To cite package ‘animalcules’ in publications use:

  Zhao, Y., Federico, A., Faits, T. et al. animalcules: interactive
  microbiome analytics and visualization in R. Microbiome 9, 76 (2021)

A BibTeX entry for LaTeX users is

  @Article{,
    title = {animalcules: interactive microbiome analytics and visualization in R},
    author = {Yue Zhao and Anthony Federico and Tyler Faits and Solaiappan Manimaran and Daniel Segrè and Stefano Monti and W. Evan Johnson},
    year = {2021},
    journal = {Microbiome},
    doi = {10.1186/s40168-021-01013-0},
    volume = {9},
    issue = {1},
    pages = {76},
  }