The Effects of Diet on the Microbiome

A couple of weeks ago in Bio120, we were assigned to read a very intriguing article by Michael Pollan called, “ Some of My Best Friends are Germs.”  In his article, Pollan describes the power and purpose of the microbiome and the significance of different bacteria in our guts, among other interesting topics3.  However, one topic that caught my attention was the observed difference in the microbiota present in our microbiomes and others in America and Europe compared to those in Africa. The American and European guts tend to have more Bacteroids and Firmicutes with low levels of Prevotella, whereas African and Amerindian guts have much more diversity in their microbiome and also have high levels of Prevotella3.  This interesting fact led me to study published in the Proceedings of the National Academy of Sciences of the United States of America (PNAS) that may link this difference in microbiota to our diets.

To identify the effects of diet on the microbiome, a study was conducted to compare the gut microbiota of children from the ages of 1-6 years old living in a rural African village called Boulpon to children of the same age group living in Florence, Italy to represent western European children2.  According to the study, children from the Boulpon village had diets that consisted of all food that was produced locally, low in fat and animal protein, and rich in starches, fiber, plants, cereals, legumes, vegetables, carbohydrates, fibers, and non-animal proteins.  The European diet was characterized by high amounts of animal protein, sugar, and fat, and low in fiber. Breastfeeding was also noted and recorded for the two groups.  It was noted that Africans typically breastfeed up to 2 years old while Europeans breastfeed up to 1 year of age2.

After identifying their diets, scientists categorized the microbiota of the children from their fecal matter.  The results describe that “More than 94.2% of the sequences in all of the Boulpon and European samples were found to belong to the four most populated bacterial phyla, namely Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria, in agreement with previous studies describing such phyla as those contributing to the majority of human gut microbiota2.”  It was further noted the Bacteriodetes were much more popular in the Boulpon children, whereas Firmicutes and Proteobacteria were much more common in European guts2.  Researches rationalized that as soon as breastfeeding is substituted by solid foods, the differences in microbiota among the Europeans and Africans begins to increase because Europeans stop breastfeeding sooner than Africans2.  This reflects the dietary and environmental separation that results in the difference in abundance of the Bacteriodetes and Firmicutes.

It is later noted in the article that “Exposure to the large variety of environmental microbes associated with a high-fiber diet could increase the potentially beneficial bacterial genomes, enriching the microbiome2.”  A decrease in the microbial richness may be an undesirable effect of globalization and eating highly processed, uncontaminated, and very nutritious foods.  This decrease in microbial richness can be observed in European as well as American bacterial genomes2.  According to their research, “[They] hypothesize that the reduction in richness we observe in European compared with Boulpon children, could indicate how the consumption of sugar, animal fat, and calorie-dense foods in industrialized countries is rapidly limiting the adaptive potential of the microbiota2.”

Another test was conducted to research one’s ability to extract calories from polysaccharides.  From their studies they have observed a correlation between polysaccharide-degrading microbiota and the calories that the host can extract from his or her diet, which may influence the survival and fitness of the host.  “We can hypothesize that microbiota coevolved with the diet of Boulpon individuals, allowing them to maximize the energy intake from indigestible components, such as plant polysaccharides, by producing high levels of short-chain fatty acids (SCFAs) that supply the host with an additional amount of energy2.”

Overall there is a strong correlation between diet and the microbiota that dominate a person’s gut according to the data collected in this study.  There is also a clear message from all of this research that we must protect the diversity of the microbiome and that there is a great importance of these microbiota to our health.  Now that you know how your diet can impact your microbiome what can you do?  Well, you actually have the opportunity to be a participant in research yourself!  “The American Gut” is a project that sets out to compare the microbiota of people from around the U.S. to help collect data to find correlations between environmental factors, like diet, and the micrbiome1.  Through this project you can send in some of you own samples and find out what microbiota live in your gut, and find out what you can do to improve your microbiota, while also contributing to data for their research1!  For more information go to


Source: Human Food Project, American Gut

Here are the simple steps you need to follow to participate in the American Gut project to find out the microbiota that make up you microbial ecosystem!

Works Cited

1. “American Gut.” Human Food Project RSS. N.p., n.d. Web. 03 Mar. 2014.

2. Cavalieri, Duccio, Et Al. “Impact of Diet in Shaping Gut Microbiota Revealed by a Comparative Study in Children from Europe and Rural Africa.” Impact of Diet in Shaping Gut Microbiota Revealed by a Comparative Study in Children from Europe and Rural Africa. Proceedings of the National Academy of Sciences of the United States of America, 17 Aug. 2010. Web. 03 Mar. 2014.

3. Pollan, Michael. “Some of My Best Friends Are Germs.” The New York Times. The New York Times, 18 May 2013. Web. 03 Mar. 2014.

Microbes in C-section Babies

Recently in Bio 120 we read an article by Michael Pollan, entitled “Some of My Best Friends Are Germs”.  This article discusses the prevalence of microbes in human bodies. Pollan states that people are in reality only 10% human, because for every human cell that a person possesses there are about ten resident microbes as well (1). An aspect of this article that I found particularly interesting was the section where Pollan mentioned how human babies tend to acquire a large number of microbes during birth through obtaining their mother’s vaginal and intestinal microbes (1). This is something that scientists have begun to see as problematic for babies born through cesarean sections because a C-section is a very sterile procedure therefore babies born this way do not acquire any of these important microbes.

Pollan mentions how Knight, the head of the lab discussed throughout this article, “inoculated” his newborn baby with his wife’s vaginal secretions at birth because his baby was born through an emergency C-section and he wanted to insure that she’d still have proper colonization of these microbes (1). The fact that Knight, a well renowned scientist, believes that these microbes are so important, and believes this strongly enough to inoculate his own child with them, made me wonder what other scientists think about this issue, and what research has been done on it. A study done at a hospital in Venezuela featured nine women and their 10 newborn babies. Four of these women gave birth to their babies vaginally, while the other five gave birth via C-section (2). The results from this study showed that vaginally delivered babies possessed bacterial communities similar to those found in the mothers vaginal communities whereas c-section babies mostly possessed bacterial communities similar to the bacterial communities on their mother’s skin (2).

This further proves that certain communities are transferred through vaginal birth. The article concludes that a mother’s vaginal microbiota gives the baby its first natural microbial exposure. The article also states “in C-section babies, the lack of a vaginal exposure leads to first microbial communities resembling the human skin microbiota, with an abundance of Staphylococcus spp” (2). This can be problematic because as a result of their lack of vaginal microbiota, C-section babies are more susceptible to certain pathogens. An example of this phenomenon that was found in this study is that “64 to 82% of reported cases of methicillin-resistant Staphylococcus aureus (MRSA) skin infections in newborns occurred in Cesarean-delivered infants” (2). These infections may not have occurred if these babies had received the defensive vaginal microbiota that vaginally delivered babies possess.

An NPR broadcast on this subject discusses and confirms the fact that babies born via C-section lack vaginal microbiota but posses microbiota similar to what is found on the skin. Yet, this broadcast takes a different stand on whether or not this is harmful for the C-section babies. This broadcast talks about how the theories that believe that the babies who lack these microbes have weakened immune systems all really relate to the hygiene hypothesis, meaning that the more that people restrict their exposure to microbes, the less the immune system will know how to deal with them (3). This study doesn’t necessarily support this view because it doesn’t believe there is any long-term evidence to show that the C-section children are actually affected by the lack of these microbes later in life. However, the broadcast does suggest that if further studies do demonstrate that there is a benefit to babies being exposed to vaginal bacteria then it is a possibility that doctors will find a way to expose C-section babies to these bacteria after birth (3).

Overall, it is clear that there is enough evidence to recognize a significant difference between the microbiota in C-section babies compared to the microbiota in babies delivered vaginally, but it does not seem like any studies have been done that follow these children later in life to conclude whether or not their immune systems or health in general are actually affected by this difference in microbes. Until further studies are done, I don’t think any real conclusions about the benefits of babies possessing certain types of microbiota can be officially confirmed.

Works Cited

(1) Michael Pollan, “Some Of My Best Friends Are Germs”, The NY Times, May 15, 2013.

(2) Maria G. Dominguez-Bello, Elizabeth K. Costello, Monica Contreras, Magda Magris, Gilda Hidalgo, Noah Fierer, and Rob Knight, “Delivery mode shapes the acquisition and structure of the microbiota across multiple body habitats in newborns”, Proceedings of the National Academy of Sciences of the United States, June 29, 2010.

(3) NPR Staff, “Study: C-Section Babies Skip The Bacterial Slide”, NPR, June 28, 2010.

Fecal Transplants: Yes-Poop Can Be Good For You

The main focus of Micael Pollan’s New York Times article is the microbiome, which consists of the of hundreds of millions of microorganisms that live within the human body and aid in many functions, such as supporting the immune system and synthesizing essential nutrients. Pollan discusses many ways to protect the microbiome, such as probiotics and fecal transplants. In this blog post, I will discuss fecal transplants. I believe that many of us were unfamiliar with this procedure before discussing it in class, and still find it to be a shocking form of treatment. I hope to clear up any lingering questions that anyone in the class still has regarding fecal transplants, specifically, what they are, why they work, and whether they are beneficial or not.

The primary source that I used to follow up on Pollan’s discussion regarding fecal transplants is a study performed in 2010 by Grehen et al. at the School of Biotechnology and Bimolecular Sciences at the University of New South Wales. Fecal transplants are a form of bacteriotherapy, the premise of which is to use bacteria to help treat diseases. The goal of this study was to determine if fecal transplants from healthy donors can be effective in changing the microbiota of patients with microbiota-related disorders (C. Difficile, ulcerative colitis, etc.). The logic behind the study is the theory that these diseases are caused by a lack of “good” bacteria in the intestines that help to maintain high levels of diversity within the microbiome. Having a diverse microbiome is a critical part of being healthy. The microbiome has been linked to supporting numerous aspects of human health, such as “obesity, behavior, heart disease, and cancer” (Stein). If one has a low level of biodiversity within their microbiome, then “bad” bacteria, such as C. difficile, are able to flourish, perhaps due to a lack of competition, and wreak havoc on the human body.

To perform the study, participants with colonic symptoms were first screened for factors such as drug and alcohol addictions and recent antibiotic use. The sample for this study was 10 people, 6 of which were male and 4 of which were female. The participants were first infused with blended mix of donor stool and saline through a colonoscope on the first day, and on consecutive days, a nasojejunal tube was used to infuse the fecal matter into the patient for 5-15 days.

The results of this study show that the participants yielded fecal banding patterns more similar to the donor’s sample than their own original fecal matter. This shows that when a donor’s healthy and diverse stool is inserted into a person with a microbiome-related disorder, the sick person will absorb the good bacteria, which in turn can be used to help treat their disease. The results of this study are consistent with our class discussions regarding the healing effects that fecal transplants can have.

In his paper entitled “Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome,” Martin Floch reviews this study. He considers it a landmark study because it explores, and is successful in, manipulating the microbiome of the colon. This is important because it can lead to promising new treatments for those who have yet to find relief from typical treatments for these types of diseases. For example, a pill form that relies on the principles established by fecal transplants. These pills contain encapsulated bacteria concentrate, prepared from donor stool, within three layers of a gelatin capsule. A University of Calgary research study reported “a 100 percent success rate — none of the 27 patients who took the tablet-sized pills had a recurrence of C. diff, even though all of them previously had had at least four bouts of the infection” (Infectious Diseases Society of America). It is important that we begin to study treatments for microbiome-related diseases due to the rise of the antibiotic resistance epidemic. C. difficile, for example, kills nearly 14,000 Americans every year (Infectious Diseases Society of America) and can severely affect the quality of life for those who suffer from it. Researchers are just beginning to discover the microscopic ecosystem that resides within the human body, and still know very little about how it affects the rest of the body. It is theorized that treatment of the microbiome can help treat diseases that are not necessarily associated with the intestines, such as Multiple Sclerosis and Autism. Hopefully in the future, more studies will be performed in order to learn more about the microbiome and all the impacts it can have on human health, and treatments can be developed to aid those who suffer from these serious diseases.

 Works Cited:

Floch, Martin H. “Fecal Bacteriotherapy, Fecal Transplant, and the Microbiome.”Journal of Clinical Gastroenterology 44.8 (2010): 529-30. Print.

Grehan, Martin J. “Durable Alteration of the Colonic Microbiota by the Administration of Donor Fecal FloraAuthentication Required.” Journal of Clinical Gastroenterology 44(8) (2010): 551-61. Weblogin:. Sept. 2010. Web. 10 Mar. 2014.

Infectious Diseases Society of America. “Fecal transplant pill knocks out recurrent C. diff infection.” ScienceDaily. ScienceDaily, 4 October 2013.

Stein, Rob. “Staying Healthy May Mean Learning To Love Our Microbiomes.” NPR. NPR, 22 July 2013. Web. 10 Mar. 2014.

C-sections or Vaginal Deliveries?

A baby is born every 4 seconds. Every 4 seconds, what was once a single cell becomes its own being. But to reach that stage they must be removed from the mother’s body one way or another. Cesarean sections are becoming an increasingly popular choice over natural vaginal deliveries. Although this type of birth may be less stressful for both the mother and the child, there are side affects that can make themselves known later in life.

The Pollan article about microbes and their effects in the human body brings up the difference a C-section can make in the development of the gut in babies. Pollan says that natural birth is “a microbially rich and messy process that exposes the baby to a whole suite of maternal microbes.” [3] On the other hand, C-sections are relatively sterile and deprive babies of the microbes they acquire while traveling through the mothers vaginal tract. But why exactly do we want these microbes? The Hygiene Hypothesis tells us that we are more susceptible to diseases because we live in an overly clean society. These microbes are necessary to prevent the development of long-term medical problems like asthma and allergies.

To test if babies are truly affected by this difference in mode of birth, a study was conducted and published in Clinical and Experimental Allergy. The population used was a large health maintenance organization named Kaiser Permanente Northwest Region. An extensive background check was done on the mothers of the children that were to be monitored ranging from their education and ethnicity to history of allergies and diseases. The models used were an “uncontaminated” C-section versus a vaginal birth or an “uncontaminated” C-section versus a contaminated one [1]. A “contaminated” C -section means that vaginal microflora have been exposed to the baby.

What came from this experiment was both expected and unexpected. Results of the study showed that children born by C-section had a much higher risk of being diagnosed with allergic rhinoconjunctivitis (AR) than vaginally delivered babies. This supports the initial hypothesis that babies born by C-section are more susceptible to allergies. The results for asthma cases were similar, however, when gender of the baby was looked at more closely, they noticed that C-section and asthma were linked only significantly in girls. This relation to sex is surprising seeing as the data from this study does not show that there is any difference in the “immunological make-up” of boys and girls.

Okay so we know that C-section generally means a higher risk of allergies and asthma, but why? According to the study conducted above, intestinal flora affects immune responses, especially the function of helper-T cells that help other white blood cells release antibodies and kill infected cells. A difference in the intestinal flora can be seen in people who have allergies as opposed to people who don’t. As stated in this study, intestinal flora is adaptable throughout life but has the most significant effect when the gut is first colonized with bacteria. That is why it is so important that babies are introduced to these microbes naturally. A sterile C-section deprives them of the whole microbial cocktail leading to a greater risk of allergies.

Many of the effects of a C-section birth cannot be seen until later in life. There is however, one thing that new, frightened parents may have to deal with. Colic is an illness where a baby cries for hours at a time for many consecutive days due to gas pains. According to Health and Wellness, a C-section can interfere with the diverse bacteria that should be present in the baby’s gut and result in more bad E. coli bacteria than good lactobacilli [2].

A C-section may be easier on the mother or in some cases may simply be the only option because of complications, but it can have adverse affects on children immediately or in the future. Maybe a messy start is what it will take for a person to brave such a sterile world.

Consider taking a look at this video. This TED talk is about why microbes are good for us. Skip to about 7:30. Here, this TED speaker lists all of the positive effects of the microbes we receive at birth.


1) Renz-Polster, H., M. R. David, A. S. Buist, W. M. Vollmer, E. A. O’Connor, E. A. Frazier, and M. A. Wall. “Caesarean Section Delivery and the Risk of Allergic Disorders in Childhood.” Wiley Online Library. Clinical and Experimental Allergy, 9 Nov. 2005. Web. 10 Mar. 2014. < >.

2) Roizen, Michael, and Mehmet Oz. “Managing Baby’s Colic.” Ocala StarBanner, 18 Feb. 2014. Web. 10 Mar. 2014. <>.

3) Pollan, Michael. “Some of My Best Friends Are Germs.” The New York Times, 15 May 2013. Web. 10 Mar. 2014. <>.

Gut Wrenching Germs – not so bad?

Let’s be real for a second. If I told you that you were going to have a baby right now, how much of your thought process is going to be devoted to how you’re going to deliver this baby? Of course you’re going to consider your options, naturally, with an epidural, or cesarean section (C-section). But maybe your reasons are because you don’t want to feel the pain of child-birth, or maybe you like the idea of a cesarean section because it’s a quicker process where you can go in and just get’er’done when you plan it unlike a natural birth that could take hours and hours and hours at any given time. However, there is SO much more to consider.

Studies are constantly being conducted that pertain to health and the future of our lives. Anything and everything can affect our health and our individual futures when it comes to diseases and illnesses, so it seems only necessary that we start the research from the exact moment we are introduced into this very world, our birth.
In regards to the article “Some of My Best Friends Are Germs” by Michael Pollan, we were briefly introduced to the study of babies and their specialized diet and the idea of breast-feeding. By deepening our understanding of breast milk and the pros and cons that associate with it, we learned about a so-called “pointless” carbohydrate in breast milk that an infant cannot digest. Scientists saw this as odd since the process of evolution over the last few thousand years would have changed this component of breast milk if it did not benefit the child. Looking further into this, we learn that this carbohydrate nourishes a gut microbiome that in fact helps protect the lining of our intestines from infections and inflammation. A gut microbiome, where everything pertaining to health begins.

Similar to this idea of receiving beneficiaries from mom, scientists looked further into this idea of the gut microbiome that quietly and effectively protects us from the inside out. Considering the idea of how we are born, we look at our very first interaction with mom and at how she has been there helping us since day one. (You rock, mom!) When having a baby, it’s obvious that the baby comes into full contact with the mother regardless of the method of delivery, the contact is simply with different parts of the mother’s body. Should a baby be born by C-section, it’s easy to understand why scientists say that the baby is introduced to the skin cells of mom, which come with the skin bacteria. Likewise, it’s easy to understand the correlation with babies that are born vaginally and how they are introduced to the bacteria within the mother’s birth canal. This simple choice in method of how to bring your baby into the world, the way in which you introduce them to their first contact with anything after their nine months in the sterile and enclosed environment within the womb, can influence their health for the rest of their life. The initial introduction of bacteria is what shapes the baby’s gut microbiome and determines their capability to fight off disease and other health factors for the rest of their life.
A study conducted in the Puerto Ayacucho hospital in Venezuela, studied nine women who ranged in age, race, and delivery method(1). Vaginally delivered babies acquired bacterial communities that resembled their mother’s vaginal microbiota. Similarly, babies born via C-section acquired bacterial communities that reflected the bacterial community found on their mother’s skin surface, which is almost completely sterile. These bacterial communities that are acquired by the babies are their first introduction to bacteria after the last nine months in sterile solitude and it is this bacterial community that they are basically given by mom that forms their tolerance to disease and other health factors.

The idea of delivering a baby vaginally is considered to be ‘better’ for the infant due to the amount of bacteria that the baby is introduced to in the birth canal in comparison to the lesser amount of bacteria on the skin that a baby born via C-section is introduced to. Basically, a baby born by C-section goes from a sterile womb to a sterile world initially. The babies that are born vaginally go from a sterile womb to a bacteria filled birth canal that introduces them first thing to the bacterial taxa and sets up a gut microbiome community most similar to their mother’s within the birth canal that will be better prepared to fight future disease and other health risks.

So, pregnant or thinking about having kids? Consider their future health by considering how you want to introduce them to our disease infested world.
Have a mom? Let her know how awesome she is since she’s been helping prevent you from getting sick since before your first official breath of air on earth!

Works Cited;
1) Dominguez-Bello, Maria, Elizabeth Costello, Monica Contreras, Magda Magris, Glida Hidalgo, Noah Fierer, and Rob Knight. “Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns.” National Academy of Sciences of the U.S.A. Jeffrey l Gordon, 24 MAY 2010. Web. 9 Mar 2014. <>.

2) Pollan, Michael. “Some of My Best Friends Are Germs.” The New York Times. The New York Times, 18 May 2013. Web. 09 Mar. 2014. <>.

3) Palmer, Chana, Elisabeth M. Bik, Daniel B. DiGiulio, David A. Relman, and Patrick O. Brown. “Development of the Human Infant Intestinal Microbiota.” PLOS Biology:. N.p., 26 June 2007. Web. 09 Mar. 2014. <>.

The Secret To Clear Skin

Recently in Biology 120 we read an article called “Some Of My Best Friends Are Germs” by Michael Pollan. Throughout the article he talked about the different microbiota on our skin and in our gut and mouth. He did not, however, directly discuss the relationship between these microbiota, which left me wondering how they are related. More specifically, I was particularly interested in the gut and skin microbiome. So how exactly are the gut and skin microbiota related?

To investigate this, I found a study that examined small intestinal bacterial growth (SIBO) and rosacea. In the study, patients (as well as controls) went through lactulose and glucose breath tests to evaluate the presence of SIBO. Those who tested positive were placed into random groups to either receive rifaximin therapy or a placebo, and after 1 month the patients were assessed to see if the disease had been treated. In addition, before and after the treatment, two dermatologists evaluated rosacea patients. It turned out that after patients had been treated for their SIBO, skin lesions had cleared in 20 of 28 and greatly improved in 6 of the 28, while those who received the placebo saw no change in their skin condition or it got even worse. The placebo patients were later given rifaximin therapy and 17 of 20 recovered from SIBO, and 15 of them had their rosacea virtually disappear. In summary, this study showed that those with rosacea generally have a greater prevalence of SIBO than those without rosacea. It also showed that helping to cure SIBO can completely, if not mostly, get rid of skin lesions.

So this provides evidence that there is a prominent relationship between the gut and the skin. But what are the mechanisms behind this relationship? There is something called the gut-brain axis, which essentially says the gastrointestinal tract, i.e. the gut microbiota, and the nervous system are connected through biochemical signaling. But I won’t go too much into that as this is not my point of focus. You can take a look at the video below that goes a bit more into depth on the connection between the gut and brain.

Elaine Hsiao from Caltech giving a TED talk on how the microbiota in the gut is connected to the brain. Video from http: //

More recently people have begun to investigate the addition of the skin to this axis, making it the gut-brain-skin axis instead. There is a neuropeptide called substance P that is produced in the gut, brain, and skin and plays an important role in skin conditions. Altered gut microbiota can increase the release of substance P in both the gut and the skin. In addition, the gut microbiota has an influence on the production of lipids and sebum, which is possibly why gut microbiota-altering disorders such as SIBO on skin conditions such as rosacea and acne. For example, sugar and grain carbohydrates cause a sudden increase of insulin in your body, which leads to an excess of certain hormones, which causes the pores on your skin to secrete sebum, and this ultimately causes acne by attracting certain bacteria. On the other hand, raw cultured dairy (such as yogurt), fermentable fibers (such as yams and bananas), and foods that contain omega-3 fatty acids can help to restore your gut microbiota.

I have always heard that a poor diet can lead to acne, but I never knew why this was true. Understanding the gut-brain-skin axis and eating the right foods can help heal your gut and ultimately improve your skin. After years of searching for the secret to clear skin, it turns out the easiest way to get better skin is simply to fix your gut.

Works Cited

Kresser, Chris . “The Gut-Skin Connection: How Altered Gut Function Affects The Skin.” Chris Kresser: Health For The 21st Century. N.p., n.d. Web. 15 Mar. 2014. <;.

“Optimizing Your Gut Bacteria Can Help Reduce Acne.” N.p., 21 July 2011. Web. 7 Mar. 2014. < 2011/07/21/simple-acne-treatment-works-by-helping-your-gut-brain-connection.aspx>.

Parodi, Andrea. “Small Intestinal Bacterial Overgrowth in Rosacea: Clinical Effectiveness Of Its Eradication.” Clinical Gastroenterology and Hepatology 6.7 (2008): 759-764. Clinical Gastroenterology and Hepatology. Web. 3 Mar. 2014.

Pollan, Michael. “Some of My Best Friends Are Germs.” The New York Times. The New York Times, 18 May 2013. Web. 5 Mar. 2014. <;.

The Impact of Diet on Gut Microbiota

In the article, Some of My Best Friends Are Germs, Michael Pollan discusses the relationship between the gut microbiota and bacteria. There are several factors that affect the gut microbiota, such as antibiotics, pathogens, and diet. Pollan explains that the gut microbiota differs significantly depending on geography; diversity in the Western gut is much lower compared to the guts of Africans and Amerindians. Pollan attributes diet as one of the reasons for this difference (1). I found this intriguing and was curious to know exactly how and in what ways diet impacted gut microbiota. What does the gut microbiota of an African child compare to that of an European child? Does diet play a significant role in this difference? A study published in 2010, Impact of diet in shaping gut microbiota by a comparative study in children from Europe and rural Africa, investigates and compares in depth how diet affects the gut microbiota of children aged 1 to 6 in rural Africa with that of Western European children (2).

In this study, researchers compared the fecal microbiota of 14 children from a village in Burkina Faso (BF) with that of 15 European children (EU) in the urban area of Florence, Italy. The diet of BF children is predominantly vegetarian, low in fat and animal protein and rich in starch and fiber. All food is produced locally and harvested nearby the village. The diet of EU children is high in animal protein, sugar, starch, and fat and low in fiber. The amount of fiber in a BF diet is 2.26% in 1 to 2 year old children and 3.17% in 2 to 6 year old children. The amount of fiber in a EU diet is 0.67% in 1 to 2 year old children and 0.9% in 2 to 6 year old children. In both cases, the amount of fiber in a EU diet is significantly lower than in a BF diet. (2).

The researchers then generated a dataset of gene sequences to characterize the bacterial lineages in the fecal microbiotas. They found that more than 94.2% of the sequences in all of the BF and EU samples belonged to the four of the bacterial phyla: Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. Actinobacteria and Bacteroidetes were more abundant in BF microbiota, whereas Firmicutes and Proteobacteria were more abundant in EU microbiota. EU children have twice as many Firmicutes; the ratio between Firmicutes and Bacteroidetes in EU children was 2.8 and 0.05 in BF children. This ratio increases with weight gain on a high-calorie diet and decreases with weight loss on a low-calorie diet. Therefore, it can be concluded that the higher ratio in EU children is influenced by their high-calorie diet and will predispose them to obesity (2).

The researchers also compared the microbial richness and biodiversity. They found that microbial richness and biodiversity in BF samples were higher than in EU samples. A high-fiber diet could increase beneficial bacterial genomes and enrich the microbiome, which is why scientists believe that the striking absence of non-infectious colonic diseases in Africans could be due to a high-fiber diet low in sugar, fat, and animal protein (2).

I found a video on YouTube that describes more in detail Firmicutes and Bacteroidetes (3). To briefly summarize, this video states that the gut flora of obese people have high numbers of Firmicutes than Bacteroidetes. People on diets for a year can change this proportion, while giving people certain antibiotics may actually trigger obesity. We can improve this ratio by ingesting more polyphenol, a natural nutrient found in certain fruits, green tea, and vinegar. Polyphenols do two things: they preferentially feed Bacteroidetes while at the same time suppress the growth of Firmicutes.

Whether it be fiber, as in the case of the study of children, or polyphenol, as mentioned in the video, the commonality between these two is that they increase the proportion of Bacteroidetes in the gut, which researchers believe evidence of this link may combat obesity. This then got me thinking: if having more Bacteroidetes supposedly helps with weight loss, why isn’t there a capsule or supplement of Bacteroidetes bacteria? Sure enough, on Google search I was able to find a website that sells Bacteroidetes supplement powder. Instructions say to mix one tablespoon of the supplement with 5 to 7 ounces of water. The website states that natural long-term usage of this supplement is very safe and claims to “change the bacteria in your gut to change your body” and “extract less calories from the same meal” (4). Granted, the validity and source of the website is questionable, but the idea of obesity not only being caused by overeating and inactivity, but also the idea that some people are predisposed to obesity because of the ‘makeup’ of Bacteroidetes and Firmicutes in their gut microbiota, is a fascinating and revolutionary idea. This got me further thinking about the relationship between genetics and weight. Many people who are naturally thin attribute this to their “genes” and “fast metabolism”. What does this actually mean? Could it be possible that Firmicutes and Bacteroidetes in the gut microbe play a role in this? Do these people “start off” with more Bacteroidetes in their gut? I believe it would be worth studying to further understand this relationship—if there is one.


1. Pollan, Michael. “Some of My Best Friends Are Germs.”New York Times 15 05 2013, n. pag. Web. 11 Mar. 2014.

2. De Filippo, Carlotta, Duccio Cavalieri, et al. “Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa.”PNAS. 107.33 (2010): 14691-14696. Web. 11 Mar. 2014.

3. “Tipping Firmicutes to Bacteroidetes.” Online video clip. YouTube. YouTube, 30 Aug. 2012. Web. 6 March 2013.

4. “Weight Loss.” ProBiotic-Lab. ProBiotic Lab. Web. 5 Mar 2014. <;.