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In vitro ecology: a discovery engine for microbiome therapies

Nature Reviews Gastroenterology & Hepatology volume 17, pages 711–712 (2020)Cite this article

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To therapeutically modulate gut microbial ecosystems, a better understanding of gut ecology is key. High-throughput in vitro ecology provides a tool with the necessary power to address these needs and interpersonal treatment response variation.

Disturbances of the gut microbiota are associated with a wide range of diseases, and the gut microbiota has become a target for novel therapeutics in intestinal pathologies and beyond1. Current strategies for gut microbiota modulation range from dietary interventions, prebiotics, phages, small molecules and drugs to faecal microbiota transplantation (FMT) and live biotherapeutic products (LBPs). However, focusing on specific modulation approaches is premature, as their advantages, challenges, functional mechanisms and application scope differ. Also, targeted microbiota modulation remains challenging owing to interindividual microbiome variation and a poor understanding of the associated responses. Here, we argue that incorporating ecological principles regulating microbe–microbe interactions and ecosystem dynamics governing treatment response, while embracing the interindividual and temporal variability of the whole ecosystem, is essential for successful modulation of the gut microbiome.

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Fig. 1: Microbiome therapy development.

References

  1. Vázquez-Castellanos, J. F., Biclot, A., Vrancken, G., Huys, G. R. & Raes, J. Design of synthetic microbial consortia for gut microbiota modulation. Curr. Opin. Pharmacol. 49, 52–59 (2019).

    Article  Google Scholar 

  2. El Hage, R., Hernandez-Sanabria, E. & Van de Wiele, T. Emerging trends in “smart probiotics”: functional consideration for the development of novel health and industrial applications. Front. Microbiol. 8, 1889 (2017).

    Article  Google Scholar 

  3. Clemente, J. C., Manasson, J. & Scher, J. U. The role of the gut microbiome in systemic inflammatory disease. BMJ 360, j5145 (2018).

    Article  Google Scholar 

  4. Mills, S., Ross, R. P. & Hill, C. Bacteriocins and bacteriophage; a narrow-minded approach to food and gut microbiology. FEMS Microbiol. Rev. 41, S129–S153 (2017).

    Article  Google Scholar 

  5. Vieira-Silva, S. et al. Statin therapy is associated with lower prevalence of gut microbiota dysbiosis. Nature 581, 310–315 (2020).

    CAS  Article  Google Scholar 

  6. Vrancken, G., Gregory, A. C., Huys, G. R., Faust, K. & Raes, J. Synthetic ecology of the human gut microbiota. Nat. Rev. Microbiol. 17, 754–76 (2019).

    CAS  Article  Google Scholar 

  7. Tramontano, M. et al. Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies. Nat. Microbiol. 3, 514–522 (2018).

    CAS  Article  Google Scholar 

  8. Maier, L. et al. Extensive impact of non-antibiotic drugs on human gut bacteria. Nature 555, 623–628 (2018).

    CAS  Article  Google Scholar 

  9. Hernandez-Sanabria, E. et al. Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation. NPJ Biofilms Microbiomes 6, 1–12 (2020).

    Article  Google Scholar 

  10. Muller, E. E. et al. Using metabolic networks to resolve ecological properties of microbiomes. Curr. Opin. Syst. Biol. 8, 73–80 (2018).

    Article  Google Scholar 

Download references

Acknowledgements

The authors are grateful to the Raes lab members for many stimulating discussions in this area, in particular A. Biclot, G. Huys, G. Vrancken, G. Falony, S. Vieira-Silva, A. Gregory, as well as K. Faust and T. Rask Licht. E.H.-S. is supported by the Novo Nordisk Fundation (PRIMA Project).

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  1. VIB – KU Leuven Center for Microbiology, Laboratory of Molecular Bacteriology, Rega Institute, Leuven, Belgium

    Emma Hernandez-Sanabria, Jorge Francisco Vázquez-Castellanos & Jeroen Raes

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  1. Emma Hernandez-Sanabria
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  2. Jorge Francisco Vázquez-Castellanos
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  3. Jeroen Raes
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Correspondence to Jeroen Raes.

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Competing interests

J.R. has acted or is acting as scientific advisor to Aphea.Bio, Biofortis, GSK vaccines, Janssen Pharmaceuticals, Merck, MRM health and Takeda. E.H.-S. and J.F.V.-C. declare no competing interests.

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Hernandez-Sanabria, E., Vázquez-Castellanos, J.F. & Raes, J. In vitro ecology: a discovery engine for microbiome therapies. Nat Rev Gastroenterol Hepatol 17, 711–712 (2020). https://doi.org/10.1038/s41575-020-00364-7

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