An exploration into a pharmacist’s microbes


An exploration into a pharmacist’s microbes



As an area of intrest, I isolated a bacteria from the contents of my father’s pocket, a practicing pharmacist as from the options available around me it presented itself as the most microbially interesting area available, both from having possible unusual outliers and from being socially relevant. This paper details my efforts in this endeavour and what I found (Spoiler: as can be seen in the picture for this post, I found a nice example of Staphylococcus epidermidis).


Google Drive Link:


A2: Microbes on the News!

Autism symptoms reduced nearly 50% two years after fecal transplant


April 9, 2019

—  Summary:

Researchers first compared the microbiota diversity between normally developing children and children diagnosed with autism spectrum disorder (ASD). They found that there was a significant difference in the diversity of the gut microbiome between these two groups. Next, with the help of the doctor who pioneered fecal transplants, children diagnosed with ASD were treated with fecal microbiota transplants (FMTs). They found that years after the treatment, there was a 45% decrease in chronic GI problems and a 58% reduction in the severity of ASD symptoms. 90% of the children in the study benefitted from this treatment plan.

—  Connections:

Several diseases stem from problems in the human gut microbiome, however, we have not discussed the effects on the mind. The researchers mentioned that they want to do more research to determine what these microbes are and what chemicals they are producing in children diagnosed with ASD. This leads me to believe that these anaerobic microbes are using several different metabolic pathways that produce gut-distressing products, as well as chemicals that could have an abnormal mechanism of action in the brain. These pathways can either be anaerobic respiration, via using a different terminal electron acceptor than oxygen or engage in fermenting which can produce several different compounds.

—  Critical analysis:

I have a cousin who was diagnosed with ASD and I recognize how much of a struggle it is to both treat and manage his disease. This FMT treatment provides a somewhat universal approach to reducing the symptoms and GI trouble associated with ASD. I had also never realized or recognized, the mental effects the microbiome can have on humans. This article was definitely credible and scientifically accurate based on the researchers’ credentials and experience. The author also did an excellent job at explaining the motivation for this study, elucidating the microbiome, and finally conveying the results of the study and future directions. The article could be well understood by someone without a background in microbiology.

—  Question:

What kind of products could one speculate are being produced in the gut microbiome of children diagnosed with ASD? Is it different for adults with ASD? How could one identify and quantify the products produced by the gut microbiome in children with ASD?


A2: Microbes in the News (#2)

Bacteria in probiotics can evolve in your gut and turn nasty, study shows  (The Independent)


Summary:  This article talks about a study performed at the University of Washington in Missouri where a probiotic evolved to attack the protective coating of the intestine in the mice they tested. Unhealthy mice with low gut microbial diversity were more likely to develop an evolved strain of the  E. coli Nissle bacteria that was used in the probiotic they studied. According to the researchers, their findings have implications for the development of safer probiotics in the future.

Connections: This article is very relevant to the human microbiome section that we covered in class. It involves the gut microbiome and the ways it can be more or less healthy, and more or less diverse. I think the way microbes can change and evolve right under our noses is fascinating!

Critical analysis: This was certainly an interesting piece and the writing style flowed well. However, this study is only one of many and might mislead readers to think that all probiotics can “turn bad.’ It could also be confusing to the regular reader, because the wording of the article makes it seem like probiotics are drugs that can change inside your body. Of course we all know that probiotics are made up of living bacterial cells that are supposed to help enhance the diversity of your gut microbiome. It was also unclear whether the  E. coli strain always evolved in a negative direction or if it was simply more prone to evolve in an unhealthy gut microbiome (toward good or bad characteristics, we don’t know). Overall, this was a well-written article, but I think the writer conveyed what he wanted the readers to believe and not necessarily the actual truth of the study.

Question:  What were the exact parameters of the evolution of  E. coli Nissle observed in this study?

Pumping May Alter the Microbes in Breast Milk

Article: “Pumping may be linked to an altered microbial mix in breast milk” by Laura Sanders

Source:  Science News

Date Published:  April 1, 2019

Summary:  A study compared the microbial makeup of breast milk from mothers who do not pump at all to breast milk from mothers who pump.   Although the microbes in breast milk is fairly unique from person to person, the researchers found two main differences.   The milk from women who pumped had more bacteria that could cause infections under optimal conditions and fewer bifidobacteria, which are thought to be beneficial bacteria.   It is still unknown as to what impact these differences have on the children, if any, and the origin for these bacteria is also under debate.   Some believe the bacteria from the gut travel to the breast and get into the milk, while others think that babies’ oral bacteria affects the bacteria in the breast.   There is some evidence that ‘baby backwash’ might trigger infection-fighting proteins in milk when the baby is fed directly from the breast, so this would not occur in milk that is pumped.

Connections:  This is related to what we were talking about with the human microbiome and how it can be affected by many different factors.   The way a mother feeds her baby not only affects the microbiome of the baby but the microbiome of her breast and breast milk, as well.

Critical Analysis:  I did not know that the way a baby receives breast milk can change the type of bacteria that occur within the breast milk itself.   Since the milk is made within the mother, I thought that only factors within the mother would affect it, so it is really interesting that babies play such a large role in that microbiome.   The information appears to be scientifically accurate since the author included some quotes from one of the scientists who did the research and did not add much of her own opinion when talking about the information from the research.   It was written well to relay the information from the scientists to people who may not have any science background.   It was easy to understand and follow.

Question:  Once the mother is done breast feeding, do any of the microbes remain in the breast?   Do they get flushed out with the milk or die?   If they do remain, are they there for the rest of her life or will they eventually go away?

A2:Microbes in the News

Title:  Specific Gut Microbes Linked With Depression: Study

Source:  The Scientist

Author:  Ashley Yeager

Date Published:  February 4, 2019

Article Link:–study-65427

Summary:  This is a small article that nicely states some findings from a project called the Flemish Gut Flora project. The results seem to conclude that two types of bacteria, in the gut are depleted in people who suffer from depression the bacteria, Coprococcus and Dialister, were found to be two of the main bacteria that were missing in those with depression. The article states if the results are further confirmed (as this is one of the first major studies and findings of its kind) it could lead to a plethora of information about the gut-brain connection and further provide new solutions for mental illness. Concluding this article are a few different statements from different scientists, both involved in the study and not, on its importance as being the first step in discovering the major role the microbiome plays in health and disease.

Connections:  This article connects very closely to what we’ve been talking about in class in the sense that an argument could be made for microbes ruling the world. If this study is further confirmed it would be a stepping stone to realizing that almost all of the problems people have are on a microbe level. Every decision people make, that changes the world, is influenced by their mental clarity and how they are feeling. Therefore, I would say microbes do rule the world, as they influence every aspect of the people, animals, plants and everything that make up the world.

Critical Analysis: I found this article interesting because of the implications it was hinting towards. Saying that this was the first real stab at understanding a huge unknown microbiome and that it could be a tool to cure mental illness. I had heard this theory of the gut biome having more of an influence on the entire body before, but it was very interesting to see an article talking about a large scale study that had been done. I believe the story was accurate scientifically, it was a smaller article, but all the information on the study and the results can be found quite easily. It was written in a fairly easy to read way, where anyone in the general public could understand the general idea that the gut biome plays a role in depression. So I think it does a good job communicating science to the public, however I will say it definitely is trying to paint a much bigger picture for people to grasp on. While this research was a big project, it is one of the first and much more needs to be learned about the gut biome before one can truly say a link for depression is only these two gut bacteria.

Question: Do you think one-day, microbial gut ‘supplements’ could be a viable cure to mental illness or other disease?

Microbes in the News

Article Link:

Title: Germs in your gut are talking to your brain. Scientists want to know what they’re saying.

Date: January 28, 2019

Source: The New York Times

Author: Carl Zimmer

Summary: In this article, Carl Zimmer describes how scientists have begun considering the role of microbes in behavior and their connection to the brain. Recent evidence suggests that the microbiome could have connections to mental health conditions. Several experiments have been conducted to study this hypothesis. For example, a study conducted by Dr. Mauro Costa-Mattioli found that some mice that showed autism symptoms lacked a specific microbe. In other studies, the presence of microbes was associated with various brain related conditions.

Connections: As we covered in the history portion of class, our understanding of microbiology has increased over time and we have acquired an increasing amount of technology, which is monumental in our study of microbes. Although microbiologists in previous centuries have made fundamental contributions to our current knowledge, we are continually better equipped to make observations on the functions and effects of microbes. This article highlights this reality, as the author discusses how recently the hypotheses and research discussed have begun to be accepted. In class we have also discussed the prevalence of microbes and how we have barely scratched the surface on understanding all there is to know about them.

Critical analysis: Overall, I found it interesting that microbes could potentially be involved in brain components, as I have never considered this type of connection. I was compelled by the research that was mentioned in this article, especially concerning the suspected role of microbiology in depression and anxiety disorders. More specifically, one part of the reading that fascinated me was that mice that are given fecal transplants from individuals with major depression are more likely to demonstrate depressive tendencies.

Although the article was very intriguing, most of the comments were based on speculation, and consequently, there were a minimal number of concrete conclusions. The scientists that were included in the article recognized their lack of knowledge regarding the connection between microbiology and the brain, as well as the limitations of their research. However, this did not seem to take away from the scientific accuracy or importance of the research and the foundation it can provide for future studies. By recognizing the limits of the research, I think that the article communicated the information to the public well because it showed that science is not always as definitive as some people seem to think, especially upon initially exploring topics. Furthermore, the text was mostly void of scientific jargon and condensed into an easy to digest article.

Question: Relatively early in the article, the author asserts “none of these associations proves cause and effect’ regarding some initial research he describes. Considering this, can any of the research mentioned in this article strongly support a connection between microbes and brain and behavior mechanisms? If not, how might the role of microbes be incorporated into alternative hypotheses to explain their apparent associations with the brain?

A2: Microbes in the News!

Article and link:

“The bacteria in your gut may reveal your true age”, by Emily Mullin from on Jan. 11th, 2019

—  Summary:  Researchers at Insilico Medicine  in Maryland are investigating what the microbiomes within our guts can tell us about our age and health. Using AI, correlations were made between reported ages and the frequencies of specific bacteria species within the gut. The algorithm formulated from these results was found to be accurate within four years of an individual’s true age.

—  Connections:  Microorganisms are everywhere, even within our bodies. Although some bacteria can be pathogenic, several species can be beneficial, like the ones in our colon. As mentioned in our textbook, “[t]he gut microbiome develops from birth, but it can change over time with the human host. The composition of the gut microbiome has major effects on GI function and human health”(2019).

—  Critical analysis:  A piece of information I found most fascinating in this article was the idea that the bacteria in our colon not only could provide details  on our age, but also our health. The prevalence or lack of certain bacteria could explain the rate at which our gut is aging, as well as “whether things like alcohol, antibiotics, probiotics, or diet have any effect on longevity” (Bullin, 2019).   Furthermore, the researchers  mentioned that association studies could show changes  in bacteria  frequencies  within the colon due to certain diseases, drugs, and other substances.

I believe that article was scientifically accurate. The source of the bacteria (I assume fecal matter) came from over 1,000 individuals around the world, but sampling biases could always be present. It would have been informative to provide a link to the scientific  paper to ensure the validity of sampling and statistical testing.

I also believe that the author did an excellent job introducing her readers to the subject with the first paragraph and then began describing the main idea with non-jargon language. The author was also able to connect this finding with the ideas from several others (i.e. biomarkers, biological aging estimators).

—  Question:  If one’s colon health and age can be predicted by the frequencies of certain bacteria using AI, could medications replenish the bacteria populations to prevent colon aging, which could allow aging individuals to absorb more nutrients from their diet and decrease their risks of ulcerative colitis and other GI diseases.

A2: Microbes in the News

Article and Link: The article I found was published in the New York Times by Richard Klasco, M.D. on December 21, 2018 titled Does the Gut Microbiome Ever Fully Recover From Antibiotics. The article can be found here but just a warning; The New York Times only allows so many article views per day before you have to pay for them.

Summary: The overview of the article is that studies are reviewing how the gut microbiome recovers from a course of antibiotics and questioning if the microbiome ever fully recovers to the same flora as prior to antibiotic treatment. The article gives basic information of the function of the microbiome in regards to human health and how the usage of antibiotic treatment indiscriminately kills bacteria regardless of being natural flora are harmful; it also has links to five different studies involving the microbiome and human health. The linked studies reviewed infant antibiotic treatment and breastfeeding, intestinal metabolism, effects of antibiotics on the gut microbiome analyzed by sequencing, and the microbiome showing incomplete recovery from repeated antibiotic treatment. The information being presented is stating that there is an increased risk for chronic health diseases with the use of repeated antibiotic treatments because the natural flora of the gut might not fully recover.

Connections: I will edit this post to add a question once we have progressed in our course.

Critical analysis: I found the study that analyzed infant gut microbiome, breastfeeding, and antibiotic usage very interesting. I’m glad that this article posted the link to PubMed so I was able to read the abstract. From the basic information in the article (without reading all the linked studies) I learned that there has been links between a disrupted gut microbiome and heart disease, obesity, asthma, and inflammatory bowel syndrome; I was surprised about the asthma and heart disease. I found that the article made some very bold statements that I could not directly find in the abstracts of linked studies but would be interesting in doing a bit more research.

Question: Given that we know that antibiotics are necessary in some cases but bacteria are increasingly becoming antibiotic resistant, I wonder if it more stress on prevention of unnecessary antibiotic usage should be given to the public. If the gut microbiome has such a difficult time recovering fully from antibiotic treatment should more research be conducted to alternatives to restoring proper function.