The EMP Ontology (EMPO) is used to assign samples to habitats in a hierarchical framework that captures major axes of microbial community diversity. Four fields are used: empo_0 (level 0: root), empo_1 (level 1: Free-living, Host-associated, Control, or Unknown), empo_2 (level 2: Saline, Non-saline, Animal, or Plant), and empo_3 (level 3: most specific habitat name).

Circle area in the below network diagram is proportional to the number of samples in the “QC-filtered” set of samples inĀ EMP 16S Release 1 (Thompson et al., under review).

EMPO network and distribution for EMP 16S Release 1

 

empo_0 empo_1 empo_2 empo_3 Examples
EMP sample Free-living Non-saline Water (non-saline) fresh water from lake, pond, river (<5 psu)
EMP sample Free-living Non-saline Sediment (non-saline) sediment from lake, pond, river (<5 psu)
EMP sample Free-living Non-saline Soil (non-saline) soil from forest, grassland, tundra, desert, etc.
EMP sample Free-living Non-saline Surface (non-saline) biofilm from wet (<5 psu) or dry surface, wood, dust, microbial mat
EMP sample Free-living Non-saline Subsurface (non-saline) deep or subsurface environment
EMP sample Free-living Non-saline Aerosol (non-saline) aerosolized dust or liquid
EMP sample Free-living Saline Water (saline) salt water from ocean, sea, estuary, mangrove, coral reef (>5 psu)
EMP sample Free-living Saline Sediment (saline) sediment from ocean, sea, estuary, mangrove, beach (>5 psu)
EMP sample Free-living Saline Hypersaline (saline) water from hypersaline sample or brine (>50 psu)
EMP sample Free-living Saline Surface (saline) biofilm from wet or underwater surface or microbial mat (>5 psu)
EMP sample Free-living Saline Aerosol (saline) seaspray or other aerosolized saline material (>5 psu)
EMP sample Host-associated Animal Animal distal gut feces, stool
EMP sample Host-associated Animal Animal proximal gut gut intestine, gizzard, crop, lumen, mucosa
EMP sample Host-associated Animal Animal secretion saliva, breast milk, vaginal secretion
EMP sample Host-associated Animal Animal surface skin, sebum, mucus, slime
EMP sample Host-associated Animal Animal corpus tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal
EMP sample Host-associated Plant Plant secretion pollen, sap
EMP sample Host-associated Plant Plant surface leaf or kelp surface biofilm
EMP sample Host-associated Plant Plant rhizosphere plant root system, may include some soil
EMP sample Host-associated Plant Plant corpus tissue of leaf, stem, fruit, algae
EMP sample Host-associated Fungus Fungus corpus tissue of mushroom or other fungi
EMP sample Host-associated Fungus Fungus surface biofilm of mushroom
EMP sample Control Negative Sterile water blank sterile water blank used as negative control for extraction, PCR, and sequencing
EMP sample Control Positive Single strain known single strain used as positive control
EMP sample Control Positive Mock community known mixed community used as positive control
EMP sample Unknown Contradictory Unknown (contradictory) unknown sample type because other metadata is contradictory
EMP sample Unknown Missing Unknown (missing) unknown sample type because metadata is unavailable