Using phyloseq for metagenomic data without actual OTUs

[CETHuyghe]

In my Eukaryotic metagenome dataset, it is impossible to identify most samples to species level or to cluster them in OTUs. I have many reads that are for example only identified to class or phylum level. Is it possible to actually use the full abundance table with all reads (so e.g. including class, species, order, phylum,..), and have analyses that take into account the taxonomy and taxonomic level to which the reads are identified? For example in an ordination plot? Or is the only way to select a taxonomic rank per analysis?