Our ontology follows a modified version of the Earth Microbiome Project's Ontology (EMPO) with four levels:

• Realm: Mineral
• Environment-Broad: Crude oil
• Environment-Broad: Microbial mat
• Environment-Local: stomatolite
• Environment-Broad: Sand
• Environment-Broad: Sediment
• Environment-Local: Brackwater
• Environment-Local: Freshwater
• Environment-Local: Glacier
• Environment-Local: Hot spring
• Environment-Local: Lake
• Environment-Local: Mudflat
• Environment-Local: River
• Environment-Local: River delta
• Environment-Local: Salt lake
• Environment-Local: Salt water
• Environment-Local: Stream
• Environment-Local: Sweepings
• Environment-Local: Volcanic
• Environment-Broad: Soil
• Environment-Local: Agricultural
• Environment-Local: Desert
• Environment-Local: Embankment
• Environment-Local: Floodplain
• Environment-Local: Forest
• Environment-Local: Grassland
• Environment-Local: Mountain
• Environment-Local: Peatland
• Environment-Local: Stream shore
• Environment-Local: Tundra
• Environment-Local: Urban
• Environment-Local: Wetland
• Environment-Broad: Rock
• Environment-Local: Lava
• Environment-Local: Mofette

• Realm: Organism
• Note : host associated microbiomes follow the taxonomic hierarchy of the host. Rhizosphere samples are categorized as plant-associated.

• Realm: Water
• Environment-Broad: Freshwater
• Environment-Local: Borehole
• Environment-Local: Delta
• Environment-Local: Ground water
• Environment-Local: Hot spring
• Environment-Local: Ice
• Environment-Local: Lake
• Environment-Local: Rain
• Environment-Local: River
• Environment-Local: Sewage
• Environment-Local: Stream
• Environment-Local: Tap water
• Environment-Local: Waste water
• Environment-Broad: Saltwater
• Environment-Local: Seawater
• Environment-Local: Sediment

• Realm: Other
• Environment-Broad: Air
• Environment-Broad: Biofilm
• Environment-Local: Epilithon
• Environment-Local: Microbial mat
• Environment-Local: Rock
• Environment-Broad: Carcass
• Environment-Broad: Compost
• Environment-Broad: Evaporite
• Environment-Broad: Fermented food
• Environment-Local: Daqu
• Environment-Local: Doubanjiang
• Environment-Local: Must
• Environment-Local: Wine
• Environment-Broad: Microbial cultures
• Environment-Local: Frac fluid
• Environment-Local: Winogradsky column
• Environment-Broad: Microbial fuel cells
• Environment-Broad: Reactor
• Environment-Local: Anaerobic digester sludge
• Environment-Local: Grass anaerobic digester
• Environment-Local: Industrial anaerobic digester
• Environment-Local: Rumen fluid
• Environment-Local: Sludge
• Environment-Local: Wastewater treatment plant