A2: Microbes in the News – Post 3

A new plastic film glows to flag food contaminated with dangerous microbes

Maria Temming – April 17, 2018

Summary: This article discusses a flexible film coated in molecules that glow when they come into contact with E. coli, and the presence of molecules secreted by E. coli which allows for the material to detect food contamination without being in direct contact with bacterial cells.

Critical Analysis/Connections: This article does an excellent job of providing a lot of information about the technology to detect E.coli and also how many individuals are killed due to foodborne illnesses. I personally would love to see this technology in the upcoming future in all packaged food. The only downside is having access to an ultraviolet lamp, but they are easily purchasable at the store and online. The article also mentioned a convenient smartphone fluorescent light attachment which could be used. In class, we discussed proper hygiene and contamination of food products. We also have discussed about how dangerous E.coli can be. This invention is a groundbreaking achievement that will save lives in years to come.

Questions: Could this be used to detect other bacteria? How much does it cost to manufacture the film?

A2: Microbes in the News – Post 2

Can You Change Your Microbiome?


Summary: In this article, the author discusses alteration of the human microbiome. In particular, a microbiome-augmenting treatment was performed on an autistic patient, which drastically improved the behavior of the child. The article further explains how altering the microbes living inside us can have “wide-reaching consequences- sometimes for the better.”

Critical Analysis/Connections: Not only does this article give a great insight of the possibilities of altering the human microbiome for beneficial effects, but it also shows current success in helping an autistic child. The article captures the reader’s attention within the first sentence of the article. After the first paragraph, we get into examples of current microbiome treatments and the future of altering the human microbiome. The article discusses the current and future uses of synbiotics which can be used to reduce cases of sepsis and mortality in premature babies. These topics all connect to our lectures on the human microbiome and the possibilities of future developments

Questions: Are there more than just one success story of the microbiome-augmenting treatment?

What are the negative effects of the microbiome-augmenting treatment?

A2: Microbes in the News – Post 1


Title: “Could You Fight Off Worms? Depends On Your Gut Microbes” – Nadia M. Whitehead

Source: NPR.org

Date: 4/7/18

Summary: This article discusses a discovery of individuals infected with parasites share common microbes even though the individuals live in different geographic locations. The article further discusses how certain bacteria known as  Lachnospiracae is associated with individuals who can fight off worms naturally.

Connections: This article is focused on the microbiome and the possibility of altering the human microbiome to fight parasites naturally without the use of drugs. We have discussed in class about the human microbiome and our bodies natural defenses over disease.

Critical Analysis: I liked how the author explains that 25% percent of the world’s population is infected with parasitic worms. The author further explains how these worms are contracted and that despite decades worth of deworming efforts to exterminate the world of worms, people in developing countries continue to be reinfected. I wish the author would have included graphs/charts on the research that was associated with the article. It would help further explain the research and engage the reader. The writer gives credit to Makedonka Mitreva, the lead researcher on the study reported in the article. Mitreva suggests a great way to rid the world of worms. She hopes to use fermented foods to plant “worm-defending” microbes inside of individuals to help fight worms.

Questions: Can we use the same plan of attack against worms to alter the human microbiome to fight other diseases, such as cancer or common infections?


Researchers discover ‘switch’ that allows microbes to recognize kin

Researchers discover ‘switch’ that allows microbes to recognize kin

Published: March 27, 2017


In our microbiology class, we learn a lot about how bacteria will interact with each other, but don’t really mention how they might be recognizing their own kind.   A plasmid shared among your species is much better than one shared with a competitor in the end.   And we also learned how beneficial a biofilm is, but not how a bacteria would know it can be a part of the biofilm.   In this article, we learn of TraA receptors —the cause of this recognition.   Digesting a study that looked at Mycococcus xanthus, this particular receptor was discovered to help recognition of M. xanthus cells for outer membrane exchange.   Additionally, different strains of bacteria have different TraA sequences, further supporting this receptor as a receptor to help with recognition of other bacteria of the same strain.   An interesting reason for the recognition receptor had to do with outer membrane exchange (OME).   The paper discussed that if different bacteria were to go through OME with each other, there might be toxins exchange that the recipient (being of a different bacterial strain) would then have no antidote to.

The article also discussed that the bacteria in question are phagocytes, and so they are of interest in the agriculture world.   So, as these would be great for getting rid of plants’ pathogens, it only makes sense that there would be interest in how they distinguish each other from other microbes.

One confusing part of the study is the way they present the ability to recognize different TraA sequences, saying one amino acid (AA) changed is enough to cause no recognition.   The way that the information was presented had me asking myself, “Is it a specific AA that when changed makes it so that the bacteria don’t recognize each other or is it that changing any AA would be enough?’

Waste-munching bacteria could make nuclear stores safer

Waste-munching bacteria could make nuclear stores safer

Published: 11 April 2017


As we learned about in class before, through research shown to us by Dr. Leigh, that some microbes use Uranium or other such things as a food source.   For that reason, when I was this article, I thought it might be interesting to see it there was any progress made.

As part of a radioactive waste disposal plan, the UK is hoping to put the radioactive waste deep underground and to cover it with cement.   The problem with cement (as stated by the article) is that it will create conditions too alkaline for microbes to grow.   To test this theory, a research team studied a similarly-conditioned site.   It was seen that there were microbes that were able to withstand such conditions.   In alkaline conditions, there is a possibility of the uranium to form soluble complexes with isosaccharinic acid and to leak out, but with the presence of microbes, the isosaccharinic acid would be degraded by them, which would help to stop these leaks.   An additional benefit of the microbes is that some break down H2, which would stop the gas from building up pressure and causing a radioactive gas leak.

One nice thing about this study was seeing the use of the words “carbon source,’ as well as the author describing that the bacteria that break down uranium and other metals (such as neptunium) use it “in place of oxygen’ thereby representing the use of oxygen as an electron acceptor.   The way it is presented is very interesting and makes me thing that it does a good job of making the information accessible to the public.   The paper also expands on the findings, suggesting using them for decontamination of drinking water, such as we saw in the study presented by Dr. Leigh.

One thing that is lacking in this paper is differentiation of microbes, albeit this might make the article harder for the general public to consume.   For this reason though, I wonder, are the microbes mentioned through the paper the same microbes or are different ones used in different scenarios (I find the latter more likely)?   Additionally, I wonder, are the microbes ones that would naturally be present and persist in the given environment or are they being introduced?

Microbes in the News: Post #3

Article and link: “Microorganisms Make a House a Home?” — https://www.the-scientist.com/?articles.view/articleNo/43840/title/Microorganisms-Make-a-House-a-Home-/


Summary: This is a brief article which overviews a study in which dust from homes were analyzed for bacterial and fungal species. The results indicate that the presence of certain fungal and bacterial species can indicate the geographical location you live and even the house’s inhabitants, from pets to people.


Connections: Using the presence of certain bacteria to ascertain information is similar to the idea of the human microbiome, as well as using the presence of certain fungi to determine geographical location.


Critical Analysis: The study found that, using the fungal data, one could predict the exact geographical location in which the home was located. Furthermore, they could predict using bacterial data whether or not there is a dog in the household — with 92% accuracy. The scientists could even predict if the house’s inhabitants were predominantly male or female, based on the presence of bacteria typically found in fecal matter (males) or the vaginal canal (females). The article itself was very brief and written for non-scientists, but it didn’t seem to have any inaccuracies. It was very interesting and insightful.


Question: What else could microbes be indicative of in everyday life?

Updating the Hygiene Hypothesis

From  The New York Times  on June 3rd, 2016 – Educate Your Immune System


This article summarizes recent research done on the development of autoimmune diseases (Type I diabetes, celiac disease, severe allergies, etc.) in children who grew up in different microbial environments – represented by households in Finland, Estonia, and the Karelia region of Russia. Studies found that, when factors such as diet and breastfeeding were controlled for, toddlers  who grew up in Finland were four times as likely as those in Karelia to develop precursors for Type I diabetes, and the two groups had very few similarities between their microbiomes. Karelia is a significantly poorer area than most of Finland, and many households drink untreated well water, so researchers hypothesized that early exposure to microbes from the environment “taught” the toddlers’ immune systems how to respond appropriately to common environmental pathogens, and so they developed fewer autoimmune issues.


We’ve discussed acquired immunity in class, but this area of research takes it a bit farther, and suggests that our microbiomes and  when we are exposed to certain microbes may play a larger role in our immune development than previously thought. Other studies mentioned in this article found that children who were exposed to certain pathogens at a young age were much less likely to develop autoimmune diseases than those that first encountered the same pathogens as teenagers or adults. This updates the hygiene hypothesis (which I think we discussed briefly?), which essentially says that people exposed to fewer kinds of microbes during their development tend to be sicker than those that were exposed to a wider variety of microbes.

Critical Analysis:

I appreciated  the angle this article took, describing autoimmune diseases and decreased exposure to diverse microbial communities as an issue of the 21st century. The author did an excellent job of defining terms and ideas that may be foreign to the lay reader, and I think this article is accessible to a wide range of audiences. However, the article implicitly assumed that the relationship between early microbial exposure and autoimmune disease was proven, and I don’t think any of the studies examined in the piece proved a causal relationship. Popular science writing needs to be careful not to assume causation when it has not been proven!


How might we (ethically) prove a link between childhood microbial exposure and autoimmune disease?

Microbes in the News Assignment: Post #3

Article and link: “Too Clean for Our Children’s Good? The Checkup’ by Perri Klass, MD, The New York Times, April 17, 2017.


Summary: This article talks about the many various ways in which our children are protected from interaction with microbes, including giving birth by caesarian section, bottle-feeding, and possible exposure to antibiotics. Such protection on the one hand affords protection from disease but on the other hand offers greater risk that children may experience complications of the “built environment.’ It is a concern that living in such a clean, controlled environment could lead to an underdeveloped immune system and subsequent health problems which may have otherwise been avoidable had the body been exposed to a diverse array of microbes at a young age. In order to combat this problem, it is recommended that young children be introduced to these microbes in the outside environment through “controlled exposures’ in the form of either “natural exposure’ consisting of interaction with their environment or through a type of vaccine yet to be developed.


Connections: This article include discussion of the development of the human microbiome, its importance in the overall health of an individual, the avenues by which children are typically first exposed to microbes, and also the concept of vaccination with microbes in order to improve health. All of these are topics which have been mentioned or discussed over the course of the semester.


Critical analysis: I liked the contrast that the author provided between the microbes found outdoors as opposed to those found within the “built environment.’ While I had naturally assumed that the inside of a house or apartment may be “cleaner’ than the outside world, I had not given much thought to the members of the microbial populations to be found in each of the two environments; in reality, the inside of a dwelling is not necessarily any more microbe-free than the outside, it is instead simply inhabited by a different, and possibly narrower, variety of microbes. I did not detect anything scientifically inaccurate or confusing in this article, and think that it did perform an adequate job in relaying this information to the public. The author did not get too technical in any of their explanations, yet clearly stated the anticipated problem, reasons behind that belief, and also the possible solutions to the problem.
Question: Are researchers suspecting that the health problems mentioned are primarily due to inadequate exposure to pathogenic bacteria? Or do interactions with the non-pathogenic bacteria also play a role in shaping the immune system of children? What kinds of “natural exposures’ are parents advised to pursue in order to assist their child’s immune system to develop properly?

A2: Microbes in the News

Antibody helps detect protein implicated in Alzheimer’s, other diseases


Summary: The article discusses research looking to find less invasive ways to identify and then track the progress of neurodegenerative diseases like Alzheimer’s. They have accomplished the first step by crafting an antibody which binds to the protein tau, which is present in tangles when damage to the brain is occurring. The antibody allows tau to stay present in the blood and accumulate long enough to be observable via blood tests.

Connection: The article discusses the use of an human antibody, but in a way we didn’t really cover in class. The antibody is not used as a flag for the destruction of a microbe or “not-self” entity in the body, but rather keep an entity around long enough to track its concentrations.

Critical Analysis:  This article does an excellent job of explaining the issues related to diagnosing neurodegenerative diseases, as well as the way in which the protein tau is associated and was identified as a potential measurable product for blood tests. Though the study has only done limited preliminary human trials, they were able to magnify the presence of tau in the blood of individuals with known neurodegenerative diseases. I believe the article did a great job of translating the innovative way in which scientists approach problems like that of diagnostics, and the interdisciplinary cooperation and literacy that is at the command of these researchers to accomplish what was discussed.

Question:  Would this antibody have the ability to track damage as it accumulates in individuals like football players, perhaps as a longitudinal study to gain more data and a predictive model for brain damage?

Microbes in the News: Post #2

Article and link: “The Mycobiome” — https://www.the-scientist.com/?articles.view/articleNo/45153/title/The-Mycobiome/


Summary: This article discusses the commonly overlooked mycobiome, which is those fungi which are in and on our bodies. In recent years the microbiome has gained much more attention in both health and human medicine, but the mycobiome is still very much understudied. This article characterizes the human mycobiome and asserts that it is similarly important to human health, and even influences microbial communities. The researchers explored the presence of many different fungi in the oral cavity. As of yet, this field is still in need of scientific development and research.


Connections: I connected this to our brief lectures on fungi, and also to the attention on the human microbiome.


Critical Analysis: I found the idea of the human mycobiome to be interesting. The author ascertains that most people, scientists included, often overlook it. I had never thought of a mycobiome until reading this article myself. I think that the article is well written. It is more directed to readers who have some scientific background, as he provides a detailed outline of his research involving the mycobiome.


Question: What are the implications of the mycobiome, and how much influence does it have on the microbiome and overall human health?