When I look at the file, I am a little confused about the classification of the OTUs. There are some OTUs that are classified as the same with a 100% confidence threshold. Eg:

OTU1: Otu00001 22860 Bacteria(100);“Bacteroidetes”(100);“Sphingobacteria”(100);“Sphingobacteriales”(100);Cytophagaceae(100);Microscilla(100);

OTU13: Bacteria(100);“Bacteroidetes”(100);“Sphingobacteria”(100);“Sphingobacteriales”(100);Cytophagaceae(100);Microscilla(100);

I am not sure how to interpret this, especially if I am interested in knowing the most abundant species in some of my samples. OTUs were constructed at 97% similarity. Therefore, shouldnt the two Microscilla be included under the same OTU?


I just realized that MIcroscilla is at the Genus level. Sorry and thanks!