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Microbiological Examination of Feces

For medical students2 min readUpdated 2026-10-10

Microbiological examination of feces is a key laboratory method aimed at evaluating the intestinal microbial landscape. It helps determine the etiology of inflammatory conditions such as enteritis and colitis, and serves as a primary diagnostic tool for intestinal dysbiosis.

Delivery timeThe sample must be delivered to the laboratory strictly within 2 hours after collection.
Prohibited substancesLaxatives, rectal suppositories, mineral oil, and castor oil must be discontinued 3–4 days prior to the analysis.
Inflammation criterionDetection of an atypical microorganism or a sharp increase in the concentration of a single opportunistic species.
Bedpan preparationThe bedpan must be disinfected, washed with running water, and thoroughly scalded with boiling water.

Indications and Patient Preparation

Ordering a fecal microbial culture serves two main purposes: identifying pathogens of acute or chronic intestinal inflammation (colitis, enteritis) and confirming the diagnosis of intestinal dysbiosis.

To ensure reliable results, the patient must prepare starting 3–4 days before sample collection. During this period, factors affecting motility and microflora must be strictly excluded:

In laboratory practice, there are strict criteria for sample rejection. A sample will be rejected if the feces are obtained after an enema or a radiological examination using barium sulfate.

Sample Collection and Transport Protocol

The collection process requires strict adherence to hygiene standards to prevent contamination of the sample with extraneous flora. Prior urination is mandatory before defecation, as urine contamination of the stool is unacceptable.

Collection technique using a bedpan:

  1. The bedpan undergoes thorough processing: disinfection, rinsing with running water, and a final scalding with boiling water.
  2. Defecation is performed into the prepared bedpan.
  3. The sample is collected using a special spoon exclusively from areas of the stool that did not touch the walls of the bedpan.

A sterile disposable container with a screw cap is used for collection. An alternative method involves collecting material using a fecal swab or rectal loop, which is then immediately placed into a specialized transport medium.

Transportation and storage rules:

Laboratory Phase and Result Interpretation

The material received in the laboratory undergoes quantitative enumeration using serial dilutions. Inoculation is performed on selective nutrient media designed for growing specific types of microorganisms, followed by the identification of isolated cultures.

Criteria for etiological significance in purulent-inflammatory processes:

Laboratory criteria for dysbiosis:

Mnemonic

To remember what must be avoided before stool collection, use the rule of the "Two B's": no Barium contrast and no Bowel-cleansing enemas or laxatives.

Frequently asked questions

What microorganisms comprise the obligate (resident) intestinal microflora?

The obligate (resident) intestinal microflora consists predominantly of anaerobic bacteria, as well as certain aerobes.

  • Bifidobacteria (Bifidobacterium) — major microbiota (up to 10¹² CFU/g).
  • Bacteroides (Bacteroides) — major microbiota (up to 10¹¹ CFU/g).
  • Lactobacilli (Lactobacillus) — accompanying microbiota (10⁸ CFU/g).
  • Escherichia coli (Escherichia coli) — accompanying microbiota (10⁷ CFU/g).

Resident flora of the large and small intestine also includes clostridia, prevotellae, ruminococci, porphyromonas, enterococci, and propionibacteria.

What selective and differential diagnostic media are used for stool culture?

Various elective and differential diagnostic media are used to inoculate stool and isolate specific types of microorganisms.

  • Blaurock medium — for isolating bifidobacteria.
  • MRS-2 medium — for cultivating lactobacilli.
  • Anaerobic blood agar — for bacteroides.
  • Levine or Endo media — for enterobacteria.
  • Bile-blood agar — for enterococci.
  • Meat-peptone agar with furagin — for Pseudomonas aeruginosa.
  • Sabouraud medium — for fungi.
  • Yolk-salt agar — for staphylococci.
Which microorganisms belong to the opportunistic flora causing dysbiosis?

Opportunistic microorganisms whose increased concentration serves as a criterion for dysbiosis include various bacteria and fungi.

  • Staphylococci (Staphylococcus) — cause dysbiosis when their concentration rises sharply.
  • Clostridia (Clostridium) — Gram-positive spore-forming anaerobic rods.
  • Fungi of the genus Candida — yeast-like fungi capable of causing candidiasis when mucosal resistance is lowered.

Dysbiosis is characterized by a simultaneous increase in the concentration of these microorganisms alongside the disappearance or reduction of resident microflora.

How is quantitative enumeration of microorganisms performed using serial dilutions?

Quantitative enumeration of microorganisms is performed using the serial dilution method.

Can stool be collected directly from the toilet bowl?

No, the material must be collected only in a pre-processed bedpan (disinfection, water, boiling water), taking samples from areas that did not touch the bedpan walls.

How much time is available to deliver the container to the laboratory?

The container must be delivered within 2 hours. Storage exceeding 5–6 hours and freezing of the biological material are strictly prohibited.

What changes in flora composition indicate dysbiosis?

The diagnosis is supported by a decrease in resident flora levels (bifidobacteria, lactobacilli, E. coli) alongside an increase in opportunistic microorganisms (clostridia, staphylococci, Candida species).

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