Writing Exercise #15

If I was the head of a funding agency and I needed to decide on a research project to award funding to I would give funding to the project that looked into probiotics and their efficacy. The project would probably have something to do with being prescribed in conjunction with antibiotics, possibly probiotic vs placebo after completing a course of antibiotics. The study would collect various biological samples to try to ascertain the affect on the microbial populations and it would track other effects such as diarrhea, etc. I think what we would likely learn from this kind of project is that probiotics are beneficial to those with depleted microbial diversity, especially those who have just completed a full course of antibiotics. This would be important for the future of healthcare because it would alter how we treat different diseases.

Writing Exercise #14

Some human non-infectious diseases that are influenced by microorganisms are diabetes, irritable bowel syndrome, allergies, alzheimers, and various cancers, such as mouth cancer and cervical cancer.

Looking back to my response to Writing Exercise #1 I feel that my list has come a long way from where I once started. Before, I was unable to list a single non-infectious disease that was affected by microbes with certainty. I am now much more aware of the impact microbes can have on various non-infectious diseases and am able to create a reasonably sized list of various non-infectious diseases where microbes play an important role.

Writing Exercise #13

The first question “can experiments detect differences that matter?” is important because if your experiment isn’t going to yield any useful information then it’s kind of a shot in the dark, it is essentially useless till you find out that the results matter. The second question “does the study show causation or correlation?” really brings to light the importance of the data, causation is very hard to prove scientifically, where as correlation is much easier. However, correlation doesn’t have the same large impact that causation does. The third question “what is the mechanism?” is important because without the mechanism we aren’t truly sure of the science behind the data. The mechanism is useful in determining how we can use the acquired data to our benefit, to positively impact human health. The fourth question “how much do experiments reflect reality?” is a strong question because if the data you’re acquiring isn’t realistic in the real world then it’s not a good model for how the real world works. The whole point of experiments is to be able to put together a model of what happens in the real world. The last question “could anything else explain the results?” brings about the potential for confounding variables. If the experiments conducted did not have good controls while keeping all other variables stable then the results could be due to other variables, meaning the data is essentially useless to the hypothesis being tested. I feel that the last question is most important when discussing controversy because if your data isn’t done with solid methods, then the data is essentially useless in terms of discussing controversy objectively.

  1. Hanage W. 2014. Microbiome science needs a healthy dose of scepticism. Nature 512:247–248.

Writing Exercise #12

Microbial communities in the body could influence brain and mental states by affecting emotional behaviors and other related brain systems.Researchers conducted large-scale population-based studies of the gut microbiome and brain imaging studies trying to determine the effects of the gut microbiome and how it affects the brains responses to emotional stimuli. They are hoping to show that the gut microbiome can affect disease by altering the development of autism spectrum disorder, anxiety, depression, and chronic pain [1]. From the alternative perspective, brain and mental health states could influence microbial communities by changing gut microbial populations of those with disease.  Some scientists believe that some credit should be given to the alternative hypothesis. Instead of the microbes causing the disease, the disease could be changing the microbial population in the human gut [2]. For example,  a child with many ear infections may require multiple courses of antibiotics. This can promote further worsening of disease by altering the gut microbiome and causing the child to become susceptible to other diseases and infections.


  1. Mayer E, Knight R, Mazmanian S, Cryan J, Tillisch K. 2014. Gut Microbes and the Brain: Paradigm Shift in Neuroscience.
  2. Hanage W. 2014. Microbiome science needs a healthy dose of scepticism. Nature 512:247–248.

Writing Exercise #11

I felt that the peer-review process was easier when the writing was better. It can be really difficult to effectively critique someones paper when there is no real focus or direction in the writing. It can also be difficult to provide useful critique when a paper is already really well written. I learned that I should be extra mindful of my organization and clarity because while it may seem clear to me because I wrote it, others may not be able to interpret the purpose of my writing as easily as I can. I’m also going to double check my transitions because those aren’t always smooth and concise.

Writing Exercise #10

Peer review is when a scientific article is sent to other people, usually scientists in the same field of study, who have extensive knowledge on the topic of the paper. This is done to help improve the quality of the paper being published.

Some pros of peer review is that you know the evidence presented is of quality and has credibility behind it. Peer review also helps the author to check themselves in case they may have missed something or weren’t aware of some other sort of scientific evidence in the scientific community. Some cons of peer review is it can be a lengthy process and in some cases people may have a different opinion than the writer and that may make the review process difficult and unfavorable for the author.

Writing Exercise #9

In recent years, we have seen human behaviors change and develop, with this change we see an increase in technology usage, as well as, dietary fads and a decrease in outdoors activities. The development of new technology has lead to many adolescents staying indoors. With the internet and video games that plague out generation, many children aren’t going outside to play anymore. They also aren’t participating in outdoors activities like hiking, hunting, fishing, and camping. While these activities were popular many years back, now a days it is rare to see a child participating in outdoor activities. There has also been an uptick in health consciousness but not the correct kind. Many parents follow fad diets now a days, some believe specific foods are bad for them and their children, yet they have no real allergic reaction or intolerance to the food. All of these factors could lead to a decrease in exposure to microbes.

Writing Exercise #8

Some of the most interesting and surprising things I learned about in regards to microbes and human health is that periodontitis has shown to increase your risk of developing cardiovascular disease.  This was especially interesting to me because the article mentioned a large percentage of the population having periodontitis at some point in their lives. I also found the information regarding probiotics to be quite interesting. I wish there was more information about probiotics like how much and what types of bacteria are best for you. I would also like like to know more about the specific mechanisms behind the probiotics and how they benefit human health.

Periodontitis has shown to increase your risk of developing cardiovascular disease. This could be especially concerning to those with gum disease and gingivitis. The good news is that gingivitis is reversible! The bad news is once a bacterial infection reaches the pulp the risk of having a stroke significantly increases. I wonder if these cases of cardiovascular disease being linked to periodontitis have any relation to tobacco use.

For my final paper I think I might focus on tobacco usage and how it can alter human microbial populations. I will most likely tie in the data showing an association between periodontitis and cardiovascular disease. I will also look to see if there is any measures that can be taken to reverse the effects, such as the use of probiotics.

Writing Exercise #7

Certain factors that may influence the colonization of the microbial community in newborn infants can be positive and/or negative. Diet is the most obvious factor that could influence colonization of the gut in pregnant women. Studies showed that mice fed a high-fat diet showed changes in their gut flora as their pregnancies progressed. It wasn’t entirely clear if these changes were positive or negative, it was just clear that the diet had an impact on the gut flora [1]. Another obvious impact on the microbial population of an infant occurs after the first trimester. There appears to be an increase in the amount of  Actinobacteria and Proteobacteria, and a decrease in alpha diversity in the mom [1]. This could typically seen as bad since it isn’t consistent with that of a healthy non-pregnant woman, however, these changes are helpful for a pregnant woman because they are needed for the baby. Another influence that occurs in the third trimester are the levels of anti-inflammatory Faecalibacterium being reduced [1]. This is interesting because this bacterium is typically lower in metabolic syndrome patients which would give the impression that this would have a negative impact on the mother. However, the change is needed to prepare for the birth of the baby so it is therefore positive in terms of the birthing process. In the third trimester there were other factors that also appeared to influence the microbial population.  There was an increase in beta-diversity,  weight gain, insulin insensitivity, and an increase in fecal cytokines, which indicate inflammation. These all seemed to create changes in the microbial population that are needed to have a healthy pregnancy.


  1. Nuriel-Ohayon M, Neuman H, Koren O. 2016. Microbial Changes during Pregnancy, Birth, and Infancy. Frontiers in Microbiology.

Writing Exercise #6

As much as I know about the health care field, I am aware that I don’t go to the doctor as often as I should in terms of preventative care. Part of the reason for this is because I haven’t had any serious illnesses requiring medical intervention. When I get the common cold, I feel that I should let my body fight it off on its own. Unless I have a high grade fever, tachycardia, vomiting, and diarrhea (to the point of dehydration), feel that I have the flu or pneumonia, I typically won’t go. I know that for viral respiratory illnesses the treatment is to typically wait it out.

My general rule of thumb is if I haven’t started feeling better after a week or so, I’ll consider getting it checked out. I am not one to run to the doctors over every cough and sneeze. I feel that antibiotics are typically over-prescribed and can do more harm than good if you are not careful. A couple of the pediatric research studies I am working on are testing 10 vs 5 days of antibiotics and antibiotic vs placebo to see if the guidelines we have for treating certain illnesses, such as ear infections and sinusitis, are the most beneficial. While the final analysis of our data isn’t complete, I feel that once it is, I will be more concrete in my feelings towards antibiotic treatment.