Microbiome analysis provides in-depth insight into the complex ecosystem of the gut and its impact on both physical and mental health. The gut microbiome consists of billions of microorganisms—bacteria, fungi, and viruses—that play essential roles in digestion, immune function, energy metabolism, and psychological balance.
Recent research has revealed strong links between microbiome imbalances and the development of various diseases, including autoimmunity, depression, anxiety, irritable bowel syndrome (IBS), chronic fatigue syndrome (CFS), autism, metabolic disorders, and cardiovascular disease.
How Microbiome Analysis Work
Microbiome analysis evaluates the composition and function of intestinal microorganisms and how they influence health. The test is typically performed using a stool sample, which is analyzed for the presence of specific bacteria, fungi, and viruses.
📌 Read more about how results are used to guide targeted therapy
Key parameters include:
- Microbial diversity
High diversity protects against inflammation and disease; low diversity is associated with obesity, diabetes, and chronic inflammation. - Beneficial bacteria
Includes butyrate-producing strains such as Faecalibacterium prausnitzii and Eubacterium rectale, which support the intestinal lining. - Harmful bacteria
Includes sulfate-reducing bacteria (Desulfovibrio piger) and pathogens that may trigger inflammation. - Mucin-degrading bacteria
Akkermansia muciniphila maintains the gut mucus layer but, when imbalanced, may weaken the intestinal barrier. - Short-chain fatty acids (SCFAs)
Such as butyrate and propionate, with anti-inflammatory properties and gut-supportive effects.
Clinical Relevance of the Microbiome
Microbiome analysis can reveal hidden contributors to a wide range of health issues, including:
- Digestive disorders – IBS, bloating, constipation, and food intolerances
- Mental health conditions – Depression, anxiety, autism, and ADHD, where the gut–brain axis plays a role
- Autoimmune diseases – Hashimoto’s thyroiditis, celiac disease, rheumatoid arthritis
- Metabolic disturbances – Obesity, insulin resistance, metabolic syndrome, diabetes
- Inflammatory diseases – Crohn’s disease, ulcerative colitis, and CFS
- Cardiovascular disease – Certain gut bacteria may increase TMAO production, linked to cardiovascular risk
Functional Roles of Specific Bacteria
- Butyrate producers
Faecalibacterium prausnitzii and Eubacterium rectale produce butyrate, which supports mucosal integrity and reduces inflammation. - Akkermansia muciniphila
Stimulates renewal of the mucus layer but may contribute to “leaky gut” if imbalanced. - Equol-producing bacteria
Adlercreutzia spp. convert plant isoflavones into equol, which has antioxidant and hormone-modulating effects. - Sulfate-reducing bacteria
Desulfovibrio piger produces hydrogen sulfide, which can damage the gut lining in high concentrations.
Diversity and Microbiome Health
High microbial diversity is one of the strongest indicators of robust health. Studies show that individuals with a rich microbiome have a lower risk of chronic illness. A fiber-rich diet including prebiotics and probiotics supports microbial diversity, while antibiotics, dietary monotony, and stress reduce it.
Examples of prebiotics that support gut flora:
- FOS and GOS (Fructooligosaccharides and Galactooligosaccharides) – Promote growth of bifidobacteria
- Resistant starch (RS3) – Increases SCFA production
- Acacia fiber – Stimulates butyrate and strengthens the gut barrier
- XOS and AXOS (Xylo-/Arabinoxylooligosaccharides) – Improve the gut environment and encourage microbial diversity
Personalized Treatment Based on Microbiome Analysis
Following testing, therapy is adapted to the individual’s needs:
- Dietary modification – Increased intake of fiber, prebiotics, and probiotic foods
- Probiotic supplements – Specific strains selected according to results
- Reduction of harmful bacteria – Targeted strategies using natural antimicrobials
- Gut barrier support – Using L-glutamine, butyrate, and diet-based methods
- Inflammation regulation – Through tailored anti-inflammatory nutrition
📌 Read more about microbiome therapy and its personalized application