New initiative to support data STREAMS for environmental, synthetic, and non-human host-associated microbiomes

With growing recognition of the need for open and accessible science, a question we frequently discuss within the National Microbiome Data Collaborative (NMDC) community and with the broader research community, is “how can we work towards a Findable, Accessible, Interoperable, and Reusable (FAIR) data lifecycle together?” Important aspects of the data lifecycle include communicating findings to the community and managing data responsibly, beyond the life of the project. However, there is little guidance for what information should be reported to fully describe a microbiome study, and there are many options for data management. For epidemiology and human microbiome research, STrengthening the Reporting of OBservational studies in Epidemiology (STROBE) and Strengthening The Organization and Reporting of Microbiome Studies (STORMS) were developed to provide their respective communities with publication and reporting guidelines. These two reporting guidelines have served their respective fields well and other domains of microbiome research could similarly benefit from an expanded set of reporting guidelines. To initiate a community-driven effort to expand reporting guidelines to environmental, non-human host-associated, and synthetic microbiomes, New Mexico Consortium Scientist Julia Kelliher led a National Science Foundation (NSF) workshop grant to bring together key decision makers in microbiome science including researchers, publishers, funders, and data repositories. When asked about her motivations for initiating this work, Kelliher said, “It can be really difficult for researchers to navigate how to best manage their microbiome data and report on their associated metadata and study information. We want to help make that easier by bringing together representatives from across the microbiome research field to generate and implement this consensus set of guidelines.”

Group photo of the Microbiome Data Management in Action workshop participants.

To kick off these efforts, Kelliher worked with Steering Committee members Emiley Eloe-Fadrosh (National Microbiome Data Collaborative, Berkeley Lab), Lynn Schriml (University of Maryland School of Medicine, President of the Genomic Standards Consortium), Chloe Mirzayi (CUNY Graduate, School of Public Health & Health Policy), and Scott Jackson (National Institute of Standards and Technology (NIST)) to organize a workshop bringing together 50 microbiome research stakeholders to discuss the current challenges surrounding microbiome data management. The Microbiome Data Management in Action workshop was held in the days leading up to the American Society for Microbiology’s annual conference, ASM Microbe 2024. 

Due to the interdisciplinary nature of the microbiome research field, participants were invited from across institution types, career stages, expertise, and environment types. The group discussed data management best practices for researchers, publishers, data repositories, and funders. They then dove into the STORMS guidelines and discussed how these guidelines could be modified to better support environmental, synthetic, and non-human host-associated microbiome research. Discussion from the breakout groups helped shape the first version of the Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies (STREAMS). A report from the workshop was recently released.  

Luke Thompson (National Oceanographic and Atmospheric Association) presenting the brainstorming outcomes of his breakout group at the Microbiome Data Management in Action workshop.

We asked Mirzayi what she learned from developing STORMS and how those takeaways can help with STREAMS. She reflected, “I think STREAMS has already done an amazing job taking the lessons I learned from STORMS and avoiding some of the pitfalls. They have done a wonderful job ensuring that STREAMS represents the best efforts of a diverse, engaged set of scientists from around the world. My one hope is that we continue to foster the adoption of STREAMS after it’s published. That is perhaps the one small regret I’ve had when it comes to STORMS. I hope the STREAMS team can make it into a living standard that evolves as the field does.”     

Following the workshop, a subset of the participants continue to meet regularly to refine the draft STREAMS guidelines, which has now been broadly shared with the research community to solicit feedback and build consensus. We encourage any researcher interested in joining this initiative to comment directly in the STREAMS guidelines or through the reporting form. We anticipate the STREAMS reporting guidelines to be made available in 2025 and all contributors to be recognized for their involvement in this initiative. 

Breakout groups discussing the formulation of STREAMS at the Microbiome Data Management in Action workshop.

This work is supported by the National Science Foundation under Award No. 2422717  

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