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Intestinal bacteria analysis: doctor's answers to frequently asked questions
Bloating, rumbling, unstable stools, skin that suddenly started reacting to familiar foods - all this can be a consequence of a violation of the intestinal microflora. In such cases, gastroenterologists often advise to undergo intestinal bacteria analysis. To understand when it is really needed and what its results mean, we have prepared a format FAQ (questions and answers).
What is intestinal microflora?
About 100,000 live in your intestines. 100 trillion microorganisms. It's not just bacteria, but also fungi, viruses, archaea. Together they form microbiome — a complex ecosystem that:
helps digest food;
produces vitamins B and K;
supports immunity;
regulates mood and sleep (through the production of serotonin).
If the balance of microflora is disrupted, it is felt not only in the stomach - the whole body suffers.
When does a doctor order a test for intestinal bacteria?
This test is not needed by everyone, but it is especially indicated if:
worries bloating, gas, discomfort after eating;
є unstable chair (frequent alternation of constipation and diarrhea);
you recently took antibiotics or hormones;
are observed skin reactions — rashes, itching, allergies;
є decreased immunity or chronic fatigue;
the child has frequent colic, poor digestion, or weight loss.
What are the types of microflora tests?
Modern laboratory diagnostics offers several approaches:
| Type of study | How is it done? | Advantages | Disadvantages |
|---|---|---|---|
| Bacteriological culture (classical) | A stool sample is plated on nutrient media. | Determines live bacteria, their ratio | Result in 5–7 days, does not detect all microorganisms |
| PCR analysis | Detects bacterial DNA in a sample | High accuracy, speed | Does not show the number of bacteria |
| Metagenomic analysis (16S rRNA) | DNA sequencing of the entire microbiota | The most complete picture of the composition of the flora | High cost, not available in all laboratories |
How to prepare for the analysis?
Stop taking after 3–5 days antibiotics, laxatives, probiotics.
Do not do enemas or use rectal suppositories.
Collect the sample in a sterile container and deliver to the laboratory within 2–3 hours.
In infants, the material is taken from a diaper or potty, without urine impurities.
What do the results look like and how to interpret them?
The result is a table that lists the types of bacteria and their number in CFU/g (colony forming units per gram).
Approximate norms for an adult:
| Bacteria | Norm | Role in the body |
|---|---|---|
| Bifidobacteria | 10⁹–10¹⁰ | The main "protectors" of the intestine, vitamin synthesis |
| Lactobacteria | 10⁷–10⁸ | Maintain acidity, inhibit pathogens |
| Escherichia coli (E. coli) | 10⁶–10⁸ | Produces vitamin K, maintains balance |
| Enterococci | 10⁵–10⁷ | Conditionally useful, but excess is a signal of dysbiosis |
| Pathogenic bacteria | Normally - absent | Their appearance indicates infection or inflammation. |
Important: There is no «absolutely correct» ratio of bacteria. Your doctor will evaluate the results based on your age, diet, past illnesses, and even your stress level.
What does the diagnosis of "dysbiosis" mean?
This is not a disease, but state of microflora imbalance. The reason may be:
improper diet (excess sugar, fatty foods);
frequent antibiotics;
stress, insomnia, hormonal changes;
infection or poisoning.
Symptoms are often similar to irritable bowel syndrome: flatulence, alternating constipation and diarrhea, and a feeling of "heaviness" after eating.
How to restore balance after analysis?
After receiving the results, the doctor may advise:
Diet correction — more fiber, vegetables, and fermented foods.
Probiotics — live beneficial bacteria in the form of capsules or yogurts.
Prebiotics — substances that «feed» the microflora (inulin, fiber, bananas).
Enzymes — if digestive problems are detected.
Is it possible to do the analysis for prevention?
Yes. Especially if you often feel tired, have skin rashes or intolerance to certain foods. For prevention, it is enough to check the microflora once a year, especially after courses of antibiotics.
Why is it important to know your microbiome?
Microflora is your «inner world.» It affects not only digestion, but also immunity, mood, energy. WHO and Mayo Clinic studies show that the state of gut bacteria is even linked to risk diabetes, adiposity and depression. Taking care of your intestines is not a fad, but part of taking care of your own health.
Sources
WHO. Gut Microbiome and Human Health Report, 2024.
Mayo Clinic. Microbiota testing and stool diagnostics: clinical overview.
FDA. Laboratory standards for microbiological analysis, 2023.
