Sequencing and beyond: integrating molecular 'omics' for microbial community profiling

Nat Rev Microbiol. 2015 Jun;13(6):360-72. doi: 10.1038/nrmicro3451. Epub 2015 Apr 27.


High-throughput DNA sequencing has proven invaluable for investigating diverse environmental and host-associated microbial communities. In this Review, we discuss emerging strategies for microbial community analysis that complement and expand traditional metagenomic profiling. These include novel DNA sequencing strategies for identifying strain-level microbial variation and community temporal dynamics; measuring multiple 'omic' data types that better capture community functional activity, such as transcriptomics, proteomics and metabolomics; and combining multiple forms of omic data in an integrated framework. We highlight studies in which the 'multi-omics' approach has led to improved mechanistic models of microbial community structure and function.

Publication types

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

MeSH terms

  • Gene Expression Profiling / methods*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Metabolomics / methods*
  • Metagenomics / methods*
  • Microbiota / genetics
  • Microbiota / physiology*
  • Proteomics / methods*
  • Systems Biology / methods*