Hello there!
I am wondering if, somebody is using GSR database for phylogenetic classification?
Currently I use SILVA with consistent results, but GSR (GreenGenes, Silva, RDP) database (GSR database), should be better because of composition. Their article state that is robust and outperforms all databases...
Please let me know if you use it and if really improves classification.
Hello Gustavo,
Welcome to the forums! 
I've not seen this database before! Thank you for sharing this.
- Article on Pubmed: PMC10946287: GSR-DB: a manually curated and optimized taxonomical database for 16S rRNA amplicon analysis - PMC
- Code on GitHub: GitHub - ManichanhLab/GSR-16SDB
- Google Scholar: 22 citations so far https://scholar.google.com/scholar?cluster=8723533819171860138
Yeah, they really do say that.
"Our evaluation analyses showed that GSR-DB outperforms existing databases in providing species-level resolution,"
They also say
"Based on the most unbiased experimental evaluation, GSR was only outperformed by Greengenes 2, with the exception of the region V1–V3."
This matches Figure 2B:
Zooming out a bit, I don't think a better database will fix the species concept.
If it helps you find a key microbe or is a better match to your positive controls, then it's worth using I guess.
Thank you for your response. Definitely, species resolution is difficult, but should help to get better picture in ecosystem if traditional methods help to characterize key participants.
Authors need to update bacterial nomenclature!
Lets give a try and see the data.
Greetings from México!