The great Sulfolane degrader of the Subarctic.

Article and Link:

Identification and Characterization of a Dominant Sulfolane-Degrading  Rhodoferax sp. via Stable Isotope Probing Combined with Metagenomics

by Christopher Paul Kasanke, R. Eric Collins &  Mary Beth Leigh

published 2/28/2019

Summery: Researchers were able to identify and obtain metagenomics on a microbacteria within the microbial community of the Sulfolane contaminated water aquifer in North Pole, Alaska that is naturally degrading the Sulfolane contaminate.     While microbacteria in other temperate regions of the world: Illinois, Canada and Japan, have identified Sulfolane degraders this is the first in a subarctic climate.   This bacteria, Rhodoferax sp. is found to be the Sulfolane degrader able not only to survive in the subarctic conditions and persist at 4o C, the average temperature of the aquifer year-round, it also

Connections:   This information connects to what we have covered in class in that the identification of Rhodoferax sp. is a further example of niche evolution and how there are different bacteria that evolve doing the same job in different areas in different ways.

Critical analysis: I think it is interesting and exciting that this is the first subarctic microorganism of its kind identified.   I think this paper is scientifically accurate.   The paper has many references, was a continuation of earlier research, processes were explained well and thought through.   I think the researcher does a good job of communicating science to the public, while there were parts that might be a little in depth, I believe that even if someone read it that did not understand exactly what everything meant, they would be able to understand the overall message.

Question: I am curious to know, where is Rhodoferax sp. found around the world, besides Alaska?

Painting with Microbes

Cristina Mondelli


My artwork was supposed to depict a bumblebee and a flower. I used M. luteus for the “yellow’ stripes on the bee and the center of the flower, but it did not grow very well. It might have needed more time in the incubator, but I was worried about the C. violaceum taking over and overcrowding the stripes, so I placed it in the fridge prematurely. The E. coli grew well, but got contaminated in the white of the wings. My flower was disappointing because I used S. marcescens which I expected to turn pink. For some reason, it failed to turn pink and left me with a white flower. Additionally, the M. luteus did not grow in the center of the flower.


While I did grow other pictures on the differential media, I liked how the TSA grew the best. The TSA was not extremely selective and was designed to allow the majority of culturable microbes to sustain life for lab purposes. TSA remains the same color regardless of what grows on it, even though the colonies themselves have color. It does not change color to indicate a change in the pH or only encourage a certain characteristic of microbe to grow. Because growing microbes on the TSA plate does not indicate any special characteristics of the microbes, it is not differential either.

A2: Microbes in the news — Yeast produce low-cost, high-quality cannabinoids


Yeast produce low-cost, high-quality cannabinoids


Synthetic biologists at UC Berkeley have engineered brewer’s yeast to produce some of the main components in marijuana including THC and CBD among others.


The developing field of synthetic biology is based on taking the tools that we are using in class, such as whole-genome sequencing, and our knowledge of how microbiology works to modify and create solutions to modern problems.

Critical Analysis:

Synthetic biology is an amazing and quickly developing field with the potential to take   a future we have only seen in science fiction and turn it into reality. This is an incredible technical achievement showcasing our developing mastery over the fundamental building blocks of life. I knew something like this was coming, I can see the economic incentives for this, I am sure the people behind this will end up fabulously wealthy, but I still can not stop myself from facepalming. Of all the amazing and wondrous potential synthetic biology holds… this had to be the top of my news feed today.


I cannot begin to imagine the legal ramifications, how the hell do you regulate something like this?

Painting with Microbes – How to create your post

Rachel Alexander Painting with Microbes

In Lab 6, you created microbial art using various bacterial strains on TSA, EMB, and MacConkey’s agar. In order to earn credit for this activity (10 pts), you must create a post for the website. Here’s what to include in your post for full credit:

  • Your name
  • Your lab section (F01, F02, F03)
  • One or more photos of your Painting with Microbes artwork. Artwork doesn’t always work out as you’d hoped, so that’s why you can choose 1 of your 3 to post.   But you’re welcome to post all 3 if you’d like.
  • Explain your artistic intent(s)
  • Explain the role of the differential or selective media in contributing to the color spectrum of your works. What type of medium was the work on? Did the medium change color? If so, how? What does that say about the strains that elicited this change or lack thereof? If it was on TSA, then just explain that it’s not differential.
  • Categorize your post by checking the “Painting with Microbes” box (see categories on the right of the screen when you’re creating your post) for full credit and to ensure that others can find it.


For the test plates created with your isolate: For the test of your isolate’s physiology using EMB and MacConkey agars, just note down the results following growth on these media and include them in your lab report. They do not need to be included in your Painting with Microbes post.

New technique provides a better understanding of bacteria evolution


New technique pinpoints milestones in the evolution of bacteria
Results show bacterial genomes provide “shadow history’ of animal evolution.
Jennifer Chu, MIT News Office February 7, 2019


Danielle S. Gruen, J. M. (2019, January). Paleozoic diversification of terrestrial chitin-degrading bacterial lineages. BMC Evolutionary Biology, 19-34. Retrieved from


—  Summary:  Researchers from MIT have established organism relationships between fungi and bacteria by reviewing the gene for chitinase (an enzyme which helps to break down chitin). Their review of the mutations, and similarities across different species has allowed them to create an evolutionary tree which correlates microbial evolution with fungal evolution. They found that approximately 450 to 350 million years ago, diversification of three separate bacterial groups diversified as the result of gene transfer with a chitinase utilizing fungi. Below is the resulting evolutionary tree with the fungi identified by purple lines and bacteria with blue lines.

(Gruen, et al. 2019)

—  Connections:  This connects with: Microbial evolution, metabolism, and diversification.
Chitinase allows these bacteria to metabolize chitin as an energy source. This allowed diversification of microbes into new niches ones chitin became more prolific in the environment. Gene transfer was said to make it difficult to genomically identify or differentiate bacterial strains, but here the gene transfer has allowed a better understanding.

—  Critical analysis: I found this article very interesting because, most evolutionary trees are based on rRNA sequencing (highly conserved due to form/function). The use of chitinase to correlate evolutionary relationships between fungus and bacteria is interesting. Especially since the origin of chitinase was in a Fungi (a microorganism that doesn’t look like a microorganism) and the gene has been horizontally transferred to bacteria.

The story was very well written and after reading the original journal publication, it was factually and accurately written. The author did as great job in conveying the information to the general population without losing the integrity of the research. I appreciate the writing style and how it helps those (like myself) who aren’t as well versed in the scientific nomenclature, to understand the information and findings from the research.


—  Question:  How many other highly conserved coding regions can we isolate and use in this manner? Are enzymes such as chitinase always highly conserved, or is there slight variations in the conformation, allowing it to mutate without ruining the function of the enzyme?

-Samantha Smith

Microbes in the News: Immune responses in Periodontal Disease

Researchers identify immune culprits linked to inflammation and bone loss in gum disease

Wednesday, October 17, 2018

Vicki Contie and Dr. Catherine Evans


Summary: Researchers at the University of Pennsylvania and the National Institute of Dental and Craniofacial Research have discovered the reason behind inflammation in periodontitis in a joint study between mice and humans. An unhealthy oral microbiome may trigger T helper 17 cells to begin an immune and inflammatory response, even if proper oral care is being undertaken. Mice with knocked out Th17 genes were compared to a selection of patients who also were missing the gene. They found a lack of periodontitis in those missing the Th17 cells when compared with those in their age bracket.

Connections: We have not covered the immune system, but we have spoken about how important microbes are. These researchers are suggesting that without the proper diversity in an individual’s oral microbiome, other diseases can arise. We’ve talked about how plaque occurs from biofilm buildup, however there are good things in the mouth that work to keep inflammation and other diseases from occurring. This is just another example of how microbes really run the world.

Critical Analysis: This news release was very interesting because it paints the oral microbiome as the good-guy in this situation, even though we often think of it as the enemy. I felt the story was scientifically accurate because they explained how the researchers came to the conclusion they did and how the study was set up. The article was written in such a way as to describe what the researchers did in case anyone wanted to question their methods. I felt the article was well written, but it may be harder for individual’s without scientific backgrounds to understand. It was easier to read than a journal article, but harder to read than the average newspaper. This article did a good job communicating to the people it was aimed at: dental professionals.

Question: How does mouthwash and brushing your teeth affect an individual’s oral microbiome?

Using natural remedies for blasting biofilm

Article and link:

“Blast Biofilm this Winter: New Tulsi Holy Basil Benefits’

Summary: John Douillard, of John Douillard’s Lifespa, claims making tea using Tulsi Holy Basil (Ocimum sanctum), breaks down the biofilm on your teeth that causes plaque.   He says that the herb contains eugenol and ursolic acid. Both are known biofilm disruptors and powerful cleansers.   He says ursolic acid is a quorum sensing inhibitor which enables the ability of the bacteria to communicate so that the biofilm is unable to form.

Connections:   We spoke in class about ability of some bacteria to “talk’ to each other through quorum sensing and their ability to create biofilms through this.   We also spoke about how these biofilms can be harmful or helpful depending on their location and the effects they have on the environment they have established themselves in.

Critical Analysis: While John Douillard has included science in his writing, and he does include scientific references for his information.   Though in these studies they found there was no statistically significant difference between using regular store-bought mouth wash and Ocimum sanctum, they did find that using Ocimum sanctum was better than the studies that used a placebo.   I am a bit skeptical because he wrote the article for his own business on his business page and there is a disclaimer at the bottom of his page that state “The entire contents of this website are based upon the opinions of John Douillard. They are not intended to replace a one-on-one relationship with a qualified health care professional, and they are not intended as medical advice. They are intended as a sharing of knowledge and information from the research and experience of John Douillard and his community. John Douillard encourages you to make your own health care decisions based upon your research and in partnership with a qualified health care professional.’   There is also a disclaimer stating that no part of the information on his page have been evaluated by the FDA.  Though this does not mean he is not pushing other products that do not work and feeding off desperate people.

Question: If people can easily get mouth wash that scientifically works, breaking down the biofilm and inhibiting other biofilm (plaque) from forming, why bother going this route?

A2: Microbes in the News – New Anti-CRISPR Proteins in Soil Bacteria

Article and Link: New anti-CRISPR proteins discovered in soil and human gut (ScienceDaily)

Summary: CRISPR is a natural bacterial immune defence, but some bacteriophages (or viruses) have developed anti-CRISPR genes that cause bacteria to lose immune defence when infected. New anti-CRISPR proteins were discovered by using protein functionality tested across a variety of environments, rather than using DNA and culturing. Their discovery could lead to the development of better technologies in the emerging field of CRISPR gene editing.

Connections: This article demonstrates the prevalence and possible uses for bacteria in today’s medical world. If bacteria could be used to produce proteins that create more precise gene editing with CRISPR, gene editing may have a very real future in human society. The way the researchers discovered new anti-CRISPR proteins is also a testament to the diversity of microbial life and how not all microbes can be cultured.

Critical analysis:  I find this article fascinating, because I am very interested in how cellular function, protein production and genetics can be used in the medical world to produce new treatments, drugs and cures for disease. With improved CRISPR technology, it may be more realistic to use gene editing to treat diseases such as cystic fibrosis. Unfortunately, this article was not very well written and did not explain the methods of the researchers in a way that is accessible to the public. The writing was very hard to follow and I had to read it multiple times before I began to understand the premise of the article. However, from my level of understanding there were no factual inaccuracies even though it oversimplified genetic editing and the way CRISPR works.

Question: How does the presence of anti-CRISPR genes in bacteria affect their susceptibility to antibiotics? Could they be more susceptible since anti-CRISPR proteins target bacteria’s “immune systems’?

A2 Microbes in the News

“Why your kid’s strep throat keeps coming back,  A combination of genetic and immunological factors makes some children susceptible to the bacteria that cause strep throat” by the La Jolla Institute for Immunology, published 6 Feb   2018. Found:

Streptococcus pyrogenes causes a number of diseases, but when found in the throat it is known as strep throat.   The scientist gathered 100 children who had undergone tonsillectomies and tested their immune response.   They had a less robust response to Strep.   Additionally, their parents also had a decreased reaction to the strep toxins released by the virus.

This, I think, connects to the class in the development of vaccines.

I think it is quite interesting how how we don’t really have a clear understanding on how the immune system responds to the removal of the tonsils, a thing we have been doing for nearly 2000 years.   It wasn’t really well written, I think because it was trying to water down a scientific publication.   It didn’t really give me as much information I wanted, but I imagine, that for a person with a less deep understanding of immune response as me, a person who, admittedly, doesn’t have a great grasp of the subject, would be able to get the gist.   However, the article could have been better organized.

“SpeA” is a toxin given off by the microbe, I wonder how the immune response acts on that, rather than the microbe itself.

A2: Microbes in the news – Study: Gene Drive Wipes Out Lab Mosquitoes



A gene editing technique called a Gene Drive which is based on the well known CRISPR technique has been shown to be able to completely eliminate a mosquito population in the lab.


We have been learning about the various techniques used through history to prevent diseases, from antibiotics to vaccines, this represents another potential tool capable of having a similar impact.

Critical Analysis:

The prevention of deadly diseases has been and continues to be one of the greatest goals of the study of microbiology and malaria is currently one of the most deadly infections still at large in the world with  219 million cases of malaria in 2017, up from 217 million cases in 2016 despite incredible continued efforts to prevent its’ spread. A commonly targeted element of the disease is the delivery method, mosquitoes. However while previous efforts have failed to slow the spread, this technique has demonstrated the potential to not just slow them but to precisely and completely eliminate an entire species.


What other populations can this be applied to? For instance, would it be appropriate to eliminate the populations of rats devastating island bird populations?