Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science

Kathryn C. Milligan-McClellan, José Pablo Dundore-Arias, Jonathan L. Klassen, Ashley Shade, Linda L. Kinkel, Benjamin E. Wolfe

Research output: Contribution to journalReview articlepeer-review

4 Scopus citations


The diversity and functional significance of microbiomes have become increasingly clear through the extensive sampling of Earth's many habitats and the rapid adoption of new sequencing technologies. However, much remains unknown about what makes a "healthy"microbiome, how to restore a disrupted microbiome, and how microbiomes assemble. In December 2019, we convened a workshop that focused on how to identify potential "rules of life"that govern microbiome structure and function. This collection of mSystems Perspective pieces reflects many of the main challenges and opportunities in the field identified by both in-person and virtual workshop participants. By borrowing conceptual and theoretical approaches from other fields, including economics and philosophy, these pieces suggest new ways to dissect microbiome patterns and processes. The application of conceptual advances, including trait-based theory and community coalescence, is providing new insights on how to predict and manage microbiome diversity and function. Technological and analytical advances, including deep transfer learning, metabolic models, and advances in analytical chemistry, are helping us sift through complex systems to pinpoint mechanisms of microbiome assembly and dynamics. Integration of all of these advancements (theory, concepts, technology) across biological and spatial scales is providing dramatically improved temporal and spatial resolution of microbiome dynamics. This integrative microbiome research is happening in a new moment in science where academic institutions, scientific societies, and funding agencies must act collaboratively to support and train a diverse and inclusive community of microbiome scientists.

Original languageEnglish (US)
Issue number5
StatePublished - Sep 2022

Bibliographical note

Funding Information:
The 2019 workshop, this editorial, and all Perspective pieces in the Deciphering the Microbiome mSystems special issue were supported by a grant from the National Science Foundation (Award number 1944020 from the Division of Integrative Organismal Systems in the Directorate for Biological Sciences). We thank the participants for their rich discussions, which informed this paper. Technical and scientific support from Marian Bolton, Michael Millican, Matthew Michalska-Smith, and Mike Fulcher was critical to the success of the workshop and is gratefully acknowledged.

Publisher Copyright:
© 2022 Milligan-McClellan et al.


  • collaboration
  • ecology
  • evolution
  • integration
  • microbiome
  • technology
  • theory


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