How to Maintain a Healthy Gut Microbiome with Antibiotics, Probiotics, Prebiotics, Symbiotics and Others

Heather Campbell
 min read

How to maintain a healthy gut microbiome is essential for overall well-being.

How to Maintain a Healthy Gut Microbiome with Antibiotics, Probiotics, Prebiotics, Symbiotics and OthersAntibiotics, prebiotics, probiotics, and symbiotics are all different active ingredients whose mission is to support our intestinal microbiota.

A healthy gut microbiome is essential, and having a diet enriched with probiotics, prebiotics, symbiotics, and postbiotics is favorable for intestinal microbiota composition and bacterial diversity. These can be ingested either through diet or else by over-the-counter supplements.

We often talk about these active agents without knowing their usefulness and the impact they can have on our bodies.

If it’s health you’re after, read on to understand more about our second brain and its importance.

How to maintain a healthy gut microbiome: Introduction

A scientist once said: “In reality, we fight our germs with germs.” Indeed, our body is composed of billions of bacteria that are both good and bad for the human body.

To rebalance our intestinal flora, we are often invited to consume probiotics, and antibiotics are recommended for specific pathologies.

But do you know the difference between all these terms: antibiotics, probiotics, symbiotics, or prebiotics?

Do you know the benefits of these active agents to keep your body and digestive system healthy?

This article will define these terms and explain their function for the human body and how to maintain a healthy guy microbiome.


A lousy diet temporarily modifies our intestinal microbiota. But antibiotics will disrupt our precious bacteria, which can also unbalance our intestinal flora and cause severe dysbiosis.

However, they can also improve certain dysbiosis, characterized by the multiplication of pathogenic bacteria and/or intestinal permeability disorders. These are suspected to be signs of inflammation in the blood related to bacterial translocation.

Examples include depression, autism spectrum disorder, and bipolar disorder.

Concerning the symptoms of the autism spectrum, they often evolve in parallel with digestive disorders and are associated with inflammatory signs.

Studies have reported a beneficial but short-lived effect of antibiotics on digestive and autistic symptoms in children who were treated orally with an antibiotic that was not absorbed from the digestive tract.

An improvement in mood has also been observed after antibiotic treatment in patients with depression or bipolar disorder.

These observations provide valuable information about the impact of the gut microbiota on mental disorders. However, they do not allow us to recommend this type of treatment in the absence of well-supervised therapeutic trials.

The beneficial effects observed are often temporary, and the use of antibiotics in the case of intestinal dysbiosis and intestinal permeability disorders is certainly not without risks.


Prebiotics are food substrates whose purpose is to promote the growth of certain bacteria of the intestinal microbiota that are beneficial to health.

The most commonly used prebiotics are complex sugars, oligosaccharides, or polysaccharides, which are substrates for bacterial fermentation.

Many prebiotics target two families of bacteria, the Bifidobacteria and Lactobacilli.

Studies have shown that using prebiotics alone to improve the quality of the intestinal microbiota is not enough. On the other hand, they seem to be more effective in combination with probiotics, whose growth they promote.


The World Health Organization (WHO) describes probiotics as “living microorganisms (usually bacteria and yeast) that, when ingested in sufficient quantities, exert positive health effects beyond the traditional nutritional effects. ”

Numerous studies have been conducted and have demonstrated the benefits of probiotics on our organism, such as anti-inflammatory benefits or those that reinforce our immunity.

The nature of probiotics

Most probiotics are composed of bacteria such as Lactobacilli and Bifidobacteria. Some species of Escherichia coli, Bacillus, and yeast (Saccharomyces cerevisiae) are also present.

Probiotics and epigenetics

Like certain intestinal microbiota bacteria, probiotics can indirectly modify the epigenetics of the cells with which they are in contact through the secretion of various substances.

For example, the bacterium Lactobacillus acidophilus, which acts on DNA methylation, has a protective effect against colorectal cancer because it increases the activity of suppressor genes of this cancer.

Other bacteria such as Lactobacillus rhamnosus GG and Nissle’s Escherichia coli also alter epigenetics by interfering with microRNAs, decreasing intestinal inflammation.

Anecdote on one of the first commercialized probiotics: Escherichia coli from Nissle 1917

Still made to this very day, this probiotic bears the name of its inventor Alfred Nissle and its date of discovery.

Nissle was a bacteriologist researching the resistance of intestinal flora to infection by the typhoid fever agent.

During the first world war in Germany, many soldiers were confronted with epidemics of dysentery, which is an inflammation of the intestines and is accompanied by diarrhea.

A young German officer, wounded and repatriated to the hospital, had a particularity that immediately interested Alfred Nissle. This patient had gone through the worst epidemics of dysentery without ever being inconvenienced.

On physical examination, his stool contained unusual amounts of a particular, non-pathogenic bacterium of the Escherichia coli family.

Since then, it has been referred to as Nissle 1917 Escherichia coli, marketed under the name “Mutaflor” and consumed by many people today.

Recently, scientific research has demonstrated its effectiveness in reducing pain in people suffering from disabling digestive disorders and reducing inflammation in patients suffering from inflammatory colitis.

Other studies have also identified the mechanism of action of this bacterium, whose effectiveness was linked to the secretion of a substance, colibactin.

The beneficial anti-inflammatory properties of this bacterium are inseparable from a toxic effect that exposes users of the probiotic to serious risk. Indeed, it can cause DNA damage to intestinal cells, increasing the risk of colon cancer.

However, in 2019, a group of researchers created a Nissle 1917 strain of Escherichia coli that cannot make colibactin while retaining its beneficial anti-inflammatory probiotic properties.

The story of Nissle’s Escherichia coli 1917 shows the need to confirm the efficacy of probiotics through well-conducted studies and determine their mode of action before their widespread use.


Symbiotics are defined as the association of a probiotic with the nutrient (prebiotic) it is fond of.

Indeed, symbiotics will contain both probiotics and prebiotics. They are also defined as a mixture of living microorganisms and one or more substrates selectively used by the host microorganisms.

These host microorganisms refer to the human microorganisms and come from outside by the probiotics. There are two types of symbiotics:

  • A synergistic symbiotic, composed of a probiotic (a microorganism) and its specific substrate (prebiotic).
  • A complementary symbiotic, containing a probiotic combined with a prebiotic designed to target microorganisms.

In many research studies on symbiotics, species such as Lactobacillus, Bifidobacterium, and Streptococcus are the most commonly used live microorganisms in the formulations tested.

The substrate components are often galacto-oligosaccharides, inulin, or fructo-oligosaccharides.


Often misjudged in how to maintain a healthy gut microbiome, postbiotics are beneficial substances resulting from food fermentation by a healthy intestinal microbiota.

These active substances are mainly short-chain fatty acids (SCFAs) that act locally in the intestine and remotely on other organs. One of the most frequently researched chain fatty acids is butyrate.

Indeed, the latter constitutes the principal source of energy for the colon cells and improves the impermeability of the intestine. Therefore, it will reduce the passage of toxins, pollutants, and bad bacteria in the bloodstream.

The butyrate also improves transit by facilitating movement in the digestive tract. It has an anti-diarrhea effect and soothes intestinal disorders by rebalancing the intestinal microbiota (dysbiosis).

What about vaccination?

Recent studies have identified a vaccine process that could be very effective in preventing or treating diseases that involve inflammation or abnormal permeability of the intestine.

Some bacteria use one or more flagella to actively move around instead of being tossed around.

This system is a kind of large cilium whose agitation, produced by a small motor that uses the energy generated by chemical molecules, allows the bacteria to move.

Some bacteria use the energy of their flagella to break through the mucus layer that protects the intestinal epithelium.

The mucus is strong to oppose the penetration of these bacteria. Indeed, it contains antibodies directed against the protein composing the flagella of these bacteria, named flagellin.

However, if the concentration of these antibodies is insufficient, the defense system may be overwhelmed.

The idea of these studies was to use vaccination to increase the intestinal concentration of anti-flagellate antibodies to more effectively neutralize the propulsion system of flagellate bacteria. So the researchers injected flagellin into the bellies of mice, basically as a vaccination.

By increasing the concentration of anti-flagellate antibodies in the intestinal wall it decreased the number of flagellate bacteria in the microbiota and in the intestinal wall.

Related: For more info on gut bacteria and their benefits, check our other article Benefits of Gut Bacteria and Their Surprising Role in Human Health

The results of this vaccination effectively prevented inflammatory colitis in mice genetically exposed to this disease and reduced the risk of obesity due to a high-fat diet.

These studies open up therapeutic perspectives that could be important for anti-flagellate vaccination and the prevention or treatment of inflammatory colitis.

And anti-bacterial viruses?

In the early 1920s, a French-Canadian physician, Félix d’Hérelle, realized that the stools of soldiers who had spontaneously recovered from dysentery were capable of destroying shigella colonies.

Shigella is a pathogenic bacterium specific to the digestive tract and responsible for severe dysentery. This doctor attributed this effect to unknown microorganisms, invisible under the microscope, which he called “bacteriophages” (bacteria eaters).

These bacteriophages were viruses that attacked bacteria. In shigella cultures, the areas destroyed by the bacteriophages appeared as clear patches and were easy to identify.

Félix d’Hérelle had the idea of treating patients suffering from severe dysentery by making them ingest a solution containing the material of the clear beaches.

He had tested the safety of this treatment on himself before giving the solution to a 12-year-old child hospitalized with severe dysentery. The child healed very quickly after the treatment.

He then manufactured solutions rich in bacteriophages against the bacilli of plague and cholera. He even founded a commercial laboratory specializing in the “preparations” of specific bacteriophages for different bacteria.

Even intestinal parasites!

With the improvement of lifestyle, the diversity of the microbiota has become poorer and digestive parasitosis has become rarer. But at the same time, the number of autoimmune diseases has exploded.

Numerous studies have shown an anti-inflammatory action of many intestinal parasites, the helminths. In fact, these worms reduce the immunological action of the T-helper lymphocytes that trigger the “heavy artillery” of adaptive immunity.

These parasites have been tested to treat inflammatory colitis such as Crohn’s disease and ulcerative colitis, intestinal diseases whose cause is not precisely known but which are partly due to an excess of inflammation produced by an “irritable” immunological system.

An experiment was conducted to treat Crohn’s disease. The ingestion of live eggs of an intestinal worm of the pig, the Trichuris suis, gave encouraging results on the frequency of remissions.

However, the use of parasitic worms is not without infectious risks. Namely, the immunosuppressive effect of these parasites favors the reproduction of certain bacteria of the microbiota, exposing patients to infections with an intestinal origin.

It is likely that viral infections such as hepatitis B and C or HIV, which are very common in countries where these parasites infect a large part of the population, are favored by their depressive action on the immune system.

The interest of helminths for researchers is to propose a model invented by nature to protect these parasites from attacks by the organism.

This model could make it possible to create more manageable drugs than the eggs of these little creatures to regulate immunity when it is in excess.

How to maintain a healthy gut microbiome: Conclusion

Prebiotics, probiotics, symbiotics, or postbiotics affect the composition of our intestinal microbiota and prevent the risks of dysbiosis.

Numerous scientific studies have shown that they are a promising therapeutic alternative for treating certain diseases.

Imbalance in the gut microbiota, more commonly known as dysbiosis, contributes to the development of:

Understanding how to maintain a healthy gut microbiome is essential to restore the balance of the intestinal flora to have good health.

Having a diet enriched with probiotics, prebiotics, symbiotics, and postbiotics is favorable for intestinal microbiota composition and bacterial diversity.

They can be found naturally in some of our food products, but they can also be provided by dietary supplements.

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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