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  • Perspective
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Emerging tools and best practices for studying gut microbial community metabolism

Abstract

The human gut microbiome vastly extends the set of metabolic reactions catalysed by our own cells, with far-reaching consequences for host health and disease. However, our knowledge of gut microbial metabolism relies on a handful of model organisms, limiting our ability to interpret and predict the metabolism of complex microbial communities. In this Perspective, we discuss emerging tools for analysing and modelling the metabolism of gut microorganisms and for linking microorganisms, pathways and metabolites at the ecosystem level, highlighting promising best practices for researchers. Continued progress in this area will also require infrastructure development to facilitate cross-disciplinary synthesis of scientific findings. Collectively, these efforts can enable a broader and deeper understanding of the workings of the gut ecosystem and open new possibilities for microbiome manipulation and therapy.

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Fig. 1: Areas of recent progress in research on gut microbial metabolism.
Fig. 2: Challenges to deciphering gut microbial metabolism.
Fig. 3: Constraint-based modelling of microbial metabolism.
Fig. 4: Methods for visualizing metabolic networks and associated data.

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Acknowledgements

Figs. 14 were created with BioRender.com. We thank C. Zhang (laboratory of P.J.T., UCSF) for assistance with the chemical structures in Fig. 2d. Funding was provided from the National Institutes of Health (R01HL122593, F32GM140808, to C.N.). P.J.T is a Chan Zuckerberg Biohub-San Francisco Investigator.

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Conceptualization, funding acquisition: C.N. and P.J.T.; supervision: P.J.T.; visualization, writing—original draft: C.N.; writing—review and editing: C.N. and P.J.T.

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Correspondence to Peter J. Turnbaugh.

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P.J.T. is on the scientific advisory boards for Pendulum, Seed and SNIPRbiome; there is no direct overlap between the current study and these consulting duties. C.N. declares no competing interests.

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Nature Metabolism thanks Marco Jost and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Yanina-Yasmin Pesch, in collaboration with the Nature Metabolism team.

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Noecker, C., Turnbaugh, P.J. Emerging tools and best practices for studying gut microbial community metabolism. Nat Metab (2024). https://doi.org/10.1038/s42255-024-01074-z

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