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:


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?

In India, a Renewed Fight Against Leprosy – post #3

Article & Link: In India, a Renewed Fight Against Leprosy (The New York Times; April 17, 2019)

Summary: Leprosy, which is caused by Mycobacterium leprae has been eliminated throughout most of the world. However, it is still a huge problem in India, which currently has 60% of all leprosy cases in the world. This is largely due to the stigma against people with leprosy in India, who are not allowed to have jobs or even be in public if they have the disease. This means people with leprosy won’t seek help if they have leprosy, which causes nerve and muscle damage if it isn’t treated. However, there are some doctors in India who are trying to educate people better on leprosy to treat as many people as possible and hopefully prevent its further spread in India.


Connections: We were recently learning about pathogens in class. Leprosy, or Mycobacterium leprae causes a bacterial disease which affects nerves and muscles. The article mentioned that the bacterium is not culturable which prevents understanding of the disease. This explains why scientists don’t yet understand how the disease spreads. It sometimes spreads in a seemingly random way, infecting some people but not others. Furthermore, people can carry the disease for decades, spreading it to other people without realizing they are carriers.


Critical Analysis: I found the discussion about non-culturable pathogenic bacteria very interesting, because most of the examples we learned about in class were discovered and treated through culturing. It is also interesting to see how stigma and misinformation prevents treatable diseases from being eliminated. I learned a lot about how India’s culture regarding leprosy by reading this article. Many people hide it, potentially risking the health of those around them. Others go to leprosy colonies, or secluded communities, surviving by begging and helping each other. From what I could tell this article appeared to be scientifically accurate and not misleading. I feel like the writing is both accessible and informational to general audiences. It explains what leprosy is, the common symptoms, and why it’s such a big problem in India. I think it also did a good job explaining why leprosy is hard to study (mentioning its non-culturable, explaining it can’t be found by blood tests, and talking about how people can be carriers for decades) to people who may not have a lot of previous microbiology background.


Question: How should/do doctors and scientists study non-culturable bacterial species? Especially those species that are pathogenic?

A2: Microbes in the News

Title: Microbes that live in fishes slimy mucus coating could lead chemists to antibiotic drugs

Source: The Conversation Academic Rigor, journalistic flair

Date: March 31st 2019

Finding new sources of antibiotics has become critically important in recent years in order to combat drug resistant infections. One potential source is fish mucus that covers their bodies in pill form since it is a natural anti-infective. Over 33,000 species of fish have the microbial containing the slime that can protect them from diseases and bacteria and potentially used to help humans with this as well.

In class we have discussed antibiotic sources and working around antibiotic resistance. We have looked at how different natural microbes can help with fighting off diseases and not have a resistance already built up.

I found the article to be well written and very scientifically relevant. They referenced their research at Oregon State University and the ways they have classified the different bacteria they have found taxonomic groups. They found 47 different bacterial strains gathered for the swabs they did on the fish mucus. They carried out a process similar to what we have done in lab to isolate and test them.

What do you think about using natural anti-infectives from animals to combat human pathogens?

Microbes in the News #2

Copycat fungus deceives immune system and deactivates body’s response to infection

Date: March 28, 2019          Source: University of Sheffield


Summary: New research shows fungi can make similar chemical signals as our immune system. These chemicals enter the body and make humans more likely to get an infection.


Connections: Just today in class we talked about the immune system and how it captures microbes.


Critical Analysis: Fungi have always produced chemicals similar to those released in our immune system. Up until know, we haven’t known the function of these chemicals. Now, research shows that when exposed to these chemicals the fungi can grow more easily than when the host is unexposed. I found it especially interesting that the fungus does not suppress the immune system in any ways. These fungi immune chemicals named prostoglandins activate a specific immune system pathway. This pathway prevents over-stimulation of the immune system. Ultimately this makes the body unable to fight off the fungal infection. What is even more dangerous is that opportunistic infections from usually commensal bacteria pose a danger while these postoglandins deceive the body. Once the body is tricked into shutting down the immune system, bacteria that our bodies always host begin to grow out of control.


Question: Would it be possible for microbiologists to isolate these prostoglandins in order to treat diseases in which the immune system attacks itself?

A2: Microbes in the news — Yeast produce low-cost, high-quality cannabinoids


Yeast produce low-cost, high-quality cannabinoids


Synthetic biologists at UC Berkeley have engineered brewer’s yeast to produce some of the main components in marijuana including THC and CBD among others.


The developing field of synthetic biology is based on taking the tools that we are using in class, such as whole-genome sequencing, and our knowledge of how microbiology works to modify and create solutions to modern problems.

Critical Analysis:

Synthetic biology is an amazing and quickly developing field with the potential to take   a future we have only seen in science fiction and turn it into reality. This is an incredible technical achievement showcasing our developing mastery over the fundamental building blocks of life. I knew something like this was coming, I can see the economic incentives for this, I am sure the people behind this will end up fabulously wealthy, but I still can not stop myself from facepalming. Of all the amazing and wondrous potential synthetic biology holds… this had to be the top of my news feed today.


I cannot begin to imagine the legal ramifications, how the hell do you regulate something like this?

A2 Microbes in the News

“Why your kid’s strep throat keeps coming back,  A combination of genetic and immunological factors makes some children susceptible to the bacteria that cause strep throat” by the La Jolla Institute for Immunology, published 6 Feb   2018. Found:

Streptococcus pyrogenes causes a number of diseases, but when found in the throat it is known as strep throat.   The scientist gathered 100 children who had undergone tonsillectomies and tested their immune response.   They had a less robust response to Strep.   Additionally, their parents also had a decreased reaction to the strep toxins released by the virus.

This, I think, connects to the class in the development of vaccines.

I think it is quite interesting how how we don’t really have a clear understanding on how the immune system responds to the removal of the tonsils, a thing we have been doing for nearly 2000 years.   It wasn’t really well written, I think because it was trying to water down a scientific publication.   It didn’t really give me as much information I wanted, but I imagine, that for a person with a less deep understanding of immune response as me, a person who, admittedly, doesn’t have a great grasp of the subject, would be able to get the gist.   However, the article could have been better organized.

“SpeA” is a toxin given off by the microbe, I wonder how the immune response acts on that, rather than the microbe itself.

A2: Microbes in the news – Study: Gene Drive Wipes Out Lab Mosquitoes



A gene editing technique called a Gene Drive which is based on the well known CRISPR technique has been shown to be able to completely eliminate a mosquito population in the lab.


We have been learning about the various techniques used through history to prevent diseases, from antibiotics to vaccines, this represents another potential tool capable of having a similar impact.

Critical Analysis:

The prevention of deadly diseases has been and continues to be one of the greatest goals of the study of microbiology and malaria is currently one of the most deadly infections still at large in the world with  219 million cases of malaria in 2017, up from 217 million cases in 2016 despite incredible continued efforts to prevent its’ spread. A commonly targeted element of the disease is the delivery method, mosquitoes. However while previous efforts have failed to slow the spread, this technique has demonstrated the potential to not just slow them but to precisely and completely eliminate an entire species.


What other populations can this be applied to? For instance, would it be appropriate to eliminate the populations of rats devastating island bird populations?

A2 Microbes in the News (P.gingivalis and Alzheimer’s disease)

Article and Link:

“We may finally know what causes Alzheimer’s–and how to stop it’
By: Debora MacKenzie
Date: 24 January 2019


Researchers have found that the formation of amyloid and tau proteins which are signs of Alzheimer’s disease, may be a response to bacterial infiltration. One of the major risk factors of Alzheimer’s is the occurrence of gum disease caused by the bacteria Porphyromonas gingivalis.
They have found that P. gingivalis has been found to infect areas of the brain with Alzheimer’s lesions as well as exacerbating the symptoms of Alzheimer’s in mice who have been infected with P. gingivalis as gum disease. Similarly healthy mice (who have not been engineered to have Alzheimer’s) who have been infected with gum disease and the bacteria P. gingivalis, exhibit amyloid plaques, and neural damage similar to that found in Alzheimer’s affected brains.
Enzymes which P. gingivalis uses to feed on human tissue, have been found in 96% of brains analyzed by Cortexyme and P. gingivalis proper has been found in several brains upon autopsy. Higher rate of these “feeding enzymes’ called gingipains have been higher in those with a greater cognitive decline before their death as well as greater amyloid and tau accumulations.
Cortexyme has developed a molecule with inhibits these gingipains and has shown to effectively halt P. gingivalis infection in mice including stopping amyloid production and reducing the associated brain inflammation.


                      I can see a connection with the research that they are doing with Koch’s postulates. Not only have they found the pathogen in unhealthy mice, but also upon injecting the pathogen into healthy mice, they receive the same symptoms. I don’t know their exact procedure, however that they are not only exploring what they are finding within the diseased subjects, but duplicating the symptoms in healthy subjects is similar to how they have been identifying pathogens using these postulates.

Critical Analysis

I am very interested in this news story, not only because the community is expanding their thinking on the amyloid and tau protein buildup (previously thought to build up due to cell component aging) being a response to something, rather than an inevitable state of neural tissue. I also like that it goes into light detail on the reasoning behind why they began the studies, what the studies are doing and what the future of the studies are going to be. Also, it is interesting that they have not only made this correlation, but that Cortexyme has already begun developing a vaccine and medications to stop the proliferation of P. gingivalis in the brain (which could also help with gum disease, but I really just love the brains).
As for the article, I think that it is a lot of information for one article but that it is very well put together in a manner that doesn’t overwhelm the reader. There are also links embedded within the article that reference journal articles for further reading, which is beneficial for those who would like a deeper understanding.


The main question that I have is one of correlation vs. causation. There is evidence form the research on healthy mice that the P. gingivalis causes the anomalies within the brain tissue, but they did not find evidence of the bacterium in all cases of Alzheimer’s that they studied. So my question is still the age old question: Is this THE cause of Alzheimer’s disease or is it A cause of Alzheimer’s disease? Does it simply exacerbate the disease or increase the rate at which the disease presents?


Samantha Smith

A2 Microbes in the News

Article and link

“Gene expression study sheds new light on African Salmonella’
Science Daily, January 15, 2019

Further Reading:



A variant of Salmonella typhimurium (ST) 313 is responsible for the deaths of approximately 400,000 persons ever year in sub-Saharan Africa. Researchers at the University of Liverpool are attempting to understand how the genome of African S. typhimurium, which enters the bloodstream and spreads through the body, differs from the global strains of S. typhimurium which causes gastroenteritis.

By culturing the different Salmonella strains in different environments they could simulate differences of stages within the human infectious timeline. They then analyzed the transcriptome of these two strains and found a multitude of gene expression variations as well as RNA variations. These coincided with metabolic and plasmid differences within the two strains.


This correlates with the information that we have learned about variations in culture mediums in class. As well as what we will be going over in lab. The ability to culture this bacterium in different environments allowed for the researchers to study the gene expression at essentially different time frames in the bacterial life cycle. Say, from an environment similar to that outside of the human body, and then an environment within the human body.

Critical Analysis

What I found interesting in this article is that the phenotypic expression of genes within one strain has caused such a different in its ability to act as a pathogen. I also never thought of culturing microbes in different environments to simulate gene expression. I just thought you would culture them in their ideal environment and study them as such. Thinking about it now, it makes a great deal of sense to do this, not only to study the activity of pathogens, but to perhaps study microbes and why they fit into their respective niches.

The forum for this article is a scientific forum, and though it is technical it is written in a way that someone who isn’t specifically a microbiologist (such as myself) can understand what is being studied and the accomplishments that this group of researchers have made.


The question that I have is a technical one. How is it that they were able to find out the gene expression of these bacterium from culture? I know that the genome can be sequenced using various methods, but how would one know or ascertain which portions of that genome are being expressed at any given time.

-Samantha Smith