Experimental and analytical tools for studying the human microbiome

Nat Rev Genet. 2011 Dec 16;13(1):47-58. doi: 10.1038/nrg3129.


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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • Algorithms
  • Computational Biology / methods*
  • DNA / genetics
  • DNA Barcoding, Taxonomic / methods*
  • Databases, Nucleic Acid
  • Genomics / methods
  • Humans
  • Metagenome / genetics*
  • Mouth / microbiology
  • Nucleic Acid Amplification Techniques
  • RNA, Ribosomal, 16S / chemistry*
  • RNA, Ribosomal, 16S / genetics
  • Skin / microbiology
  • Software


  • RNA, Ribosomal, 16S
  • DNA