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Challenges and opportunities in sharing microbiome data and analyses

Nature Microbiology volume 8, pages 1960–1970 (2023)Cite this article

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Abstract

Microbiome data, metadata and analytical workflows have become ‘big’ in terms of volume and complexity. Although the infrastructure and technologies to share data have been established, the interdisciplinary and multi-omic nature of the field can make resources difficult to identify and use. Following best practices for data deposition requires substantial effort, with sometimes little obvious reward. Gaps remain where microbiome-specific resources for data sharing or reproducibility do not yet exist. We outline available best practices, challenges to their adoption and opportunities in data sharing in microbiome research. We showcase examples of best practices and advocate for their enforcement and incentivization for data sharing. This includes recognition of data curation and sharing endeavours by individuals, institutions, journals and funders. Opportunities for progress include enabling microbiome-specific databases to incorporate future methods for data analysis, integration and reuse.

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Fig. 1: Steps and resources for microbial community experimental design, analysis and data sharing.
Fig. 2: Checkpoints for ensuring high-quality microbiome data generation and sharing.

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Acknowledgements

We thank E. Pelletier for providing helpful input and acknowledge funding by the German Research Foundation (NFDI4Microbiota, project no. 460129525 to A.C.M.) and the NIH National Institute of Diabetes and Digestive and Kidney Diseases (grant no. R24DK110499 to C.H.).

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Authors and Affiliations

  1. Harvard Chan Microbiome in Public Health Center, Harvard T.H. Chan School of Public Health, Boston, MA, USA

    Curtis Huttenhower

  2. Departments of Biostatistics and Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA

    Curtis Huttenhower

  3. Broad Institute of MIT and Harvard, Cambridge, MA, USA

    Curtis Huttenhower

  4. European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK

    Robert D. Finn

  5. Computational Biology of Infection Research, Helmholtz Centre for Infection Research, Braunschweig, Germany

    Alice Carolyn McHardy

  6. Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Braunschweig, Germany

    Alice Carolyn McHardy

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C.H. and A.C.M. wrote the paper with comments from R.D.F. All authors discussed the content.

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Huttenhower, C., Finn, R.D. & McHardy, A.C. Challenges and opportunities in sharing microbiome data and analyses. Nat Microbiol 8, 1960–1970 (2023). https://doi.org/10.1038/s41564-023-01484-x

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