 I have reached the pique of scientific comebacks! I have returned from the depths of long overdue work and, finally, have caught up! Nonetheless, celebratory affairs should only go on for so long, and we have a TON to talk about! This week your digital guide has been busy analyzing a fellow classmates' starters! I analyzed samples 55 and 57, the former of which being the control starter (just flour) and the latter holding blueberries. In the fruit sample, a unique microbe under the species name Pediococcus pentosaceus was found. Interestingly enough, this very same microbe is used in natural and additive fermentation to release flavor compounds into various food groups such as meats and dairy! Even more exciting, the fermentation of blueberries with this microbe helps to unlock the probiotic potential of the fruit... scrumptious! This was found in a study linked below (in citations!).  Now, in the actual process of fermentation, this microbe does its best work. They perform phosph
Post a Comment
Read more

We got BUBBLES, BOYZ!!

  As one travels along the soul-searching path of growing sourdough starters, one must also update his loyal fanbase on the progress that has been made. Similarly to Odysseus, my starters have been through the absolute ringer. Starting at the end of last week, I forgot to feed and water my starters, effectively missing one whole day. The starters were.... rough looking, to say the least. Dried up and brittle, the collective crust of the three trials was looking rather dire. I recognized the mistake and set out to correct it with the correct portions of food and dechlorinated water, hoping that I wasn't too late, being a day off of schedule and all (sweats nervously). Lo and behold, for I have salvaged the scraps of my experiments and prevailed! Three days after my experiment's beginning, a revival occurred and my three starters have... risen (that pun was soooo intended)! Feast your eyes on my beautiful bubbly boys! (Control Group) (Banana Variable) (Mango Trouble Child) (all p
Post a Comment
Read more

Final Blog Post ( A tear-stricken farewell)

 I have completed my final project, my coup de grace , as it were. It is a magnificent, illustrious podcast of my own design, and I hope my attentive readers and loyal listeners alike enjoy it! The link to the podcast (discussing and analyzing the general summary of this semester's lab, entitled Sourdough Center Episode 2) is posted below this paragraph. I have also made a blog post with a transcript of the episode in the previous post.  https://anchor.fm/joseph-lewis65/episodes/Sourdough-Center-Episode-2--Finale-evfkcg This semester has been delightful, challenging, and, at times, tedious, but I have loved this course and making these blogs all the same. Thank you, all my readers, for sticking along. Love you guys!
Post a Comment
Read more