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!

Fungi have enormous potential for new antibiotics


Summary: This article explores recent research into the genome of 24 different fungal species in order to identify antibiotic and other bioactive compound production genes. This study has resulted in the discovery of over 1000 pathways for generation of bioactive compounds with pharmaceutical application.

Connection:  The article could be characterized as part history of the use of antibiotics and the rise of antibiotic resistance. We have at length discussed the prevalence and mechanisms for bacterial antibiotic resistance as well as the known pathways for antibiotic production in microbes like fungi.

Critical Analysis:  The studied referenced in the article shows the promise of new antibiotic and even anti-cancer medications as a result of identifying these genomic pathways in fungi. The researchers believe that the knowledge gained from these sequences will also improve the efficiency of production and efficacy of existing antibiotics. At one point in the article, they refer to the predictive capability of the researchers experiments with the new sequencing data, claiming that not only could they predict the chemicals these fungi were capable of making, but identifying new versions of the same antibiotic chemicals. The reader must infer from the phrasing of this part that the researchers were able to trace the gene and find fungi that were previously unknown to have the ability to produce that particular antibiotic. The implications of information like that open the door wide to not only new means of production, but new variants of chemicals that have otherwise been fighting an uphill battle against antibiotic resistance.

Question:  If it is true that the researchers found antibiotic production previously undiscovered in some fungi, they use the example of the chemical yanuthone, are these inactive genes that must be activated, and how are they accurately and consistently activating these genes to produce this chemical?

Microbes in the News Assignment: Post #2

Article and link: “New HIV reservoir discovered: Findings reveal a second target for cure research’, Science Daily (it should be noted that the article on Science Daily sites the University of North Carolina Health Care as their source and mentions that the original findings were published in Nature Medicine on this same date), April 17, 2017.




Summary: This article describes scientists’ recent discovery that there is another cell within the human body which can act as a reservoir for HIV in addition to T cells: the macrophage. This discovery that macrophages are susceptible to infection by HIV is very important to current research focusing on the treatment of AIDS: this tells researchers that a successful treatment or cure would have to be effective in ridding the virus from both T cells and macrophages. One investigation found that viral replication within macrophages is effectively repressed when antiretroviral therapy is administered; however, the study also found that this effect is only temporary. Following treatment conclusion, macrophages still act as reservoirs for the virus and therefore remain capable of reinfecting the host. More research must be conducted in order to find the most effective way to resolve HIV infection of macrophage cells.


Connections: This relates to information we have discussed over the course of the semester in that it discusses a virus, HIV, and also cells involved in the immune response (T cells and macrophages). It also relates to the resolution of disease through treatment and also the ways in which viral cells can find ways to persist inside a host even following treatment; both of these are subjects which were briefly touched on in class this semester.


Critical analysis: I found it interesting to learn that HIV can also afflict host macrophage cells in addition to the host’s T cells. It has been known for some time that HIV targets T cells, but I had not heard of any other types of cells being specifically targeted by the virus. I also found it interesting that the antiretroviral therapy typically used in treating HIV infections in T cells does not work effectively on macrophages. I expect that the story is scientifically accurate as I have not seen indications to the contrary. I also did not find anything confusing in the article that would need to be corrected.  I believe that they did a good job in relating this news; it seemed as though they kept their audience in mind, and focused on relating the pertinent details and implications of this discovery without making the article too technical for those who may not have the background to understand a technical explanation.
Question: What are the most significant differences in terms of structure between T cells and macrophages which would cause antiretroviral therapeutic (ART) agents to be effective on T cells but ineffective in macrophages? Which ART’s were tested on the macrophages? What is their mechanism of action? Are scientists already aware of the specific reason that the ART does not work on macrophages?

Researchers Discover Antifungal Agent from Pathogen Box Project

Article:Researchers Discover Antifungal Agent from Pathogen Box Project                

Source: American Society for Microbiology



The pathogen box, which is  an open-source drug discovery project, is seeking to find/create solutions to under-researched/neglected diseases. Researchers can receive this pathogen box, which is composed of 96 well plates with different compounds (thought to be anti-microbial agents, or known to have certain effects on microbes), for free as long as they report any findings within 2 years. In recent tests, a compound targeting cell walls and membranes in fungi (with low toxicity to humans) could potentially be used to treat common fungal infections Cryptococcus neoformans and Candida albicans.


In class we have discussed finding different antibiotic targets for fungi, and the difficulty with doing so due to the physiological similarities between  humans and fungi.

Critical Analysis:

I found it interesting that there is an ongoing project like this, with seemingly high potential, that is actually providing a vast amount of knowledge on antibacterial targets. This is actually a really great idea, the fact that the boxes are free to researchers as long as data is shared in order to add to a database is really creative and cool. I feel like techniques like this could really be used to stimulate interest and action in certain subfields and topics. This article was well written, interesting and pertinent to bio students, but simple enough  for non-bio folk to have no problems reading and comprehending.


I would like to know how popular the pathogen box is (as far as how many people are using it) and what data they have gathered thus far (since its start in 2015).

The Influence of the Microbiome on Allergic Sensitization to Food

Article: The Influence of the Microbiome on Allergic Sensitization to Food
Source: The Journal of Immunology

Within the last 50 years, there has been a major increase in the frequency of allergic diseases in developed countries such as the US. Genetics, combined with diet changes/improved sanitation/increased antibiotic and vaccination use, can be attributed with this change. These changes lead to a change in the makeup of the human microbiota, altering not only diversity but frequency as well. Specific species of bacteria can have a multitude of different effects on the body. The presence of certain gut microbes, such as E. coli, can help to stimulate a state known as “endotoxin tolerance,” which is thought to provide a protective effect against inflammatory responses. On a similar note, individuals with a lower risk of food allergies were found to have a higher prevalence of Bifidobacterium while those with a higher risk of food allergies was found to have a higher prevalence of Bacterioids. The makeup of your microbiota can have major impacts not only on your overall health but also on the way your body reacts to certain chemicals.

The article discusses the human microbiome and the effects of its’ diversity and makeup on health and inflammatory response.

Critical Analyses:
I enjoyed the connections made between the human microbiota and human health/wellness. There is such a large connection between these, yet the field is so understudied it’s difficult to see its’ potential. One of the coolest thing I learned from this article is that when colonized with low-immunostimulatory microbiota in early life, aspects of immune education can be impaired resulting in predispostions to inflammatory diseases. This article is not a good read for those not strongly versed in scientific terminology, and is somewhat difficult for even bio students to fully comprehend due to terminology used.

How much of the field of preventative medicine is focused on the connection between the microbiota and human health? I’m curious about this because I feel like the field has so much potential, yet there doesn’t seem to be much emphasis on the microbiota and overall health.

A2: Microbes in the News- Using tropical microbes to improve the environment

Article Title: Using tropical microbes to improve the environment

Source: phys.org

Date: 4-12-17

Link:  https://phys.org/news/2017-04-tropical-microbes-environment.html

Summary: Researchers have been investigating ways to use the rich and diverse microbiome of the tropic region to help advance farming and agriculture, often finding ways to use them to protect against disease or increase efficiency in some way. For example, the scientists cultured the bacterium found in the guts of tropical fish, which can possibly be probiotics for commercially grown fish by inducing it into their guts through their food. This would protect them from the same diseases that the bacterium prevent in the tropical fish, enhancing survivability and resistance to diseases that could otherwise wreak havoc on the fish. A similar method is also used to protect banana crops, using the Streptomyces bacteria as an antifungal and antibacterial in the soil.

Connections: This is similar to what we have studied about both oil spills and microbiomes, as they are using microbes to reduce man made chemical use and are introducing these bacteria to the microbiomes of the fish and the plants.

Critical Analysis: I thought it was interesting to see how microbes can be used to protect against disease and how introducing them to the guts of the fish is almost like a vaccine for the fish. Although the article is about a developing way of helping agriculture and farming, there is a good amount of depth and explanation to the story to explain what is going on to the reader. It provides what may otherwise be a little technical to read for the general public into an interesting read that explains what it is saying well.

Question: In hat other ways could this be applied? Could it be used in place of certain vaccinations in humans? Even if it is just temporary, it would be interesting to see if this could be used for things like traveling. Because different people, especially of different cultures, have different microbiomes, could this method make it easier to travel and tolerate things such as drinking water and foods in different countries?

Neanderthal Tooth Plaque Hints at Meals and Kisses

Neanderthal Tooth Plaque Hints at Meals-and Kisses

Nature 08 March 2017



Summary: The plaque of teeth from Neanderthal remains discovered in  El Sidrón cave in northern Spain, which are estimated to have been from 50,000 years ago, were used to reconstruct the first microbiomes from extinct species. The researchers were able to determine their diet consisted of mushrooms and plants while Neanderthals from Spy cave ate wooly rhinoceros and mushrooms all from sequencing of the DNA from the plaque. The data also suggests that Penicillium mold was consumed along with aspirin from poplar trees to treat infections. The genetic analysis also suggests that Neanderthals and humans were kissing or sharing food as well since they both shared the same species of microbe in their mouths as modern humans. This is supported by the fact the strains did not split off until Neanderthals went extinct.

Connections: In lab we tested for some of the types of bacteria often found in the mouth using a variety of differential and selective agars. Though we were testing specifically for opportunistic pathogens, we discussed the amount of bacteria that is found in the mouth. In class we discussed the necessity and dangers of the bacteria that live in and on us and also the transfer of bacteria between people such as mother and baby. In addition, we learned about using penicillin as an antibiotic.

Critical Analysis: I found it very interesting that they could sequence DNA from such a long time ago. I thought the DNA would have degraded too much to get whole reads. It is amazing that they learned more about the social behavior of Neanderthals and humans just by the transfer of microbes. Since kissing means an intimacy during mating instead of the aggressive way they thought Neanderthals mated, the relationship between the two species is now considered different than what archaeologists previously thought.

Question: How did they track the split of the bacterial strain found in the ancient Neanderthals and humans from the same species of bacteria found in modern humans?

A2: Microbes in the News- Scientists find a new treatment for antibiotic-resistant bacteria


CTV News

Article published April 3rd, 2017

Researchers from Birmingham University in the UK have developed an interesting alternative to using antibiotics for a certain rare lung disease that can be caused by several bacterium including P. aeruginosa. They would run a similar process to dialysis, called plasmapheresis, but instead of removing waste from the blood they would remove a certain antibody from the blood that was in excess, which prevented them from fighting the infecting bacterium. They would run this several times a week, replacing antibodies via blood transfusions, and this reduced hospitalization time and reduced the effects of it significantly, all without antibiotics. Research is being done to see if this is a viable replacement to some antibiotic treatments.

This relates to class material because we covered usage of antibiotics and how to prevent resistance. This would be a very good way to eliminate adding resistance to bacterium that can be fought this way significantly by not even using antibiotics.

I thought it was interesting how they are trying to find ways to avoid antibiotics completely, which would significantly decrease the worry of antibiotic resistance. It is a fairly new treatment, but it looks very plausible and accurate based on the reasoning in the article. It is fairly simplified for the public but is in depth enough so that the treatment process can be understood.

One question I would ask is how this could be expanded upon to more diseases beyond just filtering out antibodies from the blood. Could this be applied to other immune response diseases? People who are immune suppressed?