Hi @nico,
Just a quick drive by comment here...
It is generally not possible to obtain species and subspecies level classification with 16S rRNA amplicons, especially with variable regions like V4 etc... It is even difficult to do this for some taxa when you have the full 16S rRNA gene sequence.
SILVA (currently up to version 138.2), as far as I am currently aware, still only curates taxonomy to the genus level, even if they provide species level information. Mainly for the reasons I mentioned above.
Here are some links to the topic that discuss (in part, or in full) that over-, under-, and mis-classification of taxa is a real issue encountered by many tools and curation practices (there are many more articles on this topic):
- Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin
- RESCRIPt: Reproducible sequence taxonomy reference database management
- Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences
- Taxonomy annotation and guide tree errors in 16S rRNA databases
- SINTAX: a simple non-Bayesian taxonomy classifier for 16S and ITS sequences
- Embracing Ambiguity in the Taxonomic Classification of Microbiome Sequencing Data
I am not familiar with AmpliSeq, or how their reference database was curated. My off-the-cuff response would be that many species, and sub-species classifications you are observing, are likely over-classifications and not real. Just because a classifier returns a species-level classification does not mean they are necessarily correct.
My 2 cents... , I'd caution against obtaining species specific taxonomic classification with short amplicon reads. If you truly require species and strain level identification, then I'd suggest looking into shotgun metagenomic sequencing.
I'm sure others will have thoughts to add. 