Hi,
Is there a database that I can use to determine whether the bacteria are Gram-positive or Gram-negative?
I would also appreciate it if you can tell me how to use it.
Thank you.
Cheers,
Adria
1 Like
Hi @adriaeda
Maybe this can be helpful: https://doi.org/10.1093/nar/gki027
I found older discussions mentioning this database might be helpful. Will link more if I come across any!
Thanks 
Anirban
4 Likes
Hi Anirban,
Thank you for your reply. I have seen this option form other discussions too but I don't know how to put into commands. Could you help with that?
Thank you very much! 
-Adria
Hi there!
I just found this toppic in the forum and I'm also interested in this kind of classification. Did you get a solution for it?
Thank you in advance.
Ana.
I haven't used the tool that was referenced above, but BugBase should do this.
3 Likes
Adding to that discussion, I've faced a similar problem before as my own initiative to please clinical collaborators. I failed, so to save everyone their time, here are the main takeaways:
While BugBase does the trick, it wasn't updated since 2015. Additionally, it uses PICRUSt predictions, which itself was updated recently (PICRUSt2 for prediction of metagenome functions | Nature Biotechnology), and doesn't perform well in environments other than the human gut.
For sequencing data there are a lot of issues:
- Gram staining is a technique from 1884 done on a culture, thus cannot be applied to uncultured species captured by sequencing.
- The traditional Gram-staining procedure does not accurately denote the structure of bacteria and there are "Gram-variable" species (more on that in PSORTdb—an expanded, auto-updated, user-friendly protein subcellular localization database for Bacteria and Archaea - PMC)
- The mapping from PSORTdb requires a lot of data wrangling and only maps sensibly with a species-level resolution, which is rare in 16S, becoming unreliable at the genus level.
I'd start with a basic question:
Why Gram staining information is required in your research question?
Because there might be a better way to get the info you need. Gram staining is quick and useful in a clinical setting, where the time is critical (rapidly developing infection, sepsis, etc.). But it is not suited for research purposes in 2022.
To browse a single bacterium I would use https://db.psort.org/
Cheers
Valentyn
3 Likes
Its just a curiosity... I understand that all minor uncultured species would not be classified as gram. How ever, I'm interested in a general vision of gram behaviour. I work with soil samples and it has been always said that tillage managements and soil pH effects differ on gram species... so I just wonder if this could be applied to metataxonomic analisys to see if this is really true or not... but as said, just curiosity.
Thank you in advance.
Sincerely,
Ana.
Hi @Anuka
In that case you could just look at phylum-level classifications. This is generally what Gram staining delineates (with some notable caveats).
Good luck!