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Fecal microbiota (16S rRNA or shotgun-metagenomics)

Fecal microbiota analysis (16S rRNA or shotgun-metagenomics)

Why is it needed?

This test evaluates the composition and diversity of gut bacteria, identifying an imbalance (dysbiosis) that is associated with:
✔ Digestion (IBS, bloating, diarrhea/constipation).
✔ Immune system problems(autoimmune diseases, allergies).
✔ Metabolic disorders(obesity, diabetes).
✔ Mental health issues(depression, autism).
✔ Synthesis of vitamins (B12, K2, short-chain fatty acids).

Methods of analysis

MethodWhat it revealsAccuracy
16S rRNAMajor bacterial groups (genus/family level)Cost-effective but less detailed
Shotgun metagenomicsAll microorganisms (including viruses, fungi, archaea) + metabolic genesMost comprehensive and accurate

Symptoms of dysbiosis

With a deficiency of beneficial bacteria (lacto -, bifidobacteria):

  • Bloating, constipation/diarrhea.
  • Food intolerances (lactose, gluten).
  • Reduced immunity (frequent colds).
  • Vitamin deficiency (B12, D).

With an excess of pathogens (Clostridium, candida, proteobacteria):

  • Chronic inflammation (colitis, Crohn’s disease).
  • Autoimmune reactions (rheumatoid arthritis).
  • Skin problems (acne, eczema).
  • Anxiety, depression.

Norms in analyses

There are no specific ‘norms’, but they are being evaluated:

  1. Diversity (Shannon index) – optimal > 3.5.
  2. Bacterial ratio:
  • Firmicutes/Bacteroides (F/B ratio) – normal ~1.5.
  • Beneficial bacteria:
    • Lactobacilli – >1%.
    • Bifidobacteria – > 5%.
  • Pathogens:
    • Clostridia – < 0.1%.
    • Candida – < 0.01%.

Sample report (shotgun-metagenomics):

What to do with dysbiosis?

1. Power correction:

  • Prebiotics: chicory, garlic, bananas (food for bacteria).
  • Probiotics: kefir, sauerkraut (Lactobacillus rhamnosus GG).
  • Exclusion of sugar/fast food(feed pathogens).

2. Supplements (as directed by your doctor):

  • Probiotics (for example, Saccharomyces boulardii for diarrhea).
  • Postbiotics (butyrate for mucosal repair).

3. Antimicrobial therapy (if there is an excess of pathogens):

  • Naturalingredients: berberine, oregano oil.
  • Pharmacological: rifaximin (for SIBR).

When is the test scheduled?

  • Chronic gastrointestinal problems (IBS, constipation).
  • Autoimmune diseases (celiac disease, psoriasis).
  • Obesity/diabetes (related to metabolism).
  • Depression, autism (gut-brain axis).

Conclusion

Microbiota analysis is key to understanding the causes of many chronic diseases.
Dysbiosis occurs when there is a deficiency of beneficial bacteria or an excess of pathogens.
📊 Rules:

  • Variety > 3.5.
  • Bacteroides/Firmicutes ≈ 1.5.
  • Lacto – /Bifidobacteria >1–5%.
    Treatment: diet, probiotics, antimicrobials.