Bacterial morphology details

Question

[Prasad]

hi,

I have a list of bacteria (~ >2000), is there a data source or a way (other than manual literature study) i can get information like- its shape (cocci, rod or spiral), whether it is gram positive or negative and respiration detail (Anaerobic or Aerobic).

[jacklukemcmurray]

Hi Both,

I appreciate this was over 6 years ago. But did you manage to find the file that 5heikki spoke about?

[predeus]

the most relevant database right now seems to be BacDive; it has a Python and R APIs and is generally maintained.

https://api.bacdive.dsmz.de/

Answer 1

[5heikki]

NCBI used to host a file called lproks_0.txt, which summarized info for thousands of prokaryotes as below:

head lproks_0.txt
## Microbial Organism Information Page
## Columns: "RefSeq project ID" "Project ID"    "Taxonomy ID"   "Organism Name" "Super Kingdom" "Group" "Sequence Status"   "Genome Size"   "GC Content"    "Gram Stain"    "Shape" "Arrangment"    "Endospores"    "Motility"  "Salinity"  "Oxygen Req"    "Habitat"   "Temp. range"   "Optimal temp." "Pathogenic in" "Disease"   "Genbank accessions"    "Refseq accessions"

They stopped updating the file some years ago, and AFAIK it is no longer in their ftp. You might find it with Google though..

[Prasad]

Thanks. It was helpful. As you mentioned it has not been updated. Google would be very difficult with such a high number. Thanks for the suggestion