Functional human microbiota analyses in vivo using ’omics technologies

Credit: Antlii / Alamy Stock Photo

Eline Klaassens and colleagues applied a metaproteomics approach to uncultured faecal microbiota, providing the first insights beyond taxonomic identification. This was followed by numerous studies using ’omics methods, such as metabolomics and metatranscriptomics, as well as the development of multi-omics pipelines; methods that are still uncovering the functions of the microbiota today.

Further reading

Verberkmoes, N. C. et al. Shotgun metaproteomics of the human distal gut microbiota. ISME J. 3, 179–189 (2008).

Jansson, J. et al. Metabolomics reveals metabolic biomarkers of Crohn’s disease. PLoS ONE 4, e6386 (2009).

Martin, F. P. et al. Topographical variation in murine intestinal metabolic profiles in relation to microbiome speciation and functional ecological activity. J. Proteome Res. 8, 3464–3474 (2009).

Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. USA 111, 2329–2338 (2014).

Bouslimani, A. et al. Molecular cartography of the human skin surface in 3D. Proc. Natl Acad. Sci. USA 112, 2120–2129 (2015).

Heintz-Buschart, A. et al. Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes. Nat. Microbiol. 2, 16180 (2016).

Franzosa, E. A. et al. Gut microbiome structure and metabolic activity in inflammatory bowel disease. Nat. Microbiol. 4, 293–305 (2019).

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