Microbiome

The microbiome is [[the-collective-cold-spring|the collective]] microbial community living on and within human tissues — bacteria, archaea, fungi, and viruses, distributed across multiple body sites with site-specific compositions [1]. The concept reframes the human body as an ecosystem rather than a single organism: the host is one species in a co-evolved community of thousands.

Scale

The numbers that changed how the field thinks about the human body [1]:

• ~38 trillion bacterial cells in/on the human body
• 30–40 trillion human cells — comparable, not orders of magnitude different
• ~100× more microbial genes than human genes — about 2 million microbial vs ~20,000 human protein-coding

The older claim of a 10:1 microbe-to-cell ratio has been refined downward as methods improved. The cell counts are roughly equal; the gene counts remain dramatically asymmetric in favor of the microbes.

Major body regions

The human microbiome is multiple distinct communities at different body sites [1]:

Site	Dominant features
Gastrointestinal tract	500-1,000 species; dominated by Bacillota and Bacteroidota; the most-studied and clinically important region — see [[gut-microbiome]]
Oral cavity	Anaerobic bacteria including Actinomyces and Fusobacterium; periodontal disease and systemic-disease links well-documented
Skin	205 identified genera across 19 bacterial phyla; site-variable (face vs forearm vs armpit)
Vaginal	Predominantly Lactobacillus species producing [[lactic-acid
Respiratory tract	Nine major bacterial genera including Prevotella and Pseudomonas; previously thought sterile, now understood as colonized
Nasal cavity	Specific to nostril ecology; influences allergic and infectious disease
Conjunctiva, biliary tract, blood	All previously thought sterile; now confirmed to harbor characteristic microbiota

A key recent finding: uterine and reproductive-tract microbiomes also exist, contradicting decades of “sterile” assumption [1]. The discovery affects fertility research, pregnancy outcomes, and gynecological disease understanding.

The Human Microbiome Project

The Human Microbiome Project (HMP), launched by the U.S. National Institutes of Health, catalogued the human microbiome at scale [1]:

• 2007 — Project launched
• 2012 — First major results: published initial findings from 242 healthy volunteers, identifying 10,000+ microbial species across body sites
• Ongoing — Subsequent phases (HMP2, the Integrative Human Microbiome Project) extended into disease populations and longitudinal studies

The HMP’s contribution was twofold:

1. Cataloguing — reference databases of what microbiomes look like in healthy populations
2. Method standardization — protocols for sequencing, analysis, and reporting that enabled subsequent research

Health contributions

Across body sites, the microbiome contributes to host physiology in characteristic ways [1]:

• [[immune-system|Immunity]] and digestion — fermentation of dietary fiber into [[short-chain-fatty-acids|SCFAs]]; immune training
• Metabolism — synthesis of B vitamins and vitamin K; bile acid metabolism; drug metabolism
• Neurological function — production of bioactive compounds including 3-indolepropionic acid (neuroprotective); 90% of body’s serotonin produced in gut; [[gut-brain-axis|gut-brain axis]] signaling
• Disease prevention — healthy microbiome correlates with reduced risk of type 2 diabetes, obesity, IBD, asthma, depression
• Pathogen exclusion — niche occupation prevents opportunistic pathogen overgrowth

The microbiome is now understood as functionally an additional organ — one that we can disturb, support, or regenerate through lifestyle and (selectively) clinical intervention.

Recent research highlights

The field has moved fast in the past decade. Notable findings [1]:

• 2024 — “Obelisks” discovery: Viroid-like RNA elements found in human microbiomes; an entirely new category of microbial entity, function unknown.
• 2024 — Cellulose-digesting microbes: Documented in non-industrialized populations but absent in industrialized ones, evidence for the “missing microbes” hypothesis.
• Vaginal/uterine microbiomes confirmed as non-sterile.
• Fecal microbiota transplant confirmed as 85-90% effective for recurrent C. difficile infections [1] — establishing microbiome restoration as a real medical intervention.

Why it matters here

The microbiome concept reframes how the wiki should think about food, plants, body, and disease. Most of what foods do in human bodies is mediated through microbiome interactions. Many traditional medical observations now have microbiome-mediated explanations. Many modern chronic-disease epidemics correlate with microbiome disruption.

The wiki’s microbiome constellation will eventually include:

• [[gut-microbiome]] — body-system entry for the most-studied region
• [[short-chain-fatty-acids]] — the metabolic currency
• Future entries for skin microbiome, oral microbiome, vaginal microbiome
• Future entries for major beneficial species (Akkermansia, F. prausnitzii, Bifidobacterium)
• Future entries for fermented-food traditions (kimchi, kefir, miso, [[sauerkraut|sauerkraut]], [[sourdough|sourdough]], kombucha)
• Future entries for fiber types (resistant starch, beta-glucan, inulin)

Lenses still to grow

• Each body-site microbiome (oral, skin, vaginal, respiratory) potentially as its own body-system entity
• The Human Microbiome Project in fuller detail
• Specific recent peer-reviewed papers (Sonnenburg lab, Knight lab, Gordon lab work)
• Industrialized vs ancestral microbiomes — Hadza, Yanomami research
• Fermented foods comprehensively
• Pediatric microbiome development — first 1,000 days
• The [[gut-brain-axis|gut-brain axis]] in clinical detail
• Modern critique — the rapid-conclusions vs slow-evidence-base tension; examples where early microbiome enthusiasm has not been borne out

See also

Auto-generated from this entry’s typed relations: frontmatter, grouped by relation type so the editorial signal isn’t flattened.

• Enables: [[gut-microbiome]]
• Founded on: [[air]] · [[water]]
• Supersets: [[gut-microbiome]]

Sources

1. Wikipedia: Human Microbiome. 38 trillion bacterial cells, 30-40 trillion human cells, microbial gene count ~100× human, body sites with characteristic communities, Human Microbiome Project (2007 launch, 2012 first results, 242 healthy volunteers, 10,000+ species), recent findings (obelisks 2024, cellulose-digesting microbes 2024, vaginal/uterine non-sterility), 85-90% FMT success rate. https://en.wikipedia.org/wiki/Human_microbiome

All sources retrieved 2026-05-02.