Five Key Questions When Interpreting Scientific Literature:

• Can experiments detect differences that matter?

In this article, the author points out that it is important to not put the cart before the horse, so to speak, when identifying the presence of certain genetic sequences and concluding what their existence in a certain situation means.   The reason scientists are able to conduct more sophisticated experiments and see causal relations between the presence of microbes, genetic sequencing, etc. and human diseases is because of the newer technology of 16S rRNA sequencing and identification.  The author points out that there are limitations when using this method in experiments, and that sometimes results can cloak finer causal relationships between gene combinations that we don’t necessarily see with this method. He further points out that our understanding of specific genes in the gut microbiome is a result of anecdotal evidence, and so it is dangerous to conjecture cause and effect relationships, in some cases invalid to do so, because in doing so we may be overlooking genetic sequencing or functional differences between genes that are not identified ahead of time.

• Does the study show causation or correlation?

This is a basic concept  that can, in the field of microbiome research,  skew many scientific methodologies and conclusions that are drawn from the data.  This is primarily because we still don’t have a good understanding of the mechanisms of the symbiotic relationships between the gut microbiome and human diseases and conditions. Scientists may see patterns, and offer a causal relationship, but there are often other factors that may contribute to or cause a particular condition.  For example, in studies suggesting that an infant born by C-section may be more susceptible to allergies as an adult than a vaginally delivered infant because of the adverse effects on the early establishment of a healthy microbiome, one would have to consider many other environmental factors and control for those in any study, including the geographical location of the subjects, exposure of lack of exposure to allergens throughout their lives, hereditary differences, etc.  It would be nearly impossible to control for all these factors and be able to say definitively that a C-section delivery is responsible for allergies later in life.

• What is the mechanism?

Understanding the mechanism plays very intimately into the first two questions brought up here. If we understood the mechanisms of the interactions between microbiomes and human disease as well as human neuropsychology, the problems of causation, correlation, and the cloaking of important genes by other dominant gene sequences would be much less of an issue.  

• How much do experiments reflect reality?

Many experiments involving microbiome research rely on germ free mice.  Also laboratory methodology often doesn’t reflect relevant situations in real life. The author argues that this is a weakness.  I think it can be if conclusions are made that are out of context with real life situations.  However, I think these experiments are vital to further progress knowledge in this area. I think of them more like pilot studies that give us information to work with to make more creative experiments with better controls for more realistic implications.

• Could anything else explain the results?

Clearly, with any scientific experiment, methodology and data, researchers must take into account the possibility of other factors explaining the results.  A good experiment and sound scientific research must include controls in the methodology.  Medical research does have a history of making erroneous conclusions based on conjecture that have affected many people in a negative way.  I feel like a warning by the author about this is definitely appropriate because there is so much still unknown about the cause and effect relationships between the microbiomes and their effects on the human condition. 

I think the most important and helpful question  to look at when discussing this controversy is the question regarding the biochemical and organic mechanisms involved in our symbiotic relationship with microbiomes. Once we understand the mechanisms better, it will help clear up our understanding of causal relationships in some cases, which will then help us understand the results of experiments, will help identify causal relations and correlations, and help us conjecture possible identification of functional groups and gene sequences involved in the mechanisms overall. 

The gut has been referred to as the “second brain,” because of direct connections found between the brain, our nervous system and the gut. There is growing evidence that microbiota can influence mind and behavior, and conversely, that mind and behavior can influence microbiota.

The vagus nerve is a cranial nerve that is routed directly from the brain to the gut. Also, various nerves in the sympathetic nervous system are routed directly from the spine to the gut. These direct pathways may allow for a direct signaling between the brain and the gut, and the gut and the brain. 

Microbiota interact with our body in complex biochemical ways with complex mechanisms that we still don’t understand.  For example, research has shown that gut microbiota can trigger cytokine reactions. Cytokines are involved in the host inflammatory response of the immune system, and cause  “activation of microbial metabolite sensor receptors that are more highly expressed on inflammatory and intestinal epithelial cells.” [1] 

Microbiota have also been shown to trigger the release of corticosteroids  and neurotransmitters which can then travel to the brain systemically. They can cause biochemical changes in the brain.

It is also believed that microbiota can be influenced by our brain and behavior.  Neurotransmitter activity has the potential to influence the behavior of microbiota through the nervous system pathways, including the vagus nerve and various sympathetic nerves. Examples of what they influence include  heart rate, breathing, sleep cycles, digestion, mood, concentration, appetite, and muscle control. They are involved in  the body’s organs, psychological functions, and physical functions. [2]

Neurotransmitters can be influenced or changed by behavior. Because of the direct connection between the nervous system and gut microbiota, the potential for microbiota to be influenced by neurotransmitter signaling is very possible. 

This is a very new area of study, one with a lot of controversy among professional peers in the field.  The thought is that altering gut microbiomes  may have an effect on mental health, possibly positively affecting or curing some mental illnesses and mental states. 

Mechanistically, most of the interaction between gut microbiota and the nervous system takes place at the epithelial cell layer of the intestine.  A healthy gut will have a healthy symbiotic relationship with the brain, but a dysbiotic gut, or one with an unhealthy amount of pathogenic bacteria, will have a disruption in the epithelium of the intestine, which has been shown in research to affect the behavior of laboratory mice in some studies. [3]

Some research has shown that when mice are given probiotics, it can reverse changes that were made to their microbiota after they were put in stressful environments.

Scientists are also noting a high correlation between disorders of the gastrointestinal system and mental conditions such as autism.

This is a very new area of study, one with a lot of controversy among professional peers in the field.  The thought is that altering gut microbiomes  may have an effect on mental health, possibly positively affecting or curing some mental illnesses and mental states. There is much research to be done, and the mechanisms of how the microbiome and the brain interact are still not well understood, but the implications of being able to manipulate behavior and mental states through a person’s microbiome could be a game changer in our understanding of human psychology and neurology. 

Citations: 

1. https://pubmed.ncbi.nlm.nih.gov/31013453/
2. https://www.medicalnewstoday.com/articles/326649#:~:text=Neurotransmitters%20are%20chemical%20messengers%20in,heart%20rate
3. Thaiss, C. A., Zeevi, D., Levy, M., Zilberman-Schapira, G., Suez, J., Tengeler, A. C., Abramson, L., Katz, M. N., Korem, T., Zmora, N., Kuperman, Y., Biton, I., Gilad, S., Harmelin, A., Shapiro, H., Halpern, Z., Segal, E., & Elinav, E. (2014). Transkingdom control of microbiota diurnal oscillations promotes metabolic homeostasis. Cell, 159(3), 514–529. 

I reviewed two papers as a peer reviewer. It felt awkward to review final essays that were based on controversies in the field of microbiology, because I don’t feel I have the expertise or professional background to make judgements on professional research that is being cited or scientific knowledge on a research level.

I also feel in some ways it’s not appropriate to peer review in an undergraduate class, because the students can be at very different levels of experience and education. They might be peers in terms of both being in the same class, but not necessarily in terms of their knowledge and experience base.

Both of the papers I reviewed had weak hypotheses and were disorganized, so it was really difficult to unravel the problems quickly. I had to sift through each paragraph and try to give suggestions of how to tie together their thoughts and ideas. I didn’t feel it was fair for me to have to put in that much time to review incomplete and disorganized papers. If they were professionally written, it would be much easier and straightforward to review them.

It was interesting and educational to read about the other topics people have chosen. I think it’s very enriching to have the opportunity to see what other’s are thinking and what drives their interests.

I think by seeing the weakness of a paper handed to me objectively it will help me strengthen the weaknesses in my paper because I will be looking for similar things that I noticed in their papers and that stood out to me as a reviewer.

A finished manuscript is submitted to a particular journal that the author or authors want to get published in. The editor of the journal reviews the article and then either passes it on to a group of usually two to four peer reviewers or rejects it. If it is passed on to peer reviewers, they will read it and give feedback as to the strengths and weaknesses of the methodology of the experiment, the content of the article, etc. After it is peer reviewed, the article goes back to the publisher again. At this point, it is either accepted with no revision, rejected, or given back to the author(s) for recommended revisions.

The first step in the process is the authors making a rough draft of the manuscript which includes all the information and details they wish to submit to a journal. Then they choose a journal based on several factors. These include the subject matter of the research, the prestige of the journal, the audience the journal reaches and impact the article might have, and past connections with a particular journal.

Journals with high impact results are considered more desirable. A journal that is considered high impact has more of their articles referenced compared to the total number of citable articles compared to other journals. This means more exposure for the authors, more notability and perhaps a better chance of being funded.

Articles are accepted based on the direction the journal wants to go in and the basic philosophy of the journal. If the article is rejected at this point, the author has to find another journal to submit to.

The peer reviewers are considered established professionals who are also published in the field related to the journal. They are chosen by the editor of the journal and are anonymous to the authors, while they are aware of who the authors of the manuscript are.

The peer reviewers watch for several things when reading the manuscript. This includes whether the research is relevant, whether data supports the hypothesis, whether the methodology is sound, whether figures and graphs match the statements in the paper, etc.

They write up their analysis of the article and give it back to the editor. At this point, the editor will accept it, reject it or return it to the author for revisions. If it is returned to the author, they can make revisions and resubmit as needed until it is ultimately either rejected or accepted for publication.

Swimming in chlorinated pools – I remember reading somewhere that when polio was spreading, they found that people who swam regularly in the rivers and lakes in the Northeast somewhere, that they did not get polio, and they hypothesized this was because they were exposed to the virus in the water and had built up immunities to it. In general swimming in a chlorinated pool will reduce exposure to microbes by the zillions.

Antimicrobial hand soap – washing with antimicrobial soap products kill all the microbes, not just the bad ones, so there has been controversy as to whether the benefit of using it to kill harmful bacteria is worth the risk of killing healthy bacteria.

Showering frequently – frequent washing will remove a lot of microbes, including those that keep a healthy microbiome on the skin. I wonder if yeast and fungal infections would be less common if people washed less. It would be an interesting experiment.

Brushing and flossing teeth – flossing is super important for removing food that gets stuck in our teeth and becomes a feast for bacteria, which can lead to periodontal disease. I feel in this case, keeping a decreased exposure to microbes is the best choice.

Washing clothes – dirty clothes have bacteria, sweat, and other microbes that , if not washed, will continue to proliferate and smell over time. I feel this another example of decreasing exposure is the more healthy choice.

Driving in cars vs. public transportation – I’m sure public airplanes, buses, and trains are teeming with beyond countable amounts of microbes. In our private cars, we are only exposed to our microbes.

Diet restrictions – our diet has a huge impact on our exposure to microbes. By restricting what we eat we automatically restrict our exposure to all kinds of microbes.

Diet variation – we can affect our exposure to a variety of microbes just based on what foods we eat. This has been proven with the use of probiotics and prebiotics.

Mask wearing – as we have seen, wearing masks reduces the amount of cross contamination by mouth in the human population. The medical community reported an extremely low rate of flu cases in 2020, attributed to high rate of mask wearing due to the Covid-19 outbreak.

Disinfecting wipes – wipes with ammonia such as Clorox wipes, as well as wipes with alcohol, are being used in high volume because of the covid pandemic and I am sure overall we are enjoying much cleaner public establishments than we used to.

Parts 1 and 2: 

• How microbes can affect our hormones
• How a particular bacteria influences our body to make morphine
• How a few bacteria can kill off our appetite hormones
• The unknowns regarding transfer of bacteria into the placenta
• How we are each carrying around an ecosystem in our body unique to us, we are each a micro ecosystem of our own on the planet.  We think of ourselves as a body and soul but this changes perspective about what our body actually is.
• How 50% of world has H. pylori implying there’s an evolutionary advantage to having, it must have symbiotic relationships
• How in pregnancy the body has the same conditions as found in metabolic syndrome, but it affects the mother and baby in a positive way rather than negative. 
• How probiotics could potentially be as powerful as antibiotics once the mechanisms of the gut microbiomes are understood better
• Shocked at how little research has been done on hospital inpatient microbiomes
• Happy to see how two researchers linked cervical cancer to HPV and saved thousands of lives.
• Shocked how two researchers’ research and hypotheses about the correlation between bacteria and GI diseases were rejected by peers for years, then ended up with the Nobel Prize fifteen years later for their work.
• How closely the microbiome interacts with the immune system and details with that
• Surprised at the number of different species of dominant pathogenic bacteria found in PICU patients, I would like to see studies done across hospitals.  Because they found the same pathogenic bacteria regardless of their individual illnesses.

Part 3:   The unknowns regarding the transfer of bacteria into the placenta and breastmilk.

It is well known that there is a barrier between the fetus and the mothers immune system. It was thought that the mothers immune systems and digestive system, which are directly involved with microbiota, were kept separate.  We read that they have found bacteria from mothers with oral disease in the microbiome of their fetus’s meconium.  There were other examples of mothers bacteria being found in the infant microbiome, I think mainly in their meconium, and they are not sure about the mechanisms of the transfer.  I think it’s very important to understand better how mothers bacteria is getting through the placental barrier.  I recall an experiment where bacteria from the mother was tagged and they later found some of it in the baby’s meconium.

I am also interested in looking more thoroughly into how individual our microbiomes actually are, maybe find a way to blueprint the array of species in each individual’s gut.  I would like to look into the methods used to analyze individual full gut microbiomes and see if there is a correlation with psychological, cultural, lifestyle differences. Kind of like medical anthropology.

Part 4:  To begin preparing for my final paper, I will research publications in the area of my interest, look to see if there are missing aspects to research, or an area that needs more research. Because the transfer of bacteria from mother to fetus isn’t well understood, there is definitely controversy over how it happens.  I will also look into research regarding the establishment of individual microbiomes, how they are analyzed and look to see if any studies have been done on correlations between particular types of microbiomes with culture and behavior.

• Vaginal birth vs. C-section birth: The microbiota of the infant born vaginally is much different than one born via C-section. The microbiota of vaginally born infants is similar to that of the microbiota found in the mother’s vagina and gut, including Prevotella, Sneathis, and Lactobacillus genera.  The vaginal microbiome of the mother is very important for development of defense mechanisms against disease in the infant. The microbiome is abundant in Lactobacillus, bacteria that produce lactic acid that can create a protection against pathogenic bacteria.  In one study, vaginal fluids were given to C-section infants after birth.  They found the microbiomes changed to that of vaginally delivered babies after one month. The microbiota of infants born by C-section is different from those born vaginally.  The bacteria found in the microbiota of C-section infants resembles that of the mother’s skin and oral microbiota, including Propionibacterium, Corynebacterium and Streptococcus genera. The study we read says that a higher number of C-section babies contract MRSA (Staphylococcus aureus) infections, attributing that to their exposure to bacterial antibiotic-resistance genes and their higher “abundance” of Staphylococcus.  The authors also state that C-section infants have a delayed “colonization of Bacteroidetes” and lower diversity of alpha bacteria groups in their first 2 years. Also, after a few months, the oral microbiome of C-section infants shows less diversity than vaginally delivered babies. There is some thought that because of less exposure to the mother’s vaginal microbiome as a baby that C-section babies may have a higher correlation with disease down the road, such as celiac disease, obesity and asthma etc.  I’m not sure I agree with these projections, because there are many factors to take into account and they would need a very large control sample to prove or disprove long term effects.  They did say that after a few months, most of the discrepancies between the microbiomes of vaginally delivered and c-section infants are resolved.

• Breast fed vs. bottle fed newborns:  Infant diet is one of the most important factors in the development of their microbiome.  Maternal milk has been thought of as sterile from bacteria, but it has been shown recently that it contains bacteria important for establishing a healthy microbiome in the infant. The first milk a newborn drinks, called colostrum, contains a variety of bacteria, including Weisella, Leuconostoc, Staphylococcus, Streptococcus and Lactococcus.  Later it changes to a flora more resembling oral cavities.  It is believed that the source of the bacteria in the mother’s milk comes from the microflora of the mother’s gut, which is dependent on hormonal influences. The bacteria that the infant gets from breastfeeding helps the baby digest oligosaccharides, and smaller sugars.  The bacteria in the milk helps the baby digest the nutritional contents of the milk in a symbiotic way.  Studies show that the most prevalent bacteria found in the breast fed babies guts are Bifidobacteria, and in formula fed infants they are Enterococci and Clostridia.  Formula fed infants also have a greater species diversity.  The bifidobacterium and the bacteria important for aiding in the digestion of oligosaccharides.  I am not sure how well formula fed babies are able to digest sugars.

• Antibiotics given to infant or mother: Antibiotics are known to kill pathogenic bacteria, and any use of them will notably affect the microbiome of whoever is taking them. In a study done with rats, the use of common antibiotics (azithromycin, amoxicillin and cefaclor), was shown to change fecal microbiota, reduce bacteria diversity and cause weight gain.  It is common for doctors to recommend taking probiotics along with antibiotics to replenish healthy bacteria, but I am not sure how safe they feel it is during pregnancy.

• Oral microbiota and/or oral infection of the mother:  The article we read states that they have found a similarity between the microbiota of the oral cavity and the placenta in the mother.  The placental microbiome resembles the microbiome of the oral cavity more than anywhere else in the mother’s body.  There is apparently a correlation between mother’s with periodontal disease and pregnancy complications.  One study showed an increased risk of preterm birth with maternal periodontal disease. 

• Mothers diet: Obviously diet is one of the most important factors affecting a pregnant woman’s microbiome, which then affects the fetus. Bacteriodes and Staphylococcus levels were shown to be significantly higher in obese pregnant women compared to pregnant women that were normal weight.  A healthy diet in general probably promotes a healthier microbiome for the mother, which can indirectly affect the fetus with a healthier pregnancy in general.

• Maternal weight:  Studies have shown that overweight and obese pregnant women have a higher number of bacteria from the genus Staphylococcus, including S. aureus, as well as more Lactobacillius.  There is concern about the long term effects of the presence of larger amounts of S. aureus in maternal milk because of a correlation that has been made with the presence of S. aureus in the microbes of overweight children. Metabolic hormones in overweight women are thought to alter the mothers’s microbiota which could then affect the fetus. 

• Probiotics:  A study was done where pregnant women were given probiotics and the probiotic bacteria were found in the infant meconium and placenta.  This implies again that bacteria can travel from the mother and colonize in the placenta as well as break the barrier into the infant’s GI tract. The mechanisms of how this happens are still not understood.  Another study showed that probiotics changed the expression of Toll-like receptor genes in the infants placenta and meconium. In addition, in another study where probiotics were used, there was a correlation between mother’s with allergic diseases taking probiotics and a reduced risk for eczema in the infants. There appears to be a number of studies on the use of probiotics and its effects on the microbiomes of mother and infant during pregnancy .

• Maternal hormones: The mother’s hormones have  a huge impact on her microbiome that can then affect the infant’s microbiome.  The study we read says that hormonal and metabolic changes that take place during pregnancy resemble those that you see in metabolic syndrome. This involves changes in hormones intricately involved with the immune system as well.  In the case of pregnancy, though, these changes are said to be healthy and supportive of the bodily changes that have to occur during pregnancy, such as inflammation required during implantation of the fertilized egg, then changing to an anti-inflammatory state later in pregnancy that allows the fetus to grow. In the third trimester of pregnancy the gut microbiota changes dramatically which would be in alignment with the fluctuation of maternal hormones.