The community of trillions of microorganisms -- bacteria, archaea, fungi (mycobiome), viruses, and bacteriophages -- inhabiting the human gastrointestinal tract, with the highest density in the colon (~10^11 cells/g). The gut microbiome encodes 100-150 times more genes than the human genome and functions as a metabolic organ producing vitamins, short chain fatty acids, indoles, secondary bile acids, neurotransmitters, and other bioactive compounds.
Composition
The healthy adult gut microbiome is dominated by two bacterial phyla:
- Bacillota (Firmicutes): Includes key SCFA producers -- faecalibacterium prausnitzii, Roseburia, blautia, Eubacterium, Coprococcus, and lactobacillus.
- Bacteroidota (Bacteroidetes): Includes bacteroides fragilis, Prevotella, and bacteroides thetaiotaomicron, important for polysaccharide degradation and propionate production.
Minor but functionally important phyla include Actinobacteria (bifidobacterium), Pseudomonadota (Proteobacteria), and Verrucomicrobiota (akkermansia muciniphila).
Core Functions
1. Colonization resistance: Commensals outcompete pathogens for nutrients and attachment sites; produce bacteriocins.
2. Metabolite production: Fermentation of dietary fiber yields short chain fatty acids (acetate, propionate, butyrate); amino acid metabolism yields indoles and p-cresol; choline metabolism yields TMA/tmao.
3. Immune education: Shapes both innate and adaptive immunity; drives Treg differentiation (via butyrate/GPR109A); calibrates Th17/Treg balance.
4. Barrier maintenance: SCFA-fueled colonocytes maintain tight junctions; akkermansia muciniphila promotes mucus layer integrity.
5. Neuromodulation: Produces serotonin precursors, GABA, dopamine; signals via vagal afferents (see gut brain axis).
The Metal-Microbiome Interface
This wiki focuses specifically on how the gut microbiome interacts with metals -- both essential and toxic. For the detailed treatment, see gut metal microbiome. Key principles:
- Metals reshape the microbiome: Toxic metals (Pb, Cd, Hg, As, Ni) selectively eliminate SCFA-producing commensals while enriching metal-tolerant, LPS-producing pathobionts [anchidin norocel 2025 heavy metal gut probiotics biosensors].
- The microbiome modulates metal handling: Bacteria biosorb, bioaccumulate, biotransform, and precipitate metals, altering their bioavailability and toxicity.
- Essential metals feed the microbiome: iron, zinc, manganese, nickel, and cobalt are required cofactors for microbial enzymes including urease, hydrogenase, and siderophore biosynthesis.
Dysbiosis
When the microbiome's composition or function is disrupted -- by metals, antibiotics, diet, infection, or other stressors -- the result is dysbiosis: loss of diversity, loss of SCFA production, barrier breakdown, endotoxemia, and systemic inflammation. This is the common denominator linking the gut microbiome to virtually every disease in this wiki.
See Also
- gut metal microbiome -- metal-specific microbiome interactions
- dysbiosis -- microbiome disruption
- short chain fatty acids -- key metabolites
- probiotics -- therapeutic restoration
- fecal microbiota transplant -- community-level restoration
- mycobiome -- the fungal component