Direct and indirect functions of the bacterial flora within the human gut

Heather Campbell
 min read

What are the direct and indirect functions of the bacterial flora within the human gut?

Direct and indirect functions of the bacterial flora within the human gutThe bacteria of our microbiota contribute to the physiology of our gut, which occupies a central and multifunctional place in our body.

They originate in the richness of our microbiome:

  • Direct, the bacteria depend on their own activities
  • Indirect, bacteria result from their collaboration with our cells

In general, bacteria allow us to benefit from the food we consume while also avoiding wasting part of it. They have an essential and intricate role to play in our immune system and, together with the right nutrition, will determine our physical and mental good health.

But if bacteria control and modulate some of our functions, these controls and modulation can be inversely related.

Indeed, if bacteria can influence our physiology, we can, in turn, influence the composition and functionality of bacteria in ways you couldn’t imagine possible. Read on to learn all about it.

Bacterial flora in the small intestine and the colon: Introduction

Direct and indirect functions of the bacterial flora within the human gut is a complex matter.

The main functions of our small intestine are digestion and immunity.

The contribution of bacteria to digestive functions is limited because they have their own chemical and enzymatic arsenal.

The transit is fast, which reduces the possibility for bacteria to intervene. Bacteria remain, however, an essential player in our immune activities.

It is, in particular, the implantation of bacteria that triggers our immune system after our birth. Then, bacteria contribute to its maturation and intervene in its functioning throughout our lives.

In our colon, or large intestine, the situation is different. Indeed, bacteria are an essential actor in many of its functions.

Their interventions are direct and indirect and are not limited to the colon’s digestive functions.

They can concern several other physiological activities in which they participate:

  • The activities of its autonomic nervous system
  • Endocrinology
  • Immunity
  • The barrier function

Functionality of bacterial flora in the gut

Our gut ensures or contributes to several important functions of our body.

If, with regard to the functionalities of the small intestine, the role of bacteria is undoubtedly limited, the situation is very different in the colon, where they ensure or actively contribute to several of its physiological functions.

Their multiple functionalities originate from their huge gene pool. Direct and indirect functions of the bacterial flora within the human gut is therefore also of a genetic disposition.

This genetic richness allows them to directly exercise or participate and modulate several colonic functions and, through it, of the whole body.

In turn, this can also influence their activities. Bacterial functionalities add a dimension and complement the colonic functional diversity.

They are:

  • Direct when they provide them alone
  • Indirect when they result from symbiotic associations with its own cells

Direct functionality of bacterial flora in the gut

The synthesis of amino acids, vitamins and neurotransmitters


Some bacteria produce several molecules that participate in the transmission of our nerve impulses. These molecules are called neurotransmitters.

They also produce a large number of other molecules that, when resorbed and passed into the bloodstream, act as signals to stimulate or inhibit various cellular activities in the tissues of our body, including our brain.


A vitamin is a molecule that is essential to our life but that our body does not have the capacity to produce itself.

Therefore, it is imperative that we obtain them in our food or the form of food supplements.

This is where bacteria come in again to help us, at least partially. Some bacteria in our colonic microbiota have the ability to make and supply us with some of these vitamins.

Of course, this source does not generally cover all of our needs, but it contributes significantly. Therefore, we must always make sure to acquire the missing balance in our diet.

Direct and indirect functions of the bacterial flora within the human gut therefore also contribute to the activities of our nervous system.

Amino acids

Amino acids are the small molecules that build our proteins.

For example, our digestive enzymes are the main components of our muscles. Our bacteria help to produce some of them.

The transformation of non-nutritive chemical compounds

Some foods may contain (often if industrially produced) non-nutritive, sometimes undesirable chemical compounds, usually present in mixtures.

Their origins are either accidental (environmental toxins) or the result of:

  • Industrial processes using various additives (colorants, emulsifiers, taste and texture modifiers, etc.).
  • Intensive agricultural practices that use many chemical inputs (fungicides, pesticides, fertilizers, herbicides, etc.)

They can also be generated by certain culinary practices (e.g. barbecuing) or by industrial techniques.

As often in biology, nothing is simple. Indeed, when we ingest them, these chemical compounds are, for us, generally biologically neutral.

The benefit or toxicity

Direct and indirect functions of the bacterial flora within the human gut may be beneficial or harmful to us (humans) and/or to bacteria.

For this, they must first be transformed into more reactive intermediates, which are the real beneficial or toxic agents. But often, these too can undergo transformations that render them inactive and facilitate their elimination.

The benefit or the toxicity is thus, very frequently, the result of a set of reactions, present in the organism which they attack, and which increase or decrease them.

Because of our great genetic diversity, some of the bacteria that make up the microbiota of our colon and probably also of our small intestine may be involved in these complex processes.

This involvement can either increase or decrease in the beneficial action or toxicity of some of these chemicals. By directly influencing this balance, they can therefore increase or reduce the risks of a benefit or toxicity.

But there is more to these mechanisms than meets the eye.

Apart from their potential role in chemical toxicity, some activities of our bacteria contribute to preventing a toxic action or, even better, to make possible the beneficial action of chemical compounds present in certain foods.

Without their presence, these compounds would not be able to give us the benefit of their positive effects.

These examples once again confirm the complexity of our contributions to colonic functionality. They are rarely the result of one but usually of several activities, sometimes contradictory, for which some of our bacteria are responsible.

Related post: What are the consequences of imbalance of intestinal microflora?

Resistance to intestinal infections

The second direct and major role of bacteria in our digestive tract is protection against intestinal or colonic infections, whether they are of food or environmental origin.

This again shows some of the many direct and indirect functions of the bacterial flora within the human gut.

In fact, in the arsenal of bacteria, they have different means of defense, generally effective, to fight and prevent the implantation and proliferation of bacteria and other undesirable microorganisms that can cause us diseases, sometimes very serious.

These roles are grouped under resistance to colonization.

Among our efficient bacteria in this matter, we know of at least one, the bifidobacteria species (commonly called bifidus that we consume in different fermented milk products).

Several mechanisms are involved in this resistance:

  • Cannibalism
  • Competition for sites of adhesion to the epithelium
  • Production of acids or antibacterial compounds called bacteriocins
  • Competition for nutrients

A well-diversified and properly nourished microbiota can provide effective protection against the proliferation of these pathogens and ensure effective resistance to colonization.

This way you are protected from intestinal infectious diseases and you resist certain food poisoning, two indicators of good vitality.

Colonic fermentation and stool production

Despite all the powerful digestive mechanisms that act throughout our digestive tract, some complex components of our food remain undigested and unabsorbed.

It is this fraction that is called dietary fiber. It is recommended that you consume at least 1.06 ounces each day.

Characterized as non-digestible, it have been crushed, kneaded, triturated but could neither be decomposed into assimilable elements, nor absorbed.

It arrives chemically intact in our colon. Then, bacteria intervene to break it down by subjecting it to a different and complementary digestive process called fermentation.

Thanks to the great genetic diversity of bacteria, fiber can encourage fermentative activities, none of which is encoded in our own genome.

The presence of bacteria offers us the possibility of supplementing our diet with non-digested, non-digestible food that would be worthless and eliminated without bacteria.

A specific function of the colon linked to the presence of bacteria is to receive an undigested residue of the food bolus, entrusting certain bacteria with the task of degrading and transforming it.

Other bacteria can then absorb the products of this transformation and benefit from its food value.

Related postHow does nutrition affect the microbiome? 4 vulnerable areas of concern

Difference between digestion and fermentation

Starch is a good example to understand the difference between digestion in the upper part of the digestive tract (stomach and small intestine) and fermentation in our colon.

This very large molecule, which we consume daily, is composed of hundreds or even thousands of copies of a small molecule called glucose (one of the two components of what is commonly called sugar).

It is the favorite food of the majority of our eukaryotic cells. Starch is present in many common foods, such as cereals and starchy foods, especially potatoes, making up most of the raw mass.

Eat hot cooked potatoes

When we eat hot cooked potatoes, the enzymes in our small intestine completely break down the starch in the upper part of our digestive tract.

All the glucose molecules thus released are absorbed and enter the bloodstream.

They feed the majority of our cells including our brain. They have no nutritional value for our colonic microbiota.

Eat cold, cooked potatoes

If we eat our cooked potatoes after letting them cool down to make a salad, then everything changes!

Indeed, because of a physical modification of its structure, the cooked and cooled starch has become resistant to intestinal digestion because our enzymes no longer recognize it.

As a result, it remains chemically intact throughout its journey through our stomach and small intestine and transferred chemically intact into our colon. And that’s where the bacteria come in.

In fact, most of the bacteria feast on it, break it down and transform the glucose molecules thus released into different products.

For the most part, these are absorbed in our colonic epithelium before being carried by the blood and feeding our cells, thus creating a complex food web.

Some bacteria feed on the rest. The intervention of the bacteria has, therefore, avoided food waste. At least for those who like potato salad.

But this is just an example to help people understand what is going on in our colon. In total and thanks to the bacteria, a little more than 55% of the dry weight of the undigested food bowl entering the colon is finally used.

The bacteria thus contribute to the completion of digestion.

The undigested and unfermented residue

Despite the great metabolic diversity of all our bacteria, this is not enough. An undigested and unfermented residue always remains.

Cellulose, for example, is not digested in the upper part of the digestive tract, but it is also resistant to attack by our bacteria.

Indeed, because of a subtle difference in chemical structure and although composed of the same molecules as its cousin starch, cellulose also resists fermentation in our colon.

This explains why if we eat a sheet of paper (composed mainly of cellulose), it will have no food value. It will be excreted in its entirety in our feces, although physically different and not visually identifiable, but chemically intact.

You have to be a ruminant (a cow or a sheep, for example) and have two stomachs and special microbiota to digest it and thus feed on it, which allows your animals, but not humans, to graze on the grass.

There are many other examples of these undigested and unfermented residues in our food. This does not mean, however, that they are useless to us.

On the contrary, together they form an indestructible matrix that plays an important role in our colon and the whole economy of our body.

They serve as a solid support on which certain bacteria and other microorganisms, sometimes pathogenic, but also various molecules, sometimes toxic, are adsorbed.

They help to facilitate the elimination of pathogens or toxic chemicals by adsorbing them before excreting them in our feces. Retaining water, they also contribute to the mechanoreceptive excitation of the submucosa and to the distension of the colonic wall and thus facilitate fecal transit.

These non-digestible and non-fermentable components of the food bolus constitute at least 21% of the dry fecal weight and form a kind of ballast.

In addition to the mass of dead or living microorganisms (a little more than 55% of the dry weight of the stool), they contribute significantly to the second digestive function in which bacteria participate, namely the production of our stools and the regulation of their excretion.

In fact, their weight is directly related to the amount of non-digestible and non-fermentable compounds that we ingest each day.

Indirect functions of bacterial flora in the intestines

The contributions of indirect bacteria to the functionality of our colon involve the biodiversity of bacteria in active partnership with some of its cells. They involve the structural complexity of our colonic mucosa.

They influence all the activities to which it contributes as well as its interactive connections with other tissues and organs in our body (including our brain).

These partnerships establish and/or optimize functionalities of the colonic mucosa as important as its sealing, its immunological and endocrine activities, and, probably also, those related to the nervous system present in our gut.

The production of hormones

The most recently explored area in which bacteria play several modulating roles is that of hormone production by our small intestine and colon but also, indirectly, by certain areas of our brain.

In our colon, this activity is linked to the presence of specialized cells (called L and K cells) that derive from the stem cells of the epithelium through selective differentiation.

Through bacterial biodiversity, bacteria actively participate in the modulation of this differentiation and, therefore, in the production of these cells, known as endocrine cells, and, in fine, in the production of their hormones.

The ones they secrete are numerous and their targets are multiple and varied. The microbiota – intestine – brain – immune system axis would play a key role in our vitality.

The tightness of the colonic mucosa

The first area where bacteria are active partners of our colon is the sealing of our colonic mucosa, one of the colon’s fundamental properties.

Without being absolute, it must be selective, allowing or even controlling the transfer of nutrients while preventing the passage of microorganisms or undesirable compounds into the body with maximum efficiency.

This waterproofing is of varying nature:

  • Physical and ensured by the mucus, these sticky secretions cover the colonic epithelium.
  • Biological and linked to the presence, between the cells of the epithelium of the bacteria, of proteins which maintain them tightly stuck to each other without open space. These structures, which link cells together, are called tight junctions composed of specific proteins.

Bacterial biodiversity influences the expression of genes in the cells of our colon that control the production of proteins responsible for sealing and that are part of the composition of tight junctions.

When this expression is adequate, these proteins are produced in appropriate quantities to establish sufficiently tight intercellular connections while allowing the necessary passages.

The production of quality mucus is also dependent on the biodiversity of bacteria from the very first moments of our lives.


The most studied field, where the intestinal symbiosis is exercised, is that of immunity.

Its main mechanisms protect us against foreign bodies (inanimate like food antigens or living like viruses or bacteria).

They also neutralize and eliminate the cells which, within our body, develop in an abnormal or anarchic way (for example cancerous cells).

As far as the small intestine is concerned, this is the main function with which bacteria are associated. In the colon it is added to all the other functions.

Bacteria play a key role in our immunity from the very first moments of our extra-uterine life.

Certainly, maternal immunity guarantees the coexistence of mother-embryo/fetus who accept each other during the whole pregnancy.

But it is the digestive implantation of bacteria that serves as the trigger event for the development and subsequent support of immune activity.

This is essential for our vitality and for our survival as a single person living in an often hostile universe. This primitive immune system, which we acquire at birth, is immature.

It has been compared to a computer equipped with hardware and software but without any data, files, folders, etc. to store or process.

It is the role of bacteria and microbiota to feed the memory of this computer, in other words our immune cells, and to create the first data directory.

When it reaches maturity, our intestinal immune system recognizes and inactivates the bacteria that have contaminated our microbiota and are a risk to our health.

Indeed, it has very efficient mechanisms to identify a small number of these intruders in the huge population of our beneficial bacteria.

These activities, linked to our biodiversity, also play a key role in the opening and maintenance of an intestine – hormones – brain axis.

Indirect functionalities of bacterial flora in the gut: Recap

Indirect bacterial functionalities are active in the small intestine and/or the colon.

They involve, on the one hand, the biodiversity of microbiota.

On the other hand, they involve the structural complexity of the intestinal mucosa and all the functions to which it contributes as well as its connections with other tissues and organs in our body (including our brain).

The production of hormones

Through the symbiosis in the gut, the bacteria participate in the modulation of the production of hormones by the intestinal epithelium, mainly colonic.

These act either by direct binding to a specific target controlling a particular metabolic process, or indirectly through the vagus nerve which connects to the brain.

After stimulation by the hormone, this nerve sends a signal to the brain, which in turn stimulates an organ via an afferent nerve or the production of other hormones.

Recently, other complex mechanisms involving gut bacteria in hormone-immune system interactions and even psychosocial behaviors have been discovered.

The sealing of the mucosa

The first area where this indirect functionality is exercised is that of the sealing of the intestinal epithelium designed to prevent the passage of microorganisms and undesirable compounds.

It is selective and involves two mechanisms depending on the biodiversity of microbiota.


The most important area remains immunity.

It is exerted from the time zero of the extra-uterine life when the bacteria implant in the digestive tract, implantation which triggers its activation and its development.

This intestinal immunity quickly becomes the most important branch of all the body’s immune activities, occupying a little more than 20% of the intestinal mucosa and ensuring more than 65% of all its activities.

Gut microbiota are, throughout life, one of the key factors in the modulation of our immune responses.

Functions of bacterial flora in our gut: Conclusion

Many are unaware of the importance of the direct and indirect functions of the bacterial flora within the human gut.

They are the first thing to be absorbed when passing from a sterile environment before birth, and continue to accompany us throughout our adulthood.

They help with our mental health, and are essential in the fight against free radicals so freely distributed in the Western world.

About Heather Campbell

As a nutritionist, my field of specialization is science-based nutritional advice but more importantly, it is my goal to share capturing and inspiring stories, examples and solutions which can help plus-size individuals overcome their specific difficulties. Read More