Determining uncultured bacterial group/clade from GTDB data

GTDB
1

Hello everyone,

I’ve downloaded the metadata for a particular bacterial group from the latest GTDB release (R220). I’m now interested in confirming whether this group has any cultured representatives. Could you advise on which column(s) would provide this information? I understand that the column titled “ncbi_genome_category” might be relevant, as entries labeled “derived from metagenomes” could indicate that the group lacks cultured representatives.

Thanks in adavance…

2

Hi Raaj,

The “ncbi_genome_category” field is the most relevant. It will indicate if a genome is derived from a metagenome or single cell based on metadata at NCBI. The assumption is that all other genomes are isolates.

Cheers,
Donovan

3

Hii Donovan,
Thanks for clarifying this.