Why are the number of species less than the number of families in my dataset?

Depending on the sequencing technologies used (which determine the taxonomic resolution that can be obtained), it is possible that there will be more OTUs can be confidently assigned at family levels, but less number of them can be assigned at the species level, maybe none at strain level. In such cases, the unassigned species will be collapsed under “Not_Assigned” category which vastly reduces the number of features available for comparison and exploration.