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Environ Microbiol Rep. 2009 Jun;1(3):191-7. doi: 10.1111/j.1758-2229.2009.00030.x. Epub 2009 Apr 29.

EnvDB, a database for describing the environmental distribution of prokaryotic taxa.

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1
Instituto Cavanilles de Biodiversidad y Biología Evolutiva, Universidad de Valencia, Polígono La Coma s/n, 46980 Paterna (Valencia), Spain. Centro Superior de Investigación en Salud Pública (CSISP), Dirección General de Salud Pública, C/San Vicente 83, 46007 Valencia, Spain. CIBER en Epidemiología y Salud Pública (CIBER-ESP), Spain.

Abstract

EnvDB is a database that classifies the environmental samples and their associated 16S rDNA sequences currently stored in GenBank. The samples were categorized in a three-level, hierarchical classification of media: the five upper levels (terrestrial, aquatic, thermal, host-associated and other) are further decomposed in 20 intermediate (such as marine, marine sediments, freshwater, soil, gut, etc.) and 47 lower levels (for instance, soil is further decomposed in forest, agricultural, wetlands, grasslands, tropical, arid, etc.). Each sample was also characterized with nine environmental features: polluted, diseased (for clinical samples), acidic, alkaline, hot environment, cold environment, saline, anoxic and restricted (when the study is focused only in particular taxonomic groups). The classification of samples was aided by text-mining techniques, complemented with careful curation and completion by human experts. EnvDB currently includes 359 928 sequences from 3502 samples. The sequences were clustered at several identity levels to obtain operative taxonomic units (OTUs). Sequences and OTUs have been taxonomically assigned to the maximum possible resolution by different procedures. The user can obtain information about sequences, OTUs, samples and environments, combining these tables using a flexible querying system that allows generating very diverse queries. Thus, the user can easily inspect the presence and abundance of particular taxa in particular samples and environments. The database also allows the users to run analyses with their own data: users can input their sequences and find the closest sequences or samples in the database. EnvDB can be accessed in the web address http://metagenomics.uv.es/envDB.

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