About the microPITA category

Name: microPITA
User manual || Tutorial

Description: microPITA is a computational tool enabling sample selection in two-stage (tiered) studies. Using two-stage designs can more efficiently allocate resources, reducing study costs, and maximizing the use of samples. From a survey study, selection of samples can be performed to target various microbial communities including:

  • Samples with the most diverse community (maximum diversity);
  • Samples dominated by specific microbes (targeted feature);
  • Samples with microbial communities representative of the survey (representative dissimilarity);
  • Samples with the most extreme microbial communities in the survey (most dissimilar);
  • Given a phenotype (like disease state), samples at the border of phenotypes (discriminant) or samples typical of each phenotype (distinct).

Additionally, methods can leverage clinical metadata by stratifying samples into groups. This enables the use of microPITA in cohort studies.


Tickle T, Segata N, Waldron L, Weingart U, Huttenhower C. Two-stage microbial community experimental design. ISMEJ 2013