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

Nature Reviews Gastroenterology & Hepatology volume 9, pages 312–322 (2012)Cite this article

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Abstract

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 20th 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.

Key Points

  • A fraction estimated at <30% of the gut microbiota has been cultured to date; new culture-independent techniques have been developed that have revolutionized our knowledge of the gut microbiota

  • The majority of these techniques are based on the extraction of DNA and amplification of 16S ribosomal RNA genes

  • 16S rRNA genes are highly conserved between bacterial species, but vary in a manner that allows species identification

  • Different techniques can phylogenetically identify and/or quantify the components of the gut microbiota

  • Metagenomics is the most recent development in the study of the gut microbiota and is defined as the study of collective genomes from the environment

  • Metagenomics will further expand our knowledge of the association between the gut microbiota and disease, and help identify causative mechanisms

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Figure 1
Figure 2
Figure 3: Extraction of nucleic acid and amplification of 16S rRNA genes.
Figure 4: Terminal-restriction fragment length polymorphism.
Figure 5: Fluorescence in situ hybridization.
Figure 6: DNA microarrays.
Figure 7: Sanger sequencing with capillary electrophoresis.
Figure 8: 454 pyrosequencing®.

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Acknowledgements

The authors thank Dr J. O'Callaghan, Paul O' Toole's laboratory, University College Cork, Ireland, for the microarray image in Figure 6. Microbiota studies in the authors' laboratories are funded in part by awards from Science Foundation Ireland, the Health Research Board and the (Government of Ireland) Department of Agriculture, Food and Fisheries.

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  1. Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland

    Marianne H. Fraher, Paul W. O'Toole & Eamonn M. M. Quigley

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Fraher, M., O'Toole, P. & Quigley, E. Techniques used to characterize the gut microbiota: a guide for the clinician. Nat Rev Gastroenterol Hepatol 9, 312–322 (2012). https://doi.org/10.1038/nrgastro.2012.44

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