Writing Exercise #15

If I was the head of a funding agency, and it was my job to determine which research projects to fund, I would have to choose studies on microbial influence on mental health. There is already a lot of current research on bacteria’s influence on our digestive health, and much is known about its influence on our immune system, but there has been fairly little investigation into the microbial influence neurologically. In the future, this research could show that treating certain microbes within our bodies could alleviate some mental health problems. Maybe this could even lead to procedures like microbial or fecal transplants to alleviate conditions. This could be a stark shift from the use of pharmaceuticals to treat mental illness, therefore I believe that this would be a worthwhile pursuit.

Writing Exercise #14

Part One

A few non-infectious diseases that are influenced by microbes include:

  • Crohn’s Disease,
  • Diabetes Mellitus,
  • Anxiety Dsiorders,
  • Depressive disorders,
  • Asthma,
  • Allergies,
  • Atopic Dermatitis (eczema),
  • Liver Disease,
  • Gastritis and peptic ulcer disease,
  • Obesity,
  • and certain cancers.

Part Two

In Writing Exercise #1, the examples that I came up with were Chronic liver disease, cervical cancer, chronic gastritis and peptic ulcers, lymphoma, asthma, and Diabetes. While I restated many of these diseases and conditions again, this time it was much easier to think of them. I remember at the beginning of the term having to look at multiple sources before coming up with this list, and even then being really unsure how they were caused by microbes. Today, this list came very natural and I would feel much more comfortable explaining the connections between the disease and how microbes contribute to the pathology.

This term I learned so much about how microbes influence our health, and I think that it will help me in the future as I embark on a career in the medical field. This class has given me a better understanding about the plethora of ways that microbes influence our health beyond their infectious qualities. As a future physician, the things that I learned in this class could influence how I choose to treat certain conditions, including not prescribing antibiotics as often or limiting cesarean sections to situations where they are deemed medically necessary.

Writing Exercise #13

  1. When discussing whether or not experiments can detect differences that matter, it is crucial to look at the results of the experiment and think about them critically. In a statistics class I once took, my professor presented data that about commute times by route taken. The data showed that there was a statistically significant difference in the time between each route, but when further analyzing it, the data actually showed that the time difference was less than twenty seconds. He cautioned us that while data may be significant, it also may just be pointless.
  2. When considering whether the study shows correlation or causation, you must consider how the data was collected and whether other variables were controlled for. If they were not, it is not accurate to say that it is causation.
  3. When discussing the mechanism of relationship, Hanage proposes returning to a reductionist approach. Often, it is necessary to look at the big picture, but here it is important to pinpoint little details in order to determined the true nature of the relationship between findings.
  4. When thinking about how experiments reflect reality, it is important to consider the findings within the bigger picture. What are the real consequences of the work, and how could they potentially be expanded upon to further the field in which they were presented and beyond. I think that this is the most important of the five questions, because without real world application, many findings are not useful.
  5. When considering whether anything else could explain the results, it is necessary to look at the experimental design and think about whether or not any confounding variables exist.

Writing Exercise #12

The microbes inhabiting our bodies have a profound influence on our physical health, but they are also highly involved in our mental health. An obvious influence is that bacteria can often make humans ill, which then can cause health anxiety, and in some cases, depression. However, there is also evidence that microbes can alter personality in mice. Mice kept in germ-free environments tended to be more hyperactive and daring than mice with more developed microbiota. Additionally, there has been a correlation between autism development and altered microbiomes. The behaviors of a certain subsection of mice very much mimicked those seen in autistic humans, and the imbalances seen in their gut microbiomes could potentially be a cause of their behavioral symptoms. Furthermore, it appears that gut microbiota communicate with the brain via the vagus nerve, which ultimately alters the permeability of the blood-brain barrier.

Writing Exercise #11

I really enjoyed the peer reviewing process. I think that it’s extremely helpful to see examples of strong writing from your classmates while also working to revise your own work. It also helped me notice flaws in my own final essay. Things that I pointed out in other peoples’ papers were also flaws that I noticed in my own writing. Although it can sometimes be difficult to give constructive feedback in a respectful tone, those are the most helpful pieces of advice that can be given. Overall, I enjoy the peer reviewing process, commenting on others’ writing and receiving comments on my own work.

Writing Exercise #10

The peer review process is used by scientific researchers and journals in order to test findings and ensure that the research published is credibly and accurate. First, a researcher writes an article after compiling all of their data and findings. Then, the article is sent to a journal of relevant subject matter and the editor screens the paper. The editor can then decide whether to reject the submission, or send it to anonymous reviewers. Typically between two and four reviewers read the paper in its entirety and make suggestions for reviews and edits, which they then submit to the editor. The editor then has three options. They can choose to accept the paper without revisions, reject the paper completely, or send the article back to the author with the recommended revisions.

Some of the benefits of the peer review process are they can increase the validity of an article. Because it has been reviewed by an anonymous source that generally has a lot of experience in the same field, it also ensures that journals are publishing only accurate information. However, it in some ways creates a culture of secrecy. Many people criticize the process for being too closed-doored. Additionally, it limits the amount of research that is published.

Writing Exercise #9

  • Excessive use of hand sanitizers: while hand sanitizer and other soaps can be necessary, their excessive use can lead to decreased exposure to microbes because they tend to kill a wide range of bacteria.
  • Excessive use of antibacterial cleaning supplies: in peoples’ homes, the use of cleaning supplies can kill many bacteria, creating nearly sterile environments. This causes a decreased exposure to microorganisms.
  • Less time spent playing outside: people, especially children are exposed to a plethora of microbes when playing outside, and over the course of the past few decades with the introduction of video games and the internet, children have spent less time playing outside.
  • Increased antibiotic use: antibiotics often kill a wide range of microbes, many of which are beneficial symbionts of humans. By taking antibiotics unnecessarily or for prolonged periods of time, a person is selecting for microbes with the capacities to evade these antibiotics.

Writing Exercise #8

I thought it was really interesting to learn about how delivery method influences the development of a baby’s gut microbiome. I never really thought about it until a few weeks ago, but now I am wondering whether or not the higher rates of C-sections are a contributing factor to increased rates of metabolic diseases and obesity in American kids. Today doctors perform a lot more unnecessary C-sections. Sometimes it’s merely out of convenience, without thought about how it actually can influence a child’s health. I read in an article recently that kids born via C-section have a way higher chance of developing childhood obesity. I wonder if there will ever be a way to help inoculate children who were born via C-section by necessity in order to help them be healthier in the future.

I highlighted the word unnecessary because I think as humans we do a lot of things in the name of “being healthy” that we really don’t need to be doing. Our bodies are amazingly capable of maintaining our health and homeostatic balances. For millions of years we survived without the need of many treatments we use daily. I’m not at all saying that we should cut out many of the medical treatments and remedies that have saved and improved so many lives, but I think that we do live in a time where so many things are overly medicalized. It seems that so many things that used to be treated with at-home remedies now require doctors visits and prescription drugs.

I think that one of the most unnecessary treatments that we see today is the overprescription of antibiotics. Often, physicians will prescribe antibiotics for illnesses that aren’t even caused by bacteria. I think that this could be a really interesting topic for my final paper, and I will look further into it in the coming days. Things I could talk about in the paper could be why doctors are so quick to prescribe antibiotics, what causes bacteria to become resistant, what next steps could be, and what the future looks like for the field of medicine with respect to antibiotic treatment (will it be phased out, will we develop new ones, will there be new/better ways to treat infections in general?)

Writing Exercise #7

  • Method of delivery: when infants are born vaginally, they harbor vaginal microbes that begin to colonize their gut microbiome. However, in infants born via C-section, there is a disruption of transmission of these microbes. Instead, they often are first exposed to skin, not vaginal, microbes. Furthermore, the maternal vaginal microbiome changes during pregnancy, apparently in order to provide the fetus with a specific microbial inoculum at birth.
  • Maternal weight: mothers who are obese often have disrupted vaginal microbiomes, which can contribute to the differential infant microbiome development compared with mothers who are not obese.
  • Breast feeding and bottle feeding of newborns: breast milk contains certain probiotics that colonize the infant’s gut prebiotics that help nourish these microbes. This combination is usually not present in formula, and aids in the development of a more uniform gut microbiome than that found in formula-fed infants.
  • Perinatal antibiotic treatment: if a mother undergoes antibiotic treatment soon before giving birth, the vaginal microbial community could be greatly disrupted. Also, antibiotic treatments could cause a change in uniformity of the breast milk, which could have a differential effect on the development of the infant’s gut microbiome.


Mueller NT, Bakacs E, Combellick J, Grigoryan Z, Dominguez-Bello MG. 2014. The infant microbiome development: mom matters. Trends Mol Med. 21(2): 109–117.

Writing Exercise #6

Personally, I take antibiotics whenever they are prescribed to me by a physician, and I am pretty diligent in making sure that I take the entire course. Before a tonsillectomy, I often got strep throat multiple times a year, and each time I was prescribed a course of antibiotics. Generally, I tend to trust my physicians, as they have gone through extensive training and education, and I try to follow their advice as closely as I can. However, among many physicians there is a growing concern about the over-prescription of antibiotics. Just today I shadowed a physician who was wary about the negative consequences associated with the over-prescription of antibiotics, and even she said that there are some infections for which an antibiotic regimen is unavoidable (i.e. urinary tract infections). When contemplating whether or not to take antibiotics, it is important to weigh both the pros and cons of the treatment, and also to consider the negative consequences of neglecting to follow a physician’s recommended course of treatment.