Earth Microbiome Project Ontology (EMPO)

Qiita supports using the EMPO classification of samples as it provides and easy way to group samples and has resulted extremely helpful for meta-analyses and searching and finding similar samples in the database.

The current version can be found here: Making data Public in Qiita and/or send data to EBI-ENA and below you can find older version, for your reference.

EMPO 1 (first release)

empo_1

empo_2

empo_3

Examples

Free-living

Non-saline

Water (non-saline)

fresh water from lake, pond, or river (<5 psu)

Free-living

Non-saline

Sediment (non-saline)

sediment from lake, pond, or river (<5 psu)

Free-living

Non-saline

Soil (non-saline)

soil from forest, grassland, tundra, desert, etc.

Free-living

Non-saline

Surface (non-saline)

biofilm from wet (<5 psu) or dry surface, wood, dust, or microbial mat

Free-living

Non-saline

Subsurface (non-saline)

deep or subsurface environment

Free-living

Non-saline

Aerosol (non-saline)

aerosolized dust or liquid

Free-living

Saline

Water (saline)

salt water from ocean, sea, estuary, mangrove, or coral reef (>5 psu)

Free-living

Saline

Sediment (saline)

sediment from ocean, sea, estuary, mangrove, or beach (>5 psu)

Free-living

Saline

Hypersaline (saline)

water from hypersaline sample or brine (>50 psu)

Free-living

Saline

Surface (saline)

biofilm from wet or underwater surface or microbial mat (>5 psu)

Free-living

Saline

Aerosol (saline)

seaspray or other aerosolized saline material (>5 psu)

Host-associated

Animal-associated

Animal distal gut

feces, stool

Host-associated

Animal-associated

Animal proximal gut

digesta

Host-associated

Animal-associated

Animal secretion

gut intestine, gizzard, crop, lumen, or mucosa

Host-associated

Animal-associated

Animal surface

skin, sebum, mucus, slime

Host-associated

Animal-associated

Animal corpus

tissue of sponge, coral, gill, siphon, carcass, etc. or whole small animal

Host-associated

Fungus-associated

Fungus corpus

tissue of mushroom or other fungi

Host-associated

Fungus-associated

Fungus surface

biofilm of mushroom

Host-associated

Plant-associated

Plant secretion

pollen or sap

Host-associated

Plant-associated

Plant surface

leaf or kelp surface biofilm

Host-associated

Plant-associated

Plant rhizosphere

plant root system, may include some soil

Host-associated

Plant-associated

Plant corpus

tissue of leaf, stem, fruit, or algae

Control

Negative

Sterile water blank

sterile water blank used as negative control for extraction, PCR, and sequencing

Control

Positive

Mock community

known mixed community used as positive control

Control

Positive

Single strain

known single strain control culture

Unknown

Contradictory

Unknown (contradictory)

unknown sample type because other metadata is contradictory

Unknown

Missing

Unknown (missing)

unknown sample type because metadata is unavailable