We are excited to share that the manuscript, “STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies” was recently published in Nature Microbiology. The STREAMS initiative provides standardized reporting guidelines for environmental, synthetic, and non-human host-associated microbiome researchers to support robust metadata capture and inclusion of important factors in scientific manuscripts. This effort began with the NSF-funded workshop led by New Mexico Consortium’s Julia Kelliher and National Microbiome Data Collaborative (NMDC) Program Lead Emiley Eloe-Fadrosh. Read more about the workshop and efforts to unite microbiome interest-holders to develop a consensus on reporting standards in our previous blog.
“The STREAMS guidelines offer the first comprehensive set of standards for data sharing and reporting for microbiome studies in non-human hosts and environments. It’s an exciting development that will improve the consistency, reproducibility, and access of data among environmental microbiome researchers. With STREAMS, researchers can follow a useful checklist during manuscript preparation to ensure transparency and clarity in sharing information about their environmental microbiome project. Reviewers can also use STREAMS to guide their evaluation of submitted manuscripts, flagging authors if certain standards are not met to encourage adequate data sharing. If widely embraced, STREAMS will be revolutionary for the field of environmental microbiome science!” -Zoe Hansen
A working group of attendees from the Microbiome Data Management in Action workshop was formed to bring together microbiome researchers across disciplines and tap into their insights on how to ensure microbiome publications contain critical contextual information. Through the incorporation of over 1100 pieces of feedback from 248 microbiome researchers across 28 countries, and multiple revisions by the STREAMS working group, the current set of guidelines took shape. One STREAMS author, Aaron Oliver, was quick to join the effort, explaining, “On a weekly basis I run into interesting studies that I cannot incorporate into my own work because data is not accessible or poorly described. And microbiome science is so interdisciplinary… A unified, standardized set of guidelines for environmental microbiome research, built by the community, makes that interdisciplinary nature a strength rather than a barrier.”
The final guidelines include 67 Items organized into categories that align with the typical format of a scientific manuscript. For more information on the guidelines themselves, visit the STREAMS website to access and download the STREAMS guidelines template, a user guide, example use cases of the guidelines, and other supporting files. Additionally, the guidelines are available as a Supplementary Table in the STREAMS manuscript, and are accessible through Zenodo (https://doi.org/10.5281/zenodo.15014818) and a data management plan (DMP) building site: DMP Tool as the “STREAMS Microbiome Guidelines” template. To make the guidelines as accessible, easy to use, and complete as possible, they will be periodically evaluated and updated based on advances in the field and user feedback which will be collected through an ongoing feedback form. Moving forward, the guidelines will also be streamlined between the STREAMS and STORMS efforts. Strengthening The Organization and Reporting of Microbiome Studies (STORMS) is a reporting checklist for human-associated microbiome studies, published and adopted by multiple journals, funding agencies, and researchers in the field. Among other avenues for continual improvement, the STREAMS Consortium is also working on a large language model (LLM) to make assessing manuscripts with the guidelines even easier for authors and reviewers. The LLM will allow users to feed in their manuscript, and receive an itemized assessment of elements that are missing.
“The whole team realizes that this publication is only the beginning of STREAMS. Once this resource gets into people's hands, we will have a better idea of how people are using it, and what the community wants to add. In the meantime, we have folks continuing to build a resource ecosystem around STREAMS to make sure it is as useful as possible. The passion around this project hasn’t gone anywhere, so STREAMS will continue to evolve as the community needs change and as microbiome science changes.” -Aaron Oliver
Beyond data reusability and accessibility, STREAMS author Sarah Bordenstein envisions these efforts as a valuable educational resource, stating, “I am particularly excited about the impact STREAMS will have on microbiome education and training. The easy-to-use template guides researchers through all stages of the scientific process and promotes the organization, communication, and reusability of microbiome data.”
We would like to thank all of the workshop participants, working group members, co-authors, and STREAMS consortium members for their hard work on the creation of the STREAMS guidelines!
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