Human microbiome

The human microbiome refers to the collective community of microorganisms—including bacteria, archaea, fungi, protists, and viruses—that reside on or within various tissues and biofluids throughout the human body. These microbes inhabit sites such as the gastrointestinal tract (especially gut), skin, oral cavity, respiratory tract, urogenital tract—including mammary glands—and more. The term also encompasses their collective genomes ("metagenomes"). Bacteria are numerically dominant among these organisms. The human body contains roughly equal numbers of microbial cells and somatic cells; this vast ecosystem plays essential roles in health by aiding digestion/metabolism; synthesizing vitamins; modulating immune function; protecting against pathogens; influencing inflammation; impacting drug metabolism; and potentially affecting neurological function. Disruption ("dysbiosis") has been linked to diseases including infections like Clostridioides difficile colitis treated with FMT,[7] inflammatory bowel disease,[3] metabolic disorders,[5] some cancers,[5] neuropsychiatric conditions,[5] among others. While individual bacterial enzymes/proteins within this community may serve as drug targets—such as dihydrofolate reductase inhibited by trimethoprim—the "human microbiome" itself is not a single molecular entity nor a conventional therapeutic target like an enzyme or receptor.[2] Instead it represents an ecological system whose balance can be therapeutically manipulated through diet changes,[7] pre/pro/syn-biotic supplementation,[7] phage therapy targeting specific pathobionts,[3] live biotherapeutics using selected strains,[7], postbiotic metabolites that modulate host pathways without introducing live organisms,[6], or fecal transplants. Because "human microbiome" does not refer to a discrete molecule/receptor but rather an entire ecosystem/community comprising thousands of species with millions of genes—each potentially encoding distinct targets—it should not be classified under standard molecular target categories used in pharmacology.[1][2][5] In summary: "Human microbiome" is not itself a therapeutic target but rather an aggregate descriptor for all resident microbes on/in humans. Individual components within it may serve as drug targets but require much more precise specification than "human microbiome."[1][2][5]

Other names

Human metagenomeHuman microbiotaMicrobiome (when referring to humans)Normal flora (historical/clinical context)

Not applicable for the human microbiome as a single target. However, mechanisms for drugs/interventions affecting the microbiome include: Modulation of microbial composition via antibiotics or probiotics/prebiotics; Eradication or suppression of pathogenic bacteria using phages or antibiotics[3][6][7]