Techniques used to characterize the gut microbiota: a guide for the clinician

Nat Rev Gastroenterol Hepatol. 2012 Mar 27;9(6):312-22. doi: 10.1038/nrgastro.2012.44.


The gut microbiota is a complex ecosystem that has a symbiotic relationship with its host. An association between the gut microbiota and disease was first postulated in the early 20(th) century. However, until the 1990s, knowledge of the gut microbiota was limited because bacteriological culture was the only technique available to characterize its composition. Only a fraction (estimated at <30%) of the gut microbiota has been cultured to date. Since the 1990s, advances in culture-independent techniques have spearheaded our knowledge of the complexity of this ecosystem. These techniques have elucidated the microbial diversity of the gut microbiota and have shown that alterations in the gut microbiota composition and function are associated with certain disease states, such as IBD and obesity. These new techniques are fast, facilitate high throughput, identify organisms that are uncultured to date and enable enumeration of organisms present in the gut microbiota. This Review discusses the techniques that can used to characterize the gut microbiota, when they can be applied to human studies and their relative advantages and limitations.

Publication types

  • Research Support, Non-U.S. Gov't
  • Review

MeSH terms

  • DNA Fingerprinting / methods
  • DNA, Bacterial / genetics
  • Gastrointestinal Tract / microbiology*
  • Humans
  • In Situ Hybridization, Fluorescence
  • Metagenome* / genetics
  • Metagenomics / methods*
  • Metagenomics / trends
  • Microbiological Techniques / methods*
  • Microbiological Techniques / trends
  • Oligonucleotide Array Sequence Analysis
  • Polymorphism, Restriction Fragment Length / genetics


  • DNA, Bacterial