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Community-led, integrated, reproducible multi-omics with anvi’o

Nature Microbiology volume 6, pages 3–6 (2021)Cite this article

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Big data abound in microbiology, but the workflows designed to enable researchers to interpret data can constrain the biological questions that can be asked. Five years after anvi’o was first published, this community-led multi-omics platform is maturing into an open software ecosystem that reduces constraints in ‘omics data analyses.

Generating hundreds of millions of sequences from a microbial habitat is now commonplace for many microbiologists1. While the massive data streams offer detailed snapshots of the lifestyles of microorganisms, this data revolution in microbiology means that a new generation of computational tools is needed to empower life scientists in the era of multi-omics.

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Fig. 1: Integrated ‘omics with anvi’o.

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Acknowledgements

The URL http://anvio.org/authors serves as a dynamic list of anvi’o developers. We thank the creators of other open-source software tools for their generosity, anvi’o users for their patience with us, and K. Lolans for her critical reading of the manuscript and suggestions. We gratefully acknowledge support for anvi’o from the Simons Foundation and Alfred P. Sloan Foundation.

Author information

Authors and Affiliations

  1. Department of Medicine, University of Chicago, Chicago, IL, USA

    A. Murat Eren, Evan Kiefl, Alon Shaiber, Iva Veseli, Samuel E. Miller, Matthew S. Schechter, Isaac Fink, Jessica N. Pan, Mahmoud Yousef, Emily C. Fogarty, Florian Trigodet, Andrea R. Watson, Özcan C. Esen & Jessika Fuessel

  2. Committee on Microbiology, University of Chicago, Chicago, IL, USA

    A. Murat Eren, Matthew S. Schechter, Emily C. Fogarty & Andrea R. Watson

  3. Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, MA, USA

    A. Murat Eren & Lois Maignien

  4. Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA

    A. Murat Eren, Evan Kiefl, Alon Shaiber & Iva Veseli

  5. Center for Bioinformatics and Computational Biology, University of Delaware, Delaware, DE, USA

    Ryan M. Moore

  6. Department of Biology, Institute of Microbiology, ETH Zurich, Zurich, Switzerland

    Quentin Clayssen

  7. Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA

    Michael D. Lee

  8. Blue Marble Space Institute of Science, Seattle, WA, USA

    Michael D. Lee

  9. Department of Microbiology, Oregon State University, Corvallis, OR, USA

    Veronika Kivenson

  10. Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA

    Elaina D. Graham

  11. Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, USA

    Bryan D. Merrill

  12. Department of Microbiology, University of Helsinki, Helsinki, Finland

    Antti Karkman

  13. Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA

    Daniel Blankenberg

  14. Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA

    Daniel Blankenberg

  15. Daniel K. Inouye Center for Microbial Oceanography: Research and Education, University of Hawai’i at Mānoa, Honolulu, HI, USA

    John M. Eppley

  16. Division of CBRN Security and Defence, Swedish Defence Research Agency - FOI, Umea, Sweden

    Andreas Sjödin

  17. Smithsonian Tropical Research Institute, Bocas del Toro, Republic of Panama

    Jarrod J. Scott

  18. NSW Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, New South Wales, Australia

    Xabier Vázquez-Campos

  19. Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA

    Luke J. McKay

  20. Department of Land Resources and Environmental Sciences, Montana State University, Bozeman, MT, USA

    Luke J. McKay

  21. Department of Bacteriology, University of Wisconsin–Madison, Madison, WI, USA

    Elizabeth A. McDaniel

  22. Wisconsin Institute for Discovery, University of Wisconsin–Madison, Madison, WI, USA

    Sarah L. R. Stevens

  23. American Family Insurance Data Science Institute, University of Wisconsin–Madison, Madison, WI, USA

    Sarah L. R. Stevens

  24. Department of Biology, Carleton College, Northfield, MN, USA

    Rika E. Anderson

  25. Lundbeck GeoGenetics Centre, The Globe Institute, University of Copenhagen, Copenhagen, Denmark

    Antonio Fernandez-Guerra

  26. Laboratoire de Microbiologie des Environnements Extrêmes (LM2E), Univ. Brest, CNRS, IFREMER, Plouzané, France

    Lois Maignien

  27. Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris–Saclay, Evry, France

    Tom O. Delmont

  28. Department of Biostatistics, University of Washington, Seattle, WA, USA

    Amy D. Willis

Authors
  1. A. Murat Eren
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Contributions

A.M.E., E.K., A. Shaiber, I.V., S.E.M., M.S.S., I.F., J.N.P., M.Y., E.C.F., F.T., A.R.W., O.C.E., R.M.M., Q.C. and A.D.W. coded and documented anvi’o, contributed to the implementation of new analytical strategies and engaged with the anvi’o community. M.D.L., V.K., E.D.G., B.D.M., A.K. and J.J.S. wrote blog posts and tutorials to make anvi’o accessible to the broader community. D.B., J.M.E., A. Sjödin, X.V.-C. and L.J.M. helped with technical issues and testing of new features on GitHub. E.A.M., S.L.R.S. and R.E.A. created undergraduate and graduate-level educational material and taught anvi’o. L.M. organized workshops for the training of research professionals. J.F., A.F.-G., L.M. and T.O.D. made intellectual contributions that influenced the direction of the platform. A.M.E. wrote the paper and prepared the figure with input from all authors.

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Correspondence to A. Murat Eren.

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Eren, A.M., Kiefl, E., Shaiber, A. et al. Community-led, integrated, reproducible multi-omics with anvi’o. Nat Microbiol 6, 3–6 (2021). https://doi.org/10.1038/s41564-020-00834-3

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