Greetings fellow microbial researchers, do you prefer to use Greenegenes or SILVA as a reference database for bacterial (16S) microbiome studies? Why? One obvious advantage of SILVA is that it has been updated fairly recently, whereas Greengenes hasn't been updated since 2013, but other than that, I'm not sure which is better.
I ran both on my data and compared the results (just the OTUs, not any actually community comparisons), and at the genus and family levels, SILVA annotates almost twice as many OTUs as Greengenes. At the class level, however, Grenngenes annotates nearly 100 more OTUs than SILVA. So for my data set, it is not clear which database will do a better job. Also, when both databases annotate a given OTU, they frequently disagree, and it's not clear to me which database in more reliable.
Thanks for the help.
P.S. these are Illumina MiSeq data.
I would suggest you the RDP database, since it is better updated. Here's the link
https://rdp.cme.msu.edu/
Cheers
Dear Donald,
Choosing a database for bacterial 16S analysis is a vast discussion.
Personally, I would recommend SILVA for several points:
First, the database is maintained and updated regularly and second, the sequences are quality checked. Meaning that when you blast you have a more accurate result and you can be sure that the sequences (and so your alignment) are reliable. You can check directly on the Silva website for more informations (https://www.arb-silva.de/documentation/). After I do not really know Greengenes but if it was not updated since 2013 I would not rely on it.
Concerning RDP, although the database is updated regularly, it is more suitable for taxonomy analysis than metaprofiling. I did not used it in a while so you would need to have a look at how they are building their database but from my personal experience I have also noticed that the annotation was not that accurate at the OTU level as it is mostly based on NCBI data sequences which are not always reliable. That said it is a really good database for fungal data.
After it is all a matter of choice, every database has its pros and cons, it also depends if you want to compare your data against some other studies, therefore it is better to use the same database. SILVA is usually a reference among microbiological researchers, especially for bacterial 16S analysis.
Hope this helps,
Regards
This paper has just been published. Right what are you asking.
Article SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomi...
Could anyone help me in training my soil microbiome? Which database I must use for 16sRNA based microbiome?
If used in conjunction with DADA2 ASVs it is very useful, since with this approach species level annotation is sometimes possible (of course not recommended for OTUs, but possible for ASVs). When exact species annotation isn't possible, SILVA has the advantage of sub-classifying genus annotations according to predicted species groups, for example Prevotella_7 and Prevotella_9, so that when species level annotation wasn't possible, you can often pick up that you actually have different species associating with your phenotype. This can be very useful for avoiding misinterpreting results! So, I recommend SILVA.
Hello dear colleagues,
I hope you are doing well!
I need to start my functional gene analysis, but as you know SILVA and GreenGene databases are dedicated to 16S rRNA gene analysis. I am going to ask you how to provide a database for a functional gene like SILVA and GreenGene? Or Are there other ways and methods to do that? Your help is much needed!
Thanks a lot.
Mehrdad
Mehrdad Rabiei I guess these are used for that.
https://www.ebi.ac.uk/arrayexpress/
https://david-d.ncifcrf.gov/
https://www.ncbi.nlm.nih.gov/geo/
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