3rd Microbes in the News: Bacteria partners with virus to cause chronic wounds

Bacteria partners with  virus to cause chronic wounds

Summary:  The common bacteria, Pseudomonas aeruginosa,  is a  drug-resistant pathogen that causes bacterial infections of those who are immunocompromised. It commonly harbors a bacteriophage, Pf, that occupies the immune response and allows the bacteria to grow at an exponential rate. A vaccine generated by the scientists for the bacteriophage caused a significant decrease in the ability for the bacteria to grow, showing a direct correlation between the bacteriophage/bacteria and how infection can spread because of how Pf and the bacterium working together.

Connections: We have discussed bacteriophages and bacterial infections amongst humans. We have also discussed how bacteria can grow at an exponential rate.

Critical analysis: It is incredible that this was discovered. Amputations are very common amongst diabetic patients with an infected foot ulcer and a vaccine preventing the bacteriophage from infecting the immune cells could help prevent this from being so common in the future. I believe this article is easy to understand and would be easily digestible by the common public.

Question:  Do you think the vaccine could prevent amputations and severe infections in diabetics? Please explain your logic.

A2: Microbes in the News (Post 2)

Harnessing Soil Microbes to Enhance Crop Performance


March 28, 2019


This article explains that some organizations (the organization they used as an example was the Agriculture and Food Development Authority (TEAGASC)) have been using bacteria to modify different plants’ genome. This has been done for a while using Agrobacterium tumefaciens, but because of limitations, they were looking into alternative bacteria that could perform the same function. They found a bacterium, Ensifer adherens, which can modify a plant’s genome easier than A. tumefaciens. Plants treat A. tumefaciens as something to guard against, which makes modifying certain plants difficult because some plants have a resistance. On the other hand, many plants recognize E. adherens as a symbiotic bacterium. As such, they do not have the same resistance as they do with the A. tumefaciens. The article then discusses some practical applications that E. adherens has been used for already.

We have been covering in class recently how humans control the growth of bacteria with many different antibacterial methods. I found it interesting that even plants have antibacterial methods that make them resilient to certain strains of bacteria. I believe that this story was scientifically accurate, I just would have liked more information on how E. adherens differed from A. tumefaciens to result in more of a symbiotic relationship. Although, I believe that editing out all of the information would make it so a wider variety of audience would be more likely to read the article. All in all, I found this article interesting and informative.

My question is: Is there any other widely-used bacterium that has been identified that can genetically modify plants?


Bacteria That Target Tumors




A genetically modified strain of Salmonella enterica serovar Typhimurium (S.Typhimurium) is being studied as an anti-tumor agent.


Over the last few weeks it seem like the over whelming topic in class is about how bacteria is going to get us, how to we kill it, there are a few good ones but only because the keep the bad ones from taking root, but in a classic cold war style operation these researchers have flipped a strain of bacteria to our side.

Critical Analysis:

When I first read this article I thought it was like something from a science fiction novel but this type of treatments are over 100 years old. William B. Coley was injecting streptococcal into patients over 100 years ago. While I’m not sure exactly why, this type of treatment gave way to expensive cancer fighting drug and radiation treatments. Now this particular case was more successful in lab animals than human trails this approach is making a come back.


Do you think the answer to killing cancer is bacteria and is just not pursed because there no money in it?



Savanna’s Flower

Savanna Ratky F03

My artistic intent for this project was to make a flower out of microbes, I put micrococcus luteus in the center with the intent that it would turn yellow (it didn’t really), I put serratia marcescens for the petals because its supposed to be red/pink (also didn’t become pink), and I put citrobacter freundii for the little swirls around the flower with the intent that they would be white. This was on a TSA plate because the list of microbes with their colors are on TSA plates, so I chose this because I thought the colors would change to the colors on the list, the color of the plate didn’t really change and I didn’t expect it to.

Painting with Microbes

Samantha Smith F01

Just a wink and a nudge to my favorite book “East of Eden” by John Steinbeck. I have a a pretty cross stitch of this at home, which admittedly looks a lot better. Perhaps I will stick to my day job and leave the microbe painting to those more artistic than myself.

I used the Eosin Methylene Blue Agar plate for this painting, hoping to achieve a stark different in coloration from the two sources I chose. The lettering and the vine were done with Escherichia coli.  This bacteria is gram negative so is not inhibited by the eosin or methylene blue of the medium. It also produced a deep black color with a metallic green sheen as it ferments lactose with strongly acidic end products. (The green sheen is actually quite pretty, though you can’t tell from the photo). The filigree and leaves are colonies of  Enterobacter aerogenes  which is also gram negative. It produces a pink color because it does ferment lactose, but the end products of fermentation are much less acidic than that of  E. coli.

I would like to add that I had a lot of fun in this assignment and seeing the variety of agar art from the ASM Agar Art Contests.


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?

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 https://bmcevolbiol.biomedcentral.com/articles/10.1186/s12862-019-1357-8


—  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

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)  https://www.sciencedaily.com/releases/2019/02/190205144338.htm

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’?

Microbes Can Prevent Potholes…?

Article: “Scientists hope bacteria could be the cure for potholes” by Talia Kirkland


Source:  Fox News

Date Published: Feb. 5, 2019

Summary:   This article/news story explains how bacteria may be an answer to preventing potholes.   Scientists at Drexel University in Philadelphia have found that bacteria (they did not mention a specific species), when mixed with CO2 and calcium, can change the environment around them to self-produce limestone.   When spread out on a road, they can make the road material stronger and more able to withstand damage that would cause potholes.   The technique is not yet being used, but it may be an alternative for better roads in the future.

Connections:    This article relates to what we have been talking about in class because they are introducing CO2 and Ca2+ to the bacteria to (I assume) get them to use a specific metabolic pathway and get the desired product.

Critical Analysis:   I think it is really interesting that it only requires two simple ingredients (CO2 and Ca2+) to get these bacteria to produce limestone.   There may be other underlying factors that contribute to the production of the limestone, but the fact that they figured this out with these simple ingredients that are extremely common is pretty impressive.   The information seemed to be scientifically accurate since they actually interviewed the scientists who did the research; it makes the article a little more credible.   One thing that I found misleading, and a bit frustrating, was that within the article, they kept using the terms pavement and concrete interchangeably, but concrete and asphalt are different materials that are made in different ways.   I don’t know if they actually tested this bacteria mixture on actual roads or not, but I think there would be a difference if they tested them on concrete versus asphalt.   The scientist kept saying “concrete”, which leads me to believe that they experimented with concrete, which is not the same material that roads are usually made out of, as far as I know (I would be surprised if roads in Philadelphia are made out of concrete, although it is possible).   If that is the case, then this mixture may not actually work on pavement (asphalt) to fix potholes, as they are claiming.   It is also possible that they were actually working with pavement and are just using ‘concrete’ incorrectly, which would be confusing to people who know the difference between the two materials!   Other than that, I think the author did a really good job at keeping the information simple enough for any person to understand it.   I think someone who knows nothing about biology would still be able to follow along and understand what they are talking about.

Question:    The scientists say that the bacteria are changing the microenvironment around them to self-produce limestone, which made me wonder- are the bacteria that they are adding the ones who are actually producing the limestone?   If not, then what changes are they making that cause other organisms to produce limestone?

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:  https://www.sciencedaily.com/releases/2019/02/190206144503.htm

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.