It's hard to assign taxonomy to species level with the use of any program (Mothur, Qiime).
Changes between sequences at species level are so small that can be compared to sequencing errors. Very popular is assigning taxonomy to even higher phylum level or if we have very good quality of reads to genus level.
Even when you assign species taxonomy the probability that those species are in your sample is small. That's my opinion. Maybe somebody has different, I will be happy to read.