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Writing Exercise # 15

Obesity are one of the most concerned diseases in healthcare. Obesity can lead to other serious diseases that affects human health as diabetes, cardiovascular diseases. Obesity in children is the issue of modern society relating to high consumption of sugar, fat in diet. As the head of a funding agency, I would look at proposal for the research project that study the effect of probiotics, prebiotics and synbiotics on obesity.

Many studies confirmed the role of gut microbe obesity. The research about the gut microbes by fecal microbiota transplant from twins in mice mentioned that there was the invasion of Bacteroidales from the mice colonized by lean co-twin to the mice colonized by obese co-twin (1). From the research, Bacteroidales could be suggested as factor that help to prevent an increased adiposity phenotype. If the project confirms the role of Bacteroidales in the decrease of body mass, then we could consider Bacteroidales as probiotics. The project of the probiotics with Bacteroidales will help to reduce the risk of develop body mass. A mechanism about the role of fat metabolism of Bacteroidales or gut microbe could be given in the study.

If the project is successful, then we can apply Bacteroidales to food products, especially high fat diet food to help reduce the risk of weight gain related to high fat diets. Healthcare system can refer food production companies add probiotics to foods, it will help low the rate of obesity in children that help to reduce the risk of developing diseases related to obesity.


Ridaura VK, Faith JJ, Rey FE, Cheng J, Duncan AE, Kau AL, Griffin NW, Lombard V, Henrissat B, Bain JR, Muehlbauer MJ. 2013. Gut microbiota from twins discordant for obesity modulate metabolism in mice. Science. 341(6150):1241214.

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Writing Exercise # 14

A list of human non-infectious diseases are influenced by microorganisms


Peptic ulcer disease

Gastroesophageal reflux disease

Gastric ulcer

Crohn’s disease


Food allergies

Atherosclerotic diseases






Inflammatory bowel disease

Ulcerative colitis

Gastric cancers

Oral infection

Cardiovascular diseases

Multiple sclerosis

When looking back the list of week 1, I learn more diseases and disorders that are influenced by microorganisms. Most of diseases does not have clear mechanisms and the relationships between microbe and diseases as chicken and eggs. Studies showed that there was a less diverse microbiota and/or altered microbial composition relates to the diseases. Changes in human behaviors such as antibiotic usage, c-section birth, formula feeding, use of antibacterial soap, septics techniques have made people less exposure microbial community that explain for the increase of some diseases related to microbe like asthma, allergies.

Topics about microbiota and human diseases are controversial. All articles we read during the course, most of them showed that there were changes of the relative abundance of microbial community in observed diseases, but they could not explain the mechanism. Some species are referred as beneficial microbiota so there are many products that supply microbiota for human body as probiotics, prebiotics and synbiotics.

A diverse microbiota will give human benefits in many ways. Although the role of microbes to human health have not completely understand yet, an early exposure should be for children to improve their gut microbiota. Children microbial community are influenced by both maternal and environmental factors.

There are many ways to modify gut microbial community. Most effective ways are obtain a diverse microbes through the diets. Diversity of diets intake, high fiber diets, fermented products are sources that provide good microbe for human.

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Writing Exercise # 13

Five questions of William P. Hanage when interpreting scientific literature keep scientists from exaggerating the results of studies and help them convey exactly the findings from research.

1.Can experiments detect different matter?

Microbiota have multiple species. A alternation or unbalance of the ratio is not clear communications about the changes of microbial community. The development of technologies allow us to identify the genomes of microbes. Genomes could make for important differences in what metabolic network do. The microbial community is various from individual to individual, experiment has to detect the alternation in term of significant amount, ratio across the network.

2.Does the study show causation or correlation?

It is important to distinct the causation and correlation. Correlation related to the observation, it is not the caution. In microbiology, the relationship between microbial community and health state is like chicken and eggs. It is hard to define which one lead to the changes on the another. In microbial studies, it is hard to eliminate the confounding variable due to the number of microbes and their characteristics. An exaggerating from association into causation can causes confusion.

3.What is the mechanism?

Mechanism is important to help scientists design experiment to the detect the relationship between microbiota and diseases. Sometimes, correlation can imply some of sort of causal relationship. Understanding the mechanism help to interpret the result more accurate.

4.How much do experiments reflect reality?

Most of studies of the role microbial and diseases were done on animals. The response mechanism of animal and human are different. The effects on mice may not cause symptoms on human. The results from mice can not generalized to human. Free-germ mice is phenomenome that not realistic because they do not represent the animal’s’ natural state.

5.Could anything else explain the results?

There are many factors or compounding variables occurs in microbial researches. Microbial composition are influenced by environmental factors. If we have most of factors can influence the microbial community in the studies, then we can interpret the data in correct ways.

To controversy, we need to apply all five questions. To me the most helpful is the mechanism. Usually, a controversial topic doesn’t have a clear mechanism, and many confounding variables that the experiment can not eliminate. If there was a clear mechanism, then scientist could define what are confounding variables and design experiments to detect the matter and eliminate the outside affecting factors that leading to correctly interpret the result and conclusion about the caution or correlation.

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Writing Exercise # 12

Microbiota have significant role in many diseases related to digestive, cardiovascular and  immune system. Now, more recognitions of the role of microbes in the central nervous system like brain.

  1. Microbial communities could influence brain and mental health.
  • Microbiota triggers the lymphocytes of immune system release the cytokines that commute back to the brain. Those cause changes the signalling of cell expression.
  • Some microbes release the neurotransmitters that affect the activity of the brain
  • Some products are produced by microbes can trigger the sensory part of vagus nerve.
  1. Brain and mental health states could influence microbial community.
  • Corticosteroid and other neurotransmitter released by nervous system can modulate the microbiota.
  • Chronic stress increases the levels of corticosteroid in the blood that can affect the gut microbes because corticosteroid can suppress the immune system, the body is more susceptible to pathogen.
  • Acute stress activates the sympathetic system that lead to change the body responses and change the gut microbiota
  1. There are several disorders of mental health related to gut microbes:
  • Pain: Intestinal microbiota can influence central and peripheral mechanism in visceral pain perception. Probiotics with species Lactobacilli and  Bifidobacteria can alleviate visceral pain. Ingestion of probiotics B.infantis increases the pain threshold.
  • Stress, anxiety and depression: Gut microbiota regulates stress, anxiety. Many studies suggested that germ-free mice have over hypothalamic-pituitary adrenal axis responses to restraint stress. However, the consistent reductions in anxiety-like behavior were observed in germ-free mice when they exposed to novel and aversive environment. Specific region of brain on germ-free mice altered neurotransmitter signaling.
  • Cognitive function: Different mouse trains have different aspects of microbial composition, and they have different behaviors. Germ-free mice that were colonized with microbiota from other strain have a behavioral profile similar to donor strain. Germ-free mice have decreased hippocampal expression of key protein evolved neural cognition.
  • Autism spectrum disorder: gastrointestinal symptoms are frequently reported in children with ASD. ASD individuals have changes in gut microbial composition. Faecal concentrations of the short-chain fatty acids highlightly changed in ASD children suggesting that such altered microbial metabolites is as a neuroactive mechanism by which microbes changes brain function.
  • Multiple sclerosis: the disease is characterized by the progressive deterioration of neurological function. Microbiotas can have protective role in multiple sclerosis. There was a study showed that germ-free mice have development of autoimmune encephalomyelitis, and specific pathogen free mice remained fully protects from autoimmune encephalomyelitis.

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Writing Exercise # 11

The peer review process is so useful and interesting to me. Both papers introduced new and current controversy topics, and I gain some knowledge in microbiology. Look at the paper for the reviewer position to consider the author’s hypothesis, their supporting evidences, their references help me improve my paper by finding what I missed and how to add more information to my paper.

When reading and critique someone else’s writing, I have chance to think and look back about my paper. I learn what is important to help the audience can understand the author’s thesis. In scientific paper, the question of interest and hypothesis must be clear and relevant to the topic. While reading and valuing the paper, the audience will tie evidences back to the hypothesis. Each long paragraph should have topic sentence and a sentence to close the paragraph’s concept and open to new concept in the next paragraph. Transition words are also important to help the audience follow the author’s thesis. Evidences supporting the thesis have to be convincing. Citation used in the paper should be valuable carefully, if the paper uses primary researches, the author should talk a bit about the experiment and the statistics of the data instead of just using the conclusion to help the audience understand the concepts and given evidence are more reliable. Use studies or other review papers have to be selective to avoid the paper going off the main findings. A conclusion also important to remind the audience what is the main idea that the author wants the audience to carry after reading the paper. These things will help me better to correct my final paper, I can use the view document to valuate my own final essay.

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Writing Exercise # 10

A peer review process is the process that the authors of scientific paper submitting their studies to the editors or publishers to be reviewed before the paper is publicized. There are many steps of the process. After the author submits paper to the editor, the paper is sent to reviewers who are experts in the field of the paper’s topic. Peer reviewers are usually anonymous. After the review step, the paper can be rejected, further reviewed or issued to the public. The review step included many concepts. The reviewers carefully consider the author’s hypothesis. Hypothesis is the main statement or conclusion of the paper basing on what the author found from their researches. The reviewers usually want to answers questions about paper such as is the hypothesis is clear to represent for the author’s thesis? Is it relevant to the topics or question of interest? What are the evidences that the author gives to support or reject their hypothesis? If the paper is primary research. Primary research is used to describe paper that the author directly did the study, they had their hypothesis, formed the method to find the answers through collecting and analyzing the data. In the primary, the reviewers value the method to find if there is bias or not, the strength of data to see if given data convincing or not. Reviewers go through all evidences that author provides to decide the paper have enough evidences to support their hypothesis. The peer review process has pros and cons.


  1. One or more people in the field have examined independently one research before publication.
  2. The peer review ensure the author carefully discuss and explain their hypothesis .
  3. The peer review ensure given conclusion is exact and precise.
  4. Peer review helps the audiences define the knowledge given in the paper is value, right and convincing.


  1. It takes times to have feedback for reviewers.
  2. The process sometimes takes years after the paper submitted to editors.
  3. Sometimes, the reviewers is hard to determined the value of research without replicating the experiment. There is still fraud data from studies.
  4. No grading systems about the quality of the peer review.

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Writing Exerciser # 9

Sanitation: sanitation is important practice because it will helps us stay in healthy, prevents many infectious diseases. Clean water, safety food, sanitized hospital environment and et al are so necessary since sanitation kills or reduces bacteria and avoids transmission of diseases in the community. However, sanitation is non selective so it kills all microbes which made reduce good or harmless microbes. Too much clean decreases microbial community would make human less exposure to microbes.

Antibiotics usage: antibiotics is considered a magic that helps reduce the infectious diseases from the time they are discovered. Besides increasing of multiple drugs resistant bacteria, antibiotics makes lots of changes in microbial community. Antibiotics uses reduce the diversity of microbes, some beneficial species disappear under the effectiveness of antibiotics.

Stay in house, not outdoor activity: Children and adult contact more “dirty” things with outdoor activity. Soils, plants, animals are sources with a diversity of microbiomes. Human are exposed to many microbial species. Technology improved children usually play inside the house which less contacted with nature things lead to be less exposed to microbes.

Eat less diversity of foods, less vegetables, fruits and other fiber source: Diversity of foods provide human with many microbes species. Eat less diversity, some species can be missed.

C-section delivery birth: Vaginal delivery baby are exposed to a diverse microbial community than baby was born by C section method. Composition of microbes in baby with vaginal born are similar to mother’s vagina.

Reduced breast feeding and increase formula milk: Breast feeding provides healthy microbes. Formula milk is processed or sterilized, it provides microbes different from breast milk and less diverse.

City or urban development: children are grown up in farms have higher diversity of microbial community than ones live in cities. It dues to less outdoor activity, polluted air. Urban life make human be less exposed to microbes.

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Writing Exercise # 8

The most surprising things the important role of gut microbes to the health of human. Changes in microbial community related to some diseases in digestive system. The changes of microbiota in obesity mouses, microbes affect on diabetes patients, the inference of microbe in the insulin pathway lead to insulin resistance. It is new things is microbes and allergy and asthma disease. There is a research about the use probiotics on pregnant woman, the result show that there is a reduce allergy condition and asthma on children. This is interesting because asthma and allergy is hard to cure, just there is the drugs that helps reduce the symptom, it is the new finding the roles of probiotics in these disease will help many children. Children and food allergy is a worry for patients and especially in family have history of food allergy.

Gut microbes in important in helps to digest some foods, it might related to food allergy. In the other sides, allergy relate the response of immune system. There is a research suggest that intestinal bacteria play role in determining the strength of anaphylactic reactions to food allergy. Antibiotic uses, cesarean birth and formula feeding are associated with increased susceptibility to asthma and allergies later life. These factors affects the colonization of microbio on infants. There is different microbial community between allergic and nonallergics children. Mom takes probiotics during gestation period can reduce the risk of allergy and asthma development.

Base on the above writing, I think the topic of gut microbes and food allergy is the one I want to write for my final paper, I want to research further about how intestinal microbial community changes on food allergy children and the role of probiotics taken during pregnancy helps reduce the allergy in child or not.

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Writing Exercise # 7

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.

Mode of birth: gut microbiota of vaginally born infants is colonized by bacteria from maternal vagina and infants born by C-section indicates a relative resemblance  to maternal skin and oral microbiota from mom. And more bacterial taxa in the infants delivered vaginally compared with infants delivered by C-section. This can be considered as a protective factor for vaginally born infants when C-section born children acquired infection 1 year earlier than vaginally delivered infants in dental cares.

Diets and new environmental exposures during first two years: alpha diversity of gut microbes of infants increases over time. The methods of feeding as breast milk, formula and then solid foods. A diversity of food increases the diversity of gut microbes. Breast milk provides healthy microbes for the newborn and they are extremely diverse and dominant microbes change over the course of lactation period.

Breast milk and formula feeding: Bifidobacteria are the most abundant organisms in breast-fed infants guts comparing to Enterococci and Clostridia in formula-fed infants, but gut of formula-fed infant contains fewer bacterial cells and more species diversity. Breast-fed infants contain oral lactobacilli with antimicrobial properties that are not found in formula-fed infants

Hormonal, immunological and metabolic changes on mother: Immune system changes strictly as female is pregnant, some degree of suppression to accept the growing of fetus and other remain to protect the mother and body. During pregnancy, implantation and parturition are considers as inflammatory stage. Inflammation can lead to changes which negatively affect on mother and baby as less alpha diversity or change the contribution of microbes. For example, from the first to third trimester, increasing Actinobacteria and Proteobacteria phyla abundance in mother’s gut microbes, and also reduce the number of taxa groups. Metabolic changes can result in weight gain, elevated blood glucose levels, insulin resistance and low grade inflammation. Weight gain and increased blood glucose related to the change gut microbial community on mother. Gut microbes change to enhance glucose absorption and increase fasting-induced adipocyte factor secretion. It finds that maternal weight is a major influencing factor in shaping milk bacterial composition.

Mother’s diets: High fat diets of mother during gestation changes gut microbe of mom. Diets of mom during feeding period can changes the microbial composition in milk.

Antibiotics use during pregnancy: antibiotic treatment during pregnancy reduce bacterial diversity, it causes the normal abundance of species changes as increase Proteobacteria and enterobacter while reducing Firmicute Sand and Lactobacillus.  A certain change in microbial community on mother affects offspring’s microbiota.

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Writing Exercise # 6

Penicillin used to be the miracle drug for infectious diseases in the first time it is introduced to Vietnam. Then many other generations and kinds of antibiotics have been coming to Vietnam. In a country where we can have antibiotics without prescription from doctors. Antibiotics can be dispensed easily to someone just step in the pharmacy with running-nose or sore throat symptom. I was not sure the first time I used antibiotics, but I think it was when I was just a kids since now I see doctors and pharmacists in my country, they use antibiotics even on the children without careful consideration. Although more tools to access to the world’s knowledge about the consequence of improper antibiotic usage, many people in my country still want to take antibiotics when they have just a cold, flu or viral infection. Amoxicillin seems to be ineffective and multi-drug resistant bacteria is huge current issue in Vietnam. I remember the time as I took antibiotics was many years ago. When I has high fever, sore throat, and cough for a couple days when painkillers didn’t work and cough became worse, I went to talk to a pharmacist and she gave me three days of antibiotics with other painkillers and vitamins. After taking all, I felt better. Now, look back it was really bad experience. I think I might have a flu, but I took antibiotics, and it was coincidence that make me feel that antibiotics was effective in flu. Therefore, I can understand why many Vietnamese people think antibiotics help with all diseases, they do not know what is drug resistance and how dangerous it is. If I did not have a chance to study about antibiotics, I would believe that antibiotics are effective in flu.

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