Writing Exercise #15 – Research

Imagining that I am the head of a funding agency that is looking at research project proposals, and based on what we have learned this term, a research project that I would be interested in funding is one that studies how sanitation affects exposure to microbes when we are young. I think it would be interesting to gain a better understanding of the interactions and mechanisms behind establishing the microbiota at a young age. This would give us a better understanding of what behaviors are important to keep, change, or actually stop doing.

As we have seen throughout this class, having a diverse microbiota is essential to human health and thus understanding how to maintain or establish this is crucial to understanding how to have better health and avoid potentially dangerous diseases. By establishing a better microbiota at a younger age, it may lead to less risks for microorganism influenced diseases later on in life.

Understanding more about this can also impact healthcare decisions, both in a professional healthcare setting and in day to day healthcare related decisions. For example, understanding more about how current healthcare practices influence the ability to develop our microbiota may lead to changes in protocols. More specifically, because much of our microbiota is initially developed at a young age, this may mean changes in hospital (and home life) procedures following birth. By having a greater understanding of the interactions and mechanisms behind establishing a healthy microbiome equilibrium, we can make more informed and guided decisions within healthcare.

Writing Exercise #14 – Human Non-infectious Diseases and Reflection

Part 1:

Through the course of this class, we have learned about tons of different human non-infectious diseases that are influenced by microorganisms. There are some diseases which are more obvious such as those associated with out gut, such as Irritable Bowel Syndrome (IBS) or different gastrointestinal diseases. However, our microbiota is actually connected to a more diseases and health related responses within our body. For example, microorganisms affect diseases such as diabetes or obesity which have to do with our glucose and nutrient intakes. Surprisingly, microorganisms have also been tied to influencing human mental health such as Autism Spectrum Disorder (ASD).


Part 2:

Looking back at my first writing exercise where we also made a list of non infectious diseases that are affected by microorganisms, I can see that my knowledge has become more broad. I remember when I first the first writing exercise I felt pretty clueless and didn’t know where to begin until I had done some preliminary research. However, for this assignment I was able to reflect back to the past 10 weeks and remember different diseases we had learned about.

I think the most important thing I will take away from this is that the gut microbiota affects just about everything that is related to our health: from gastrointestinal diseases to mental health to our sleep and circadian rhythm. Therefore, it is extremely important to take care of our gut microbiota and make sure it is diverse and has proper levels of healthy bacteria. Just from this class, I have already started to be more mindful about what habits I have that affect my gut microbiota, such as my diet, daily behaviors, and any routines I might have. From initially being something that I rarely thought about at all, I am now realizing how impactful the gut microbiota is in our lives and how many factors can affect it.

Writing Exercise #13 – Interpreting Scientific Literature

In an article titled “Microbiome science needs a healthy dose of scepticism” by W. P. Hanage, the author discussed five key questions we should always remember when interpreting scientific literature.


Can experiments detect differences that matter?

Hanage discussed how it is often hard to distinguish functional differences in the world of microorganisms when we don’t already know what to look for or have characterized the network well already. Hanage discusses that until we can identify differences from gene sequences alone, we need to realize that any similarities we might notice may actually be hiding important differences that we haven’t realized yet.


Does the study show causation or correlation?

This question is important to take into consideration because often times a microbiome we see in correlation with a disease may actually just be a bystander in the diverse microbiota of our body. While explanations may fit the data, research often times doesn’t explore the reverse causality, so it is important to pay close attention to other factors that may be affecting the microbiome.


What is the mechanism?

Although we all know that correlation does not always equal causation, Hanage discusses how correlation usually implies some sort of causal relationship. Therefore, Hanage advises that the use of careful experiments to determine the mechanism and understand biochemical activity is crucial to understanding the true causes microbial influences may have.


How do experiments differ from reality?

Often times, microbial studies try to isolate only what is being examined to show more causation and understand the specific effects of a specific microbe – which is why the use of germ free mice is so popular.  However, it doesn’t accurately represent an animal’s natural state or the responses an animal normally might have with their diverse microbiome.


Could anything else explain the results?

Because current experimental procedures are not always the most developed or sophisticated due to the nature of exploring microbiotas, there are often many other factors that can influence results such as diet or other environmental factors. Hanage also stresses that findings tend to be exaggerated in the media and thus individuals may make decisions without knowing everything. Therefore, it is always important to consider other contributors.


Out of these five questions, I think the most helpful in discussing controversy is what is the mechanism. A lot of the uncertainty and questions about other potential factors comes from not knowing the specifics of what is happening because there are so many contributors. Therefore, knowing the exact mechanisms that are occurring and the roles they play in the larger microbiome will help provide clarity and a deeper understanding of microbial science and influences on diseases.

Writing Exercise #12 – The gut and the brain

The gut is often referred to as the second brain. There are tons of nerves and neurons found in the gut that are connected to the brain through either vagal and sympathetic nerves and thus these two areas of our bodies are intricately intertwined. Neurotransmitters, cytokines, and other small molecules create systemic connections between the gut and brain, making both of them important influencers of each other.

For example, some microorganisms can trigger immune cells to release cytokines and then the brain can respond to this release through signalling of other cell types. Some microorganisms have also been shown to produce corticosteroid and neurotransmitters directly which can then influence brain states through these systemic connections. With such a diverse gut microbiome, there are tons of byproducts produced by the gut microorganisms which can alter and affect brain states. Additionally, since the gut and brain and so connected, it is also then possible for the changes in brain state and release to cause changes in the gut microbiota.

We have seen how significantly the gut microbiota has been able to control human health, immune responses and diseases. However, with this new information on the gut’s ability to influence brain, it is clear that the gut microbiota may also be able to influence mental health states as well. Several studies have shown that different bacterial species have been able to affect things like depression and autism spectrum disorder (ASD). Therefore, understanding the way in which specific bacteria interact with the brain and different neurotransmitters could be a crucial turning point in promoting mental health and aiding different diseases.

Writing Exercise #11 – Peer Review Reflection

Completing the peer-review process as a reviewer was a long process but one that is very valuable for both the peer-reviewer and the author. As a peer-reviewer, I found reading the papers to be very interesting. I believe it made me think more critically about what I was reading while also staying open minded when I was reviewing the work. It made me more critical because instead of simply reading and absorbing the information, I was paying more attention to how the topics all flowed together and how it developed the thesis – it made me a more actively engaged reader. I think it also made me more open-minded because I was trying to think about both sides of the topic and how they worked together.

The peer-review process also helped me figure out a few ways I could improve my own writing. For example one paper I peer-reviewed set up the paper really well by adding a quick statement of what the paper would examine. I think this helped the paper flow easier because I had an idea of what to expect. I also noticed that it is easy to focus a lot on one thing but then cut short others and so when I look over my own essay I want to make sure I am not spending too much time being redundant in one area and to include a diverse variety of evidence. For example, including multiple studies that say about the same thing is not as effective or useful as using different types of evidence.

Although it was a long process, I think peer-reviewing is a very valuable resource and way to review work and find what is lacking and what was done well. I can imagine that the peer-review process with experts in this field is even more valuable tool because they can check the validity and understand the importance of the evidence to a greater extent than we can as students.

Writing Exercise #10 – Peer Reviews

In many academic fields, we look to peer-reviewed articles for credible sources of information. For scientific articles which explore new findings and groundbreaking discoveries, this is crucial to making sure that the information shared is trustworthy and accurate.

The peer review process includes an author submitting their paper to a major journal, which then sends out the article to reviewers to look over if the editor approves the paper. The reviewers make comments and edits, or bring up questions or concerns they may have and then the original author can then edit their paper with these comments. The peer-reviewers are all established and published authors themselves, further validating the credibility of the process.

The pros of using the peer review process is that it increases credibility of the findings by having multiple experts in the field look over the data and conclusions. Especially in new discoveries in scientific fields with complex concepts and high levels of education and research to understand, having reviewers check the validity of the findings against scientific backings can be an extremely valuable step.

However, especially because this process does tend to deal with groundbreaking new discoveries, it is also possible that a paper may challenge current thinking and concepts because of new data. If these findings go against current scientific beliefs, it may receive backlash and harsh reviews. However, this is also why the peer review process is so important. In order to disprove current knowledge, it is important to have strong evidence and data to back it up. By having such a thorough review process, it ensures that only results and conclusions strongly supported by data can be approved.

Writing Exercise #9 – Decreasing Microbe Exposure

Microbes are everywhere and as tiny organisms typically unseeable by the human eye, we may not realize all of the ways in which our behaviors contribute to our exposure to microbes.

Some behaviors are obvious – such as the ones where we take actions to physically block microbes from reaching us. For example, we wear gloves when handling something that may transfer dangerous microbes. In more specialized activities we may wear safety goggles or personal protective gear to prevent exposure to microbes. Another behavior that doesn’t necessarily block but rather removes the microbes before you can be exposed is sterilizing an area before you come into contact in it.

Other behaviors are less obvious but lead to decreased exposure as well. For example, avoiding very public places such as a school or workplace decreases being exposed to microbes from other people. These can be harmful, or could be pathogenic microbes which may cause you to become sick. Similarly, exposure to pets or other animals may lead to increased microbe exposure. Another behavior which leads to decreased exposure is limiting time outside or in the outdoors such as in parks, trails, or natural areas.

Writing Exercise #8 – Interesting topics and reflection

Step 1:

This class has taught me a lot about the impact microbes have on our health. Before this class, I knew that they were important and had some effects, but I did not realize the extent to which they control human health and the development of diseases. Thinking about it now, it makes sense that microbes that live in our gut can trigger inflammatory responses or immune responses just as other chemicals or compounds do in other places in our body. I think what has been most interesting to me is the use of microbes for treating diseases. I think it is a very smart but potentially risky route to take because we are dealing with live organisms which can evolve or develop traits or behaviors that we can’t always control once they have entered our body. It is amazing to me that we have been able to identify ways in which microbial communities can interact with our gut and we have specified which species promote human health and which trigger dangerous effects. However, in cases such as antibiotic resistant bacteria, we must be careful to not introduce threats to our body that would make it harder to heal or alleviate symptoms. I think I would want to learn more about the use of probiotics and antibiotics in alleviating diseases and the mechanisms behind it.


Step 2:

“I think it is a very smart but potentially risky route to take because we are dealing with live organisms which can evolve or develop traits or behaviors that we can’t always control once they have entered our body.”


Step 3:

Something I have wondered throughout the past modules in which we have learned about using probiotics is how physicians are able to control the effects of the probiotics. Unlike standard drugs which have a formulated chemical structure and dosage, probiotics are live bacteria which may have slightly different genomes and phenotypes, so the exact effect can not be guaranteed in the case that the species evolves and differentiates away from the intended use. Also, because probiotics are living, how is the dosage controlled? Bacteria typically have fairly fast life cycles and so the dosages can potentially vary – or do later probiotic pills begin with a smaller number of individuals so that by the time the patient takes the probiotic it is at the intended dosage? Additionally, each person has a unique microbiome, so are probiotics personalized to the patient or are they standard prescriptions? Probiotics seem to have a lot of uncontrollable features and so I would want to learn more about these factors and how they are controlled. I would also want to understand more of the interactions and mechanisms so that I can understand which factors are necessary to control and which are less significant.


Step 4:

For our final paper, I think I definitely want to look into either the use of probiotics for disease/infection treatment or prevention. I am extremely interested in disease pathways and how they can be affected and so learning about the ways in which physicians interact with these pathways in patients is something I am very curious about. Because our final paper is supposed to be about a controversial topic, I think I will begin doing some research about probiotics and what controversies surround it. Then for my paper I will explore the two sides and weigh the pros and cons of both. This will be a very good learning experience for me because I am neither for nor against probiotics at the moment so I will be able to develop my opinion on them through this paper.

Writing Exercise #7 – Maternal and infant microbiomes

As we have previously learned, our gut microbiomes can be incredibly diverse and have a significant impact on human health. However, as infants there are some factors that may affect our microbiota that we likely do not realize

Some of the more obvious ways our infant microbiomes can be affected is through diet and antibiotic use. As a baby, one of the most heavily consumed items is milk. Interestingly, the microbiota depends on whether the baby is fed with breast milk or formula milk. Breast milk contains certain probiotics not present in formula milk and thus enhance the growth of healthy bacteria.

Diet during the first couple of years is especially important in characterizing the microbiota as the baby is most sterile when born and in the next few years its gut microbial communities will develop to be what they will be as the infant grows to be an adult. For antibiotic use, something that is interesting is that if a mother took antibiotics during the pregnancy, this could impact the antibiotic interventions during childbirth.

Another notable way which could influence the colonization of the microbial community is the mode of delivery. Whether the baby is delivered through vaginal birth or a C-section affects the first exposure to a microbial community. If the baby is born vaginally, they will adopt a microbiota similar to the mother’s vaginal microbiota, but through a C-section will result in the infant having a microbiota more similar to the skin microbiota.

Writing Exercise #6 – Antibiotics

Antibiotics can be used for a wide variety of bacterial infections and diseases and with more advancements, more antibiotic treatments have become available. However, we must be careful about our antibiotic use and make sure to be intentional so that it does not become dangerous. I have never had to use antibiotics, but my personal philosophy about how and when to take antibiotics is that it should only be used when there is a guarantee that it will achieve its desired response (curing, treating, or alleviating an infection/disease). Antibiotics can be very beneficial for our health and should not be dismissed or overlooked, but if there is another method of treatment that works as well or better, I would suggest using that treatment instead.

The danger with using antibiotics is that it is meant to interact with living bacterial species and thus there is the possibility that the species may evolve to become resistant to that antibiotic. Bacterial species often proliferate very quickly and thus new generations can quickly evolve with genes that allow it to resist and survive antibiotic use, rendering the antibiotics useless and making it even more difficult to eradicate the invasive infection. Therefore, in cases where antibiotic use is the best approach, the patient should make sure to follow the instructions closely to ensure maximum effectiveness.