Writing Exercise #15

One project that I would be most excited about funding would be how microbes during pregnancy and birth could affect one’s life down the road. There seem to be a few different consequences resulting from a newborn’s microbiome that can affect their life down the road. For example, being born via C-section seems to be correlated with asthma and allergies that are usually life-long diseases. Additionally, being babies born via C-section seems to contain a higher proportion of bacterial antibiotic-resistance genes compared to vaginally delivered infants. This could lead to more infections as an infant, risking the child’s life. Also, being breastfed vs formula fed has an impact on the microbes colonization of the mouth, with breast-fed infants containing oral lactobacilli with antimicrobial properties. Additionally, when mothers have oral infections it seems to have negative effects on their child such as pre-term births. The extent of how microbes colonizing newborns is varied and can have many long term effects that I would be interested in learning about. I think we would learn how specific behaviors that affect microbiomes, ultimately influence the lives of newborns. For example, if infants are colonized with skin bacteria in C-sections and not vaginal bacteria, then shortly after birth doctors should consider somehow inoculating the child with their mother’s vaginal fluids so they get the benefits and prevent asthma/allergies. Or, if it was proven that mouth infections of the mother can cause pre-term births then the doctors could work towards ridding the mother of the infection before it negatively affects their child.


Writing Exercise #14


-stomach cancer

-cervical cancer

-irritable bowel syndrome

-inflammatory bowel disease





Most of the diseases that I listed in week one did not pertain as much to the gut as the ones I have listed here. But, there are a few similarities in the non-infectious diseases I listed in both posts. Some fo the similar diseases are asthma, cancer, and depression. The ones I failed to mention were one such as irritable bowel syndrome, inflammatory bowel disease, obesity, and allergies.

I think the most important topics I will take away from this course will be obesity and asthma, with obesity being the one that sticks with me the most. Obesity will probably stick with me the most because I wrote my final essay on it but it also has some of the most interesting mechanisms. The way that microbes can influence gut hormones is astonishing. Additionally, asthma is a disease that has been correlated with C-section births. I was born via C-section and also live with asthma so I wonder if this relationship was the cause of my asthma and look forward to future research on this topic.


Writing Exercise #12

Microbes have been shown to have a relationship with stress and anxiety-related behaviors. Studies have shown exaggerated neuroendocrine responses to stress and anxiety-like behavior in germ-free mice. This observation was reversible when mice were colonized with bacteria, reducing anxiety-like behaviors. But, this phenomenon is thought to only be possible if mice are colonized in a critical time window during the early-life/adolescence. Additionally, there has been evidence of the microbiome modulating emotional behavior. Probiotics with Bifidobacterium and Lactobacillus have shown to have beneficial effects on anxiety and depression in a few different studies. Another mental state that microbes seem to influence is that of autism spectrum disorder. ASD-like behavior of mice was associated with alterations in the gut microbiome. A study also showed that germ-free mice showed reduced sociability and had social cognition deficits compared to conventionalized mice. These social deficits were reversed by the colonization of bacteria. Lastly, gut microbes have been shown to exert influence over leptin and ghrelin, appetite-regulating hormones. There have been shifts in science that indicate microbes do indeed affect the brain and a persons’ mental state but much of the research done has been on rodents. More research is required to truly prove this causational relationship in humans and understand the mechanisms at which microbes affect the brain.


Writing Exercise #13

Can experiments detect differences that matter?

  • This question is very significant because experiments seem to find differences in bacteria diversity amongst obese and healthy individuals. But the question is how significant are those differences? There is great diversity amongst healthy individuals bacteria itself, and there isn’t an established “healthy” microbiome that all others can be compared to. Microbiomes vary from person to person. So, do the differences between obese and healthy person microbiomes even matter if there are already established differences from person to person? Being able to label a specific difference in the microbiome as causational for a disease isn’t possible if there isn’t even an established and well-characterized network to compare it to.

Does the study show causation or correlation?

  • When interpreting scientific literature this is a very important question to consider. While the results may show a correlation between a certain microbe and outcome, it can not be labeled causal until the reverse causational relationship is explored. If a journal states a microbe causes an outcome/disease, they must be sure to rule out the disease or outcome isn’t causing the presence of the bacteria. Additionally, Microbes could be mere bystanders during certain outcomes and just measuring whether they are present or not does not allow for the relationship to be named causational. The literature must have real proof of causational relationships by providing mechanisms of action. This leads to the next question to consider.

What is the mechanism?

  • This question is very significant in evaluating scientific literature. Without evidence of the mechanism, the relationship can merely only be correlational. Observing the correlation between microbes and certain outcomes is a step in proving a causal relationship. But, the mechanism behind how microbes can cause certain outcomes is ultimately the best evidence of labeling the relationship as causational. By conducting experiments that rule out certain taxas and confounding factors, allows researchers to pinpoint whether a certain microbe affects human health and then study how it does so.

How much do experiments reflect reality?

  • The significance of this question lies within the methods and conduction of the experiment. It seems that in many experimental studies the setting is so fabricated and unrealistic that their findings may be worthless. If researchers are implanting germ-free mice with microbes and observing what happens to them, they are completely ignoring other factors and creating a very unrealistic setting. No person is going to be “germ-free” such as these mice, so the results of the experiment might not even be applicable if they can’t repeat such results in a human.

Could anything else explain the results?

  • When studying the microbiome, it would be foolish to think that bacteria cause outcomes without any other contributing factors. Diet is a very important factor that researchers seem to neglect when conducting an experiment. They transplant microbes into mice, observe reduced fat, and publish all these articles that people can lose weight with a fecal transplant. The media then takes these reports and blows them up even further, all without taking into consideration one’s diet and how that could influence the gut microbiota rather than a transplant.

I think the most helpful question when discussing controversy is the mechanism of action. Like I said before, you can observe relationships between microbes and outcomes but that observation only provides evidence for correlation. Knowing the mechanism and explaining it provides a piece of whole new evidence for a side of the controversy. If one side can only support their claim with correlations while the other actually has a real mechanism of action, then the side with a mechanism explanation is much easier to believe. The mechanism can actually explain and support their thesis, which is why I think it the most important thing to consider when discussing a controversy.


Writing Exercise #11

It felt a bit odd doing the review of someone else’s paper in such a formal way by filling out a review form. It kind of made me rethink some of the areas in my paper that could use improvement. I have never done such a detailed review before, looking for very specific things in people’s papers. Most reviews I have done before involve mostly just reading through someone else’s paper and checking boxes such as grammar, structure, answering of the prompt. But this review had us looking in-depth at how the author of each paper found evidence surrounding controversy using primary research and the way they were able to convey it to their audience. Additionally, it incorporated a review of how they used their evidence to support a thesis and a recommendation for health in regard to their specific topic. Some things I learned to apply to my essay is to look over the way I explain research to the audience to make sure it is appropriate and understandable. Additionally, look over and make sure I tie that evidence back to my thesis and recommendation in a way that supports the bigger picture and context of my topic.


Writing Exercise #10

Peer review is a process of verification of studies before they are published for the general public. Typically, a group of researchers conduct a study and write their results in the form of an article. That article is submitted to a journal for publication. The editors of the journal send the article to other scientists in the same field. If those scientists feel that the article is of high enough quality and meets good scientific standards they will approve the publication of it. The pros of this method of peer review are allowing other scientists to review the work done by researchers before their work is made public. That way some random joes don’t run an experiment from their home and publish the results of a poorly ran study as conclusive evidence for various topics. It is a verification process in that sense. The cons are that the approval is subjective as it isn’t the same group of people in each field who follow a specific set of standards. The results of a study could seem plausible to some scientists who support that sort of research while others might refute it and find flaws in the methods. Overall, the subjectivity of the scientists doing the review could impact the credibility of the results.


Writing Exercise #9

cleaner water:

-Although cleaner water normally sounds like a good thing, the ingestion of water from rivers and wells that indigenous people consumed had many more microbes from the environment. The water consumes now is so highly processed and removed of microbes we have much less exposure.

Smaller families:

-With couples choosing to produce less offspring for financial purposes, there are fewer microbes that can be exposed to people at younger ages. As siblings may live in the same environment, they are not glued to each other and tend to make different friends, hang out in different places, and do different activities. This increases the exposure of various microbes to individuals from their siblings who experience different environments. The exchange of microbes between siblings is a factor.

Born via Cesarian section:

-Being delivered by c-section changes what microbes an individual is immediately exposed to at birth. It has been shown that vaginal bacteria are very beneficial to infant development. People who are born via c-section do not get exposed to this beneficial bacteria and are instead immediately exposed to skin bacteria. By missing out on being colonized by vaginal bacteria, those individuals miss out on the health benefits that come with them.

Antibiotic exposure:

Taking many antibiotics as a child or infant changes the stable structure of microbial communities. They can kill healthy bacteria that are used in immune defense or metabolism and have co-existed with humans for thousands of years, such as H.pylori. The use of antibiotics selectively permits certain microbes to inhabit while others cannot, which can last for years after ceasing the use of the antibiotic.

Decline in breastfeeding:

-The decline in breastfeeding and increase in formula feeding has decreased microbe exposure. The oral microbiome of infants will have greater colonization of microbes from the breast and from the milk that is beneficial, while formula infants will not. Additionally, the gut microbiome is further matured in infants who drink breast milk and need to breakdown the sugars/fats that are present in breast milk.

Playing outside as a child:

-Children who play outside are exposed to many more microbes than those who stay inside. Acts such as eating dirt as a child can expose an individual to many microbes as there is a lot in soil. Additionally, playing with other children outside can increase the likelihood of exchanging microbes and being exposed to germs from the other child’s environment.


Writing Exercise #8

  1. There have been many things that have been very interesting to me in my time of this course. The first of them being how microbes of the gut have influence over obesity. Another one is how the dysbiosis of microbiota cause/have heavy negative influence over gastrointestinal diseases and cancer but probiotics are able to restore microbial communities and have positive impacts on diseases. The way probiotics and antibiotics are heavy influencers over gut microbiota, with antibiotics actually having a more negative effect than positive. The way microbes influence our metabolism has always amazed me thus far and I am most impressed by how the microbes in obese people are different than in healthy people and break down molecules differently.

3. The influence of microbes over obesity has been particularly interesting in this class. Some experiments have shown that the fecal transplant of obese people’s microbes into germ free mice has had increased adiposity when compared to mice inoculated with lean persons feces. The microbial community of obese people are usually at a dysbiosis and don’t have microbes that can metabolize certain compounds that are important in preventing adiposity development. Lean microbial communities have microbes that produce short chain fatty acids and metabolize simple carbohydrates and are insulin sensitive while many bacteria found in obese individuals are insulin resistant and do not promote the uptake of glucose like they do in lean individuals.

4. To begin preparation for my final essay, I will start to research and look for articles about microbes influence over obesity. I will find articles that explain the dysbiosis prevalent in obese individuals and how the microbes or lack of microbes affect the molecules metabolized by an individual. I also want to find out how the microbes of obese individuals affect their insulin sensitivity. Lastly, I will explore articles on how microbes affect inflammation in obese individuals and the consequences of that induced inflammation.


Writing Exercise #7

Diet of the mother:

-The diet of the mother during gestation and before pregnancy showed changes in microbial composition in their feces. Obese pregnant women showed significantly more Bacteroides and Staphylococcus in their feces in comparison with normal weight pregnant women. A study of diet induced obese rats revealed that when these rats were fed oligofructose prebitoics during pregnancy and lactation, the cecal microbiome of the offspring was altered. The result was that it prevented increased adiposity in the both the dams and offspring. This implied an early maternal effect on offspring microbiota


-Antibiotics given to pregnant mice showed a few negative effects such as decreased bacterial diversity. Researchers also observed that maternal antibiotic administration during pregnancy decrease immune response in the infant mice. Lastly, non-absorable antibiotics given to pregnant maternal mice altered offspring behavior, showing decreased locomotor activity and lower levels of exploratory activity.

Mode of delivery

The type of delivery seems to have an affect on the bacteria that infants are exposed and colonized with when they are first born. The two modes discussed are vaginal vs. Cesarean section birth and how they affect the gut microbiota of an infant. The infants delivered via the vagina displayed colonization of vaginal and maternal gut bacteria in their gut. Infants who were born via C-section were colonized by bacteria that resembled skin and oral microbiota. This is interesting because the microbiome of c-section infants contained a higher proportion of bacterial anti-biotic resistant genes than vaginally delivered infants. It has been suggested that disruption of vaginal bacteria transmission due to C-section can cause long-term medical implications.

Breast Feeding vs Formula:

-Breast milk contains sugars that cannot be digested by infants so bacteria such as Bifidobacterium, Lactobacillus, and Bacteroides help break down the polysaccharides to be used as an energy source. This gives them an advantage over competing bacteria. As a result Bifidobacterium are most abundant in breast-fed infants while Enterococci and Clostridia are dominant in formula fed infants. Three month old breast fed infants had oral bacteria that contained antimicrobial properties that were not found in formula fed infants.


Writing Exercise #6

My personal philosophy about taking antibiotics is to only take them when they are prescribed to me by a physician and to follow the directions the pharmacist gives me when I pick up the prescription. I don’t usually go to the doctor when I am sick as I just try and strengthen my immune system to fight the sickness and overcome it, instead of just running to the doctor every time so they can give me me antibiotics to feel better. I believe I formed this philosophy because I always assumed the doctors knew what they were doing and would only prescribe antibiotics if they deemed it necessary. I also am pre-pharmacy and have always been interested in that field, so I also trust that the pharmacist’s extensive knowledge about the drugs and their directions are worthy following down to the tee. I feel like I always trusted these healthcare providers because of their credentials, knowing that they both have doctorates in their respective professions gave me a perception that they are always doing the right thing. The older I have got and the more I have educated myself I have found that not to be true, as physicians and pharmacists alike can make mistakes. In the case of antibiotics, it seems like doctors largely over-prescribe these drugs and it is causing a large problem of antibiotic resistance which could easily be avoided with other treatment options.