Gut Microbiome 101

In the last 15 years, there has been a huge increase in scientific research related to the gut microbiome. Even for the general public, an Internet search using words like “gut microbiome” or “gut microbiota” generates between 1 and 2.2 million results. Of course, the food industry took advantage of it. Probiotics supplements (see previous article)  and ”fermented food” can now be found in almost every drugstore and natural health products store. Health gurus are also all over the place with many claims of the ”superpowers” of the gut microbiome on our health. But what is true and what do we really know about it? Let’s dive deep on everything gut microbiome.

What is the Gut Microbiome?

The term ”gut microbiome” is defined by the great and diverse community of microorganisms that is found in the human intestinal tract. This includes bacteria, fungi, viruses, and protozoa. We can count over 100,000,000,000,000 (1014) microorganism in the human body. Just to give you an idea, it’s 10 times more microbial cells than the number of cells in the human body.

Are we born with it a microbiome? Does it develop through life?

Previously, it was thought that the first colonization of the gut microbiome was during the birth process. Nevertheless, science constantly evolves and new studies showed that there are actually microorganisms in the amniotic fluid, umbilical cord and placenta. More studies are needed to have a better understanding, but this work opens a door to the importance of maternal gut microbiome health. This being said, the delivery mode influences the baby’s microbiota during the early stages. An infant born by vaginal way will be exposed to vaginal microbiota which is quite different from skin and operation room bacteria’s during a caesarian section.

Story Time: In ancient times, when a woman would give birth, the oldest member of the family (the grandfather or great-grand-father) would spit in the newborns mouth in order to transfer the good bacteria. This was believed to increase the child’s immunity.

Breastfeeding has shown some beneficial effects over formula feeding in newborns on their proportion of good bacteria such as Bifidobacteria in the gut. This is shows us how important the diet is on our microbiome composition (we will be addressing this later in this article). As babies grow up, their microbiome grows too. An adult will have about 1,000 different species in their gut microbiome compared to about 100 in a young infant. The new microbes are introduced through various environmental factors, and especially by the foods we eat.

The changes in a child’s microbiome often mimic their changing diet. For instance, babies get their dose of vitamin B9 (folate) from their own gut microbes (as they don’t get much B9 from their nutrition). However, as adults, we’re able to get it from the foods we eat and therefore, as we grow older, we have fewer folate-producing microbes and more folate-harvesting microbes. Furthermore, ageing has a critical impact on its composition and changes are generally observed after age of 65.

Did you know the people you live with also continue to impact your microbiome profile? Yes! Whether it is parents, siblings, or roommates, people who live together tend to have more similar microbiome compositions than those who don’t. Our microbiome composition is always changing and adapting to our environment and our nutrition.

How does our gut microbiome impact the way we digest & absorb nutrients? (We are about to geek out here)

Digestion is the process by which food is broken up physically and chemically into absorbable components. It starts in the oral cavity with physical digestion by the action of our teeth and tongue (aka chewing), then goes to the pharynx, esophagus and arrives in the acidic environment of the stomach where an important part of the chemical digestion occurs. The mostly digested food (aka bolus) moves to the small intestine which is the main site of absorption in the body, especially for lipids and simple carbohydrates. However, not all substances are digested or absorbed at this point. Dietary fibre, resistant starches, and non-carbohydrate substrates travel to the large intestine before the digestion process ends with the elimination of solid waste. Gut microbiome plays a key role in aiding in the digestion of these compounds. Different microorganisms are found through the GI tract (i.e. enzymes and bacteria) but our main focus will be in the large intestine. In fact, the colon is the most important site of bacteria in the entire body and also, the most studied. These bacteria play an important role for several body’s functions.

Indeed, colonic bacteria help to increase the body’s absorption of remaining lipids, proteins, and minerals such as iron, magnesium, and calcium. The gut microbiome in the colon produce vitamins from B complex (thiamine, riboflavin, niacin, biotin, pantothenic acid, and folate) and also vitamin K. Vitamins from our food intake are absorbed in the small intestine, while the one produced by the bacteria are absorbed in the colon.

When dietary fibre, resistant starches, pectin gums and cellulose arrive in the large intestine, colonic bacteria generate enzymes (i.e. protein that breakdown foods) that will ferment these components. The metabolic waste products from this breakdown are a major group of metabolites of great interest: short-chain fatty acids (SCFAs). These chains of one to six carbons include acetate, butyrate and propionate.

Now, what’s the deal with SCFAs? In the last decades, they became an active area of research after some studies showed that they could play a major role in the prevention and management of bowel disorders, certain types of cancers and metabolic syndrome. In fact, SCFAs constitute a source of energy for our organs that used them as substrates or signal molecules. Furthermore, the level of SCFAs in the blood is sensed by a family of receptors involved in the regulation of glucose and lipid metabolism. SCFAs modulate the balance between lipolysis (i.e. fat tissue breakdown), fatty acid synthesis (i.e. creation of fatty acids) and fatty acid oxidation (i.e. breakdown of fatty acids). By activating fatty acid oxidation, lipolysis and de novo synthesis (i.e. creation of fatty tissue) are inhibited, which lead to a decrease of free fatty acids in plasma and therefore, a reduction in body weight.

Moreover, SCFAs play a role in the development of intestinal cells and leukocyte by acting as messengers between the immune system and the microbiome. Did you ever think that fibres in your morning oat would end up doing this much? This is exciting, but further research will give us a better understanding of the complex role of SCFAs.

Can the Foods We Eat Impact Gut Bacteria?

It’s a big yes! Gut microbiome is influenced by a lot of things such as environment, genetic, stress-level, physical activity but mostly, diet! As previously explained, the gut microbiome ferment non-digestible carbohydrates. A diet high in fruits, vegetables, whole grains and fibres is associated with a more diversified microbiome and an increase production of SCFAs. On the other hand, the typical Western diet: rich in fat, sugars, animal protein and depleted of fibre is associated with a low microbial biodiversity and an increase risk of obesity, coronary vascular disease, certain cancers and metabolic syndrome. Now, let’s go deeper about the effect of certain groups of foods and nutrients.


Overall, many studies found that protein consumption was positively correlated to gut microbiome diversity. However, not all types of protein have the same effect on the microbiota composition. Plant proteins were linked to an increase of beneficial bacteria such as Bifidobacterium and Lactobacillus, a higher production of SCFAs and a decreased inflammation. On the other side, SCFAs and Bifidobacterium were reduced with animal protein and count of Bacteroides was higher. Still, it is important to nuance the fact that animal proteins are often high in saturated fats, in addition to protein. (This also does not mean to avoid animal protein as they have other great benefits- however incorporating more plant based protein could be beneficial for you)


Speaking of fats, they also have their effect on the gut microbiome. Human studies have suggested that a diet high in fat would lead to a higher amount of Bacteroides in the gut. On the other hand, a low-fat diet was noted to increase Bifidobacterium. Consumption of unsaturated fat, such as found in nuts, avocados, seeds, olive oil, would have a beneficial effect on the count of lactic acid bacteria (Lactobacillus and Streptococcus) and Bifidobacteria.


There are two big families of carbohydrates: digestible and non-digestible. Digestible carbohydrates includes starches and sugars (glucose, fructose, sucrose and lactose) and are digested in the small intestine. A study from 2014 analyzing the effect of date fruit (high in glucose, fructose and sucrose) on gut microbial profile, found that human subject had a higher count of Bifidobacteria, with reduced Bacteroide. Surprising findings were observed in another study looking at the effect of lactose supplementation. Usually thought as a GI irritant in the case of lactose intolerance, lactose supplementation has actually resulted in an increase of beneficial SCFAs in the fecal concentration. It is certainly an interesting finding, but more studies will be needed to explore further effects of lactose on gut microbiome.

As previously mentioned, the non-digestible carbohydrates are fermented in the large intestine by resident microorganisms. Dietary fibres provide energy and carbon for the host. A diet rich in non-digestible carbohydrates, such as whole grain, wheat bran and resistant starch, is known to increase beneficial bacteria in the gut. On the other side, a diet low in fibres, typically seen with the Western population that roughly eat 15 g per day while the recommended intake is being above 25 g, is linked to a lower SCFA production.

Other Dietary Compounds

Probiotics and prebiotics are a hot topic when speaking about gut microbiome.

Another food compounds of interest in the gut microbiome are polyphenols. Polyphenols are commonly known for their antioxidant properties and include: catechins, flavones, flavonols, phenolic acids, anthocyanins and proanthocyanidins. Dietary sources of polyphenols are fruits, seeds, vegetables, tea, cocoa products and red wine. Their consumption was noted to increase Bifidobacteria, Lactobacilli and decrease Bacteroides, Clostridia, Salmonella typhimurium and Staphylococcus aureus.

Is there such thing as a microbiome ”imbalance”? If so, what are the impacts? How can I ”balance” my microbiome with food?

Even with a growing number of studies saying that changes in the gut microbiome composition are linked with many diseases, the definition of ”healthy gut microbiota” stays unclear. However, a condition called ”dysbiosis” is used to describe the opposite of a healthy microbiome where there is sort of an imbalance between the ”good” and the ”bad” bacteria. Several diseases have been linked to dysbiosis, such as obesity, inflammatory bowel disease, allergies and some mental illnesses. Even if it appears that changes in microbiome composition have an impact on human health, it is still unclear if dysbiosis is the result of chronic inflammation caused by those diseases or if dysbiosis act as a trigger (a classic case).

Many factors can negatively affect the gut microbiome, such as a sedentary lifestyle, use of antibiotics, and as previously discussed, a poor diet. A study from 2014 stated that dietary changes, strictly from animal-based protein to plant-based in that case, can alter the microbiome compositions within 24 hours. The return to its initial state has been seen within 48 hours of diet interruption in this study. Basically, a shift back to your good eating habits could help pretty quickly your gut microbiome.

What kind dietary habits improve our gut microbiome?

Eating a lot of vegetables, fruits and whole grains to reach at least 25-30 g of fibres per day, limit red meat, high-fat milk produces, sugar and processed foods and add some fermented foods to your diet, such as kefir, kimchi, pickles, sauerkraut, tempeh, miso and yoghurt.

Eating Disorders and Gut Microbiome

Eating disorder and gut health are very much interconnected. Check out this article to learn more


Even with data about the gut microbiome is rapidly growing, many questions are still left unanswered. Further research is needed to clarify the mysterious subject of the gut microbiome. The future of this area can’t be more exciting! In the meantime, keep a critical mind about what you read, don’t fall in the trap of health gurus and enjoy whole healthy foods!

Questions? Comments? Don’t hesitate to reach out!

The Balanced Practice is a team of professionals specialized in eating disorder outpatient treatment. We strive to provide evidence based nutrition counselling to support you, or your loved one, in achieving full recovery. Schedule a connection call now.

Marie-Pier Pitre-D’Iorio, RD, B.Sc.Psychology
Lead Registered Dietitian & Founder at The Balanced Practice

A BIG thank you to Myriam Beaudry for this article.


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Eid N, Enani S, Walton G, Corona G, Costabile A, Gibson G, et al. The impact of date palm fruits and their component polyphenols, on gut microbial ecology, bacterial metabolites and colon cancer cell proliferation. J Nutr Sci. 2014;3:e46.

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The Gut Microbiota | Elsevier Enhanced Reader. (s. d.).

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