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...

Introduction to the Gut Microbiota

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

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 millilitre 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).

Symbiosis in the Gut Microbiota

Microorganisms inhabiting our gut are symbionts. They live in symbiosis with us, stablishing beneficial 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.

Variability of the Gut Microbiota

Human microbiome, specially the gut microbiota varies widely between subjects.

Every 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.

Development of the Gut Microbiota

When is the gut microbiota formed? How do they get there? When is the symbiotic relation stablished?

mode of delivery and gut microbiota

Mode of Delivery

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. 

Childs delivered "naturally" showed a higher number of Bifidobacterium and Bacteroides, related with a healthy gut microbiota (study)(study).


Child Feeding

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).

Breastfeeding could also ameliorate the possible disruption made to those childs being born by Caesarean section (study).

The oligosaccharides contained in human milk are not digested by the child, acting as prebiotics for our gut microbiota.

Breast milk results in higher immune system activity and proliferation of IgA (study)



The high subject variability in microbial composition and richness also depends on the family genetics and genome. Human genetics shapes microbial composition (study)


  • 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 the Gut Microbiota

Factors Modulating Gut Microbiota

The gut microbiota changes along lifespan, and we are able to modulate and make slight changes in our lifestyle and habits to avoid the possible adverse effects of dysbiosis (unhealthy microbiota)


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).

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 fibre content and protein. Diets high in fibre have shown an increase in beneficial species (study).

Fibre 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, regulating and improving the immune response and intestinal barrier (study).

A western diet is not of interest when trying to achieve a healthy gut microbiota.

Usually being high in simple sugars and trans-fats, it leads to an increased production of insulin and bile acids. These will lead to a proinflammatory immune response and deteriorated intestinal barrier.

High intakes of protein, mainly coming from red meat, may lead to overdose of amino acids. 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).

Certain nutritional protocols like paleo diets also showed to improve gut microbiota composition and richness

Physical Activity

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.

Physical activity and body composition modulate and improves your microbiota (study).

High caloric intakes coming from 'real foods' also lead to the production of higher amounts of SCFA and other metabolites that can be beneficial for our organism.

Probiotics and prebiotics have been highly consumed by athletes lately, being a cause of improved microbiota composition and diversity.


Chronic stress is considered a dysbiosis promoter (study). Many of the metabolic consequences of stress implicate systemic inflammation, including intestinal inflammation (study).

Stress has a negative impact on your gut microbiota. Inflammation increases cytokines and interleukins, associated with a change in gut microbiota (study).

In this study, stress could increase the phyla Clostridium and decrease Bacteroides, leading to dysbiosis and higher risk of diseases related with the gut microbiota.


Antibiotics are pharmaceutical products used against microbial species to cure or improve disease status.

Most of these antibiotics are non-specific, and act on more than one different microbial species.

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).

After antibiotic exposure the gut microbiome fully-recovers within approx. 6 weeks (study)


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 environment 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.

We have seen that dietary habits, stress levels, physical activity, antibiotic exposure and hygiene play a role modulating and shaping your microbiota.

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

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