Ecosystem-specific microbiota and microbiome databases in the era of big data

Lobanov, Victor; Gobet, Angélique; Joyce, Alyssa

doi:10.1186/s40793-022-00433-1

Environmental Microbiome

Table 2 A selection of published ecosystem-specific databases

From: Ecosystem-specific microbiota and microbiome databases in the era of big data

Ecosystem-specific database	Target ecosystem(s)	Target organisms	Meta-omics approach used	References
Biomes of Australian Soil Environments (BASE)	Australian subcontinent, terrestrial systems	Prokaryotes and fungal-specific eukaryotes	Sanger sequencing Metabarcoding Metagenomics Environmental measurements	[214]
Dictyopteran gut microbiota reference Database (DictDb)	Dictyopteran gut microbiota	All microorganisms	Sanger sequencing Metabarcoding Metagenomics	[215]
Earth Microbiome Project (EMP)	EMP Ontology (EMPO) ecosystems	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[34, 216]
Genome Repository of Oiled Systems (GROS)	Crude oil contaminated environments	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Environmental measurements	[217]
Global Ocean Sampling (GOS)	Open ocean ecosystems	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[218]
Human Food Project	Human gastrointestinal tract	All prokaryotes	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[219]
Integrative Human Microbiome Project (HMP)	Human body microbiome environments	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[181,182,183]
Human Oral Microbiome Database (HOMD)	Human oral environment	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics	[220]
Maarja Öpik arbuscular mycorrhiza database (MaarjAM)	Arbuscular mycorrhizal fungi associated environments	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Environmental measurements	[221]
Marine databases; MarRef, MarDB, MarCat	Open ocean ecosystems	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[184]
METAgenomics of the Human Intestinal Tract (MetaHIT)	Human gastrointestinal tract	All microorganisms	Metagenomics Metatranscriptomics Metaproteomics Metabolomics	[222]
Microbial Database for Activated Sludge (MiDAS)	Activated sludge	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metabolomics Environmental measurements	[223]
Rumen and Intestinal Methanogen- DB (RIM-DB)	Ruminant gastrointestinal tract	All microorganisms	Sanger sequencing Metabarcoding Metagenomics	[224]
Tara Oceans project	Open ocean ecosystems	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metatranscriptomics Metaproteomics Metabolomics Environmental measurements	[35, 225, 226]
Unified Human Gastrointestinal Genome (UHGG) collection	Human gut	All microorganisms	Sanger sequencing Metabarcoding Metagenomics Metaproteomics	[227]

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ISSN: 2524-6372

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