How to Identify bacterial strains that cause human diseases?

01 January 1970 3 3K Report

Hello!

I am working with a considerable list of bacterial genomes, and I need to create subsets as commensal, environmental, and pathogenic lineages. I know its possible to get this data from the genome page (per example, https://www.ncbi.nlm.nih.gov/genome/182), but, as its a big list, I looking for something similar to a table because I will process this data with a script.

I can use alternative websites to get this info too, but I need to retrieve the correct annotation. So any suggestions are welcome.

Thanks!

Christian Mittermayr

Hi !

Maybe these links do not exactly provide what you need, but maybe there is an indirect link to the data you need.

Christian

BACTERIAL BIOINFORMATICS RESOURCE CENTER

https://www.patricbrc.org/

Digital Database of Microbial Phenotypes

https://github.com/rec3141/ddmp

http://reric.org/work/ddmp/

TypOn: The Microbial Typing Ontology

http://www.phyloviz.net/typon/

bacterial metadatabase BacDive

http://bacdive.dsmz.de

https://academic.oup.com/nar/article/47/D1/D631/5106998

Microbial Phenotypes Wiki,

https://microbialphenotypes.org/wiki/index.php/Main_Page

Article Hiding in Plain Sight: Mining Bacterial Species Records for ...

International Journal of Systematic and Evolutionary Microbiology (IJSEM) phenotypic database

https://figshare.com/articles/International_Journal_of_Systematic_and_Evolutionary_Microbiology_IJSEM_phenotypic_database/4272392

Any bacterial databases that contain Gram staining information?

https://www.biostars.org/p/201794/

Pathogen Host Interaction DB

http://www.phi-base.org/

Article An ontology for microbial phenotypes

Temperature data for all bacteria?

https://www.researchgate.net/post/Temperature_data_for_all_bacteria

Rafael Piergiorge

Thank you for the suggestions, Dr Christian Mittermayr

Andrei Grecu

I think you need to first create a query somehow and get the data you need from the database. Then you can put this data in a table (or other form) that is convenient for your script.

Maybe you can get some support from the maintainers of the database on how you can query it.

The answer to your question would be a list of already known bacterial strains that are pathogenic (i.e. causes disease)? Otherwise, I think that finding if an unknown strain can cause a disease would be difficult (although interesting).

Edit: I could save a search result after "Human Pathogen" into a file; there is a "Send to: " link at the bottom right of the search result. You can try different keywords for your search.

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