Deciphering the Microbiome:

Empowering theory, cross-system analyses and innovative analytics to propel advances in microbiome science

Call for Submissions, mSystems Special Collection: Deciphering the Microbiome

The NSF-sponsored Deciphering the Microbiome workshop held in December, 2019 brought together top researchers from across diverse microbiome settings to discuss critical recent advances and key conceptual, theoretical, technical, and analytical needs, and future directions in microbiome science.

Based upon the very productive interactions that emerged, we seek to publish a collection of 8-10 Perspectives pieces targeting key topics addressed in the workshop. We are soliciting contributions that integrate the rich diversity of organismal data, experimental and technical approaches, and conceptual and analytical frameworks encompassed by microbiome science. The editors especially challenge early-career authors to provide big ideas for moving the field forward. This collection is intended to leverage the rich, cross-disciplinary interactions and discussions from the workshop to produce what we hope will be a foundational series of pieces to stimulate the field. All charges for authors will be covered from the NSF meeting sponsorship.

WHAT IS EARLY-CAREER? Early Career = graduate students, post-doctoral scientists, and pre-tenure faculty, and/or within 10 years of terminal/final degree. We intend to use the LEAST restrictive categorization (e.g. if you are MORE than 10 years from final degree/Ph.D., but still pre-tenure, you will count as early-career).


We are issuing an open call for co-authored pieces. Perspectives pieces can be up to 1500 words in length and contain up to 2 figures and/or tables. Each piece should discuss the current state of microbiome science in relation to the topic (see list of potential topics below; this is not an exclusive list!), and where the field is going or should be heading. Submissions will be required to include an interdisciplinary team of authors representing at least 3 distinct disciplinary, technical, or host/organism viewpoints, and the majority of authors should be early-career scientists. Our emphasis on early-career authors, and a strong commitment of the Co-Editors to shepherd the writing process and challenge authors to integrate across disciplines reiterate primary goals of our workshop.

As a first step, co-author teams are asked to provide a 250-word synopsis of their proposed perspective piece, targeting one of our proposed foci OR an author team-proposed microbiome focus. In addition to the 250-word synopsis, the proposal should identify the core author team, and establish both the early career status of the majority of the co-authors and the interdisciplinarity aspect of the author team. Synopsis submissions will be reviewed by the Co-editor team, with feedback provided within 2 weeks of the submission deadline (see below). Synopses should be submitted to Linda Kinkel ( by February 5, 2021.

Meeting organizers will serve as Co-editors of the Perspective collection. Co-editors will communicate with the co-author teams regarding the full collection of topics and authors engaged in Perspective pieces, and provide feedback on outlines and content of the Perspective during the writing process. All Perspectives will be reviewed by at least 2 anonymous reviewers, with clear information provided to reviewers on the goals and specific topics considered in the full collection of contributions.

· Timeline:

o Synopsis Submissions: February 5, 2021

o Synopsis Decisions and Formal invitations: February 20, 2021

o Submission outlines due for review and distribution among authors: March 10, 2021

o Draft Perspective submission: April 15, 2021

o Reviews returned to authors: May 15, 2021

o Revised manuscripts returned to editors: June 15, 2021

o Publication: July 2021

· Proposed Topics (this list is not exclusive, and we encourage creative suggestions):

o The challenges/opportunities of scale (spatial, temporal) in microbiome research

o How cross-system studies can reveal 'rules of life' for microbiomes

o Resilience, stability, and perturbations in microbiomes

o Predictive ecology and evolutionary theory for microbiomes

o Communication within/across the microbiome field: what are effective ways to get scientists working across microbiome systems to talk to each other more often/deeply/effectively?

o Training programs/tools to broadly teach (the next generation of) microbiome scientists

o Tools/techniques/approaches to better define microbial traits

Questions or preliminary inquiries may be addressed to any of the Co-Editors:

Linda Kinkel (

Ben Wolfe (

Kat Milligan-Myhre (

Jonathan Klassen (

JP Dundore-Arias (

Ashley Shade (

This 2-day NSF-sponsored workshop will address critical gaps in microbiome science. Bringing together 60+ scientists in-person, and open to 1000 scientists as virtual participants, this workshop will engage researchers working on plant, animal, environmental and human microbiomes.

This workshop will bring together leading researchers spanning broad fields of microbiome research in order to advance the discipline.

Opportunities for Virtual Attendance: We welcome virtual participants to our workshop, especially early-career scientists! Virtual participants will have access to all talks and discussions in real-time, and will each be part of a 6-10 person virtual community for small-group interactions. We will use a variety of tools, techniques, and communication platforms to enhance the virtual meeting experience, and hope to stimulate development of new models to enhance participation while reducing financial and environmental costs of workshop attendance.


Organizing Committee:

  • Linda Kinkel

  • Kat Milligan-Myhre

  • Jonathan Klassen

  • Ben Wolfe

  • Jo Handelsman

  • JP Dundore-Arias

  • Ashley Shade

  • Patrick Degnan

For questions or further information contact:

Linda Kinkel