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 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?

A2: Microbes in the News – Post 2

Title: “A Teenager Was Diagnosed With Schizophrenia – but it Turned Out to Be an Infection From HIs Cat”

By” Christina Oehlea

Healthy Living Newsletter



A young Midwestern boy spent two years in and out of the hospital due to a bacterial infection.  The boy was first misdiagnosed with schizophrenia by two physicians, but later correctly diagnosed and treated for neurobartonellosis, which caused him to have psychiatric symptoms such as depression and suicidal thoughts, among other symptoms. After an antibiotic treatment, the boy made a full recovery.


The content of this article relate to our study of the human immune system and antibiotics.

Critical Analysis:

I think that the article was easy and short, which is good for accessibility, however, I think that it should have provided more information about the bacteria strain, which carry Bartonella clarridgeiae.  But overall, I think that it covered the bases for to provide readers with preventive and informative facts. I also think that the article was from a reliable source, because the author cited that the original case was published in The Journal of Central Nervous System Disease, which is a peer-revised journal publication.


How did cats become a vector for Bartonella clarridgeiae and do they infect other hosts?

A2: Microbes in the News #2

-Article and Link:

“Exploring Copper’s Potential as Antibiotic.’ Source: University of Arizona News. Link:

-Summary: An immunobiologist at the University of Arizona is studying whether or not copper could be used as an antibiotic in the future. Bacteria need certain metals, like calcium and iron, to survive, but copper is toxic to them. They have a protein called CopY that controls how their cells get rid of copper, but exactly how it works is unknown.

-Connections: We’ve talked about antibiotics in class, and about how they target characteristics of bacterial cells that are different from eukaryotic cells. We also talked about how antibiotic resistance is increasing- thus, antibiotics targeting elements of bacteria that they haven’t yet developed resistance to might soon be needed.

-Critical Analysis: I found it interesting that macrophages (at least in the lungs) “bombard’ bacterial cells with copper, while depriving them of metals they do need, in order to kill them. I think the article was scientifically accurate (I trust it slightly more than I would if it were from a “regular’ news website, because it’s from a university- though that isn’t always a sure thing). I think it was well written. Most people have heard of pneumonia, so I think mentioning it at the beginning of the article was a good way to draw readers in. I think it did a good job of communicating science to the public- for example, it defined the term “macrophage,’ and explained why research into new antibiotics is needed.

-Question: Is copper also harmful to eukaryotic cells?

A2: Microbes in the News – New Anti-CRISPR Proteins in Soil Bacteria

Article and Link: New anti-CRISPR proteins discovered in soil and human gut (ScienceDaily)

Summary: CRISPR is a natural bacterial immune defence, but some bacteriophages (or viruses) have developed anti-CRISPR genes that cause bacteria to lose immune defence when infected. New anti-CRISPR proteins were discovered by using protein functionality tested across a variety of environments, rather than using DNA and culturing. Their discovery could lead to the development of better technologies in the emerging field of CRISPR gene editing.

Connections: This article demonstrates the prevalence and possible uses for bacteria in today’s medical world. If bacteria could be used to produce proteins that create more precise gene editing with CRISPR, gene editing may have a very real future in human society. The way the researchers discovered new anti-CRISPR proteins is also a testament to the diversity of microbial life and how not all microbes can be cultured.

Critical analysis:  I find this article fascinating, because I am very interested in how cellular function, protein production and genetics can be used in the medical world to produce new treatments, drugs and cures for disease. With improved CRISPR technology, it may be more realistic to use gene editing to treat diseases such as cystic fibrosis. Unfortunately, this article was not very well written and did not explain the methods of the researchers in a way that is accessible to the public. The writing was very hard to follow and I had to read it multiple times before I began to understand the premise of the article. However, from my level of understanding there were no factual inaccuracies even though it oversimplified genetic editing and the way CRISPR works.

Question: How does the presence of anti-CRISPR genes in bacteria affect their susceptibility to antibiotics? Could they be more susceptible since anti-CRISPR proteins target bacteria’s “immune systems’?

“Does the Gut Microbiome Ever Fully Recover From Antibiotics?’


“Does the Gut Microbiome Ever Fully Recover From Antibiotics?’ Richard Klasco, M.D.

New York Times. December 21, 2018.


Summary: Although most microbes in the “gut’ grow back quickly and normally after stopping the use of antibiotics, there are some which take much longer to grow back, and some which may never grow to the same population density they once were.

This may have unknown effects on the body, but may contribute to certain health ailments, including inflammatory bowel disease and heart disease.


Connection: While microbes are generally thought to be fast growing, we have learned that some grow quite slowly, depending on their metabolism and physiology. If a microbe takes a long time to reach maximum population density, wiping them all out with an antimicrobial may have long term effects that cannot be easily undone by simply ceasing the use of the drug.


Critical Analysis: Without more knowledge on which specific species are affected long term by the use of antibiotics, it is hard to understand the full implications of the research. The human microbiome is a field with increasing focus and attention recently, and understanding the long term effects of some of these antibiotics may contribute to the development of less harmful medications which could help with the ever-growing problem of microbial antibiotic resistance.


Question: Could the use of certain probiotics help restore the population of some of these microbes in the gut following a course of antibiotics?

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.

A2: Microbes in the News Assignment

Microbes in the News !

Over the course of the semester, post 3 different stories involving microbes  from the popular media and then read and comment on 3  posts by other students.


Points: Total possible = 30 points. Earn up to 8 pts for making a post and 2 points for posting a comment. Create 3 posts and 3 comments over the course of the semester.

Deadlines: Posts can be made as soon as you’d like, but for full credit you must post them by these deadlines:

Post 1: Feb. 8

Post 2: April 1

Post 3: April 15

All comments: April 15


Learning Objectives:

– Increase your awareness of microbiology and its role in society

– Expand and apply your knowledge of microbiology

– Practice critical thinking by analyzing popular news media for scientific accuracy

– Develop questions about microbiology

– Help your peers and yourself understand microbiology by answering their questions



Over the course of the semester, create 3 separate Microbes in the News posts on the course website, and then read and comment on 3 Microbes in the News posts by other students. Be sure to follow the guidelines below in order to qualify for  full credit.


Guidelines for creating a post:

Article and link: Enter the title, source, and date of the article and create a link to it. Articles should be from any popular media source (newspaper, magazine, podcast, blog,  etc.) that others can access without hitting a paywall. Any relevant story is acceptable, but challenge yourself to find stories that are current (~within the last 3 months) and that haven’t yet been posted by your peers, whenever possible.

Summary: Write a short summary of the story (just a few sentences is sufficient).

Connections: Explain briefly how this connects to what we’ve covered in class.

Critical analysis: Explain what you found interesting about this story, and what (if anything) you learned. Comment on whether you think the story was scientifically accurate or not. If you noticed any factual inaccuracies or aspects of the story that might inadvertently confuse or misinform readers, identify those and provide a more accurate explanation. Also comment on how this was written. Do you think it did a good job of communicating science to the public? Why or why not?

Question: Write a question about microbiology that you had as a result of reading this story.

Categorize: Categorize your post as “A2: Microbes in the News’ using the categories menu on the right. This will ensure I can find it and give you credit.

Tag: Tag your post based on any relevant microbiological themes by choosing from the tag menu (below categories on the right). Use existing tags when possible, but you can add new ones if needed by clicking “+Add New Category’ link just below the list of tags. This will help us find stories on relevant themes. You can also use these tags to search for other students’ stories on themes that interest you.

Guidelines for commenting on a post:

– Read the news story and the students’ post about it

– Create a comment and write a response to their critical analysis. Do you agree, disagree, or have more to add?

– In your comment, answer their question to the best of your ability. This might require some independent research.