Taxonomic ids of all pathongenic/BSL<1 microbes.

Question

[bio.erikson]

I'm trying to identify any human pathogens in a whole genome metagenome survey of enviromental samples. Is there some list or database of pathogenic microbes? Or list of organisms greater than BSL 1? I have NCBI taxonomy ids from KRAKEN.

[Sej Modha]

If you have taxonomy identifiers for these viruses then it would be possible to download whole genome sequences using NCBI Eutils. For example:

esearch -db nuccore -query "txid11676[ORGN] AND refseq[FILTER]"|efetch -format fasta