Based on your readings this term, discuss a research project that you would be most excited about funding as they relate to learning more about microbial influences on human health. As part of your response, consider what are we likely to learn from the project and how that might be important in future healthcare decisions.
Looking at the research for the coronavirus vaccine, I think it would be extremely interesting and exciting to award funding to that project. A coronavirus vaccine is something that has been discussed regularly, but not with the certainty surrounding this one. Also, the technique of introducing mRNA to the system as a way to trigger the immune system seems very interesting. I would want to know if this project would influence the microbial colonies within the human body. I do not think it would much considering only a little is being introduced but that would be good information to know before widely distributing the vaccine. This would be incredibly important in future healthcare decisions, especially if the mRNA vaccine technique is more effective than the standard dead virus that is injected.
Part 1: Set a timer for 3 minutes, and make a list of as many human non-infectious diseases that you can think of that are influenced by microorganisms.
Part 2: Refer back to your Writing Exercise #1 that you completed the first week of class. Reflect and discuss how your responses have changed from week 1 to week 10, and what the most important topics you will take away with you once you have completed the course.
The diseases I have listed in Writing Exercise #1 were much more specific than the ones I chose for this week. This is due to my understanding of what a non-infectious disease expanding over this course. At first, I had thought that a non-infectious disease had to affect the patient immediately from the microorganisms. Now I understand that microorganisms have a long term effect that could help or damage the body long term. The most important topic I will take away from this course is the skill of analyzing different types of scientific articles and applying them to the broader topic that is discussed. Taking this class during the pandemic really helped me understand in a broader way the effect microbes can have on us as individuals and as a community.
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?
When reviewing other people’s writing, I was unsure as to how harsh I was and if I was being equally critical with both papers. Both papers I read were very different in writing style and topic so it was difficult to say how they could improve better technically other than grammar or slight changes to sentence structure. I was also wondering during the review if I was going as in-depth as other people with the reviews. Without a reference, it was hard to know what was wanted by the writer and by the reader for the questions. I would say different papers excelled in different areas for each paper I reviewed.
I was very surprised how different the two papers I read were to mine structurally. The first paper condensed their information from their sources into the majority of the paper, with their opinion on the controversy being the later part of the paper. The second paper had a good mix of their opinion and information from sources throughout the entire paper but the beginning was very slow. It will be interesting as to what the responses from the people who reviewed my paper will be like. I definitely need to bring back my idea to the main controversy more, which the two papers I read had done consistently.
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 is an important part of publishing scientific articles because this process validates a manuscript’s information. This is done through other scientists in the same field reviewing the information and confirming it is valid and not made up. If the information is rejected, it will not be published and must be rewritten and resubmitted for peer review. The process of peer review might fill in gaps that the paper might have or make it easier to read.
Pros
Establishes validity based on expert knowledge of other scientists from the same discipline, which should prevent plagiarized work from being accepted.
Allows for the researchers to revise and improve their work before actual publication.
Allows journal editors to isolate the most important research for publication from a group of papers based on the reviews of experts.
Peer review is the standard for most researchers.
Cons
The large time delay between research and publication.
Peer review takes a lot of resources to perform as well from people who have to do their own research too.
Researchers debate as to whether peer review is very effective in finding errors in academic papers.
If it is a small expert group, it might be hard to keep it anonymous,
Peer reviewers might protect current beliefs and not want to branch out to new ideas.
A rapid increase in atopic disorders, genetic developments of allergies such as asthma, started between 1960 and 1970 with progressive rises during the 1980s and 1990s [1]. The reunification of Germany proved the influence of lifestyle on atopic disease in a more homogeneous population between East and West Germany. Researchers showed hay fever and atopic sensitivity among children in the former East Germany both significantly increased between 1991 and 1996, which raised concerns of the ‘Western living’ influence on children, since there were lower rates of allergies in East Germany compared with West Germany [1]. In this post, I will describe the environmental influence on children from a young age as well as potential benefits children might gain from early exposure building immunity in the long-term.
Family size and structure and atopy: The environment and size of the family in which a child grows up are shown to have an effect on allergies that children may have as well as what they are susceptible to. In the home, having siblings, sharing a bedroom as a child, and attending daycare are all shown to have decreased the probability of developing atopy due to the wide array of microbes that the child is exposed to from a young age.
Farm and other rural exposure. Other studies have isolated farm life as a protective effect against atopy. Farm children were shown to have less atopic disease and lower levels of seroprevalence to many allergens. Environmental factors that would build this immunity include close contact with animals as a child, exposure to stables under the age of 1 year, and consumption of farm milk (presumably raw/ unpasteurized) which would build bacterial endotoxin resistance [1].
Bacterial and viral infections: Early exposure to microbes through food-borne routes protect against respiratory allergy and that “hygiene and a westernized, semi-sterile diet may facilitate atopy by influencing the overall pattern of commensals and pathogens that stimulate the gut-associated lymphoid tissue” [1]. General exposure to infections early in life is extremely important for immune system development.
Gut flora: Early exposure to intestinal microflora, like living on a farm, program the gut early against endotoxins. Probiotic research has been seen as beneficial in priming or maintain normal gut flora which may be beneficial to immune-related conditions, including the response to infection.
Sanitation, water treatment: Chlorinating water has been happening for over a century now in the US and the UK. It is unlikely this can be attributed to a decreased exposure to microbes over the last 30 years. What has contributed to a decrease in microbes change in food and water quality which reduces our exposure to pathogens? This has likely altered our exposure to commensal strains, environmental strains, and pathogens. Removing pathogens in modern water treatment will remove most benign microbial bacterial contamination as well as their positive benefits.
Immunization/vaccination: Current epidemiological studies have provided no consistent support for beneficial or adverse effects of vaccination/immunization on contracting allergies. For example, in countries with high vaccine coverage, families who choose to not vaccinate their children are unusual which increases the risk of atopy and any protective effect, depending on the population examined.
Antibiotic therapy: It is difficult to determine the influence of antibiotic therapy on microbial exposure since there is such a close relationship between antibiotics and other atopic diseases. It is difficult to determine whether the key exposure time is related to the infection or the antibiotic. Researchers suggest the antibiotic effect could be influenced by the bacterial colonization of the gut in the early years of development.
Breastfeeding: Breastfeeding transfers maternal antibodies which would affect the infant’s gut from a young age. By introducing this young, breastfeeding protects against intestinal pathogens and respiratory infections [1]. Some studies report the benefits of breastfeeding to include the prevention of asthma or atopic disorders later in life.
Citation:
[1] Bloomfield SF, Stanwell-Smith R, Crevel RWR, Pickup J. 2006. Too clean, or not too clean: the Hygiene Hypothesis and home hygiene. Clinical Experimental Allergy 36:402–425.
I am surprised as to how much research I have been doing for these writing exercises. The one this week, writing exercise 8 I believe, I basically wrote in the style of the summary article except without the 250-word constraint. Both the summary articles and the writing exercises have helped me understand how to read a research article in a more developed way and I have been able to break down an article into its main comprising parts faster and faster. My favorite subject that I have learned so far would probably be how an infant is influenced by the mother’s microbiome and the environmental factors after birth. Going in, I had a general idea that environment influenced things like allergies but the extent to which infants are affected is way more than I anticipated. I thought it was really interesting that the mother’s womb and the nutrients absorbed in development have such a huge influence on the initial microbiome of the infant. I also had not considered the large difference in nutrients between breast milk and formula.
In my research for this recent homework assignment, I learned that the common belief up until recently was woman’s wombs was considered sterile environments. I have no idea how a sterile environment exists… when it is in the human body? It was a one-sentence explanation on one of my citations but it was so confusing it threw me for a loop. Maybe sterile means something different than what I am imagining but why is it called sterile? Is it because it is technically like a protected area for a child to grow in with an epithelial layer? Even so, I would not consider that sterile considering there are many nutrients and commensal bacteria that work to help a child grow. It is probably just the common belief because research is historically created by white men who believed women hormones caused hysteria for a while. But why sterile… is it just they were too lazy/scared to research beyond that and morally just said “can’t broach that subject because of morals. we’ll just say it is sterile”?
Reflection: I probably focused too much on the most recent assignment but since it was what was fresh in my head, I would say that this was an appropriate topic to write about for the first writing session. I think in the second paragraph, it was much more rambly than the first paragraph. I was definitely running out of things to say for the phrase part so I suppose that makes sense.
List and describe potential factors that the mother or the infant could be exposed to that could influence the colonization of the microbial community in the newborn infant (in positive or negative ways).
From birth, gut microbiota has a major impact on the development of fetuses. The womb was thought to be a sterile environment up until recently. Probably because most scientists were men who didn’t know anything about periods. If they had asked a woman, she could’ve told them there are A LOT of bacteria, since they have to deal with it every month. Recently, research has revealed the necessity for the mother’s womb to develop the infant microbiome before birth. The mother’s womb transfers nutrients to the infant to breakdown breast milk and is important for the breakdown of toxins and drugs; vitamin synthesis; and ion absorption (1).
Gut microorganisms protect the infant from pathogenic organisms. The initial gut microbiome of infants develops in the first three years and is influenced by maternal and neonatal exposures, including mode of delivery, antibiotic exposure, and feeding patterns, diet, and stress (1). This gut colonization is imperative for the infant’s development and growth at the early stages of life. Colonization of the gut from mutualistic bacteria forms the basis of the immune system for homeostasis. This homeostasis also determines the oral tolerance for the mutualistic bacteria as well as the benign antigens that the immune system produces (1). If this homeostasis cannot be established, an imbalance of the microbiome could occur (dysbiosis) which would leave the infant vulnerable to allergies or pathogens. The main species of bacteria that colonize the infant’s gut are from the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria (1).
In the first month of life, the number of bacteria Enterococcus faecalis that colonized the infant gut microbiome varies based on hospital location and whether the infant was fed with breastmilk or formula (2). Bacterium Bacteroides-Prevotella influenced infant weight and the ponderal index, how lean someone is. There was strong causation between how an infant was fed in the first month of life and health issues later on (2). Altering the microbiota in an infant early in life can be dangerous. A large change in infant microbiota has been linked to a higher risk for necrotizing enterocolitis, a critical gut inflammation that can kill premature infants or cause permanent intestinal damage (3). Other less drastic microbiota changes have been linked to asthma or diabetes (3). Due to this research, feeding supplements such as formulas should not be given to infants considering the lack of nutrients that might cause dysbiosis and long-term negative effects on infants.
[1] Yang I, Corwin EJ, Brennan PA, Jordan S, Murphy JR, Dunlop A. 2016. The Infant Microbiome. Nursing Research 65:76–88.
[2] Obermajer T, Grabnar I, Benedik E, Tušar T, Pikel TR, Mis NF, Matijašić BB, Rogelj I. 2017. Microbes in Infant Gut Development: Placing Abundance Within Environmental, Clinical and Growth Parameters. Scientific Reports 7.
[3] DeWeerdt S. 2018. How baby’s first microbes could be crucial to future health. Nature.
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?
My personal philosophy on taking antibiotics is to try to limit the consumption of antibiotics when I am not very sick to keep my tolerance low and hope a resistance does not build up. For example, when taking acetaminophen or ibuprofen, I switch between the doses if I am fighting off a cold because one can burn the stomach if taken too much, I believe it is acetaminophen, and I am worried about building a resistance to it early in life. In addition, my mom has kidney damage from taking too much acetaminophen because of her chronic back pain. Due to these reasons, I am hesitant to take many antibiotics except for when necessary.
My other method is to blast my immune system with antibiotics over a short period of time to try to eliminate the infection within a few days. The previous experience that led me to treat colds this way was when I was sick on the east coast at the beginning of this year. I had developed a cold on the plane to the point my sinuses were so blocked I could not feel my body. Luckily, I had Sudafed and took multiple doses over a weekend to try to blast it out of my system. I am not sure if this method was effective or if I was just lucky, but it worked. If I get sick like that again I will probably try this method since it worked so well.
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.
My approach to food consumption and product use when considering how it will affect my microbial communities is to avoid overconsuming products I know will cause a negative effect and consume products with positive benefits when possible. For example, I do not always eat yogurt but when I am grocery shopping, but sometimes I do buy it since it is so versatile and it is a good mutualistic bacteria. This choice is more non-international because it depends on when I buy groceries and if that week I want to buy yogurt. An intentional choice that is probably beneficial to my microbial colonies is my decision to not eat junk food like cookies or chips. I have never felt the need to snack, so junk food was never something I craved. Controlling what I eat and how it has affected my microbial colonies has gotten more difficult recently since I have developed lactose intolerance which has required me to adjust the food and drinks I consume daily. While I am not the most healthy person, I do think I have a good amount of control over what I eat.
Name of author (and credentials or a phrase describing the author), genre and title of work, date in parentheses; a rhetorically accurate verb; and a THAT clause containing the major assertion (thesis) of the work.
An explanation of how the author develops and/or supports the thesis (nature of evidence)
A statement of the author’s apparent purpose, followed by an “in order” phrase.
A description of the intended audience and/or the relationship the author establishes with the audience”
(1) Kamila Goderska, Sonia Agudo Pena, and Teresa Alarcon researched as a team through the Poznan University of Life Sciences and Hospital Universitario de La Princesa that published a peer review journal article titled “Helicobacter pylori treatment: antibiotics or probiotics” (2017) which articulates why H. pylori alternative treatments have been explored and have been effective. The authors believe that probiotic treatments are an effective way to raise eradication rates of H. pylori and will reduce the side effects of treatment.
(2) Goderska provides evidence that H. pylori antibiotic resistance is over 20% in certain populations which calls for a need for a new treatment, then provides evidence by analyzing the effectiveness of various treatments such as bismuth quadruple therapy, sequential therapy, non-bismuth quadruple therapy, hybrid therapy, levofloxacin-based therapies, and probiotics.
(3) The purpose of this journal article is to provide alternative treatments for H. pylori and explain why probiotics are viable research opportunities in order to eradicate infection rates for this bacterium more effectively.
(4) Goderska intends for this article to be read by scientists and nonscientists alike through using cohesive and comprehensible language while still establishing the biological mechanisms that would be useful against H. pylori.
