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I am looking for tidy tabular dataset that contains known bacteria and fungi down to the species level. Basically a table that includes genus and species names and other higher-level information. For example, whether it is gram-positive or negative, or anaerobic etc. A database with API would work too.

I found https://bacteria.ensembl.org/, but this is not so easy to use/automate.

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You can try Entrez in Biopython. Although, there is hassle with additional information.

from Bio import Entrez

Entrez.email = "your.letterbox@any.com"
Entrez.api_key = "your_key"

TaxID = Entrez.read(Entrez.esearch(db="taxonomy", term="Hepatovirus A"))["IdList"][0]
Entrez.read(Entrez.efetch(db="taxonomy", id=TaxID))
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