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?

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?

A2 Microbes in the News

A Taste For Pork Helped A Deadly Virus Jump To Humans



In 1999, in a small town in Malaysia, a scientist named Dr. Kaw  Bing Chua made a discovery crucial for the restructuring of the agriculture and farming industry across Malaysia (as well as Singapore, the Philippines, and several other countries). Chua discovered the virus later to known by the name of Nipah. Chua, a grad student studying virology at the time pinpointed this virus as one spreading across the country, yet no one at the time believed it.  Over the course of the next year a disease more deadly than Ebola was spreading rapidly throughout the town of Nipah, Malaysia. It eventually caught the attention of the government, and since most common viruses were spread through mosquitoes, the government treated it that way. However, after months of efforts to decrease the rate of spreading, nothing was working. This is when Chua comes back into the story. Chua was adamant that the virus in question was not in fact spread through mosquitoes, but actually through pigs. He came to this conclusion when he observed that the only demographic of people not getting the disease were Muslim, and hence were not eating pigs. Chua connected with a lab in Fort Collins, Colorado where he was able to see the virus through a special camera at their lab. The virus was identified and confirmed to be one that spreads through livestock. This led to the researchers at the CO facility contacting the Malaysian government,  who then immediately switched procedures and began focusing on stopping the spread between pigs and pigs to people.

This relates strongly to what we’ve been discussing most recently in class.  Learning how a disease spreads is critical for studying how to stop or slow it. Once the Malaysian government realized that Chua’s observations were correct, they changed policies throughout their nation. The entire farming industry was turned over and reshaped in order to minimize the spread of infectious diseases, such as the deadly Nipah virus. It really struck me in this article that the key to reducing outbreaks is to start by preventing them in the first place. The article elaborates on how serious a threat diseases like measles pose for humans. Nipah, like measles, is a respiratory virus. It spreads through close proximity, like when the pigs lived in extremely close quarters, but it also can spread just through the air. This is why taking advantage of any available immunizations is key to reducing outbreaks of potentially deadly pathogens. One question that stuck with me after reading this article was how specifically is this virus adapting to its conditions? The first outbreaks of Nipah were only due to pig to human transfers, but as of late, the virus spreads from human to human.



A2: Microbes in the News #3

Meet the Obscure Microbe that Influences Climate, Ocean Ecosystems, and Perhaps Even Evolution

Elizabeth Pennisi, 3/9/17, Science Magazine



Summary: Prochlorococcus is a cyanobacterium present in the ocean. It is the smallest and most abundant photosynthesizing bacteria in the ocean and is responsible for 5% of global photosynthesis. It thrives at a depth of 200 meters and has an estimated 80,000 genes (4 times the number that humans have). Penny Chisholm and two colleagues are working to show that Prochlorococcus is a central actor in evolution. They also believe that it helped to fuel to explosion of early life in oceans and the rise of oxygen in the atmosphere.


Connections: This article talks all about how a scientist by the name of Penny Chisholm is so in love with this microbe and has devoted her life to showing the world how big of an influence it has. This to me, shows the amount of dedication it takes for one to make their work known in the science world, especially when it comes to microbes because they are so abundant and diverse. Over time, she finally showed the world her work and let Prochlorococcus show it’s worth.


Critical Analysis: I love this article because it kind of motivates me in a way. Chisholm never gave up her love for this microbe and now people everywhere are starting to appreciate the work it has done on our atmosphere. I also love that it was written in terms that everyone can understand. The author even showed that it takes 220 million Volkswagen Beetles to equal the mass of Prochlorococcus in the oceans today. This was great because it really helped me imagine just how much of it is actually out there.