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Gut microbiota

Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD

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Although metagenomic sequencing has provided unprecedented characterization of the gut microbiome, it gives only indirect evidence of the genes and pathways that might be active. Now, investigators have combined longitudinal sampling with metatranscriptomics and metagenomics in IBD to provide a high-resolution picture of the microbiome's functional dynamics.

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Figure 1: Schematic representation of different views of the gut microbiome.

References

  1. Morgan, X. C. et al. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 13, R79 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. The Human Microbiome Consortium. Structure, function and diversity of the healthy human microbiome. Nature 486, 207–214 (2012).

  3. Falony, G. et al. Population-level analysis of gut microbiome variation. Science 352, 560–564 (2016).

    Article  CAS  PubMed  Google Scholar 

  4. Schirmer, M. et al. Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat. Microbiol. https://doi.org/10.1038/s41564-017-0089-z (2018).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Schloissnig, S. et al. Genomic variation landscape of the human gut microbiome. Nature 493, 45–50 (2013).

    Article  PubMed  Google Scholar 

  6. Gevers, D. et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe 15, 382–392 (2014).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Bang, S. et al. Nociceptive and pro-inflammatory effects of dimethylallyl pyrophosphate via TRPV4 activation. Br. J. Pharmacol. 166, 1433–1443 (2012).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Franzosa, E. A. et al. Relating the metatranscriptome and metagenome of the human gut. Proc. Natl Acad. Sci. USA 111, E2329–E2338 (2014).

    Article  CAS  PubMed  Google Scholar 

  9. Vandeputte, D. et al. Quantitative microbiome profiling links gut community variation to microbial load. Nature 551, 507–511 (2017).

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Department of Medicine, APC Microbiome Institute, University College Cork, Cork, Ireland

    Aonghus Lavelle

  2. Sorbonne Université, École normale supérieure, PSL Research University, CNRS, INSERM, AP-HP, Hôpital Saint-Antoine, Laboratoire de biomolécules, LBM, Paris, France

    Harry Sokol

  3. INRA, UMR1319 Micalis & AgroParisTech, Jouy en Josas, France

    Harry Sokol

Authors
  1. Aonghus Lavelle
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  2. Harry Sokol
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Correspondence to Harry Sokol.

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Competing interests

H.S. is co-founder of Nextbiotix and has served as consultant for BiomX, Danone, Enterome and Maat pharma. A.L. declares no competing interests.

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Lavelle, A., Sokol, H. Beyond metagenomics, metatranscriptomics illuminates microbiome functionality in IBD. Nat Rev Gastroenterol Hepatol 15, 193–194 (2018). https://doi.org/10.1038/nrgastro.2018.15

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