Hi!
I'm using SILVA 138.2 and in my taxonomy table there are genera like "Synechococcus_CC9902" or "Prochlorococcus_MIT9313" etc. So there is the genus name (Synechococcus) with a code (CC9902). Looking at the literature I found that the code shuold be the strain. Wouldn't it be more correct to put "Synechococcus" in the genus column and "Synechococcus_CC9902" in the species column (which is empty)?
Thank you for any suggestions
Hi @Anna_96,
This has more to do with how the original submitter and/or the respective databases have decided to annotate the various organisms. Things can get messy when a name has not been validated yet. Mixup of taxonomic labels and ranks is quite common.
I suspect that these "strains" are not really strains, but a label given by the group that discovered them, which may not be a valid taxonomic label. They probably confirmed the genus... but are fuzzy when it comes to a species and strain labels...
For example see the NCBI Taxonomy for:
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Hi @SoilRotifer,
thanks for your quick response! At this point, I think it makes more sense to simply replace the name Synechococcus_CC9902 in the genus column with Synechococcus. I would do this because I have other similar cases in the same column, such as [Synechococcus]_spongiarum_group, which isn't very informative. I imagine that having entries like [Synechococcus]_spongiarum_group and Synechococcus_CC9902 treated as separate genera might negatively affect the statistics, rather than just having both listed as Synechococcus which is what they really are at genus level. What do you think?
Thank you! 
HI @Anna_96,
I quite agree! In fact, this is one of the reasons why we made the qiime rescript edit-taxonomy ... action. That'll probably help you batch rename many items in your reference database, etc...
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