The microbial flora refers to the collective communities of microorganisms residing on and within the human body—a generic term encompassing all local microbiomes (intestinal, skin, vaginal, oral, and respiratory). Humans harbor more than 38,000 billion microorganisms, of which the gut microbiome represents the largest and most extensively studied ecosystem. Explore our range of probiotics and prebiotics.
What is the microbial flora?
The human microbial flora includes bacteria, archaea, viruses (virome), fungi (mycobiome), and protozoa—each colonizing distinct anatomical sites with radically different compositions. The gut microbiota (predominantly Firmicutes and Bacteroidetes) primarily influences metabolism, immunity, and the gut-brain axis. The skin microbiota (Staphylococcus, Cutibacterium) protects the epidermal barrier. The vaginal flora (Lactobacillus) maintains a protective pH. The oral flora (Streptococcus, Fusobacterium) interacts with cardiovascular health. These flora communicate systemically via the circulatory system and the immune system.
Microbial Flora and Chronic Diseases: What Are the Links?
Research in microbiomics has revealed associations between dysbiosis and chronic diseases far beyond the digestive tract.
- Metabolism: An altered Firmicutes/Bacteroidetes ratio is associated with obesity and type 2 diabetes—gut bacteria influence calorie extraction and insulin sensitivity
- Cardiovascular: production of TMAO (trimethylamine N-oxide) by certain gut bacteria from choline and carnitine — associated with atherosclerosis
- Mental health: the gut-brain axis via the vagus nerve and enteric serotonin —dysbiosis associated with depression and anxiety in several clinical studies
- Autoimmunity and allergies: a depleted microbiome in childhood associated with an increased risk of autoimmune diseases and allergies (hygiene hypothesis)
- Not all of these associations are established causal relationships—research is ongoing, and clinical applications are emerging
Microbiome sequencing: toward personalized medicine?
Next-generation metagenomic sequencing has transformed our understanding of the microbial flora.
- Shotgun metagenomics allows us to identify not only the species present but also their metabolic functions—going beyond a simple bacterial profile
- Microbiome tests available in laboratories or as direct-to-consumer kits: species mapping, Firmicutes/Bacteroidetes ratio, markers of inflammation (calprotectin), and markers of intestinal permeability (zonulin)
- Selection of personalized probiotics based on individual microbial profiles—an approach currently in clinical development
- Current limitation: The correlation between the microbiome profile and the prescription of supplements remains to be validated in controlled studies for the majority of indications
Antibiotics and the Microbial Flora: What Is the Real Impact?
Antibiotics are the best-documented disruptor of the microbial flora.
- A 25–50% loss of microbial diversity occurs within the first few days of antibiotic therapy—partial recovery occurs within 1–2 months, but some species may take up to 6 months to return
- Risk of colonization by resistant species (Clostridioides difficile) after the elimination of susceptible bacteria
- Lactic acid bacteria (Saccharomyces boulardii, L. rhamnosus GG): taken starting on the first day, every 2 to 3 hours—documented reduction in post-antibiotic diarrhea and partial protection of diversity
- Continue probiotics for 7 to 14 days after the end of treatment to support microbiome restoration
Fecal microbiota transplantation: where do we stand?
Fecal microbiota transplantation (FMT) is the most clinically advanced microbiome therapy.
- Approved and reimbursed indication in France: recurrent antibiotic-resistant Clostridioides difficile infections—success rate > 80%
- Ongoing clinical trials: ulcerative colitis, irritable bowel syndrome, obesity, autism spectrum disorders—promising preliminary results but not yet validated in routine clinical practice
- Strict protocol: stool donation from a healthy donor, comprehensive microbiological screening, administration via colonoscopy or capsule
- Evolving regulatory framework — the ANSM strictly regulates FMT in France
How can you modulate your microbial flora on a daily basis?
Beyond advanced medical therapies, there are several accessible ways to support your microbial flora.
- Diet: 30 different plant-based foods per week, daily consumption of fermented foods, reduction of ultra-processed foods—dietary diversity fosters microbial diversity
- Documentedprobiotics: identified strains (genus + species + code), guaranteed CFU count until expiration, gastric resistance
- Prebiotics (inulin, FOS, GOS): substrates for bifidobacteria and colonic lactobacilli
- Regular moderate physical activity: documented to improve microbial diversity—even 30 minutes of daily walking has a measurable effect
- Glutamine: supports intestinal epithelial integrity—an essential barrier for a functional microbiome
