Gut microbiome interactions

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Gut Microbiome - The Body's Tiny Roommates

  • Microbiome vs. Microbiota:
    • Microbiota: The community of microorganisms (bacteria, archaea, viruses, fungi).
    • Microbiome: The collective genetic material of the microbiota.
  • Key Phyla: Predominantly Firmicutes and Bacteroidetes. Most are obligate anaerobes.
  • Regional Density: Microbial load increases distally:
    • Stomach: Low (~$10^1-10^3$ cells/mL)
    • Colon: High (~$10^{11}-10^{12}$ cells/mL)

GI tract microbial activity and probiotic research

⭐ The gut microbiota collectively contains over 100 times more genes than the human genome, forming a 'second genome'.

Microbial Functions - Metabolic & Immune Allies

  • Metabolic Contributions:

    • Fermentation of dietary fiber into Short-Chain Fatty Acids (SCFAs).
      • $Dietary,Fiber \xrightarrow{Bacterial,Enzymes} Butyrate + Propionate + Acetate$
    • Key nutrient synthesis: Vitamin K, Biotin (B7), and Folate (B9).
  • Immune & Barrier Functions:

    • Strengthens gut barrier integrity (e.g., butyrate feeds colonocytes).
    • Promotes maturation of Gut-Associated Lymphoid Tissue (GALT).
    • Pathogen Displacement: Competes with harmful microbes for resources and adhesion sites (colonization resistance).

⭐ Butyrate, a key SCFA, is the preferred energy source for colonocytes and plays a crucial role in maintaining gut barrier function.

SCFA production from fiber and effects on colonocytes

Clinical Correlations - When Good Bugs Go Bad

  • Dysbiosis: An imbalance in the gut microbiota's composition and function, often triggered by antibiotics, diet, or stress, disrupting host homeostasis.
  • Clostridioides difficile Infection:
    • Commonly follows antibiotic use (clindamycin, cephalosporins), which eradicates protective commensal bacteria.
    • Causes pseudomembranous colitis (diarrhea, fever, abdominal pain).
    • 📌 For C. diff treatment: 'Vanquish with Vanc' (Oral Vancomycin) or 'Attack with Fidax' (Fidaxomicin).
  • Broader Implications:
    • IBD: Dysbiosis is linked to both Crohn's disease and ulcerative colitis.
    • Metabolic Syndrome: Associated with obesity, ↑ insulin resistance, and non-alcoholic fatty liver disease.
    • Gut-Brain Axis: Microbial imbalance can affect mood and contribute to anxiety/depression.

⭐ Broad-spectrum antibiotic use is the most significant risk factor for C. difficile infection due to the eradication of protective commensal bacteria.

Endoscopic view of pseudomembranous colitis

Therapeutic Interventions - Hacking the Microbiome

  • Probiotics vs. Prebiotics
FeatureProbioticsPrebiotics
DefinitionLive beneficial organismsSubstrates for beneficial bacteria (fiber)
ExamplesLactobacillus, BifidobacteriumInulin, Fructans
  • Fecal Microbiota Transplantation (FMT): Infusion of a healthy donor's stool to restore gut flora, primarily for recurrent C. difficile infection.

⭐ Fecal Microbiota Transplantation (FMT) has shown high efficacy (>80%) in treating recurrent C. difficile infection that is refractory to standard antibiotic therapy.

High‑Yield Points - ⚡ Biggest Takeaways

  • The gut microbiome synthesizes essential vitamins, including Vitamin K and B vitamins (folate, biotin).
  • Dietary fiber is fermented into short-chain fatty acids (SCFAs) like butyrate, the primary energy source for colonocytes.
  • It is crucial for the development and maturation of gut-associated lymphoid tissue (GALT).
  • Normal flora provide colonization resistance against pathogens like Clostridioides difficile.
  • Dysbiosis is linked to IBD, obesity, and metabolic syndrome.
  • Metabolizes primary bile acids into secondary bile acids.

Practice Questions: Gut microbiome interactions

Test your understanding with these related questions

A 24-year-old woman comes to the physician because of progressively worsening episodes of severe, crampy abdominal pain and nonbloody diarrhea for the past 3 years. Examination of the abdomen shows mild distension and generalized tenderness. There is a fistula draining stool in the perianal region. Immunohistochemistry shows dysfunction of the nucleotide oligomerization binding domain 2 (NOD2) protein. This dysfunction most likely causes overactivity of which of the following immunological proteins in this patient?

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Flashcards: Gut microbiome interactions

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Toxic megacolon describes the cessation of colonic contractions by way of transmural inflammation that results in significantly increased _____ release

TAP TO REVEAL ANSWER

Toxic megacolon describes the cessation of colonic contractions by way of transmural inflammation that results in significantly increased _____ release

nitric oxide

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