BHS Writing Assignment #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.

If I could only pick one project that I would be excited to fund, I think it would be related to autoimmune diseases. AI diseases are something so prevalent in the healthcare community right now, and from my own personal experience (being a patient and working in a healthcare setting) as well as experience through classes and educational platforms, it seems like an area that most healthcare providers still have so many questions about. There is obviously a huge connection between microbes and AI diseases ranging from connective tissue diseases to neurological to skin diseases. I would like the project to look specifically at different diet protocols and how they influence microbial health within the human bodies. It would be interesting to quantify symptoms and look at correlations between types of microbes and symptoms patients are experiencing.

This would be an important project because it would provide valuable information to healthcare professionals dealing with AI diseases on a regular basis (dermatologists, GI specialists, rheumatologists, etc.) and provide an additional treatment avenue for patients. Currently, treatment options for patients with autoimmune diseases are not great. Most are immune-compromising medications that have MANY unwanted side effects. A dietary change for AI patients could be really life changing. Looking at the specific microbes associated with disease states vs AI patients with few symptoms might also be a good way to target specific microbes that could be used in FMT for this specific patient population.

BHS 323 Writing Assignment #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.

Here’s my list: Heart disease, atherosclerosis, cancers (many types!), diabetes, insulin sensitivity, obesity, IBS, Crohn’s Disease, other GI diseases, Leaky Gut Syndrome, multiple sclerosis, rheumatoid arthritis, lupus, psoriasis, eczema, rosacea, follicular diseases, Alzheimer’s disease, Parkinson’s disease, anxiety, depression, insomnia, sleep apnea.

Reflecting back on my Writing Exercise #1, I actually had a fairly comprehensive list of diseases (I’m surprised!). I was kind of impressed that I was actually able to come up with so many encompassing classes of disease. I had a good idea of what I thought microbes had the ability to influence, but I have learned SO MUCH over the course of this term. One of the most important takeaway topics from this course is just how connected all of our body systems are and how dysbiosis in a small way can contribute to some very large diseases. I also learned that it is fairly easy (if you put in the right efforts) to make choices that positively influence your microbes. Depending on lifestyle, medical, and dietary choices, each of us have a lot of control over the health of our own microbiota. In looking at my own longevity, I am most impressed with the ability of microbes to influence your health over a lifetime. As I grow older, I think about my life and things I can start doing now that will positively influence me as I age. I hope to incorporate many of the findings of this class into my life as I make choices that will impact my microbiome and my health for the rest of my life.

BHS 323 Writing Assignment #13

Prompt: In W. P. Hanage’s article, he discusses the importance of five key questions when interpreting scientific literature. Explain the significance that each of these questions have on interpreting scientific literature. Which is most helpful when discussing controversy, and why?

  • Can experiments detect differences that matter?

This is significant because it gives a study the ability to have findings that are significant. If one variable or aspect to the study changes, the results could differ drastically. Differences in the study outcomes as well as differences in the study outline and methods are equally as important. These small differences could be the key to a study being more valid or accurate.

  • Does the study show causation or correlation?

Causation shows that A directly influences B. Correlation shows that A and B are related, but it doesn’t depict how so. Causation gives us a much clearer picture of what is being shown, and proves that something is caused by a specific factor. A correlative relationship is important, but it doesn’t show us why the correlation exists. For example, a specific diet protocol may influence our gut microbiome, and specific measures might show that eating a low-carb diet has such an influence on the gut, but this is not showing us specifically why something is happening. It just shows that there is a relationship between what we are eating and how our microbiome responds.

  • What is the mechanism?

The mechanism is the process that causes a relationship between variables. The mechanism is important in that it shows how the relationship happens or why it is possible. This is important in interpreting scientific literature because it explains the conclusions made from the research article. Without a clear explanation of how A causes B, it is hard to interpret literature with a high level of reliability or validity. 

  • How much do experiments reflect reality?

This is a huge measure. If your research question is tested in an environment that is nothing like the natural environment in which this would occur, it would be hard to justify that the experiment is reliable in its natural setting. This is a significant question as it shows the ability for the results to be applied to a real-life scenario. 

  • Could anything else explain the results?

The ability for anything else to explain the results of the study limits its validity. Validity explains the accuracy of a measure and how well the study question is answered by the testing completed. If there are confounding variables or outside variables that influence the results, the study loses accuracy and validity. For the results to be valid, the question needs to be answered specifically by the variables in the study. 

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

      I think the most helpful when discussing controversy is the ability for anything else to explain the results. When reading a study that is controversial, I often ask myself if there is anything else that could give these same results. This ties in a bit with the causation vs correlation point in that causation is really what the goal of any study is. Correlation gives us some data, but doesn’t give a true answer to the research question, unless causation has been proven. In my final essay, I talk about Roundup and its active ingredient, glyphosate. The controversy is whether or not glyphosate disrupts the gut microbiome, which can then contribute to a disease state. While you can look at glyphosate ingestion and how a specific gut microbiota looks after ingestion, there are many other factors at play that need to be addressed (diet, for example). 

BHS 323 Writing Assignment #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?

Microbial communities in the body can influence brain and mental health states in a number of different ways. There is a direct connection between the gut and brain via vagal and sympathetic nerves. Small molecule byproducts made by microbes influence these nerves. Lymphocytes release cytokines, which can influence endocrine and paracrine actions, which can directly influence brain function. Systemically, production of corticosteroids and neurotransmitters can influence the brain systemically. Conversely, behavioral changes can release neurotransmitters, steroids, or hormones, which can all affect microbes in the gut.

Promotion of health and disease, then, go hand in hand. If you have good mental health with little depression, anxiety, or other diagnosed mental health conditions, you likely have a health gut microbiome. In contrast, if you actively work to increase the health of your gut microbiome, you likely reap the benefits of a good mental health state. The opposite is also true. These are a correlative relationship, meaning if your mental health starts to decline, your gut microbiome likely will too. If you eat well and focus on foods to increase your gut bacteria health, you might find your mental health and brain functioning to be better! The connection between individuals with ASD and IBD is very interesting and gives good evidence to suggest that this connection is indeed true.

BHS 323 Writing Assignment #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?

I had somewhat of a hard time with this assignment. Normally, I enjoy reading and giving feedback on peer papers, but the papers I was assigned to were not complete. This made it hard to fully assess the writing and compare it to the rubric. I am a fairly comfortable writer, I completed an undergraduate thesis during my time at Oregon State University, so writing comes easily to me. It is tough for me to “go easy” on the writing of others. During the peer review process, I had to read the papers with an open mind and try to see where the authors were coming from and their thought process in order to give them valuable feedback.

It was a good reflection for me on my own writing. I want to re-read my paper and make sure that I have good introduction and transition sentences in each of my paragraphs and that I gave enough information to support the citations I made in my paper. I also want to make sure I didn’t include too much extraneous information unrelated to my thesis statement.

BHS 323 Writing Assignment #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.

The process of peer review has 5 main steps:

  1. The author(s) submits their work to the journal of their choosing. Journals are selected based on subject manner (should relate to the topic of the manuscript), prestige of the journal, and connections to the journal or editors of the journal. The prestige of a particular journal means that there might be more exposure, if published. This would be a pro for the author because it would allow many people to see and cite their article. This might be a con because it could be harder to have their work published in a high-prestige or high-impact factor journal. For a journal to be considered “high-impact factor”, it means that the articles in that journal are the most highly-cited articles.
  2. If approved to move forward by the journal, the journal editor screens the paper to decide if the manuscript fits with the philosophy of the journal. If so, it moves on for further review by 2-4 reviewers. If not, the manuscript is rejected.
  3. These reviewers are usually well-established published researchers in the field of research of the manuscript. These reviewers are chosen by the journal editor and remain anonymous to the author, however the reviewers do know who the author is. The manuscript is evaluated for scientific merit and relevance. The reviewers write their impressions in a letter to the editor to accept or reject the manuscript. This step would definitely impact the credibility of the manuscript as it is being reviewed by experts in the field, often who have done their own research on similar subjects. This is a pro for the credibility of the research.
  4. The editor has three choices. They can accept the manuscript as is with no revisions (this is very rare), reject the manuscript (very common), or send comments back to the author to revise and resubmit the manuscript (very common). This is a valuable step for the author as it gives them a chance to often make revisions and re-submit. If there is a part of their manuscript that is unclear or needs further clarification, it gives them a chance to go back and re-write a section.
  5. The author then has the option (if given) to respond to any changes and re-submit for review again.

A con of the entire review process is there is little transparency to the general public. This might lead to a decrease in the credibility due to the public not knowing the interests of the reviewers of the manuscript.

BHS 323 Writing Assignment #9

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

  • Exposure to the outdoors- Spending your childhood indoors vs playing outside, getting dirty, exposure to bodies of natural water would likely decrease your exposure to microbes.
  • Exposure to pets and other animals– Growing up in a home rich with animals, especially those who live outdoors, and having exposure to animal saliva, cleaning animal pens, eating chicken eggs, drinking unpasteurized milk will likely increase your exposure to microbes. Growing up with no pets or animal exposure (or even indoor cats/dogs) would probably decrease your exposure to microbes.
  • Taking antibiotics-As we have learned, this will decrease exposure to microbes and decrease richness of microbes already present in the gut.
  • Eating processed, sugar-rich foods-Instead of eating pre- and probiotic rich foods, eating processed foods will decrease your exposure to microbes.
  • Home daycare as a child vs. public daycare– Growing up in your home environment without exposure to other children will likely decrease your exposure to microbes.
  • Homeschooling vs. public school-Similar to above, attending a public school with children from all backgrounds will likely increase your exposure to microbes, while being homeschooled will decrease your exposure.
  • Not breastfeeding your child-There is a decrease in microbial exposure that comes with formula or bottle feeding an infant.
  • Your work environment-Your work environment could increase or decrease your exposure to microbes depending on where you work. An office setting in your own cubicle will likely provide less exposure to microbes than say, working out in a forest or working with animals.
  • Food source-Where your food is grown and if it was treated with antibiotics is a factor that could increase or decrease microbial exposure. If your food is store-bought, treated with RoundUp or other pesticides, it is likely not going to expose you to as many microbes as if you ate homegrown, organic foods.

BHS 323 Writing Assignment #8

Prompt: Free write. This writing exercise is designed to help you begin to think about a topic you are interested in pursuing for your final essay project in the course. 

5 minute free write #1

I am interested in the role that diet plays in our gut microbiome. Nutrition is very interesting to me and especially the long term effects of a particular diet on all aspects of the body (endocrine, neurological, etc.). The ways in which the gut microbiome is affected by what we eat or ingest that can hurt or harm the microbes. I would like to know more about leaky gut syndrome and the other systemic effects caused by disruption to the gut microbiome. I am also interested in the role that pesticides (antibiotics) have played in our microbiome, if there has been a change nationally in our microbiome with the addition of more processed foods, RoundUp, etc coming into our diets. How we can eat specific foods to target good gut bacteria proliferation and reduce foods that are harmful. I know some things about leaky gut and believe it is somewhat related to the microbiome and partially related to breakdown or inflammation in the gut lining that increases systemic inflammation. Systemic inflammation as a result from dysbiosis in the gut is also something I would like to learn more about. I know there is a big correlation with neurological diseases like parkinson’s and alzheimer’s, which would be interesting to take a look at.

5 minute free write #2

I know that “Leaky gut syndrome” is caused by inflammation in the gut that causes microbes to “leak” into systemic tissues, which usually triggers inflammation and an immune response. It would be interesting to learn more about what can be done to counteract this and if there is any correlation to autoimmune diseases. Working in dermatology, I have exposure to patients with skin components of some autoimmune diseases and I know that diet can play a large role in that. It would be interesting to see if there was a microbial component to autoimmune diseases characterized by inflammation that was maybe caused by leaky gut. Is leaky gut something that can be reversed? I know there are a number of “bad” microbes that feed on simple sugars and processed foods, so eliminating inflammatory carbohydrates can be beneficial for many people. It would be interesting to look at a diet protocol for patients with lots of inflammation or immune conditions. Is systemic inflammation typically caused by the foods we eat? There is a lot of hype about “inflammation” right now and all of the “trendy” things we can do to decrease inflammation. I would like to know which microbes specifically are targeted by sugary foods and maybe lead to increased inflammation or leaky gut syndrome.


I think that writing my final paper on a particular anti-inflammatory diet protocol would be very interesting. If I could find research that talks about foods to increase “good” gut microbial communities or foods to eliminate that are more inflammatory or lead to proliferation of bacteria that contribute to inflammation in the gut or even systemically, that would be very interesting. I am drawn to nutrition, its role in our lives, and finding ways to improve our diet to increase longevity and health. I will look at information that is out there and look into more of what leaky gut syndrome is caused by (if it is a symptom of microbial dysbiosis) and see what I can find!

BHS 323 Writing Assignment #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).

  • Diet of mother-The diet of the mother controls which microbial communities are present in her gut, mouth, and vagina. Her diet also determines whether or not she will develop gestational diabetes during pregnancy.
  • Antibiotics taken by mother-If the mother takes antibiotics during her pregnancy (or prior to becoming pregnant), it is likely she has some level of dysbiosis that could affect the future microbial communities of her unborn baby.
  • Pre-/Probiotics taken by mother-If the mother takes pre-or probiotics prior to- or during pregnancy, this could help to retain or enhance her already present microbial communities.
  • How baby is born-If the baby is born vaginally, they will be colonized with bacteria from the mother’s vagina. If the baby is born via c-section, the baby will be colonized with bacteria from the mother’s skin. One way is not necessarily “better”, but vaginal births are the most “natural” birth method, so I would guess babies are exposed to more diversity of microbes if they are born vaginally vs via c-section.
  • If baby is breastfed or bottle fed-If the baby is breastfed, they are coming into microbes on the mother’s skin and in her milk, which would help to enhance colonization of microbial communities.
  • Hospital environment-The environment in which the baby is born could definitely contribute to the baby’s microbial communities, either in a positive or negative way depending on which microbes were present in the room, if the baby were born in an operating room vs being a home birth.
  • Home environment-Similar to the hospital environment, if a newborn baby comes home to a house with pets or other siblings, they will likely be exposed to a much different set of microbes than a home with no animals. A home in the city vs out in the country could change the microbial communities present too.

BHS 323 Writing Assignment #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?

I have taken antibiotics a handful of times for minor surgery precautions (wisdom teeth), staph infections of the skin, as a treatment for acne and most recently, for rosacea, facial redness caused by inflammation.

I believe that there is a time and place for antibiotics. In the case of surgeries, I think it is a necessary precaution. Infections in your mouth or near organs can be life-threatening. If it was recommended that I take antibiotics prior to, or after, a surgical procedure, I would certainly do it.

For the staph infections, topical agents such as prescription Mupirocin ointment can be used as a primary method of treating the staph (as long as it hasn’t spread or become too aggravated). This would be a way to avoid oral antibiotics with a good cure rate. I would make the change from oral to topical antibiotics to preserve my gut flora in the future.

As a teenager, acne is often treated primarily with Doxycycline 100-200mg daily. I took Doxy for several months about 10 years ago and it certainly helped to clear my skin. This is not something I would ever consider doing again, and if I had the choice to go back and avoid the Doxy, I certainly would. Because this was not crucial to my health and they are other treatment options available, I don’t think taking antibiotics for acne is a great option.

Finally, low-dose, long-term antibiotics for skin conditions such as rosacea is actually a very common treatment. For this, it’s usually a 40mg daily dose of Doxycycline that you basically take….forever. A dermatologist will tell you that taking 40mg is not an antibacterial dose, it is only an anti-inflammatory one. Even so, I don’t think I would ever take a chronic antibiotic knowing what I know now about how my gut microbiome is impacted by their use.