gut microbiota

Developing a Healthy Gut Microbiota [Science-based]

Microorganisms are generally associated with diseases and pathogens. However, there are millions in microorganisms living inside us. These form what we know as human microbiome. But for now we'll only talk about gut microbiota and its implications on our metabolic health.

Humans and microorganisms have lived in symbiosis for ages. In fact, almost our entire body surface is colonized by symbiotic microorganisms. From the skin to the colon or the vagina, there are millions of different microorganisms living and helping us carrying out the different biological functions.

If you want to know what's the gut microbiota and why it's important for our health, this 5min read is for you. Enjoy it...


For now we know that the human microbiome is a combination of all the microorganisms living in different parts of our body surface. If we look at the intestinal tract, we can find the gut microbiota.

Gut Microbiota

Although the gut microbiota inhabits all three organs of the digestive tract (stomach, small and large intestine), most of what we know refers to the microbiome of the large intestine. Densities of 10¹¹ per each mililiter are common there (source), varying between different sections of the intestinal tract. The most inhabited section is the colon, in where mostly fermentative microbial species are found. Close to 400 species inhabit our body, typically being from the BacteroidetesFirmicutesActinobacteria, and Proteobacteria phyla (source).

Microorganisms inhabiting our gut are symbionts. They live in symbiosis with us, stablishing benefitial biological interactions between two or more organisms. That is, we give them a place to live, and they in return help us achieving different functions to sustain our health.

Human microbiome, specially the gut microbiota varies widely between subjects. Each gut microbiota is unique, depending on various factors such as lifestyle, diet, location, hygiene,... The composition and richness of the microbiota are the two main aspects to control the state of our microbial communities. If they are disrupted, from low to severe adverse effects may arise.


When is the gut microbiota formed? How do they get there? When is the symbiotic relation stablished? We'll go through that in just a second...


Gut microbiota is firstly formed during birth. It has been shown that the mode of delivery is the first fact that determines your microbiota composition (systematic review).

In this systematic review performed in 2016, it was seen that childs that were born through Caesarian section showed lower abundance of Actinobacteria and Bacteroides and higher abundance of Firmicutes. On the other hand, child delivered "naturally" showed a higher number of Bifidobacterium and Bacteroides, related with a healthy gut microbiota (study)(study).


It's also believed that the gut microbiota is mainly formed and stablished during the first years of life. After birth, the main factor regulating microbial composition is feeding. When compared to formula's feeding, breast milk results in a considerably more well-established and regulated gut microbiota with higher richness of species, including Bifidobacterium and Bacteroides (study). In fact, breastfeeding could also ameliorate the possible disruption made to those childs being born by Caesarean section (study).

Being the only source of nutrient in early life, human milk shows a high-quality nutritional matrix. The oligosaccharides contained in human milk are not digested by the child, acting as prebiotics for our gut microbiota. Also, it has been seen how breast milk results in higher inmune system activity and proliferation of IgA (study)


The high subject intervariability in microbial composition and richness is also constrained by the family genetics and genome. Human genetics shapes microbial composition (study), being a factor to use when explaining why we have different microorganisms.

After the first 6-7 years of life, gut microbiota is fully-established and almost permanent. During adult ages, no severe changes are likely to happen to your gut microbiota. However, slight dysruptions in composition and richness due to changes on diet, physical activity... can compromise overall health.


  • Gut microbiota forms all the microbial species inhabiting the digestive tract

  • It's developed and stablished during the first years of life

  • The main aspects for the development is mode of delivery, feeding, and genetics


Factors Modulating Gut Microbiota

As it happens with mostly everything related with metabolism and health, we are able to modulate and make slight changes in our lifestyle and habits to improve it and avoid the possible adverse effects of dysbiosis (unhealthy microbiota)

Once the microbiota is formed and stablished during the first 10-12 years of life, it doesn't undergo huge changes along our adulthood. In fact, it' not until we start 'aging' (+40-45 years) when our gut microbiota starts deterioritating and suffering more permanent changes. This is why first years of life are crucial for having a healthy and well-stablished microbiota.

One very interesting experiment performed fecal transplants between two different species: germ-free mice and zebrafish. What they encountered was the gut microbiota of both species surprinsingly resembled to that of their own species even after the transplant (study). These findings opened a new gate to think that the host (us, in this case) have different mechanisms by which we can modulate and shape our gut microbiota to get it working as we need.


It's not hard to think that dietary habits could change gut microbiota. Microbes use and convert some of our waste-products coming from food into molecules that we can use as energy source or some other functions. Different diets have shown to modulate composition and diversity of the gut microbiota (source). However, as I explained you before, these changes are not permanent, and composition goes back to normal within 3-4 days after intervention.

The main aspects of our diet modulating gut microbiota is fiber content and protein. Diets high in fiber have shown an increase in benefitial species (study). Fiber are non-degradable carbohydrates being used by the species found in the colon to produce short-chain fatty acids (SCFA). These molecules are used by our organism to produce energy.

These SCFA can also enhance intestinal mucus secretion and antimicrobial peptides, thus regulating and improving the immune response and intestinal barrier (study).

In this image describng the main benefits / adverse effects of dietary habits on gut microbiota, you can easily see why a western diet is not of interest when trying to achieve a healthy gut microbiota. Usually being high in simple sugards and trans-fats, it leads to an increased prduction of insulin and bile acids, respectively. These will lead to a proinflammatory inmune response and deteriored intestinal barrier. High intakes of protein, mainly coming from red meat, may lead to overdose of aminoacids. The surplus will be used my our microbiota to synthesize metabolites that are toxic for our organism (source).

Lastly, there are some foods considered pro/prebiotics, such as cocoa flavanols (read about it HERE). Not only that, but certain nutritional protocols like paleo diets (read about it HERE) also showed to improve gut microbiota composition and richness


You may think that physical activity and gut micrObiota have nothing to do with each other. But it's not the case. Both aspects are highly interconnected, and one can benefit the other to a great extent. A healthy microbiota increases oxygen uptake, important aspect in cardiovascular sports and aerobic physical activity (study). It also produces sources of energy such as SCFA.

Athletes usually show higher diversity and richness of beneficial microbial species than other subjects suffering from obesit or any other metabolic disease. This suggest that physical activity and body composition modulate and improves your microbiota (study).

These subjects generally follow a well-planned diet, avoiding excess of ultraprocessed foods. High caloric intakes coming from 'real foods' also lead to the production of higher amounts of SCFA and other metabolites that can be benefitial for our organism. Additionally, probiotics and prebiotics have been highly consumed by athletes lately, being a cause of improved microbiota composition and diversity.


Chronic stress -frequently seen in actual society- is considered a disbyosis promoter (study). Many of the metabolic consequences of stress implicate systemic inflammation, including intestinal inflammation (study). As you may have guessed by know, stress modulates and has a negative impact with gut microbiota. Inflammation increases cytokines and interleukines, associated with a change in gut microbiota (study).

It was seen in this study that stressor could increase the phyla Clostridium and decrease Bacteroides, leading to dysbiosis and higher risk of diseases related with the gut microbiota.


Antibiotics, as you may know, are pharmaceutical products used agains microbial species to cure or improve disease status. Most of these antibiotics are non-specific, and act on more than one different microbial species. So if we abuse or have to take them for any reason, it would act on our gut microbiota as well.

These substances are considered the major disruptors of the gut microbiota. They can have several effects, in where we find a decreased microbial diversity, altered metabolic mechanisms and microbial metabolism, or risk of infections such as Clostridium Difficile Infection (CDI) (study). Use of antibiotics has also been linked to an increase in pathogenic species such as Salmonella typhimurium or Escherichia spp (study).

But don't worry if you have been prescribed antibiotics. It's been shown that after antibiotic exposure the gut microbiome fully-recovers within approx. 6 weeks (study). The ability of reproduction and disperal of microorganism is huge when compared to mammals or other organism. They are able to divide and create offspring within hours, and generations take place within days


Microorganism have mainly from the outside, and exposure to the environment is crucial to determine microbial composition and diversity. In fact, a correct and normal exposure to the environmet is crucial for establishing a healthy microbiota (study).

Early gut colonization and development acts as a trigger to develop and enhance innate immune system (study). If we abuse of hygienic methods and absolutely avoid public surfaces, it could compromise innate immune system, increasing the risk of autoimmune disease or diseases caused by microbial species.


  • Once gut microbiota is stablished, only temporal changes may be induced

  • Macronutrients and fiber content are the main dietary modulators of gut microbiota

  • Physical activity has been proved to improve gut health

  • Antibiotic exposure may deteriorate gut microbiota, but it's fully recovered after approx. one month


In this post we have briefly introduced gut microbiota and the main factors to determine a its health. First years of life are crucial for establishing a healthy microbiota. After those years, only temporal changes can be induced. However, we have seen that dietary habits, stress levels, physical activity, antibiotic exposure and hygiene play a role modulating and shaping your microbiota.

After reading this post I hope you learned what the gut microbiota is and how we can modulate it to achive a healthy microbial diversity and composition.

If you have any question regarding this topic (or any other) leave your comment below on the comments section!

4 thoughts on “Developing a Healthy Gut Microbiota [Science-based]”

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