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Gastrointestinal Microbiome

For medical students2 min readUpdated 2026-10-10

The microflora of the digestive tract is a complex, dynamic ecological system of microorganisms. This system performs critical physiological functions, providing immune defense for the host and actively participating in metabolism.

Large IntestineHighest density of microflora: over 10 billion cells per 1 gram of contents.
StomachDue to low pH, the environment suppresses bacterial growth (maximum up to 1,000 cells per mL).
ColonizationBegins in the first weeks of life when anaerobic bacteria enter via the oral cavity.

Topography and Distribution of Bacteria Along the GI Tract

In newborns, the digestive tube is entirely sterile. Its colonization begins in the first weeks of life when microorganisms (predominantly anaerobes) enter the body through the mouth. Subsequent distribution of bacterial populations is uneven, as each segment of the gastrointestinal tract features a specific environment.

Eubiosis and the Influence of Diet

The balance of interactions among various species of microorganisms within the GI tract is known as eubiosis. This equilibrium establishes a specific saprophytic flora and reliably protects the host organism from invasion by pathogenic bacteria. Historically, the concept of improving health through microflora was studied by É. Metchnikoff, who proposed the hypothesis of replacing pathogenic flora with beneficial acidophilic bacteria using fermented dairy products.

To maintain eubiosis, a continuous, adequate, and balanced diet is critically important. Any pronounced changes in diet (an exogenous factor) transform the bacterial landscape:

  1. Vegetarian diet stimulates the growth of enterococci and eubacteria populations.
  2. Excess animal proteins and fats lead to a pathologic increase in the number of clostridia and bacteroides.
  3. Excess animal fats alone selectively increase the bacteroides population while concurrently decreasing the number of enterococci and bifidobacteria (fat deficiency causes the exact opposite changes).
  4. Milk diet (rich in lactose) promotes the active proliferation of bifidobacteria.
  5. Non-physiological components, such as freeze-dried foods or single-cell proteins, exert adverse effects on microbial homeostasis.

Physiological Role of Microorganisms

The normal intestinal microflora performs a spectrum of tasks essential for maintaining human vitality. A key function is the development of immunobiological reactivity. Bacteria provide colonization resistance, protecting the organism from the implantation and proliferation of pathogenic agents.

In addition to defense, the microflora fulfills the following functions:

Disruption of this complex microbial biocenosis is termed dysbiosis. It arises against the background of various diseases or prolonged antibiotic therapy. This condition is dangerous due to the unchecked proliferation of opportunistic flora (Proteus, staphylococci, yeasts), which inevitably leads to complications.

Mnemonic

To remember the main functions of the microflora, use the acronym DIMS: Digestion (breakdown of fiber), Immunity (colonization resistance), Metabolism (lipid and acid exchange), Synthesis (vitamins B and K).

Frequently asked questions

What microorganisms belong to the obligate microflora of the adult large intestine?

The obligate (main) microflora of the large intestine includes bifidobacteria and bacteroides. The normal microflora also includes accompanying microorganisms (lactobacilli, Escherichia, enterococci) and residual microorganisms (Citrobacter, Enterobacter, Proteus, yeasts, clostridia, staphylococci).

What are the mechanisms of colonization resistance provided by the normal microflora?

Mechanisms of colonization resistance by normal microflora include nutrient competition and the production of substances that inhibit foreign flora: lactic and acetic acids, short-chain fatty acids, antibiotics, bacteriocins, antimicrobial peptides, and secondary bile acids.

What toxic products are formed as a result of protein putrefaction in the large intestine?

Protein putrefaction in the large intestine yields toxic amino acid breakdown products: amines, phenols and their derivatives, indole, skatole, and hydrogen sulfide. Putrescine and cadaverine are also listed among protein breakdown products in the large bowel. Indole and skatole are formed from tryptophan.

What is the role of intestinal microflora in bile acid metabolism?

Intestinal microflora participates in bile acid metabolism by converting primary bile acids (cholic and chenodeoxycholic) into secondary bile acids. Under the action of microflora, deconjugation and 7α-dehydroxylation occur in the intestine, producing secondary bile acids such as deoxycholic and lithocholic acids. Additionally, microflora regulates the enterohepatic circulation of bile components.

What leads to the development of dysbiosis?

Dysbiosis occurs as a result of underlying diseases or prolonged antibiotic therapy. This disrupts eubiosis and provokes the unchecked proliferation of opportunistic microorganisms, such as staphylococci and yeasts.

Is the intestine colonized with microorganisms before birth?

No, the contents of the gastrointestinal tract in newborns are completely sterile. The process of colonization by anaerobic microorganisms begins only in the first weeks of life via the mouth.

Which vitamins can the intestinal microbiome synthesize?

Normal microflora synthesizes vitamin K and B vitamins. This process partially covers the human body's daily requirement for these compounds.

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