Overview of Microbiome Science

Human Microbiome (gut, oral, skin, etc.)

• The human body hosts trillions of microorganisms (bacteria, archaea, fungi, viruses), roughly on the same order as the number of human cells. These microbes live in communities at various body sites.
• Diverse niches: Each body site has a distinct microbiome composition (e.g. gut, skin, oral cavity, airways, urogenital tract) with specialized microbes adapted to that environment. For example, oxygen-tolerant bacteria dominate skin, while strict anaerobes thrive in the colon.
• The gut microbiome is especially dense (up to ~10^11^ cells per gram of colon content) and plays key roles in digestion and immunity. Other sites like the oral microbiome (saliva, dental plaque) or skin surface have lower biomass but greater exposure to environmental factors.
• The human microbiome is established early in life and influenced by factors such as diet, antibiotics, and environment. Maintaining a balanced microbiome is important for health (imbalances or “dysbiosis” have been linked to diseases).

Environmental Microbiomes (soil, water, air)

• Microbes are everywhere: Complex microbial communities exist in virtually all ecosystems – in soil, oceans and freshwater, and even the air. These environmental microbiomes include bacteria, archaea, protists, fungi, and viruses adapted to their habitat.
• Soil microbiomes are among the most diverse known. A single gram of fertile soil contains on the order of 10^9^-10^10^ microbial cells and thousands of species. Soil microbes drive nutrient cycling (carbon, nitrogen, etc.) and support plant growth by processes like biodegradation and nitrogen fixation.
• Aquatic microbiomes: Oceans and lakes contain microbial plankton (bacteria, algae, archaea, viruses) distributed through the water column. For example, the Sargasso Sea seawater metagenome revealed ~1.2 million new genes from microbes[1]. Aquatic microbes are key to global biogeochemical cycles.
• Air microbiome: Even the atmosphere carries microbes (the aerobiome), such as spores, pollen, and cells uplifted from soil or water. Although low in biomass, airborne microbes can travel long distances and influence cloud formation and dispersion of pathogens.