Third Microbes in the News

Article and link: A Blazing Hot Coal Shows How Microbes Can Spring to Life   Source: Wired 04/21/19   Link:

Summary: In Centralia many single-celled microbes live in the soil that is on top of the underground mine fire in the coal seam. Due to the fire it was initially thought nothing may have lived, but instead there are many microbes. The same amount of microbes have been found to be living in very hot areas including various thermophiles that microbes that live at geothermal hot springs.

Connections: In class we have briefly studied thermophiles which are heat loving bacteria. We have also looked at the various species of microbes that live in soil, and I find it interesting how natural disasters can affect what microbes are in the soil. We studied factors that can cause microbes to go dormant, which is what can happen during a fire since there is no activity on the soil.

Critical analysis: I thought this article was interesting because it involves microbe activity when a natural disaster occurs and using spores to regrow genomes. The article was well written and contained a large amount of detailed scientific information. It could be rather difficult for the general public to read the article and understand it all though, because of all the technical terms it contains.

Question: What organisms do you think would be likely to live through a fire or other extreme natural disaster? Would they become dormant?



Microbes in the News (#3)

Emily Werner

Title: Microbes in the human body swap genes, even across tissue boundaries: study

Summary: A team of researchers from the University of Illinois developed a method that helped to identify when HGT is taking place in the human biome. They concluded that microbes with similar DNA will readily carry out HGT with each other regardless of their location in the body. Microbes with similar DNA will swap genes with each other even if one is in the large intestine and the other is on the skin. They perform HGT more than with microbes in their same location with less similar DNA (i.e. mouth, GI tract, skin.)


The shortcomings of this method don’t help to determine the ancient HGT that occurred between species millions of years ago but they do help to determine the more recent gene transfers.


Connection: We’ve learned a lot about HGT in class and that this is a method that microbes use to transfer antibiotic resistance genes from one another. This article tells about how microbes in the human gut will do the same.


Critical Analysis: This article is general and ideal for anyone wanting to learn more about what is going on in research who don’t have a deep background in natural science. They discuss that this method they created for determining HGT is best for looking at the genes that were recently inherited, but they don’t specify that timeline. I think that since they specify ancient inheritance of genes, they should also do the same to give reference.  


Question: If antibiotic resistance is such a “scary’ thing today, how were we able to survive for millions of years before modern-day soaps and antibiotics?

In the simplified version, if antibiotics were critical to our survival, we should’ve gone extinct long ago why didn’t we?



Microbes in the News 3rd Post

Bacteria harness viruses to distinguish friend from foe

April 16, 2019

Summary- Researchers have discovered that bacteria found in the gut use a virus to self-recognize using the virus to self identify.   Thomas Wood of Pennsylvania State University one of the senior authors found a demarcation line was formed when Escherichia coli K-12 strains were near each other, but not when identical clones were near each other.   They found that prophage CPS-53 and one of its proteins, YfdM, were required for the demarcation line and that CPS-53 is essentially inactive in cell lysis and phage-particle production causing them to believe this was the reason for the difference.

connection- We have discussed bacteria and viruses in detail throughout the semester.   I thought it was interesting how the viruses that attack these bacteria are being used to keep itself safe and recognize itself.

critical analysis- I thought the subject was very interesting and was something that had not been discussed previously.   I did think the article was written for people with a scientific background and that some of the details would be unknown to someone without some microbiology background.

quesiton- Are there other bacteria in the body that use this same technique?


Microbes in the News 3rd Post

Bacteria That Eat Drugs Could Help Solve the Antibiotic Resistance Crisis

Researchers design bacteria to gobble up antibiotics in the environment, before microbes have a chance to turn deadly.

By  Jonathon Keats|Thursday, November 08, 2018


Summary: Antibiotic resistance has been around for a long time; it has even existed in nature long before humans contributed more antibiotic resistant bacteria. In the year 2007, a postdoctoral researcher in the Harvard University lab of George Church named Gautam Dantas researched the bacteria that are capable of consuming and using antibiotics as a nutrition source. It was found that bacteria evolved to resist beta-lactam which is supposed to weaken their cell walls but by producing an enzyme that breaks the ringlike part if the molecular structure when it is exposed to penicillin. There is still a lot more for scientists to learn about why bacteria engage in the behavior of eating substance that are meant to kill them.

Connections: When it comes to penicillin, we learned that it also targets the peptidoglycan in bacteria cell walls, it binds to microbial tanspeptidase enzyme so it can’t cross-link peptidoglycan. We also learned in class when taking about penicillin that it will not kill Archaea because they don’t have peptidoglycan. There is also a huge problem with over prescribing antibiotics in humans and livestock that is contributing to the more antibiotic resistant bacteria that are out there.

Critical analysis: What I found interesting is that some bacteria have evolved in a way that certain antibiotics that are made to kill them, becomes a nutrition source for them. It is amazing how this can come about but it is also quite concerning because it might be even harder to find other alternative medicine in the future. However, with the increasing amount of inavation in technology, like whole genome sequencing can help with this huge problem that is still on going.

Question: What kind of other ways in the future that could help with the problem of antibiotic resistant bacteria?


“Purdue professor discovers new method to treat superbug infections”

Summary- Mohammed Saleem, a professor from Purdue, has found a new method that can treat infections by antibiotic resistant bacteria. The method involves treating the infection with blue light, which strips the bacteria of a pigment necessary for survival in the host. By removing this pigment, the bacteria are weakened to a point that traditional mild antiseptics. This has been found to be effective in mice infected with MRSA, and the researchers are looking forward to human trials.

connections- We have learned that antibiotic resistance is a major area of research of monumental importance. Because blue light is not toxic to the host, it is selective for the pathogen and is an easily accessible method of treating infections on the skin.

critical analysis- It is not explained exactly why the bacteria need the pigment, or how the blue light washes this pigment from the cell. The blue light does not kill the cell, and the use of “mild antiseptics” are still necessary. Depending on what the antiseptics are, this could still contribute to antibiotic resistance.

question- What does the pigment do to help the bacteria live in the host body?


Reducing Allergic Reactions to Cheese

Title: Certain microbes may reduce allergy-like reactions in many people

Date: April 16, 2019


Researchers at Iowa State University are studying bacteria strains of the genus Brevibacterium that have genetic pathways to reduce histamine production.   Histamine is a compound involved in human immune response and around one present of people get allergy-like symptoms from the ingestion of it.   naturally forming biofilms of bacteria and fungi have been used in the cultivation of cheese for thousands of years.   These communities develop on the surface of the cheese and slowly form the rind of the cheese.   These communities are not well studied, and researchers lead by Stephan Schmitz-Esser are working to manipulate the fermenting communities to optimize the process and reduce the histamine production.

This was a well written article that communicated the issue effectively by explaining the cause and effects that lead to the study.   I found this article interesting because it divulged that there has not been a lot of research that has been done on the communities that comprise the fermentation of cheese products.   I find this surprising given it is a product we ingest, and we don’t even know the microbial composition of their processes.   Further research into the subject reviled that histamine formation is a huge product of cheese fermentation, but it can lead to histamine intoxication.   This can halt fermentation.   If conditions become toxic for fermenting species the entire process halts.   It turns out, the sole carbon source of the Brevibacterium species being studied is histamine!   This putative metabolic pathway for histamine degradation is critical for cheese ripening and solidifies Brevibacteriums importance.   This connects to our lessons of the fermentation process and the formation of bio-films.   The complexity of this community and the interdependence that makes their variety necessary is truly amazing.   I am curious how fungal species contribute to the rind forming biofilms?   I did not find anything about their role in the microbial community but would be interested to know more.


Bacteria Could be the Key to Biological ‘Wires’

Article:  “Electricity-conducting bacteria yield secret to tiny batteries, big medical advances”

Source:  Science Daily

Date Published:  April 4, 2019

Summary:  Scientists discovered that Geobacter sulfurreducens is conducting electricity through tiny fibers made of protein that “… surround a core of metal-containing molecules.”   It was previously thought that they were conducting electricity through pili, but new technology has made it possible to examine the smaller structures within the bacteria at a higher resolution.   These bacteria live in environments without oxygen, and they get rid of excess electrons almost as a way of ‘breathing.’   It is thought that this way of conducting electricity could eventually be harnessed and used in medical devices associated with human tissue.

Connections:  This article doesn’t relate exactly to the topics we have covered in class, but it does highlight how some bacteria have unique ways of processing molecules and electrons.   It mentions that these bacteria can also be used to clean up radioactive waste, which we have briefly talked about in class.

Critical Analysis:  I was not aware that bacteria could even conduct electricity, so the fact that they can do that, and people were able to figure out how they are doing it, is pretty cool.   It is also really interesting that the same technology the scientists used for this discovery was used to find a virus that was surviving in boiling acid.   The information seems scientifically accurate since they included quotes from the scientists that performed the research, and they included the citation for the article they were explaining.   I think the author did a good job of simplifying the material as best as they could so that any person could understand it.   It would be easier to understand if you were reading it with some background in biology, but it is not completely necessary to understand the basics of what they were talking about.

Question:  Will these proteins still function the same way if they are taken out of the bacteria and used for medical purposes?   Will the entire bacterium have to be used in the medical devices in order for them to work?

Gut microbiome and preservatives

If you have kept up with my “microbes in the news” posts, you’ll probably notice a theme at this point. I’m very interested in the gut microbiome. I think this is largely just because I’m a health geek and strive to fuel my body as efficiently as possible. But with that said, also how junk food and preservatives affect the gut biome, because trust me, I still get my fair share.

“UH Maui College research finds that food preservatives kill beneficial bacteria found in humans” UHM Nov 2017


The study began out of interest for the increased number of those with food allergies, obesity, and metabolic disorders. Trying to understand what in our environment is causing this was the driver for the study. The article talks about how there is a correlation between gut microbe disturbance and consumption of common preservatives. The study showed that the gut microbes are killed or inhibited after inoculated with common preservatives in the same concentration regarded as safe by the FDA.

Connections: This is exactly what we learned about when talking of the human microbiome.

Critical analysis: Being that this study came from a university, I feel it is fairly dependable. This article seems to have been published before the publication of a primary literature paper, but otherwise interesting to know the correlations.   I also feel the article did a good job of giving the information to the public, as it did not draw any conclusions.

Question: Can we expect to gut microbes to evolve to process preservatives?


A2: Microbes in the News (#3)


As Subway Commuters Mingle, Their Microbes Do Too

Subway riders in Hong Kong. (Credit: Sean Pavone/Shutterstock)           Hand-based microbe collecting experiment on the subway

Summary: A research group in the University of Hong Kong wanted to get a holistic view of how many microbes interact with humans in a city. They specifically studied the Hong Kong metro system which provided the team with a way to look at microbe populations throughout the city. About 5 million people are riding the metro every day. In their study, they had volunteers ride the metro during the morning and during the night. They collected bacteria by telling the volunteers to hold on to the handrails and then swab their hands (palms) after they got off the metro. The goal of their study is to understand what microbes on the metro transfer onto the riders. After the samples underwent DNA sequence analysis they discovered that the microbes the riders encountered were very dependent on time. They discovered that the morning riders were mostly exposed to microbes that belonged to the same environment surrounding different metro lines. The evening riders had a mixture of microbes some also belonging to different metro lines but the majority belonged to microbes that live on human skin. Through their study, they discovered that different metro lines had distinct populations of microbes in the morning but in the evening the populations had blended together.

Connections: During lecture, we have talked a lot about how we have an immune system to protect us from microbes. Specifically, we have an innate (non-specific) immune system which consist of physical barriers such as skin and hair. A lot of the microbes found on the hands of the volunteers belonged to a mix of different microbes found in different metro lines and microbes that are found on the human skin. Without these physical barriers a lot of people will be exposed to the microbes and could potentially get sick. We have also talked about ways of disinfecting places to prevent the spread of microbes. Even though, the metro employees were cleaning the train rails that people touched throughout the day, the commuter traffic through out the day were spreading microbes along with it. So, although the rails were being cleaned through the day the microbial spreading was still occurring.

Critical analysis: We already know that microbes are everywhere. The goal of this study wasn’t to scare the metro riders. They want to educate the public that might not fully understand what microbes are, that they are everywhere and they can spread quickly. Especially in public places, through the study they wanted to help commuters understand what they can do to protect themselves and reduce the spread of bacteria.  Many people grab these rails and then might rub their eyes or eat something without washing their hands. I think this study is important so people have better hygiene after being in public spaces. Meaning perhaps washing their hands as soon as they can or having hand sanitizer handy when they can’t wash their hands.

Question: I wonder if the rails were being cleaned though out the day for the purpose of the experiment only. Are they cleaned on a regular basis though-out the day when it’s not for   study? If not, would they have potentially found other more harmful bacteria?



A2: Microbes in the News 3

Title: Is it Illegal to Refuse to Vaccinate Your Kid in New York? This Court Says Yes.

Source: Gizmodo; Date: 4.19.2019

Summary: The article explains that there is a measles outbreak in New York, so the Mayor declared a state of emergency. In response to this, the health commissioner mandated that in the areas with the highest breakout of measels, children must be vaccinated. Some conserned mothers filled a complaint with the court against this mandate, but it was upheld because their claims that the vaccinations were harmful were not upheld.

Connections: A few weeks ago we learned about vaccinations. We learned babout how they work, what they target, and why some people are wary against their use.

Critical Analysis: I thought this article was well written, and explained the situation well. It wasn’t an article that had a lot of language barriers, so I felt that anyone who read this article could understand it efficiently. It also touched on the point that vaccinations are not harmful to people, which I feel is very important.

Question: Are there any other areas that have mandated that people and their children must be vaccinated?