Nature Reviews Genetics 13, 47-58 (January 2012) | doi:10.1038/nrg3129

Article series: Study designs

Experimental and analytical tools for studying the human microbiome

Justin Kuczynski1, Christian L. Lauber2, William A. Walters1, Laura Wegener Parfrey3, José C. Clemente3, Dirk Gevers4 & Rob Knight3,5  About the authors


The human microbiome substantially affects many aspects of human physiology, including metabolism, drug interactions and numerous diseases. This realization, coupled with ever-improving nucleotide sequencing technology, has precipitated the collection of diverse data sets that profile the microbiome. In the past 2 years, studies have begun to include sufficient numbers of subjects to provide the power to associate these microbiome features with clinical states using advanced algorithms, increasing the use of microbiome studies both individually and collectively. Here we discuss tools and strategies for microbiome studies, from primer selection to bioinformatics analysis.

Author affiliations

  1. Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, 347 UCB, Boulder, Colorado 80309, USA.
  2. Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, 216 UCB, Boulder, Colorado, 80309, USA.
  3. Department of Chemistry and Biochemistry, University of Colorado at Boulder, 215 UCB, Boulder, Colorado 80309, USA.
  4. Microbial Systems & Communities, Genome Sequencing and Analysis Program, The Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.
  5. Howard Hughes Medical Institute, 215 UCB, Boulder, Colorado 80309, USA.

Correspondence to: Rob Knight3,5 Email:

Published online 16 December 2011