What is the gut microbiota composed of?
What is the intestinal microbiota composed of ? It is a complex ecosystem comprising bacteria, viruses, fungi, archaea and protozoa that colonize the entire digestive tract.
According toInserm () [1], the human gut microbiota hosts approximately 10<sup>14 </sup> microorganisms, which is ten times more microbial cells than human cells in the body. This community weighs between 1.5 and 2 kilograms in adults.
- More than 1,000 different bacterial species identified to date
- Viruses (the virome) in even greater numbers than bacteria
- Microscopic fungi (the mycobiome)
- Archaea, primitive microorganisms distinct from bacteria
- Non-pathogenic protozoa and commensal parasites
What exactly is the gut microbiota?
The term "gut microbiota" refers to all the microorganisms living in symbiosis in the digestive tract. It replaces the former term "gut flora," which was considered inaccurate because microorganisms are not plants.
Each individual possesses a unique composition, comparable to a microbial fingerprint. This uniqueness is influenced by genetics, mode of delivery, breastfeeding, diet, and environment.
ThePasteur Institute () [2] describes this ecosystem as "of incredible richness", with an organization in density gradients ranging from the stomach (almost sterile) to the colon (the most populated).
Bacteria: the heart of the microbiotic composition
Bacteria represent 99% of the biomass of the gut microbiota and constitute its most studied component. They are divided into several large taxonomic groups called phyla.
The two dominant phyla
- Firmicutes (40-60% of bacteria): include Lactobacillus, Clostridium and Faecalibacterium prausnitzii
- Bacteroidetes (20-40%): dominated by the genera Bacteroides and Prevotella
Minority but essential phyla
- Actinobacteria : notably Bifidobacterium, the stars of probiotics
- Proteobacteria : a phylum to monitor, as its increase often signals dysbiosis.
- Verrucomicrobia : Akkermansia muciniphila, guardian of the intestinal barrier
A study published in the journal Nature () [3] showed that the Firmicutes/Bacteroidetes ratio is a key marker of metabolic health. An imbalance in this ratio is associated with obesity and type 2 diabetes.
To learn more about the role of these bacteria, see our guide on what the gut microbiota is for.
The intestinal virome: billions of unknown viruses
The intestinal virome is the least known component of our digestive ecosystem. Yet it comprises tens of thousands of different viral species.
The majority of these viruses are bacteriophages — viruses that infect and regulate bacterial populations. They play an invisible, orchestrating role in the microbial balance.
- Caudoviral phages are the most abundant.
- Eukaryotic viruses (such as anelloviruses) coexist without causing disease
- The virome varies greatly depending on diet and immune status
Researchers at EMBLhave identified more than 140,000 viral species in the human gut, half of which were unknown before [3].
The mycobiome: the fungi of the gut
Microscopic fungi make up the intestinal mycobiome. Although they are a minority in number, they exert a significant influence on immunity and digestion.
The most represented genres are:
- Candida (especially C. albicans) — present in almost all healthy adults
- Saccharomyces — a yeast involved in the fermentation of sugars
- Aspergillus and Penicillium — present in small quantities
- Malassezia — a skin fungus also found in the intestine
Abnormal proliferation of Candida (intestinal candidiasis) is a frequent warning sign in dysbiosis, particularly after prolonged antibiotic therapy.
Archaea: Essential primitive microorganisms
Archaea are often overlooked in descriptions of the gut microbiota, yet they play a unique metabolic role. They are unicellular microorganisms distinct from bacteria and eukaryotes.
The dominant species in humans is Methanobrevibacter smithii. It produces methane (CH₄) using hydrogen generated by bacterial fermentation, which optimizes energy extraction from dietary fiber.
- Archaea represent 1 to 3% of intestinal microorganisms
- Their density increases with age
- A deficiency in archaea is associated with certain forms of constipation
Protozoa: discreet commensals
Protozoa are unicellular eukaryotic organisms found in small quantities in a healthy intestine. The most common are Blastocystis hominis and Dientamoeba fragilis.
Their exact role remains debated in the scientific literature. Some studies suggest that they participate in local immune regulation, while others associate them with functional digestive disorders.
Anatomical distribution: where do these microorganisms live?
Microbial density varies considerably depending on the region of the digestive tract. This distribution is directly related to pH, the presence of oxygen, and the transit rate.
| Digestive segment | Microbial density | Dominant microorganisms |
|---|---|---|
| Stomach | 10¹–10³ CFU/mL | Helicobacter pylori, lactobacilli |
| Proximal small intestine | 10³–10⁴ CFU/mL | Lactobacilli, streptococci |
| distal small intestine | 10⁷–10⁸ CFU/mL | Bacteroides, enterococci |
| Colon | 10⁹⁰–10¹² CFU/mL | Firmicutes, Bacteroidetes, Bifidobacterium |
The colon is by far the most populated segment. It concentrates more than 70% of all microorganisms in the human body. Our article "Where is the gut microbiota located?" details this anatomical distribution.
The metagenome: the collective genome of the microbiota
The complete set of genes carried by intestinal microorganisms forms the metagenome. This collective genetic heritage is 150 times richer than the human genome.
The MetaHIT () [4], coordinated by INRAE,catalogued more than 3.3 million distinct microbial genes in the human gut. This catalogue allows us to understand the collective metabolic functions of the microbiota.
- Vitamin synthesis (B12, K2, folates)
- Fermentation of fibers into SCFAs (butyrate, propionate, acetate)
- Degradation of xenobiotics (medicines, pollutants)
- Modulation of the immune response
- Production of neurotransmitters (serotonin, GABA)
6 factors that modify the composition of the microbiota
The composition of the gut microbiota is not fixed. It is constantly evolving under the influence of multiple internal and external factors.
- Diet : a diet rich in fiber promotes butyrate-producing bacteria
- Antibiotics : they can eliminate up to 30% of bacterial species in a single course of treatment.
- Chronic stress : it alters intestinal permeability and bacterial composition via the gut-brain axis
- Age : microbial diversity decreases after age 65
- Mode of delivery : Babies born vaginally inherit the mother's vaginal microbiota
- Physical activity : athletes exhibit greater microbial diversity
Many readers report that their gut microbiota has significantly improved after incorporating fermented foods into their daily diet. This observation aligns with data published by ANSESon the effects of prebiotics [5].
Discover how diet directly influences your gut flora in our guide to gut microbiota and diet.
Dysbiosis: when the composition becomes unbalanced
Dysbiosis occurs when the composition of the gut microbiota is disrupted to the detriment of beneficial species. It is associated with numerous pathologies.
- Chronic inflammatory bowel diseases (IBD)
- Irritable bowel syndrome (IBS)
- Obesity and insulin resistance
- Anxiety and depressive disorders (via the gut-brain axis)
- Autoimmune diseases (rheumatoid arthritis, multiple sclerosis)
- Allergies and atopic eczema
A review published in Cell Host & Microbe () [3] confirms that the loss of microbial diversity is the first marker of dysbiosis, even before the appearance of clinical symptoms.
Probiotics and prebiotics: nourishing and restoring the microbiota
Probiotics introduce beneficial bacteria, while prebiotics nourish those already present.
Food sources of probiotics
- Yogurt and kefir (rich in Lactobacillus and Bifidobacterium)
- Sauerkraut and kimchi (lactic fermentation)
- Miso and tempeh (fermented soybeans)
- Kombucha (fermented tea)
Dietary sources of prebiotics
- Garlic, onion, leek (rich in inulin)
- Green banana (resistant starch)
- Asparagus and artichokes (fructo-oligosaccharides)
- Blond psyllium (fermentable soluble fibers)
Our comprehensive guide to probiotics and their role in gut health will help you choose the right supplement for your situation.
Dietary supplements targeting the gut microbiota
The market for gut health supplements has exploded in recent years. Not all supplements are created equal. Here are the criteria to consider when choosing one.
- Number of strains : favor multi-strain formulas (minimum 5 species)
- Concentration : at least 10 billion CFUper dose
- Gastric resistance : gastro-resistant capsules withstand acidity better
- Prebiotic combination : symbiotic formulas (probiotic + prebiotic) are more effective
For a detailed selection, consult our gut microbiota dietary supplement guide.
The gut-brain axis: the microbiota influences your mood
The gut microbiota communicates constantly with the brain via the vagus nerve, the immune system, and neurotransmitters. This bidirectional axis is called thegut-brain-microbiota axis.
Approximately 95% of the body's serotonin is produced in the gut, partly under the influence of gut bacteria. A depleted gut microbiota can therefore contribute to mood disorders, anxiety, and sleep problems.
- Lactobacillus rhamnosus reduces anxious behaviors in animal models
- Bifidobacterium longum modulates the response to chronic stress
- SCFAs (butyrate) protect the blood-brain barrier
Microbiota and immunity: 70% of immune defenses are located in the gut
Approximately 70% of the body's immune cells reside in the intestinal mucosa. The gut microbiota plays a central role in their education and activation.
From birth, intestinal microorganisms teach the immune system to distinguish "self" from "non-self". This process is fundamental to preventing autoimmune diseases and allergies.
To boost your immunity naturally, our article on probiotic gut microbiota presents the best-documented strategies.
How to assess the composition of your microbiota?
Microbiota sequencing tests are now available in France. They analyze theDNA of microorganisms present in a stool sample.
- 16S rRNA sequencing : identifies bacterial genera (standard analysis)
- Shotgun metagenomics : comprehensive analysis including viruses, fungi, and archaea
- Metabolite analysis : measures SCFAs and other molecules produced by the microbiota
These tests are not covered by health insurance and their interpretation requires the assistance of a specialized healthcare professional.
- The gut microbiota is composed of bacteria (dominant), viruses, fungi, archaea and protozoa.
- More than 1,000 bacterial species coexist, with two dominant phyla: Firmicutes and Bacteroidetes.
- The virome (bacteriophages) regulates bacterial populations and remains largely unknown.
- The composition of the gut microbiota is unique to each individual and evolves throughout life.
- Diet, antibiotics, and stress are the main factors that alter this ecosystem.
Frequently asked questions about the composition of the gut microbiota
What is the difference between microbiota and gut flora?
Both terms refer to the same thing. "Gut flora" is the old term, replaced by "gut microbiota" since the 2000s. The term "flora" was inaccurate because it evoked the plant kingdom.
How many bacteria live in the human gut?
The human gut is home to approximately 10<sup>14 </sup> bacteria, or 100 trillion. This figure is comparable to, or even slightly greater than, the total number of human cells in the body.
What is the composition of a newborn's gut microbiota?
At birth, the gut is almost sterile. Colonization begins during childbirth (vaginal and maternal fecal microbiota) and continues through breastfeeding. The microbiota stabilizes around the age of 3.
Are viruses really part of the gut microbiota?
Yes. The intestinal virome, composed mainly of bacteriophages, is an integral component of the microbiota. It regulates bacterial populations and plays an immunological role that is still poorly understood.
Can the composition of one's gut microbiota be improved?
Yes. A diet rich in diverse fibers, the consumption of fermented foods, stress reduction and regular physical activity are the levers best documented by research.
What does the gut microbiota consist of in terms of fungi?
The gut mycobiome is dominated by the genera Candida, Saccharomyces, and Aspergillus. Although present in smaller numbers, these fungi interact significantly with bacteria and the immune system.
What is intestinal dysbiosis?
Dysbiosis is an imbalance in the composition of the microbiota, characterized by a reduction in microbial diversity and a proliferation of potentially pathogenic species. It is associated with many chronic diseases.
Are archaea dangerous to health?
No. The archaea present in the human gut, notably Methanobrevibacter smithii, are beneficial commensals. They optimize fiber fermentation and are not pathogenic in immunocompetent individuals.
How do antibiotics affect the composition of the microbiota?
Antibiotics can eliminate up to 30% of intestinal bacterial species in a standard course of treatment. Complete restoration can take several weeks to several months, and may even be incomplete for some species.
What is the role of Bifidobacterium in the microbiota?
Bifidobacterium are bacteria of the phylum Actinobacteria, particularly abundant in breastfed infants. They ferment fibers, produce B vitamins and strengthen the intestinal barrier.
What is the composition of the gut microbiota in the elderly?
With age, microbial diversity decreases. Bifidobacterium populations decline, while Proteobacteria (markers of inflammation) increase. This trend is associated with immunosenescence and metabolic disorders.
Can a healthy gut microbiota be transplanted?
Yes. Fecal microbiota transplantation ( FMT ) is a validated technique for treating recurrent Clostridioides difficile infections . Clinical trials are exploring its use in other conditions.
Key takeaways
Understanding what the gut microbiota is made of means realizing that our gut harbors a remarkably complex ecosystem: bacteria, viruses, fungi, archaea and protozoa coexist in dynamic balance to maintain our digestive, immune and neurological health.
The composition of the gut microbiota is unique to each individual and changes throughout life under the influence of diet, lifestyle, and environment. Preserving its diversity is one of the most profitable long-term health investments.
Concrete action: Starting today, incorporate 30 different plant-based foods per week into your diet—vegetables, fruits, legumes, whole grains, and herbs. This is the recommendation of the American Gut Project to maximize gut microbial diversity.
Sources and studies
- Gut microbiota (intestinal flora) — Inserm,
- Gut microbiota: an incredibly rich ecosystem — Pasteur Institute,
- Gut microbiome diversity and composition in health and disease — Cell Host & Microbe,
- A human gut microbial gene catalog established by metagenomic sequencing — Nature,
- Dietary fiber and the gut microbiota — ANSES,
This article is provided for informational purposes only and does not constitute medical advice. Consult a qualified healthcare professional before use.
