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R package to link NCBI taxonomy ID to bacterial properties (Gram stain, aerobe/anaerobe, etc)

Hi all,

I wonder if you know of an R package that would allow linking a bacterial species (e.g. by NCBI taxonomy ID, or by a full species name) to a selection of properties. I am currently interested in Gram status and aerobe/anaerobe growth requirements, but other properties (e.g. whether it's cultureable, etc) would be neat to have as well.

Thank you, as always.

r ncbi bacteria taxonomy
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updated by Philipp Bayer Philipp Bayer • written by predeus predeus

1 answer

BacDive has an API (free registration required) with a REST-R client: https://r-forge.r-project.org/R/?group_id=1573 More examples here: https://api.bacdive.dsmz.de/

It's a shame how the other efforts to unify similar databases seem to have disappeared. The Microbe Directory's web page is gone, but it seems like you can pull out the tables on Github: https://github.com/dcdanko/MD2 BactoTraits seems to have also disappeared.

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written by Philipp Bayer Philipp Bayer

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