phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data (2013) PLoS ONE 8(4):e61217 http://dx.plos.org/10.1371/journal.pone.0061217
See the microbio_me_qiime tutorial for more details and examples downloading and importing into phyloseq/R directly from this public database.
The phyloseq project also has a number of supporting online resources, most of which can by found at the phyloseq home page, or from the phyloseq stable release page on Bioconductor.
To post feature requests or ask for help, try the phyloseq Issue Tracker.