Writing Exercise #1

There is likely hundreds of human non-infectious diseases that are influenced by microorganisms, but the ones I think of when I hear this are sarcoidosis, malaria, oral thrush, yeast infections, sepsis, lyme disease, botulism, tetanus, and toxic shock syndrome.I realize after trying to write down all of the diseases that I think are influenced by microorganisms is actually slightly difficult. The most common diseases that came to mind were viruses, and while I suppose some would argue that a virus is a microorganism, I did not think it would be appropriate to add to this list. The videos provided for this week challenged my thinking though, but as of right now I figured I would keep cancer and other “non-microbial” diseases off my list as I am not well-versed in this area. After completing this activity, I noticed that the diseases I could think of were mostly communicable diseases. I think it is interesting that there are some microorganism influenced diseases that cannot spread person to person, due to the fact that the disease was most likely brought on by exposure, and then it simply inhabits only that body. However, is it possible that two microorganisms can inhabit the same body, ultimately causing two separate diseases? Does the body somehow ramp up its own immune system as an attempt to fight off an additional disease that it could come in contact with? I suppose this is why illness often confines a person to their bed, but I rarely hear of two life-threatening bacterial/fungal diseases occurring at once often. This could also simply be because it is just not very likely.

Writing Exercise #15

Prompt: Imagine yourself as the head of a funding agency (like the National Institute of Health) in which your job is to look at proposals for research projects and decide what projects to award funding to. Based on your readings this term, discuss a research project (or projects) that you would be most excited about funding as they relate to learning more about microbial influences on human health. As part of your response, consider what are we likely to learn from the project and how that might be important in future healthcare decisions.

Response: Based on my readings this term, I would be most excited about a research project concerning the gut microbial community and various psychological diseases or also concerning human nutrition and the gut. I think that there is a lot of potential within these areas that has yet to be explored, and it certainly should be explored. The gut plays a vital role within the body, so it is possible that it could be linked to more than just obesity nutrition-wise and could also be linked to other psychological diseases. From these projects, we could likely learn how to better inform the general public on their eating patterns, medication consumption, and overall gut health. These could be incredibly important to future healthcare decisions because if it turns out that antibiotics are more harmful than we initially think, perhaps these will have to start being administered in a different way. Also, on a bigger scale, if there is a connection between the gut and nutrition patterns, it could possibly control heart disease, diabetes, and obesity rates. This in turn would kill the number one killer in the United States, which would be absolutely extraordinary. If we could learn that psychological health and gut health are connected, there could be certain supplements available that focus on more of a holistic approach instead of handing out anti-depressants to people, which could likely save patients money and adverse side effects.

Writing Exercise #14


Part 1: Set a timer for 3 minutes, and make a list of as many human non-infectious diseases that you can think of that are influenced by microorganisms.

Part 2: Refer back to your Writing Exercise #1 that you completed the first week of class. Reflect and discuss how your responses have changed from week 1 to week 10, and what the most important topics you will take away with you once you have completed the course.

Response: The human non-infectious diseases that I can think of that are influenced by microorganisms are irritable bowel diseases, Crohn’s disease, obesity, diabetes, cervical cancer, cancer in general, depression, anxiety, kidney disease, periodontal disease, heart disease, herpes virus, HIV, botulism, tetanus, autism, Alzheimer’s disease, multiple sclerosis, ALS, Huntington’s disease, Parkinson’s disease.

Once I referred back to my first writing exercise, I realized how closed minded I was. I basically regurgitated everything that my microbiology class taught me and nothing else. I feel like looking at my response now, it’s certainly more engaging and entertaining. I feel like I actually have more substance within my response now and it would actually be a good conversation starter if need be. This class has really taught me to think outside of the box and expand my mind. Some of the most important topics that I will take away from this class are that the body is truly more connected than initially thought. Additionally, I feel as if the stomach is not very glorified for it’s role in the body, but now I truly feel like it should be taken care of so much more. The most important thing that I am taking away, however, is that as a human being in the medical field, I need to be more open to other possibilities than the cut and dry.

Writing Exercise #13


In W. P. Hanage’s article, he discusses the importance of five key questions when interpreting scientific literature:

  • Can experiments detect differences that matter?
  • Does the study show causation or correlation?
  • What is the mechanism?
  • How much do experiments reflect reality?
  • Could anything else explain the results?

Explain the significance that each of these questions have on interpreting scientific literature. Which is most helpful when discussing controversy, and why?


  1. The significance of this question is that, as humans, we have yet to reach the ability to fully understand genomes within microbiomes to detect differences that truly matter. The microbiome is hugely diverse and expansive, and it is difficult to observe all the changes from an experiment across the entire microbiome. Hence, we look for things that are “supposed” to change. Other factors could also change as well, and these could be even more important than what the experiment is testing. Hence, it is important to note that not all experiments are able to fully understand the extent of microbiome and not all the necessary information may be present.
  2. The significance of this question is that people need to explore the study done before taking the study’s word. The example giving within the paper perfectly describes that while the paper stated it was a “causation”, it was most likely a “correlation”. Other factors need to be considered when reviewing an experiment, especially if it can directly impact the experimental question.
  3. The significance of this question is that now that technology has advanced in such a way that allows us to pick out a taxa and see what that specific bacteria does. It is important for studies to be more precise, and not speculate on a broad range of bacteria. Having a study be more precise about a taxa or phyla is more convincing that it will have a said effect on the experimental question. Everything can have a casual relationship, and thus experiments should be exact.
  4. The significance of this question is that a lot of primary research articles are done on mice, and more often than not, they are germ free mice. This is certainly not modeled in humans. Hence, the study can be completely irrelevant to humans and this is important to consider. Humans are more complex and all come from different backgrounds that cannot be controlled.
  5. The significance of this question is that it refers to a lot of built up hype and also things that are beyond researchers controls. Therefore, when reading an article, the study needs to be big enough that it is actually a significant result and does not happen by chance. There are also needs to be a lot of controlled variables in the experiments. Additionally, those who write about the studies in a news article may not correctly interpret the results and hype up the article inappropriately.

I think the question that is most helpful for discussing controversy is, “how much do experiments reflect reality?”. I think this one does a good job of actually tackling the elephant in the room, is this even an applicable study? A lot of experiments are done in such an environment that can never be modeled for an actual human or environmental scenario and therefore is completely irrelevant.

Writing Exercise #12

Prompt: Describe how microbial communities in the body could influence brain and mental health states. Then, describe how brain and mental health states could influence microbial communities in the body. In what ways might these promote health and/or disease?

Response: Microbial communities in the body could influence brain and mental health states by way of various alterations to these communities. This is made possible because there is something called the gut-brain axis which is connected by the vagus nerve neurotransmitters, cytokines, and other small molecules. Hence, the two are then directly connected and can be affected by one another. One example is lymphocytes release cytokines, and this is caused by gut microbiota and then makes its way back to the brain systemically. Additionally, there is the more “broad” speculation of how these two could be connected due to an imbalance of the gut microbiome, and if the community isn’t harvesting nutrients very adequately, then the brain will be told that it is hungry more often than if it was functioning properly.

Brain and mental health state can influence microbial communities in the body by release of hormones or neurotransmitters. When a stressful event occurs, there is a release of cortisol and this weakens the gut microbial communities. There have also been studies that show when patients have IBD, they do not respond to stress well because their microbial community is already weakened, and stress does this even more-so.

This could promote general mental health and avoiding disease by trying to really take care of our gut microbiome. The study in the videos this week showed that when a certain probiotic was implemented, the mice became less depressed. Hence, perhaps probiotics could aid those dealing with stress or depression. This could also promote disease by taking antibiotics. As we now know, antibiotics severely alter the gut microbiome. Hence, persistent use of these or constant hospitalization perhaps can lead to depression. It is interesting to think that perhaps cancer patients and chronically ill patients could have psychological effects from an altered gut microbiome in the hospital, and not so much from the mental aspect of actually being in a hospital.

Writing Exercise #11

Prompt: Reflect on the peer-review process with you as the reviewer. How did it feel to read and critique someone else’s writing? What did you learn that you can apply to your own writing as you revise your final essay?

Response: It felt weird critiquing someone else’s writing, just because I don’t necessarily think I am the most qualified person to give advice on these things. I am okay at writing, but I certainly do not know a lot about writing essays, as being a science major, I do not really ever have to do that except for in a few classes. I felt very teacher-like which was kind of fun for a second.

Things I learned that I will be applying to my own writing is that someone made a really helpful suggestion about about including a paragraph about the cellular processes of how bacterial colonize the stomach, and it didn’t even dawn on me that this would be good a point to talk about. So far I have only gotten one reviewer, so that’s really about all I can say so far.

Writing Exercise #10

Prompt: Describe the process of peer review to someone who does not frequently read scientific articles. In your response, consider the pros and cons of peer review and how that might impact the credibility of the results that come from that scientific article.

Response: Peer review is the process of having a colleague, who typically studies the same subject as the author, read a scientific article that the author wrote. This person carefully takes into consideration of what the person is writing about and also makes sure to check the validity of what the author is saying. They comment on various aspects of the paper such as clarity, use of references, and the thesis of the overall paper.

A pro of having someone do peer review is that you get an outside perspective on your paper, and they can see things that you do not. They also can make suggestions as for what to add or subtract from the paper that are not necessary that the author wasn’t sure about.

A con of having someone do peer review is that the author and them might not always see to eye to eye, or the peer reviewer might not be as educated. Additionally, peer reviewers might not always do a great job and therefore can give you feedback that isn’t actually true.

This could impact the credibility of the paper if the author listens to bad advice or if they simply follow everything the peer reviewers says to do because the author no longer cares, or does not have appropriate confidence in their writing.

Writing Exercise #9

Prompt: List and describe as many changes in human behaviors as you can think of that contribute to decreased exposure to microbes.


  1. Going to the hospital
  2. Going to the dentist
  3. Going to the above and receiving antibiotics
  4. Having a major surgery
  5. Having a more bland diet, i.e. consuming more processed junk foods
  6. Showering a lot
  7. Using the antibiotic hand soap every time you wash your hands
  8. Cleaning with really powerful disinfectant wipes in your home
  9. Washing your clothes with bleach
  10. Not letting your kids play with other kids
  11. Not letting your kids play at the community park
  12. Isolating yourself for days on end doing homework in your room
  13. Being an only child with working parents (for the child)
  14. Not playing any contact sports as a child (for the child)
  15. Never going into the forest for a nature walk
  16. Never going to the beach
  17. Avoiding community transport

I feel like I can’t think of anymore without repeating myself.

Writing Exercise #8

Step 1: Some of the things that I’ve learned this term that are most interesting would probably be the areas concerning gut health, probably because this is mostly what we’ve focused on. Specifically, I really liked how cancer could potentially be caused by the microbes in our stomach. I also enjoyed the studies about mice and how differing microbiomes could influence their body fat mass. Recently, I have also found it interesting that take a simple vitamin supplement such as probiotics could really change a person’s gut potentially. I also think the fecal transplant stuff is kinda cool. I wrote about HPV and cervical cancer for the midterm essays, that was cool but I feel like I’m kinda tired of that subject now. It’s interesting how antibiotics really effect gut health and how it can take so long for it to recover. It also seems like gut health really has an impact on the body overall. The new stuff with skin dysbiosis and whatnot is kind of intriguing, but perhaps not as much as the older stuff to me.

Step 3: Specifically, I really liked how cancer could potentially be caused by the microbes in our stomach. I’ve always been really fascinated by cancer. In school, however, I have always been taught that cancer is simply something that happens by chance or from constant exposure to carcinogens such as cigarettes or red meat. When I first started the class I found this topic something that I looked forward to. I still think I really like it, and kind of think I’ll pursue it further. The studies that we read about make a lot of sense with how inflammation causes cells to divide and whatnot. This seems like something I should probably look into more. My parents both had cancer, so I’m a little worried about it myself even though its not genetic. Or… perhaps it can be? What if their microbiome was something that caused their cancer? They didn’t have gut cancer or anything, but maybe that could be passed down to me? I’m not too sure about that so I should probably stay on track with just the gut microbiome area.

Step 4: After reviewing my responses, I clearly should follow what interests me and pursue how microbes can cause cancer even further. To prepare for this, I should probably start finding research articles that could somehow show this. I am not entirely sure what I will find, since in class we only did stomach microbiomes. I’m not sure if I’ll find other parts of the body microbiome research and if thats associated with cancer as well, but I think just typing in key words of what I want is a good place to start.

Writing Exercise #7

Prompt: List and describe potential factors that the mother or the infant could be exposed to that could influence the colonization of the microbial community in the newborn infant (in positive or negative ways).

Response: Potential factors that the mother or infant could be exposed to that could influence the colonization of the microbial community of the infant seem as if it could be almost anything. Something that the mother could be exposed to when pregnant could be the things she eats and what these microbes are. Additionally, perhaps if the mother is in a very polluted area with dangerous breathing quality, this could potentially affect the infant. During pregnancy, if the mother takes probiotics or drinks kombucha, perhaps this could increase the infants microbiome diversity? After birth, the reasons listed before could also negatively affect the infant’s microbial community if they are directly exposed to it. However, things that could potentially positively impact the infant’s microbiome would having a formula that contains a diverse range of nutrients. Perhaps the mother’s breastmilk could be influenced by the mother eating nutritious foods as well.

Writing Exercise #6

Prompt: Describe your personal philosophy about how and when you have taken, or would take, antibiotics. What experiences or prior knowledge do you have that shaped that personal philosophy?

Response: I have taken antibiotics before, and I personally do not think that they are harmful if taken in appropriate dosages. I took them orally about two years ago and I did not have any complications. I think they are an extremely useful medical tool that can cure a lot of bacterial infections or diseases. However, I am very much so against any product that says antibacterial hand wash or antibacterial cleaner. I think this is completely unnecessary and is greatly promoting more and more antibiotic resistance in the world. It is very unclear to me how there is certainly knowledge that antibiotic resistance is a threat, yet all these mass companies keep making antibacterial products that do not even probably ever be used in an every day house hold setting. They especially do not need to be used every time someone washes their hands. Prior knowledge that has shaped this philosophy is in my microbiology course I have taken where my professor introduced this concept to me. My professor also taught us how soap works, and the importance of bacteria on our skin so it became a no brainer to say that it isn’t needed in hand-wash. I do think antibiotics are great in a healthcare setting, but not necessarily outside of it.