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Now, I admit, this may be coming out of left field, but I am most interested in further research surrounding the microbiome related differences in babies born vaginally versus those born cesarean. I understand that there is an initial difference for at least the first few minutes/hours of life, but after that, how much impact does the difference actually make?

For the research study that I would fund, I would be most interested in a longitudinal study that followed a group of maybe 50-200 children, and over the course of ten years, follow them throughout yearly check-ups and measure their oral and fecal microbiomes, as well as tracking the incidence of certain associated conditions, or immune development.

To start, you have cancer, diabetes, heart disease, obesity, and many different metabolic disorders. outside of the gut there are diseases of the mouth like gingivitis, periodontitis, and dental caries. on the skin there are things like acne or dandruff, and in places like the vagina you can have bacterial vaginosis. There’s also the case to be made for things like depression, anxiety, alzheimer’s disease, and dementia in the brain. the microbiome has also been linked to asthma. I even think that there is a case to be made for accidents being linked to the microbiome, either from stress, lack of sleep, or lack of focus due to discomfort.

I think that there wasn’t a whole lot different between the two responses. To me this makes sense, because I had just come out of the term prior studying the human microbiome with Dr. Thomas Sharpton, so I came in with a lot of knowledge about the microbiome and the way that it interfaces with disease/injury. The only major difference is that I have researched more about the microbiome and the brain for my final paper, so I have a better grasp on the way that they link up. Funnily, I also believe, now, that accidents could theoretically be caused, or at least linked, to symptoms originating from the microbiome.

Can experiments detect differences that matter?

This is significant when interpreting scientific literature because it indicates proper study design, with controls as well as controlled variables and random samples. If there were a study that happened to find a difference between two groups of individuals, but didn’t parce out what actually caused that difference, there is very little that we can draw on from that study, other than the foundations for another study.

Does the study show causation or correlation?

The significance of this phrase is more geared towards the conclusions that we can draw. There is a massive difference between the two, as well as the in the aftermath of their respective studies what we are able to do. If we determine causation, we are given clear direction, and often (but not always) the mechanisms to target, for an effective therapy. If we only find correlation, then our hands are more or less tied, as we can’t be sure that the therapies will be effective, or if they might exacerbate the issue. Overall, I feel that this is the most important when discussing controversial topics, as it helps to delineate whether or not something has been weakly associated versus strongly associated with actionable plans for the future. Also, it helps to lend credence to these more strongly associated topics, and they are less likely to be shot down by the opposing side.

What is the mechanism?

This is important for developing therapies as well. If we know that something is causing something else, but we don’t know how, we have to do further research in order to find out what to do to actually address the problem. There are certainly times where we don’t necessarily need to understand the mechanism behind a therapy to know that it works, and because of that I think that it is less important for controversial topics.

How much do experiments reflect reality?

This calls back to experimental design, but it really focuses on the applicability of the conclusions. Very rarely do scientists spend the time and money to conduct worthless, inapplicable experiments. There are times when results can perhaps be called into question, for example with animal model studies and their relation to human applications, but overall science has come to the conclusion that these are generally acceptable as experimental designs when it comes to drawing correlative conclusions.

Could anything else explain the results?

And once again, study design is in question, although this issue has to do with the thought put behind the study. I think that this is very similar to the ‘differences that matter’ and the ‘mechanisms’ issues, as it sort of combines aspects of the two. The former gives us issues with determination of results and the sample design of studies, and the latter gives us issues surrounding the next steps that we take in the future.

The microbiome and the brain both influence each other bidirectionally, that is to say that they influence each other in the same ways.

To start, we can discuss neurotransmitters. The microbiome is capable of making neurotransmitters; notably, it can synthesis serotonin out of the amino acid tryptophan. These created neurotransmitters can influence the highly innervated intestinal lining, which sends signals up to the brain via the Vagus nerve. The Vagus nerve can send down signals as well, releasing chemicals and hormones that can influence the microbiome both positively and negatively.

Additionally, there is the possibility that the two influence each other by way of inflammation. Various mental health conditions are associated with systemic inflammation, as are various dysbioses. On top of that, both of these types of maladies can actually cause inflammation, either by way of cortisol/stress hormones or by way of expressed metabolites entering the bloodstream. There is further evidence that these inflammations are intertwined, as mitigating the cause of one can help alleviate the symptoms of the other.

There may yet be more ways that the microbiome interfaces with the brain, but right now there hasn’t been enough solid research linking the two to really draw any heavy conclusions.

I am generally comfortable as a peer-reviewer, but usually that is for more pop science articles or short stories as opposed to harder science articles like these. I think that articles like these are much more difficult to review like I normally do, especially because we aren’t necessarily editing for ideas and content or word choice or what have you.

I found that in reviewing my assigned articles, I was trying to think back to writing my own article. Whether or not I had included my own thesis statement, or if I had supported the side opposite my opinion as well as I had supported my own side. All in all, I think that peer reviewing, especially in this context, does make you think about how you are as a writer yourself, and that reflection often is the basis for growth.

Peer review, generally speaking, refers to a part of the editing and revising process wherein people within the same field read an article that you’ve written, and critique it. In a scientific article, peer review means that the article is reviewed by scientists in the same field for accuracy and feasibility.

This peer review is important for ensuring that scientific journals aren’t filled with articles that aren’t scientific in nature, articles that fake or falsify their results, and articles that draw incorrect conclusions from their data. While some accidents certainly slip through the cracks, this process has been used over the years because of how effective it is at catching bad articles.

There are some drawbacks to peer review, however. The most glaring issue is that cutting edge research that fundamentally changes the way that we view a field of science may be passed on or overlooked because nobody in the peer review committee has seen anything like it, or they may assume that the data, the methods, or the conclusions drawn are bogus. If these revolutionary articles are thrown out in the peer review process, it can hold back progress in the field significantly.

There are many human behaviors that can decrease overall exposure to microbes, most of which have to do with hygiene.

The increased number and frequency of usage of cleaning products in the modern home have contributed to lower exposure to microbes, especially decreasing the variety of microbes that people experience. The household areas will get reseeded with microbes that are already in the house, such as those from the people living inside.

On the same topic, the increased frequency of bathing over the centuries have contributed to decreased microbiome exposure. Showers essentially wipe out the skin microbiome due to the soap, the high heat, and the friction of the water. This can also decrease the variety of microbial exposure, as odd microbes from the outside will get washed away in the shower before they can take hold.

Speaking of the outside, the tendency in the modern era to stay inside, especially in hotter areas, decreases the exposure to new microbes that would help to develop the immune system. additionally, modernity has allowed more and more people access to air conditioning, which limits the amount of time that windows stay open, thus further limiting the amount of outside exposure that buildings have.

Lastly, there is also a trend over the past few millennia towards more and more cooked foods as opposed to raw foods. This is overall a good thing, as it has decreased the amounts of food borne illnesses, but it has also decreased the amount of commensal microbes that people are exposed to in foods. Probiotics and the raw food diet have attempted to somewhat remedy these issues, but they have yet to grow in popularity enough to fully make up for it.

Step #1: I think that some of the more interesting microbial interactions that I have learned about have had to do with the microbiome and the way that it interfaces with mental health, specifically from the gut. I bet other microbiome dysbioses could have effects on mental health like bacterial vaginosis or acne, but the idea that the microbes that you eat would impact your brain chemistry, and vice versa, is really awe inspiring and opens the possibilities for new and interesting therapies.

Past that, I like learning about microbiomes of body sites outside of the gut, because I have much less experience with these places. Stuff like the urogenital system, the respiratory system, or the skin has been interesting to me in the past because I have more to learn about the topic.

Step #2: The microbiome and mental health

Step #3: The microbiome and mental health are intricately interconnected. This is because of the vast expanse of nerves that serve the intestines. All of these nerves send signals to and from the intestines, and they all link to the Vagus nerve which directly links to the brain. The microbiome can make neurotransmitters that send signals to the brain from the gut, and the brain can affect the microbiome as well, both by direct nervous interactions and by way of the endocrine system.

Step #4: I think that in order to prepare for the final paper I should learn more about the ways that the microbiome and the brain interact to influence brain chemistry. Right now I think that’s where I will be best able to deepen my understanding. Additionally, learning more about the specific conditions that the microbiome can impact is important as well, and getting specific sources for those topics will be imperative as well.

Colonization of a newborn infant’s microbiome depends on a number of factors, but barring odd circumstances, oftentimes the initial seeding of the microbiome comes directly from the immediate family, particularly the mother herself.

Firstly, initial colonization is impacted by the method of birth. Babies born vaginally have an initial microbiome aligned with the maternal vaginal microbiome, while babies born via C section have initial microbiomes closer to the maternal skin microbiome.

Past this first moment, much of the infants microbiome is determined by what they put in their mouth. Traditionally speaking, this could be determined by formula feeding vs breastfeeding, with the latter seeding the microbiome with a wider variety of healthy maternal microbes.

In a less elegant manner, newborns, infants, toddlers, etc, like to put things into their mouths. This serves to introduce environmental microbes to their systems which may or may not have an impact on their microbiomes or their immune systems. Therefor, any impact that a decision has on the environmental microbial community will have an impact on the infant. Anything from owning a pet to opening a window can serve to expose the infant to a broader microbial community by way of them putting things into their mouth.

There are two distinct memories that I have about antibiotics, and both of them happened within the same year.

The second time that I had to take antibiotics it was difficult but relatively non-invasive, at least as far as antibiotics go. I had caught pink eye. My freshman year of college, my dorm window looked out over the parking lot and had a view of the Hilton Garden Inn to the south of campus. The light would pour in through the slats of our blinds, and for the first few weeks of college, dramatically impacted my sleep. I had decided to buy a sleep mask to actually get rest so that I could get work done in class.

When the sleep mask arrived a few days later, I happily slapped it on my face and slept like a log for the first time in many nights. As the week dragged on, both of my eyes began to feel sore and began to make mucousy sludge that had sealed my eyes shut in the mornings. Whether it was my sleepless haze of the past few weeks or not, I didn’t identify the mask as the vector for my eye infection until after I had gone to student health services and received antibiotic eyedrops. they may have been impossible to use, but at least these antibiotics stayed in my eyes (and a little on my cheeks) and didn’t have any systemic effects.

The first time I took antibiotics was only four months earlier, right after my last day of high school. I had woken up perfectly fine. It was a brisk June morning in Oregon, nothing out of the ordinary, but as I walked to the bus I realized that I was much warmer than normal. the day dragged on, and I became clammier and more feverish. By the end of the day I was drawing concern from friends and acquaintances, and by the time I got home, I was running a high fever and sweating uncontrollably, and had developed such a sore throat that I could no longer swallow.

The next day I went to the clinic, where I was quickly diagnosed with a combination of bronchitis, laryngitis, and a double ear infection and sent home with prescriptions for antibiotics and an inhaler. I took the antibiotics without question. I understood the importance of maintaining the schedule of pills, and completed the full course of antibiotics without issue. At this time I was only acutely aware of the microbiome, and didn’t consider that systemic antibiotics would have a negative effect on that as well.

Various gastrointestinal distresses began popping up. I had previously attributed them to my liquid diet of the past few weeks, as juices and smoothies were the only things that I could actually eat, but as my normal diet resumed, it became clearer that that was not the case. It was at this point that I was introduced to probiotics, and as soon as I started substantially consuming probiotic foods in my diet, I began to feel relief from my various GI ails.

I now know enough about antibiotics to know that sometimes they are not necessary. I believe that in my lived experience, the times that I have had to take antibiotics were necessary, and I would not have benefitted from alternative treatment options due to the either the manner or the severity of my infections. I do believe that many times, doctors will prescribe antibiotics for issues that could be treated by other means, and that this can be more harmful to patients than the initial infection. In the future, I will discuss alternative options with healthcare professionals in the event that antibiotics are brought up, and if there are not alternative treatment options, I will be sure to take my antibiotics with yogurt.