Writing Exercise #11

During the peer-review process, I recognized many interesting points. First, I was so confused about the audience of the assay who is in bio-health science but not an expert in microbiology. English isn’t my native language, and I don’t know whether some words that I don’t understand other student know them. The difference is the language difference. Thus, I tried to image and pretend myself as a student who was born in U.S. before I start the process. Second, I felt so interested in reading and critiquing other students’ essays. I found the different writing styles between two essays such as the way the organize their essays and the language they use and whether they prepare and take the time to write their essays. I might know how passionate the author put into their essay. I followed the rubrics and critique the essays. I usually ask myself and search information before I write down my responses. Somehow, I try to provide the authors the clear feedbacks and not unnecessary ideas so they can have better ideas to revise their essays. I used

I also compared the essays I do peer-review and my own essay to think of how to revise my final essay. There are differences among essays, and I think that doing peer-review for other students’ essays help me to know clearly rubrics and ideas how other student work on their essays in order to improve my ideas in my essay. I found out that I lack some points based on the rubrics, so I definitely need to work on that. Also, from the essays, I learn the character of this essay based on a controversial topic. One essay is so simple and doesn’t have the controversial topic. Another essay, the student works well on supporting the thesis but not against the thesis. So I think that I should try to make a balance between pros/cons paragraph. This essay has a controversial topic which student needs to have an overview of both sides of a topic then make their own stance. If the pros are so strong and long paragraphs, and the cons are so weak and short paragraph, then the essay seems not controversial. It’s because the students don’t need to convince them in order to make a stance. Thus, after the peer review process, I carefully check my topic to make sure its controversy.  Moreover, I also learn about the tone and language. As the audience in bio health science but not an expert in microbiology, when I read the essays, I thought of my essay if I was the audience. Then I had many ideas how to change my language to be more suitable for the audience.

Writing Exercise # 10

The process of the peer reviews is a process that is designed to review the validity and quality the originality of articles for publication. The peer review process stops the substandard and poor science so as to save time and money from publication. The reviewers are experts and have updated developments in their fields in order to evaluate and reject the plagiarized and duplicate papers. Besides, the peer review process can be used to publish the journal and to apply for the grant and standard textbooks. The process is also to increase the integrity of science.

                    However, the peer review is also related to some disadvantages. There may be criticism related to human activity based on perceived faults or mistakes. Editors are the connectors between the author and referee, and the editors have decision-making power. These can lead to the misuse of authority. Because there is no grading system in the peer-review process, the different journals have different standards in order to know the expertise and quality of the reviewers or editors. Besides, the peer-review process is time-consuming and expensive. The length of time in the peer-review process, many months is before the manuscript is approved. If the researchers have experiments to do, the process may be delayed and hampered. These disadvantages affect the credibility of the results of the process of peer-review.  

                      The process of peer review has five steps which start at the submission of paper and end at the communicated decision (no revisions required for publication in the journal). The authors need to write up all information for a draft manuscript such as the relevant data, methods, observations, and discussion. Then the first step of peer review process is to submit the manuscript based on several factors including subject matter, the concern of researchers, the chance of earning funding, and connection of authors and editors. The second step is editorial office assessment. The editors check the compositions of the paper such as the focus on the clinical research, exciting research, and solid foundational research in order to make an initial decision. Based on journal’s philosophy and journal’s author guidelines the, the editors will reject the manuscript outright, so the authors need to submit their manuscript to another journal. If the editors accept the manuscript, the manuscript will get into step 3. The third step is to review the manuscript by 2 to 4 reviewers. The reviewers who have done researchers in fields related to manuscripts are chosen by the editor. The reviewers are anonymous to the authors, but the authors do oppositely. The reviewers read and evaluate the manuscript for scientific merit. The reviewers are usually based on questions such as the relevance of the question of the manuscript, the clear of the hypothesis and model, the manuscript is primary research or clinical research, and the support of data and analysis of data for the manuscript. The reviewers then summary their thoughts and evaluations. The reviewers will write a letter about their responses such as their concerns of a figure-by-figure breakdown to the editor, abstractions about the manuscript, and their recommendation for the editor whether the manuscript would be accepted or rejected. The fourth step is editor assessment of reviewers. After the editor receives the feedback from the reviewers, there are three things the editor can choose to do. First, they accept the manuscript without revision requirement. Second, they reject the manuscript. Or the third thing is to send the comments back to the authors for further revision of the manuscript. The editor will send a letter to the authors with their decision and comments. The fifth step is author’s revision. In case, the author revises their manuscript, they can contact to editors to announce their changes in the manuscript to solve the criticism. Then the author resubmits their manuscript and goes through the process of peer review again.


Writing Exercise #9

  1. Hand hygiene: practicing hand hygiene is a helpful approach to prevent bacterial infection. Hand hygiene is used to prevent the spread of germs due to killing all of them. People can use soap and warm water to clean their hands before touching and/or after using the bathroom, taking out the trash, changing a diaper, visiting someone who is infected. It’s good to make sure to wash hands after sneezing or coughing.
  2. Clean high-traffic objects in home and office: In order to reduce the number of bacteria in our environment, people should keep certain objects which people and others in their household use regularly such as door knobs, toilet handles, telephone, and bathroom. Disinfectant should be used to wipe to clean the high-traffic objects once a week
  3. Steer clear of anyone who seems sick: People should avoid contacting close to anyone who seems sick and touching people who are infected, people who have the flu or contagious illness.
  4. Stay informed about food and water recalls: It’s important to stay informed in order not to ingest contaminated water or food. Food contamination is a common issue. People can listen to the local news about contamination food and water supply. If there is the situation of food and water contaminated, people should purchase water bottle to drink and not to take shower. Staying informed about food and water contributes to protecting yourself from foodborne bacteria.
  5. Wash and cook food well: Washing and cooking food well can help to prevent bacteria from entering to digestive systems. All fruits and vegetable should be washed before consuming. All meat and fish should be cooked thoroughly to any harmful bacteria. People also should avoid eating raw or undercooked meat and eggs. Besides, people should use their own utensils.
  6. Take steps to reduce the risk of developing vaginitis, an inflammation of the vagina and/or vulva from bacteria, chemical irritants, or viruses. people shouldn’t douches in order not to change to pH of the environment in the vagina and to decrease the risk of the bacterial infections. Also, people should have one sexual partner and shouldn’t smoke due to association with risk of developing a bacterial infection.
  7. Vaccination: Getting vaccinated is a way to against bacterial infections. Bacterial vaccines are able to kill bacteria. Antibodies can against particular bacteria and prevent bacterial infections later. Some form of vaccines such as Tuberculosis vaccine and vaccines to against meningococci, pneumococci, and enteropathogenic E. coli.
  8. Mode of delivery: The vaginally born infant have diverse microbial community compared with the C-section born infant.


Writing Exercise #7

  1. Diet: Pregnancy imposes changes in the bacterial composition of pregnant women. In the article “Pregnancy-related changes in the maternal gut microbiota are dependent upon the mother’s periconceptional diet”, the authors did a study about diet and pregnancy interaction, high-fat diet intake before and during pregnancy leads typical shifts in the pregnant gut microbiota. This causes the major differences in the abundance of genes related to lipid metabolism, gluconeogenic and glycolysis metabolic pathways during pregnancy period. In the infants, the transition from milk to solid food changes in their microbial population and species. The infant’s gut microbiota has an abundance of Bacteroidetes and Firmicutes same as adults’ microbiota [4].
  2. Antibiotic use: the antibiotic use cause change in maternal microbiota and abundance of some taxonomic groups. The use of B antibiotic including azithromycin, amoxicillin, and cefaclor triggers the increase of Proteobacteria and Enterobacter and decrease of Firmicutes and Lactobacillus [1]. Besides, similar effects with normal people, antibiotic contributes in reducing bacterial diversity in the gut microbiota of pregnant women. Antibiotic also causes weight gain [4]
  3. Probiotic use: the pregnant women who used probiotics 14 days before C-section showed modulation of the infant microbiota as well as offspring’s microbiota. The probiotic treatments on pregnant women gave advantages to the offspring to have the immune system to respond to pathogens and commensal after birth and reduce the risk of eczema as well. The immune modulation affects the microbial components.
  4. Mode of delivery: The gut microbiota of infants has a relationship with mode of delivery [3]. The gut microbiota of vaginally born infant is colonized by bacteria from maternal vagina including the enrichment in the Prevotella, Sneathia, and Lactobacillus group which is a positive factor to infant microbiota [2]. The infant born by C- section has delayed colonization of the phylum Bacteroidetes and alpha diversity during first 2 years of life. Also, the infant born by C-section has higher number of antibiotic-resistance genes compared with infants born vaginally [4]
  5. The method of infant feedings: There are differences in gut microbiota between breastfed infants and formula-fed infant. The major organism in breastfed infant is Bifidobacteria while the formula-fed infants have Enterococci and Clostridia mostly. Besides, the breastfed infants have more bacterial cells and less species diversity. The methods of feeding have effects on infant’s oral microbiome also. The study shows that the three-month-old breastfed infants consist of oral lactobacilli with antimicrobial properties which didn’t appear in formula-fed infants [4].  


  1. Gonzalez-Perez G., Hicks A. L., Tekieli T. M., Radens C. M., Williams B. L., Lamouse-Smith E. S. 2016. Maternal antibiotic treatment impacts development of the neonatal intestinal microbiome and antiviral immunity. J. Immunol. 196, 3768–3779. 10.4049/jimmunol.1502322
  2. Jakobsson H. E., Abrahamsson T. R., Jenmalm M. C., Harris K., Quince C., Jernberg C., et al. . (2014). Decreased gut microbiota diversity, delayed Bacteroidetes colonisation and reduced Th1 responses in infants delivered by caesarean section. Gut 63, 559–566. 10.1136/gutjnl-2012-303249
  3. Khan I., Azhar E. I., Abbas A. T., Kumosani T., Barbour E. K., Raoult D., et al. . 2016. Metagenomic analysis of antibiotic-induced changes in gut microbiota in a pregnant rat model. Front. Pharmacol. 7:104. 10.3389/fphy.2016.00104
  4. Sela D. A., Li Y., Lerno L., Wu S., Marcobal A. M., German J. B., et al. . (2011). An infant-associated bacterial commensal utilizes breast milk sialyloligosaccharides. J. Biol. Chem. 286, 11909–11918. 10.1074/jbc.M110.193359

Writing Exercise #8 – Free write/ Brainstorm

I read through the syllabus in order to understand the final essay. The first word came to my mind is a controversial topic. It’s interesting to think of controversial topics related to the microbiome. My first thought is microbiome species, similar to biological species when I searched the definition of microbiome at beginning of the class. I found that this controversial topic brought researchers different areas and classifications for microbiome species concept (MSC). Another topic is the relationship between microbiome and disease. Researchers have been studying whether the variant microbiome are from responses of human to environmental factors or through heriterity. The variant microbiome caused disease related to immune responses in beginning to cancer period, local microenvironment, or potential inflammations. Also, the topic about the role of Helicobacter pylori in the pathogenesis of gastric reflux esophagus disease (GERD). I’m curious why eradication of H.pylori doesn’t induce in these disorders, and whether or not, antibiotic treatments work perfectly for these diseases. The “ commensalisms” suggested that eradication the H.pylori causes the worse GERD and asthma. However, H.pylori infection can lead to gastric cancer. So whether or not we should kill all H.pylori or just restrict their growth in symptomatic or nonsymptomatic individuals.

I have three topics including classification of the microbiome, the role of the microbiome in disease, and eradication of H.pylori in symptomatic or nonsymptomatic infected people related to GERD. I try to remind myself about classifications about microbiome, but I don’t have a lot of ideas about this topic. So, I start to consider about the classification of microbiome and H.pylori. Also, the variant microbiome is a new topic to me. I read the information about microbiome which is a combination of genetic material and influences of environmental factors. But How microbiome change? What trigger their changes? Besides, I did my midterms about H.pylori topic, and at that point, I focused on what is H.pylori, how people gets infected, and how treatments work in H.pylori infections. I understood about H.pylori had all negative effects and side effects from H.pylori treatments using antibiotic. However, now I’m going to work on a controversial topic about H.pylori. It sounds cool to debate myself about H.pylori. Maybe, it changes my perspective about H.pylori infections in different ways.

I think that my final essay will cover eradication or preservation of H.pylori. It’s interesting to turn my mind up and down sides about H.pylori. I may start my essay from outlining the organization of my paper such as discovery and characteristics of H.pylori related to how H.pylori affects human health, the idea of eradication of H.pylori (pros/cons), the preservation of H.pylori, and my standing side at the end. I will build my introduction, body paragraph according to ideas above, and conclusion. First, I will read again the articles which I found for my midterm and selected which one I would use for the final. Then I continue to find articles about H.pylori infections, eradication treatments, and preservation of H.pylori. I will underline main findings, howe researchers conducted their studies, and information support for my ideas also. Then I will put the information into my outline. Finally, I will write and build a completely paragraphs.

Antibiotic and My Philosophy- Writing Exercise 6

In my country, most patients are provided antibiotics when they get sick including cold, flu, sore throat. This has made my philosophy about antibiotic as a common medicine for these diseases which is wrong. When I was 18, I got a strep infection caused by streptococcal bacteria. My classmate spread the strep infection to me because I sat next to her. At the beginning, I thought that she got some common coughs. The infections made my throat and tonsils irritated, swollen, painful, and inflamed without coughing. My mouth had some road spots, and I had a hard time to swallow food. I didn’t go to any doctor and waited to recover by drinking water, but my situation got worse. Later, when I met a doctor, he said that I got strep infection, a kind of bacterial infections. He recommended me to use antibiotics such s penicillin, cephalexin, and amoxicillin, for I got many days in being infected. I asked him about the antibiotic, and he explained to me different situations for use of antibiotics which treat only infections caused by bacteria, not any viruses. And people shouldn’t use antibiotic for cold and flu if they are from viruses. Also, bacterial resistance becomes harder to treat if people use antibiotic too often or wrong way. I followed exactly my doctor’s instruction in taking antibiotic, and I recover around 2 weeks later. From that point, my philosophy about antibiotic change completely which antibiotics are used to treat specific infections from bacteria. It was so interesting to learn about antibiotics and how to use them wisely and usefully.

Probiotic Products- Writing Exercise 5

Probiotic Is defined as a live microorganism which has benefits for the human digestive system. Mono or mixed culture of organisms in probiotic improve intestinal microflora related to introduced or existing bacteria in the colon [1]. Many studied showed positive effects of probiotics such as decrease risk of childhood atopic, rotavirus shedding in infants, and diarrhea [1] There are many types probiotics in markets for both meals and medicine. My food choice to improve my microbial community is yogurt. I usually eat yogurt which made in my family. My yogurt usually made from goat milk which has a lot of proteins, vitamins, and minerals. All these increase digestive abilities and lower allergy symptoms. Also, there are abundant probiotics such as thermophiles, bulgaricus, and bifudus in goat milk [3]. Besides, fermented products such as miso soup, pickles, and kimchi are my favorite food for my gut microbiota. Miso soup is Japanese food which is made from fermented rice, bean, or rye. Miso soup had a lot of lactobacilli and Bifidus bacteria from the fermentation process, so miso soup helps to reduce stomach inflammation and improve digestion. Also, pickles from carrot and radish and kimchi from cabbage have a lot of prime probiotics as well as vitamin C, B, beta-carotene, calcium, iron, potassium, and fiber from vegetable which assists digestive system [5]. My non-intentional choice is non-dairy products including dark chocolate and ice cream which consists antibiotics from manufacturing process [1]. These were found as assistants of probiotics in order survive in extreme pHs of the stomach [6].


  1. Bhadoria PB, Mahapatra SC. Prospects, Technological Aspects and Limitations of Probiotics–A Worldwide Review.
  2. Cruz AG, Antunes AE, Sousa AL, Faria JA, Saad SM. 2009. Ice-cream as a probiotic food carrier. Food Research International. 42(9):1233-9.
  3.  Damunupola DA, Weerathilake WA, Sumanasekara G.2014.  Evaluation of Quality Characteristics of Goat Milk Yogurt Incorporated with Beetroot Juice. International Journal of Scientific and Research Publications. 2250-3153.
  4. Fujisawa T, Shinohara K, Kishimoto Y, Terada A.2006. Effect of miso soup containing Natto on the composition and metabolic activity of the human faecal flora. Microbial ecology in health and disease. 18(2):79-84.
  5. Irkin R, Songun GE. Applications of probiotic bacteria to the vegetable pickle products. Scientific Reviews and Chemical Communications. 2012;2(4)
  6. Possemiers S, Marzorati M, Verstraete W, Van de Wiele T. 2010.Bacteria and chocolate: a successful combination for probiotic delivery. International journal of food microbiology. 141(1):97-103.


Writing Exercise #4

Celli, Erramilli, and Bansil in the department of Physics at Boston University, Turner, Afdhal, Keates, Ghiran, and Kelly in Division of Gastroenterology at Beth Israsel Deaconess Medical Center and Harvard Medical School, Ewoldt and McKinley in Department of Mechanical Engineering, and So in Department of Biological Engineering at Massachusetts Institute of Technology in their study entitled “Helicobacter Pylori moves through mucus by reducing mucin viscoelasticity” (2009) find that H. Pylori has the ability to swim freely in gastric mucin by elevating pH- dependent rheology and reducing viscoelasticity. The research team provides evidence that H.pylori causes pH elevation by hydrolysis of urea through rheology studies using two-photon fluoresce microscopy. The purpose of this study is to understand the effects of H.pylori on gastric mucin as well as how H.pylori moves in the gastric mucin, so that we may learn more about H.pylori as a causative agent of gastric inflammation and H.pylori infections. The paper contributes a new finding about capability of H.pylori in the relationship with microbiological research as well as healthcare fields.

Citation: Celli JP, Turner BS, Afdhal NH, Keates S, Ghiran I, Kelly CP, Ewoldt RH, McKinley GH, So P, Erramilli S, Bansil R. 2009. Helicobacter pylori moves through mucus by reducing mucin viscoelasticity. Proceedings of the National Academy of Sciences. 06(34):14321-6.

Human Behaviors and Gut Microbial Community

  1. Excessive alcohol consumption: alcohol changes the gastrointestinal tract (GI) microbiota composition. Also, alcohol consumption disrupts intestinal barrier which against pathogens as well as alcohol-induced liver pathology including nonalcoholic fatty liver disease (NAFLD), nonalcoholic steatohepatitis (NASH), and alcoholic liver disease (ALD). There is a relationship between alcohol-induced oxidative stress, intestinal hyperpermeability to luminal bacterial products. The excessive alcohol consumptions that is detrimental to human health cause disruption of intestinal microbiota hemostasis- dysbiosis. The alcohol-induced changes can cause alcohol-related disorders, quantitative and qualitative dysbiotic changes, the development of alcoholic liver disease (ALD), and other diseases. Alcohol consumption increases GIT inflammation such as inflammatory of bowel disease (IBD), irritable bowel syndrome (IBS), celiac disease, intestinal hyper permeability and triggers tissue damage/organ pathologies and others. Alcohol consumption is associated with risk of development of cancer, abnormal function of the immune system as well as risk of acute and chronic infections, and other diseases including pancreaitis, heart disease, and circadian clock.
  2. Use of antibiotic: antibiotic affects negatively to gut microbiota, and the human microbiome is disrupted such as collection of cells, genes, metabolites from eukaryotes, and viruses). The overuse or use of antibiotic without intention which changes microbiome composition can cause health problems related to immune system, metabolic problems, disorders and infectious diseases. Antibiotic can affect caesarean sections associated with immunological disorders such as asthma and type 1 diabetes. Also, antibiotic can cause increasing the risk of overweight for boys during infancy. Using antibiotic rationally and frugally can prevent microbiome disruption and restore microbiota. The effects of antibiotics are based on concentration of drug, different microbial growth stages, and others. Besides, the combination of antibiotic and antibiotic-resistant bacteria can lead to reduction of mitochondrial gene expression and mitochondria per cell. Antibiotic that may contribute to enhance bacterial translocation out of the gut is related to bile acid-hydroxylating activity of clostridium scindens to against Clostridium difficile.
  3. Diet pattern: Diet patterns that affect on gut microbiota composition are related to combination of bacteria in the intestine called enterotypes. The three human enterotypes are Prevotella, Bacteroides, and Ruminococcus. The substrates for intestinal microbial metabolism is from food components which are indigestible for human enzymes.
  4. Fiber intake: The increasing fiber intake contributes to bacterial diversity and proliferation. The consumption of agro-pastoral-derived foods are related to the occurrence of bifidobacteria in the gut of adult humans. Bifidobacterium plays a role in preventing pathogenic infections by producing acetate. People who don’t have enough vitamin and nutrition intake lack of bacterial diversity. This triggers to GI inflammations and bowel diseases.
  5. Living environment: In article “Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ”, the study of Claesson and colleagues showed that people in long-stay care environment had high level of Bacteroidetes while people in community had high level of Firmicutes. Also, people in long-stay care environment lost community-associated microbiota associated with increased frailty and process of diseases. And, the diversity of people in long-stay care is less than people in community.
  6. Aging: Aging affects of microbiotic environment. For example, the infant has less complex intestinal microbiota than adults. By 2, the community structure related to the gut microbiota of infants evolves similar with adults. Besides, the age is associated with physiological changes in the gastrointestinal (GI) that compositions of gut microbiota in older people (over 65 years old) is different from young adults.


Engen PA, Green SJ, Voigt RM, Forsyth CB, Keshavarzian A. 2015. The Gastrointestinal microbiome: Alcohol effects on the composition of intestinal microbiota. Alcohol Res. 37(2):223-36.

Langdon A, Crook N, Dantas G. 2016. The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation. Genome medicine. 8(1):39.

Guinane CM, Cotter PD. Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ. Therapeutic advances in gastroenterology. 2013 Jul;6(4):295-308.





Writing Exercise 2

In a scenario, as a healthcare professional, a college asks my opinions about which HPV strains should be covered in a new treatment. Based on the article “Viruses and Human Cancer: From Detection to Causality” by Sarid and Gao in 2011, my recommendation that HPV strains including HPVs 16, 18, 31 and 35 because of some reasons. First, HPVs 16,18,31, and 45 strains- high risk strains are accountable for 80% of cervical cancers. The high-risks strains are linked to anogenital cancer as well as other head and neck cancers related. Other HPVs strain such as 39, 51, 52, 56, 58, and 59 are associated to cervical caner and classified as “probably carcinogenic to humans” or “possibly carcinogenic”. This means that these strains are related to cervical cancers but not casual agents. The questions I raised here is if “high risks” HPVs strains play 80% of cervical cancer cases, so the 20% left would belong to which strains. It may be strains 39,51,52,56,58, and 59, but the authors didn’t explain clearly. Instead, they counted these strains as associated agents to cervical cancers. We may need to conduct more researches about role of these strains. Beside, the cost to develop a vaccine for a strain is expensive, so the new treatment should be priority for high risk strains which are HPVs 31 and 35 due to their majority casual percentage in cervical cancer while other associated strains to cervical cancer

The treatment should be administered to both women around age of11-12. HPV which is a human virus is a representative of etiologic agent for cervical cancer, the third cause of mortalities and morbidities for women worldwide. Every year, there are around 12,000 women who are diagnosed with cervical cancer and 4,000 women die in the U.S The target of HPV vaccine is to prevent cervical cancer. The outcome of infection is related to cell cycle and body metabolism pathways, and women puberty starts around 11 which their body metabolism changes as well as cervix. Therefore, getting vaccine during puberty timeline is recommended for girls.



Sarid, Ronit, and Shou-Jiang Gao. 2011.  Viruses and human cancer: from detection to causality. Cancer letters. 305.2:218-227.

“HPV Vaccine Information For Young Women.” Human Papillomavirus (HPV). Center for Disease Control and Prevention, 28 Dec. 2016. Web. 14 Apr. 2017. <https://www.cdc.gov/std/hpv/stdfact-hpv-vaccine-young-women.htm>.