To cite phyloseq in publications, or otherwise credit, please use:

  phyloseq: An R package for reproducible interactive analysis and
  graphics of microbiome census data. Paul J. McMurdie and Susan Holmes
  (2013) PLoS ONE 8(4):e61217.

A BibTeX entry for LaTeX users is

  @Article{,
    author = {Paul J. McMurdie and Susan Holmes},
    journal = {PLoS ONE},
    pages = {e61217},
    title = {phyloseq: An R package for reproducible interactive analysis and graphics of microbiome census data},
    volume = {8},
    number = {4},
    year = {2013},
    url = {http://dx.plos.org/10.1371/journal.pone.0061217},
  }