How To Determine If A Given Species(Or Tax Id) Belongs To A Given Environment (Bacteria)

Question

[Dhruv Sakalley]

I want to determine origin of bacterial species in a certain phylum, more precisely in categories human gut; gut + environment ; non gut How can this be achieved. Thanks in advance

Answer 1

[Casey Bergman]

Try EnvDB: http://metagenomics.uv.es/envDB/

EnvDB is a database that aims to provide the most complete census to-date of the environmental distribution of prokaryotes. EnvDB connects the taxonomic identification of 16S rDNA sequences with the environmental characterization of their original samples. This is the result of a comprehensive effort to annotate all samplings and sequences stored in the ENV section of GenBank database. Currently, EnvDB contains 359928 sequences belonging to 3502 samples, classified in 46 different enviromental categories plus some environmental features.

[Dhruv Sakalley]

Yes I saw a similar approach in http://www.ncbi.nlm.nih.gov/pubmed/20197316

[Dhruv Sakalley]

Thanks, is that the best way available?

[Dhruv Sakalley]

Although informative this method does not clearly distinguish between phylum at a species level, such as when I search for phylum associated/ reported for human gut, I even get results like : Archaea Host-associated Gut Human restricted I know there are a lot of species associated with human gut in literature, but this database appears to still be under development and cannot certainly tell if a species belong to a desired enviornment