Writing Exercise #15

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.

Projects that I would be excited about longitudinal research projects that show how time and environmental conditions such as antibiotics affect a child’s microbiome as they age. I would be interested in research that had different subject groups such as those born vaginally, or through C-section, those who had illnesses at birth, and do longitudinal research through in home surveys as well as annual surveys sent to the home, and perhaps collecting samples such as fecal samples annually or when antibiotics or other intense treatments were administered to see how the microbiome changes through time/environmental conditions. The ideal study would include a very large and diverse sample size, so we could see trends across many individuals.

I think seeing the microbiome change through time, and seeing the responses of the microbiomes from environmental factors such as antibiotics would open a lot of doors for further research. If we saw trends among the young in responses to certain antibiotics or other medical treatments, and saw that these affected the microbiome/individual in harmful ways, it could be a leap into new considerations for treatment, and potentially a door to preventative care/information. If it was more of a study, rather than an experiment, and we could ethically watch the young as they develop without intervening, I think ethically it may be okay with parental consent… Perhaps a longitudinal study is what we need to really understand how human microbiomes change through time and to responses from the environment.

Writing Exercise #14

Looking back at my first writing exercise, I remember being really confused on how to answer the question of how microorganisms influence non-infectious diseases… I remember googling, and not being sure what this meant.


I know that microorganisms can influence our overall health in so many ways including non-infectious diseases such as:





Asthma (and can also help it…)

Heart disease

Mental health issues


Crohn’s disease

and the list goes on and on…

In my fist post, I only included a couple of diseases, and I wasn’t sure if this was even true. Now I know how there are strong correlations between our microbial communities and our overall health. So many studies have been conducted with different chronic illnesses, and we see actual differences in microbiomes of subjects with illnesses when comparing to control groups.  I think the most important topics are that understanding the link between ourselves and our microbiomes, could be the future of medicine, at least in some important ways… perhaps when seeing these correlations gain interest and more respect with more publications and more research, we may have new treatments for these illnesses, and they may be healthier treatments than ever before. Another really important topic was that our microbiomes coevolve with us. The microorganisms in our guts aren’t just a new hot topic in science, but they are literally part of us, and have been with us since the beginning of time. Another important topic is that it isn’t just our microbiomes affecting us, but that our choices and lifestyles are affecting them as well– hence the disappearing microbiota hypothesis…

I look forward to hearing more about these topics and I imagine as a future health care professional, that I’ll be educating my future patients on the wonders of the bacteria in their bodies.

Writing Exercise #12

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?

The gut is known as the “second brain”, therefore there must be some links between our brain brain and our gut…

The gut has neurons and nerves that are linked to our brain, thus having the gut influence mental/brain states and vice versa.

The microbiota can signal to immune cells to release cytokines which eventually gets back to the brain. Microbes can even produce neurotransmitters and corticosteroids which can influence the brain.

The mental/brain may release neurotransmitters, steroids, and hormones that effect the microbiota perhaps via the systemic interaction between the gut and the brain.

The vagus nerve serves as a connection between the gut and the brain. For example, in a study done with mice with an in tact vagus nerve, when inoculated with certain microbes, their depression decreased– showing that microbes can have an influence on the brain/mind. When the vagus nerve was disconnected the inoculation did not have an effect.

If we were to have more studies proving these connections, perhaps we would be able to help alleviate mental health/brain disorders through microbial therapies such as probiotics… or perhaps there could even be an intervention to introduce microbes at a certain age to decrease the chances of mental health disorders.

Writing Exercise #13

  • Can experiments detect differences that matter?

I think that this question has to do with are we researching things we already know, or are we exploring new ideas? And are these ideas even big enough to be spreading?

In the article they explained it as: With the technology we have right now, it can be hard to distinguish between differences in genes. Although we have gotten fairly good at determining genes, this is because we know the genes we are looking for prior to the experiment. Being able to determine functional differences in genes  is necessary to be able to tell between similarities and differences. Oftentimes things that seem similar can actually be quite different..

  • Does the study show causation or correlation?

This is a super important question in regards to did this research explain something causing another thing, or is it just association?

If one claims that something is causation, but then there is a confounding variable that also comes into play, then is it rally causation or just correlation? It’s important to keep confounding variables in mind.

  • What is the mechanism?

Explaining the causative component of correlations… Why do these things correlate? Conducting experiments to determine why certain things correlate is the background of this question.

  • How much do experiments reflect reality?

It’s important to note what the subjects are like… are these sick individuals already? Are they germ free mice? It’s important to think about if the conditions were affecting the findings in a bigger population, or if perhaps the subjects in the experiment were peculiar and maybe it wouldn’t translate to the bigger picture.

  • Could anything else explain the results?

It’s important to think about other reasons that may explain results. For example, weight loss can be correlated with the microbiome, but perhaps diet played a bigger factor.. The article said a good researcher is someone who thinks about these questions and includes them in their explanations.

I think the most important question when discussing controversy would be the last question: could anything else explain these results?

If the researchers address the question of whether or not their findings could be explained by other things, then this causes less controversy and less questions/attacking on the writer.

All of these questions are important to think about when reading scientific articles to make sure one is not oversimplifying the findings, and that we don’t take it as concrete evidence… All of these questions help keep us grounded while still feeding our brains new information/findings.

Writing Exercise #10

Peer review of a scientific journal is necessary and also pretty elaborate. The reason for peer reviews is it gives the manuscript several pairs of fresh eyes–eyes that understand the topic– and gives notes to the authors to make the manuscript better. The author begins by sending in their work, then the editor, if accepted, sends out the manuscript to several peer reviewers. The peer reviewers do know who the author is, but the author usually does not know who the reviewers are. This could potentially lead to some biases perhaps due to competition within that scientific field, or perhaps the reviewers find the particular subject boring… reviewers seem to have a pretty strong hand in what happens to the manuscript, so it is an intense process that may lead to some credibility issues if there are personal biases. The reviewers chosen are considered people in the field related to the work, and have usually been published themselves… therefore, they understand the tedious process.

Once the reviewers add in their revisions, it is sent back to the editor to accept the manuscript or decline it. If accepted, the manuscript gets sent back to the authors once they fix the things the reviewers noted, they send it back in and the review process is replicated until the paper deems fit.

Although it is a tedious process, and perhaps there is room for biases, it is a necessary process in order to make research/the manuscript the most understandable, and the most relatable in that scientific field due to the experts’ edits and advising.

Writing Exercise 11

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 always feel a sense of stress when reviewing someone else’s work. I don’t want to hurt anyone’s feelings, but at the same time, I know for my work I love and appreciate when people help my writing be better.

I believe I may have had an international student’s paper and that was kind of hard to gauge because it isn’t the grammar or sentence structure that we’re used to, but I also can’t imagine how hard it would be to write a 2000 word essay in a non-native language. I hope I gave good advice to them.

It made me want to go back and reread my entire paper to make sure my grammar and sentence structure made sense, and that my ideas flowed. I think it’s easy to read your own paper and think it makes sense, when in reality there are fragments and ideas that don’t quite flow when a reader is reviewing it for the first time.

Writing Exercise #9

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

Increased handwashing and with antibiotic soap [1]

Increased cleaning/cleaning products

Kids not playing outside

Kids not playing with other kids

Increased antibiotics [1]

Hand sanitizer

Smaller families (less children) [1]

More C-sections [1]

Less breast feeding [1]

More antibiotics during pregnancy [1]

It was also mentioned that we may have a loss of ancestral microbes (1)

Blaser M, Falkow S. 2009. What are the consequences of the disappearing human microbiota? Nature Reviews Microbiology 7:887–894.


Writing Exercise 8

Writing for 5 minutes on what I’ve found most interesting/want to learn more about:

I think the most interesting topics we’ve covered are how different compositions of the microbiota are correlated with certain diseases... we’ve talked about obesity, asthma, now stuff with the heart, and I think that the disease component on the microbiota is really interesting. I also thought this week’s information regarding pregnancy and infants and development of the child was pretty crazy. It makes sense that we get our bacteria from somewhere, so it’s cool to see that it’s literally caused by the environment and things we interact with. It reminds me of that movie boy in the bubble or whatever it’s called. What else… probiotics and antibiotics are of course really interesting and so prevalent with society today. I hear about antibiotic resistance all of the time, so it’d be cool to delve into that more— especially because I feel like I focused mostly on the probiotic portion of that module and didn’t get to learn too much about the antibiotic portion.

Step 2: Underline

Step 3: Write bout what you bolded

Antibiotic resistance: I hear about this all of the time, and it is scary. I remember doing research on it and it said something like 30% (I think) of antibiotics prescribed are unnecessary. I think this is a huge problem, and it’s really relevant in the field I’m persuing– medicine. I remember learning about plasmids in microbiology class and this class talked about how plasmids can actually transfer antibiotic resistance, so it was really cool to relate the two classes.

Diseases and the microbiota. I think that there is probably so much information on this topic. I wouldn’t be surprised if there was at least a small correlation between almost every disease with the microbiota. I think this is super interesting because I think if doctors were to educate their patients and look more into the gut microbiota, it could help a lot of people with things such as weight loss. After learning about how different the gut microbiota differs for obese people, it scared me into wanting to eat healthier and lose some weight. Obesity leads to bigger issues such as health problems, etc, and I wonder if this is partly to do with the microbiota as well and not just the visceral fat.

Step 4: Reflection

I definitely want to write on diseases and the microbiota. I think I might even emphasize on obesity. I’m going to start my research tomorrow and see if it’d be too much information to talk about several diseases, and if it is, I’ll focus solely on obesity.

Writing Exercise #7

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).

It is known that infants start becoming exposed to many different bacteria and by the moment they’re born, they are diversifying their microbiota. Being born , either vaginally or through C-section, both introduce new microbes to the infant. If born via C-section, it’s shown that those babies have more antibiotic resistant bacteria, and this could be a cause for MRSA in infants  (64-82% of the infants with MRSA were delivered via C-section) (1). Several diseases may have a higher relevance rate with C section babies such as celiac disease, asthma, and obesity. However, this is just an association rather than factual correlations.

Breast milk vs. formula as well as weaning period influence changes in the gut and oral microbiota, and differences are found in milk vs. formula babies. For milk babies, they show more Bifidobacterium, Lactobacillus, and Bacteroide species which aid in absorbing more nutrients. However, long term effects are not known (1).

The child’s environment, immune system and genes all help determine which microbes can stay and which ones won’t be able to colonize (2).

Things the mother ingests could affect the infant through breast milk, the cleanliness of the mother, the amount of things the mother let’s the baby suck on, the binky… These could all introduce positive and negative microbes.

The infant’s microbiota is almost at the same point as an adult’s microbiota by the young age of 3. Therefore, the infant’s microbiota is changing rapidly through their environment and the new things they’re introduced to, whether positive or negative.


Nuriel-Ohayon M, Neuman H, Koren O. 2016. Microbial changes during pregnancy, childbirth, and infancy. Frontiers in Microbiology 7:1-13.

lecture 6b notes: Obstetrics and Infant Microbiota Development. Obtained from: https://courses.ecampus.oregonstate.edu/bhs323/6b/

Writing Exercise #6

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?

Before coming to college, I would take antibiotics whenever they were recommended or prescribed by the doctor. Growing up, I would get strep throat all of the time and so I ingested a lot of antibiotics growing up. I remember once in a while if I had a sore throat and my strep test came back negative, they would still prescribe me antibiotics just in case.

Fast forward to my first year of college… I had pretty severe acne and so I went to see a dermatologist. The first thing she recommended was getting me on an antibiotic. Trusting my doctor, I agreed to take it. I was on it for 2 years without seeing results. After taking a few science classes I quit taking the antibiotics since I wasn’t seeing results anyway. To this day, I’m surprised at how long she wanted me to take them– I definitely don’t think that was healthy. Fast forward to this year (my last year of college) and I went in to the doctor for what I thought was extreme allergies. He said he thought it was a sinus infection and gave me  an antibiotic. Due to my misery, I took it. It did not help unfortunately, and the antibiotics gave me terrible side effects.

I’m a lot more conscientious now about what I put into my body regarding medication (especially antibiotics) due to the rising awareness of antibiotic resistance due to gene sharing and selection. While researching for the discussion post this week I found on the CDC that 30% of antibiotics prescribed are actually unnecessary, and this was definitely an “AHA” moment that I’ll keep with me for future reference (https://www.cdc.gov/features/antibioticuse/index.html).