Writing Exercise #12

PROMPT:  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?

One thing that has become increasingly studied and researched is the relation with the gut microbiome and mental health. Coincidentally, that is the exact topic of my final essay paper. Even though this is a topic which has interested me for a little while now, and I have done some independent reading on the subject, the process of gathering info for my paper has brought many new theories to my attention. Results from studies I have read have provided information about new ways of how the gut microbiota affects the brain and mental health.

The connection between the gut microbiome and the brain is referred to as the ‘Microbiome-gut-brain-axis’ and involves the bidirectional relation between the Central Nervous System, the Enteric Nervous System, and the gastrointestinal tract. (1) The Central Nervous System encompasses the brain and spinal cord and is well known. The Enteric Nervous system involves approximately 500 million nerve cells which can control all the normal functions of digestion even if separated from the brain. (2)  These two nervous systems connect via the Vagus nerve, and thus a direct line is made connecting the brain and gut.

With respect to the gut affecting the brain/mental health, one of the most fascinating facts relates to the percentage of all endogenous neurotransmitters and neuroactive chemicals that are made in the gut. 5-hydroxytryptamine (5-HT), more commonly referred to as ‘serotonin; plays a large role in our mental health. Imbalances and low concentrations of serotonin are believed to cause a wide array of mental disorders, and thus serotonergic drugs are often the most widely used treatment. When one thinks about neurotransmitters, and chemical imbalances of the brain, its easy to assume that all or a significant majority of neurotransmitters are both made and stored solely in the brain. New studies show that this couldn’t be further from the truth. Approximately 90% of ALL endogenous serotonin is synthesized in the gut! (3) A study using mice found that the presents of some microbes regulate the hosts serotonin levels, and having these microbes led to significantly higher serotonin levels than in mice birthed and raised germ free. (3) Since the microbes are able to alter the levels of endogenous serotonin, and serotonin plays a large role in mental health, the microbes have a direct influence on the mental health of their host!

As mentioned when describing the Microbiome-gut-brain-axis as a ‘bidirectional’ relation, the connection and influences go both ways. Mental health can have an impact on the make up of gut microbiomes in a few ways. Chronic stress and Anxiety due to various mental disorders can lead to an increase in stomach acid production. This changes the acidity of the stomach and intestines and impacts which microbes can successfully colonize the area. Depression can lead to a lack of personal hygiene, and poor dietary habits, which both can have an impact on an individual’s microbiota. Bulimia Nervosa, an eating disorder characterized by binge eating followed by forced self-induced emesis to prevent the absorption of the caloric contents of the food, can introduce microbes to new areas of the digestive tract as they are physically relocated during episodes of vomiting.

The microbiome of our gut, the enteric nervous system, and the central nervous system are connected in ways never thought of or studied before. Its amazing learning how two incredibly different specialized regions of the body can have such a collaborative impact on each other. As technology advances and new studies are done, its almost certain that new connections between the organs never thought of before will be discovered, and new ways of indirectly treating diseases and illness affecting different organs will be designed and target the connected organs.


  1. Mayer E, Tillisch K, Gupta A. 2015. Gut/brain axis and the microbiota. Journal of Clinical Investigation 125:926-938.
  2. https://www.youtube.com/watch?v=_PLD5RLLvfQ
  3. Yano J, Yu K, Donaldson G, Shastri G, Ann P, Ma L, Nagler C, Ismagilov R, Mazmanian S, Hsiao E. 2015. Indigenous Bacteria from the Gut Microbiota Regulate Host Serotonin Biosynthesis. Cell 161:264-276.

Writing Exercise #11

PROMPT: 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?

It was an interesting process for sure. It was difficult to critique someone else’s writing effectively without feeling rude. It was very informative, however. I feel that it helped me learn a few things to look out for as I revise my own final essay. First, I need to make sure that my language is appropriate for the audience. One way I can do this is by having someone who has no biology background read through my essay and highlight any areas they either didn’t understand or needed to really read in depth and use context to understand. If there are things they highlighted that I feel is still appropriate, I don’t have to change it, but it will still provide a useful source of information to give me an idea of how appropriate my essay is in general. Second, I am going to make sure I really emphasize the importance of thesis, and why it matters to the reader. It’s easy to just start writing when you have an idea. It’s easy to get fixated on making a solid argument to back up your claims, and completely forget to explain exactly why my thesis is important in the first place. One other thing I am going to really make sure to keep in mind as I revise my essay is making sure that I provide any background info needed to explain why it’s important, and to define exactly what I am discussing. It’s easy to assume other people will know your own definition of subjective terminology (for example, over-weight/obese can mean completely different things to different people. My classification may not match exactly what other people think.) Also, if there is a set objective number/quantity, I will be sure to provide it and explain it so I’m sure the reader and myself are on the same page.

The peer-review process was really beneficial in regard to improving my own essay. It helped highlight some things for myself to make sure to check and gave me a good idea about how to make my argument as strong as possible. It is a little scary having someone else read my paper though! Even if their response is anonymous, I still know that another human is critiquing my work, and it’s a little frightening! I look forward to finding out their thoughts and incorporating their feedback into my work though. I am sure it will help me write a stronger essay, and give some ideas where I could expand on, or where I spent too much time talking about.

Writing Exercise #10

PROMPT: Describe the process of peer review to someone who does not frequently read scientific articles. In your response, consider the pros and cons of peer review and how that might impact the credibility of the results that come from that scientific article.

Peer review provides a proof-read and a check to make sure claims being made are properly backed up with evidence. By having a qualified person review your article, it increases the credibility because they don’t carry the same beliefs, and if they agree with your points and evidence after reading your article it provides additional credibility. It also allows errors to be corrected, and suggestions for small changes. When writing an article, its easy to get caught up in your argument and lose yourself to small internal, unconscious biases. You make believe in a point you make and don’t feel the need for specific evidence to back it up. However, by having a fresh set of eyes look over your article, these unconscious biases can better be avoided, and any additional evidence necessary can be added. Another advantage to having a peer review your article is that they may be able to provide suggestions about additional sources, evidence, or areas to expand on which can lead to a stronger argument. They may also give ideas about additional potential explanations, or where to look for beneficial information to add to your article. However, having a peer review your article can have its disadvantages. First, it could cause you to question the strength of your claims/thesis to an amount not necessary to ensure an accurate paper. This could potentially cause someone to scrap their entire proposal/article for poor reasons because of self-doubt. Additionally, they could provide inaccurate input or additional biases that can take away from the strength of your argument. So it is wise to take any advice with a grain of salt and to double-check any claims they make and look into their sources to ensure that the information is up-to-date and accurate.

Writing Exercise #8

PROMPT: Freewrite/Brainstorm (No proof-read)


Step 1:

One thing that I came into this class wanting to learn about is nosocomial infections. I have been working in critical care for nearly 2 years now as a CNA2, and have been working in a hospital. One thing that we have to be careful about is any injuries/illness that can be linked to their time in the hospital wont be reimbursed, so the hospital has to pay for it. This is most often related to bed sores, pneumonia, C. diff, CAUTIs, VAPs, and other sepsis related illnesses. One thing that I never took into account with regards to infectious disease prevention and the immune system is the state of our microbiomes. I never really considered the fact that staying in the hospital can alter your microbiome, and can lead to complications, increased length of stay, and overall worsening of patient outcomes. It has been really interesting to learn about the microbiome and its impact on our health and how it can protect us from infection.

Step 2:

staying in the hospital can alter your microbiome”

Step 3:

Staying in the hospital can alter your microbiome. Due to antibiotic treatment, nutrition deficiencies, exposure to pathogens by healthcare workers, etc., the microbiome you walk into a hospital with likely is drastically different than the one you will leave with. Currently, there are not much treatment options that are used commonly to counter this inevitable change. I think it would be really interesting to learn about techniques and methods utilized by specific hospitals/clinics/centers in other areas/countries where they have spent time studying the microbiome and how to prevent dysbiosis. Im sure some great research has been done, and some other facilities utilize cutting edge techniques, but the knowledge hasn’t spread throughout healthcare.

Step 4:

In a hospital you can become really focused on numbers, observable symptoms, and the visible state of the patient and completely disregard what you cant see. Its easy to disregard this part of human biology since there are other critical things in plain view. I think this is part of the reason why the microbiome is not a larger part of the care plan in patients, especially the ones who are in Critical Care settings. Infection is very prevalent in hospitals, its not a secret that many people succumb to nosocomial infections, and some of which can be fatal. There is an underutilized natural defense system we all have, its microscopic, but it still can provide a lot of protection. By ignoring this system, and additionally altering it, we cause dysbiosis and destroy a very valuable asset. I think I will look into the strategies employed by other facilities regarding protections of the integrity of microbiome, and write my paper on how effective they are, and the importance of factoring in the microbiome in patient care plans.

Writing Exercise #6

PROMPT: 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?

Having nearly 2 years of experience in healthcare, I have become quite familiar with drug-resistant organisms. I would say that due to the various classes I have taken in addition to the time I have spent working in hospitals, my personal philosophy on antibiotic usage is quite biased. Antibiotics are an incredible resource that have drastically improved the outcome for patients around the world. While it’s impossible to calculate an exact number of lives that have been saved since the creation of the first antibiotic in 1928, estimates put the number at 80-200 million or more. (1) However, with great power comes great responsibility. The misuse of antibiotics has lead to an epidemic of infections of strains of pathogenic bacteria which have developed resistance to nearly all antibiotics. (1) This is why strict adherence to proper use of antibiotics is serious.

It is important to note that antibiotics have an incredibly important role in healthcare and treating patients suffering from various infections. If your physician EVER prescribes an antibiotic, it is essential that you follow the specific instructions for the prescription. Additionally, even if you start feeling better, DO NOT STOP taking the antibiotics as prescribed. The premature discontinuation of antibiotic treatment can cause a relatively benign infection to come back as a much more serious, drug-resistant, infection. This contributes to the problems that lead to the few cons of antibiotic usage.

Antibiotics are a double-edged sword. While they have saved countless lives as previously stated, they have lead to the rise of deadly bacteria that we either struggle to or are no longer able to treat. Had antibiotics been used only in specific cases as needed, we would not be facing this epidemic we are in today. In 2009 alone, over 3,000,000kg of antibiotics were administered to humans. Even more surprisingly, 13,000,000,000kg of antibiotics were administered to US livestock. (2) Compared to the typical 125-1000mg dosage of antibiotics, it’s clear that antibiotics were over-used and overprescribed.

The 13 billion kilograms given to livestock was primarily given as preventative treatment, rather than for treating livestock afflicted by an infection. The farms raising the livestock do this to try to prevent an outbreak of infections that can wipe out an entire farm’s cattle due to the small shared spaces livestock are kept in at factory farms.

Bacteria replicate quickly, with a high chance of mutations occurring in their genome. These mutations can either lead to no change, be harmful, or be beneficial. Since bacteria replicate so quickly, one bacteria turns to two, which turns to four, then eight, 16, 32, 64… and so on. In a relatively short time, 1 bacteria can turn into a colony containing millions of bacteria. If even as many as 1 in 1000 bacteria have a serious mutation, the amount killed off due to harmful mutations is insignificant as the colony still has 99.9% of the bacteria living without mutations. However, if that mutation happens to lead to a beneficial change in the bacteria, especially if it leads to resistance to antibiotics, that 1 in 1000 becomes incredibly significant.

Now, take those millions of bacteria in the colony, and place them in a cow at a farm. The cow then receives antibiotics, which leads to the death of 99.9% of the bacteria. However, the remaining bacteria now have all the space they need to replicate and virtually 0 competition for nutrients. Not only this, but they are resistant to the antibiotic, so treating the cattle with the same antibiotics to try and treat the infection does nothing. The resistant pathogen is now free to colonize the host without being killed by antibiotics, and without competition from other microbes.

The 1 in 1000 number I used is not a scientifically based statistic, it was used to illustrate my argument. The real number is MUCH less frequent, but it is still significant when put in a real-world context. With 3 million kilograms of antibiotics being given to humans, and another 13 billion being given to livestock, it’s clear to see how even incredibly low rates of mutation can still end up with the development of drug resistance.

As I said before, with great power comes great responsibility. We are sitting on the edge of a bubble of an epidemic that is ready to burst. If we continue to use antibiotics haphazardly, we will ultimately run out of antibiotics to treat even common infections. Antibiotics have a critical role in healthcare and should 100% be taken as directed by a physician. However, we must improve the way they are used before we are stuck in a situation we can’t get ourselves out of.

  1. Ventola, C. L. 2015. The Antibiotic Resistance Crisis: Part 1: Causes and Threats. J Clin Pharm Ther 40(4), 277–283.
  2. Spellberg B, Bartlett JG, Gilbert DN. 2013. The future of antibiotics and resistance. N Engl J Med 368:299-302.

Writing Exercise #5

Writing Exercise #5

PROMPT: What choices do you make in terms of food/nutrition/product use and consumption that may have an impact on your microbial communities? Consider choices that are intentional, and choices that are perhaps non-intentional.


There are many different products and foods which my consumption can have an impact on my microflora. A lot of these things are a part of my daily life and I don’t think twice about their implications. From medications to foods, to supplements, they all can influence the specific balance organisms that make up the composition of my microflora.

The thing that probably has the biggest, non-intentional, impact is the over-the-counter Proton Pump Inhibitor (PPI) I take daily, omeprazole. Due to my chronic gastritis, I have to take this medication daily to decrease the amount of stomach acid produced. The decrease in acid production leads to a reduction in the pH/acidity of my entire GI tract. Studies have shown that the use of antacids increases the risk of developing a C. difficile infection. (1) Interestingly, it has repeatedly been demonstrated that the specific type of medication I take, PPIs, have the highest associated increase in risk of infection. The reason these drugs cause an increased risk of infection is not explicitly apparent. However, the reasoning behind the association is clear upon further thought. Most organisms can only live in a small pH range, and their optimal environment for reproduction is an even smaller range. The pH of stomach acid can go as low as 1.5, which is incredibly inhospitable. By suppressing the production of stomach acid, the pH raises to a more neutral level. This allows other microbes to colonize an environment where they usually wouldn’t have a chance.

A more obvious influence on my microbial flora comes from some of the foods I eat. Yogurt and cheese are two food items which commonly come to mind when thinking about microorganisms in food. Bacteria is added to milk, and thru fermentation make yogurt. Fungal species, as well as bacteria, are added to milk, and perform fermentation of the lactose in the milk and make cheese. That means that if you consume cheese or yogurt, your introducing live microbial cultures to your body. This is an example of how food can have a direct impact on my microflora.

While I don’t drink often, I do have the occasional alcoholic beverage. Interesting, beer impacts my microflora in two different ways. First, beer production requires yeast, an Ascomycota fungus named Saccharomyces pastorianus, is used to ferment glucose into ethyl alcohol. That means that drinking a beer would mean drinking a beverage which contains residual yeast from the fermentation process. (However, most commercial breweries filter/remove any microbes before bottling the beverage) Additionally, another impact on my microflora stems from the ethyl alcohol, or ethanol, itself. Ethyl alcohol has antimicrobial effects, so the consumption would likely kill some of the microbes found in my GI tract.

There are many different ways which I can alter the distinct composition of my microbiome. Some ways have a more significant impact than others, and some ways are more direct than others. Additionally, some ways are less readily visible and require deeper thinking to understand their influence, but play an essential role in the balance of my unique microflora.

  1. Dial S, Delaney JAC, Barkun AN, Suissa S. 2005. Use of Gastric Acid–Suppressive Agents and the Risk of Community-Acquired Clostridium difficile–Associated Disease. JAMA. 294(23):2989–95.

Writing Exercise #4

PROMPT: Brainstorm a list of behaviors that an individual could engage in that could cause changes to a gut microbial community. For each behavior you list, discuss how that behavior could change the microbial community, and what potential health impacts (beneficial, detrimental, neutral) that change could be for the individual’s health

  1. Alterations to diet, or general poor diet

Each strain of bacteria either thrives or struggles to live in different, varying environments. Acidophilic bacteria prefer to live in more acidic environments, Neutrophilic bacteria thrive in environments with pH ranges close to neutral (pH of 7), and Alkaliphiles preferentially live in basic environments. Additionally, other bacteria thrive or are killed off by different nutrients, foods, and substances. One’s diet can have a large impact on the environment in their gut. Some dietary/medication related examples:

i.Highly Acidic Diet:
Consumption of acidic foods and drinks such as Coffee, Alcohol, Dairy Products, Tree Nuts, Tomato Sauce, Soda and even carbonated water are all common things we eat that are acidic, some being so acidic that they have a pH as low as 3. By changing the over the acidity of the one’s gut, the microbes which can and will populate the gut is altered.

ii.Overuse of GERD medication(i.e. Antacids, Proton Pump Inhibits, H2Blockers, etc.)
Many people are affected by GERD, and many take medication (both over-the-counter, and prescription) to treat the symptoms of GERD like acid-reflux. Just as the acidity of one’s diet can impact their gut pH, medications made to directly impact gut pH either directly or indirectly. Antacids like tums contain some compound which acts as a buffer to target and neutralizes stomach acid directly. HReceptor Blockers (H2RBs), and Proton Pump Inhibitors (PPIs) act indirectly by aiming to decrease the overall amount of stomach acid produced. Some studies have shown that overuse of acid-reducing medication leads to an increased risk of developing C. difficile infections. (1)

iii. Antibiotics/Probiotics
Antibiotics are another medication which can have an impact on the overall gut microflora. By killing different bacteria depending on the antibiotics and the mechanisms of its actions, different bacteria have extra space and nutrients to replicate and change the microbial community of one’s gut. (1) Probiotics are the exact opposite of antibiotics and aim to increase the presence of certain bacteria. By introducing new bacteria to one’s gut, little explanation is needed to show how this could impact one’s microbial balance.

iv. Diets High in Sugar

Certain organisms use glucose (table sugar) as a source of energy. A diet high in sugars will provide nutrients for these organisms and could lead to different organisms prospering and creating a microbial imbalance (or dysbiosis). Candida albicans, commonly referred to as ‘yeast,’ is an opportunistic pathogen that is present in nearly 100% of human gut microbiomes. High sugar diets can lead to microbial imbalances and Candida overgrowth. (2)

  1. Hygiene

Living or working in environments full of bacteria, (such as garbage men, pre-school teachers, healthcare providers, etc) leads to direct exposure to many foreign bacteria or high concentrations of various microbes. These can alter the diversity, and balance of one’s microbiome. This can be good, or bad for one’s health. By being exposed to new bacteria, one can develop a level of immunity to protect from future infections. However, the exposure can lead to infection, and other illnesses if the bacteria are pathogenic.

i. Animals

Another common source of foreign bacterial exposure is from pets. It is not rare for one to let their pet, or other’s pets, lick their face, hands, and even mouths. Dogs are known to eat just about anything and don’t understand hygiene. Thus, it is expected that these licks could pass on microbes to humans, which could then alter one’s gut microflora.

  1. Stress

Chronic stress alters the hormones which are present in the body. These hormones can impact the microbial communities of the gut. Cortisol and Adrenaline are some of the stress-response hormones that increase under times of heavy stress as part of the body’s ‘flight or fight’ response. These hormones increase the rate of production of bile and stomach acid, thus altering the internal environment of the gut. Long-term stress gives the acidophilic bacteria time to out-compete other bacteria and colonize the gut in place of the non-acidophilic bacteria. These bacteria, as well as the increased acidic conditions of the stomachs, can even lead to the development of gastric ulcers.


  1. Kwok, C., Arthur, A., Anibueze, C., Singh, S., Cavallazzi, R. and Loke, Y. 2014. Risk of Clostridium difficile Infection With Acid Suppressing Drugs and Antibiotics: Meta-Analysis. Am J Gastroenterol 107:1011-9
  2. Martins, N., Ferreira, I., Barros, L., Silva, S. and Henriques, M. 2011 Candidiasis: Predisposing Factors, Prevention, Diagnosis and Alternative Treatment. Mycopathologia 177:223-40.

Writing Exercise #3

Prompt: As a healthcare professional, a colleague asks your opinion as to which HPV strains should be covered in a new treatment. Based on your reading from the Sarid and Gao 2011 article, what would your recommendation be, and when should the treatment be administered? What evidence supports your opinion? 

Currently, vaccines protecting against HPV 16 and 18 exist and have been proven to be effective protection from those two strains. However, there is presently no single vaccine which protects against all four high-risk strains, nor the eight strains which are probably carcinogenic. These 12 strains together have been recognized to cause nearly all cases of cervical cancer, and have been linked to cases of anogenital cancer, a subset of head and neck cancers, and possibly more. Thus, we must consider investing in the development of vaccines protecting against additional HPV strains.

Unfortunately, the creation and production of new vaccines happens to be both expensive and time-consuming. So, an attempt at developing a vaccine protecting from all strains is highly unrealistic. It is much more conceivable to target a small number of additional strains first, with the other two high-risk strains (HPV 31 and 45) being the priority.

It is in my opinion that a quadrivalent vaccine protecting from all four high-risk HPVs should be the next step in treatment and protection of HPV infections. HPV is known to cause warts, which have been studied and determined to contain virus particles and to be contagious. Since HPV is a sexually transmitted disease, this vaccine would be ideally administered in the years before when a patient may become sexually active, such as during early puberty. This is so the immune system has adequate time to develop immunity before the transmission would occur. Additionally, since vaccines are known to lose their effectiveness over time, this gives the patient the most protection when they are most likely to come in contact with the virus.

In previous years, the current HPV vaccine was primarily suggested only to female patients due to the initially noted correlation of HPV and cervical cancer. However, due to the more recent evidence that HPV causes additional forms of cancer, male patients should also receive the vaccine to prevent cases of HPV-related cancers which may affect both genders, as well as to limit the overall transmission of infections.

By treating all patients, regardless of gender, with a vaccine designed to protect against the fours strains of HPV which have been proven to have a high risk of causing cancer, hypothetically we can prevent the most cases of HPV-related cancer in the most cost and time efficient manner.



Sarid, R. and Gao, S. 2011. Viruses and human cancer: From detection to causality. Cancer Lett305(2):218-27.

Writing Exercise #2

1) In the primary research paper “Symbiotic gut microbes modulate human metabolic phenotypes” (2007) Li et al determine the extent of the relation between individual gut microbiota and specific metabolic pathways which occur in the host. 2) Li et al showed that significant variations in gut microbiomic structural patterns are seen even in between family members, and gut microbiomes strongly influence host metabolic phenotypes. 3) The purpose of this study was to improve knowledge of human biology in order to allow for the creation of upgraded theories in disease prevention and treatments based upon an individual’s dysbiosis. 4) This study aims to give those working in or studying dietary and nutritional healthcare a better target for treatment based on gut microorganisms and their metabolic activity.

Writing Exercise #1

Topic: List as many human non-infectious diseases that you can think of that are influenced by microorganisms. 

It’s hard for me to think of diseases that are non-infectious, but are directly influenced by microorganisms. An infectious disease is an illness caused by pathogenic microorganisms, so the connection of infections and microbes is pretty hard to get past. However,  I can think of two cases where a non-communicable disease can be either caused secondarily to the presence of microorganisms, or worsened by the presence of microorganisms.  In this manner, these diseases are not directly caused by the microbe, and thus are classified as “non-infectious”, but are in fact still influenced by the presence of microbes.

A list of non-infectious diseases caused secondarily to the presence of microorganisms that I can think of:

1. Gastric Cancer – Can be caused by H. pylori.
2. Irritable Bowel Syndrome/Inflammatory Bowl Disease – A general term for disorders of the bowel, which can be caused by shifts/changes in one’s microbiome, leading to overgrowth of specific microbes.
3. Gastritis – the presence of specific microbes can lead to more acidic stomach contents, which can lead to inflammation of the stomach lining.
4. Dementia – I’m certain that many different organisms can cause various forms of encephalopathy, or over time can lead to degenerative brain function.

A list of non-infectious diseases that can be worsened by the presence of microorganisms that I can think of:

1. Asthma – Any infection of the lungs, sinuses, or airway can exacerbate symptoms of asthma, but the disease its self is not directly caused by an infection.
2. Diabetes Mellitus – While I don’t know for certain if this is the case, I can hypothesize that certain microbes in the digestive tract can influence Diabetes by metabolizing (or not metabolizing) glucose.


I am certain there are more, however, I’m struggling to think of diseases that aren’t infectious in nature. I may have misunderstood the goal of this exercise, but I tried my best to answer it as accurately as I can!