New Global Standards Streamline Microbiome Research, From Soil to Human Health
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A collaborative effort involving nearly 250 researchers from 28 countries has yielded a new set of guidelines, known as STREAMS – short for Standards for Technical Reporting in Environmental and host-Associated microbiome Studies – designed to standardize data sharing and improve the rigor of microbiome research across diverse environments. The guidelines,published in Nature Microbiology in early 2025,address a critical need for consistency in a field vital to understanding everything from human health and agriculture to climate regulation.
The Challenge of Microbiome Data
Microbiomes, the complex communities of microorganisms inhabiting our world, are increasingly recognized for their profound influence on life. However, studying thes tiny organisms, especially their interactions with their surroundings, presents unique challenges.
“You just don’t translate from the human side,” explained Julia kelliher, lead author of the STREAMS guidelines and a doctoral student at michigan State University. “Terminology, data types, even the way samples are collected-it’s all different.”
The guidelines are structured to align with the typical format of a scientific manuscript, ensuring that crucial details – such as permit facts and proper data citation – are not overlooked. STREAMS comprises 67 checklist items designed to promote clarity and consistency in reporting. Moreover, the framework is designed to be machine-readable, enabling computers to efficiently analyze and compare research findings.
Accessibility and Inclusivity at the Core
Kelliher emphasized the importance of making STREAMS accessible to all researchers, particularly students. “I just want to help some people, especially the students,” she said. “We’ve built tutorials,user guides,and even a list of acronyms to make sure it’s accessible. I want it to be something that makes their work easier and better.”
The development of STREAMS was a highly collaborative process,originating from a workshop at the American Society for Microbiology Microbe Conference. Participants included researchers, data repository representatives, journal editors, and funding agencies. A conscious effort was made to include researchers at all career stages. “some of the best ideas came from early-career researchers who are out there collecting metadata, and they were happy to be included, too,” Kelliher noted.
Addressing Emerging Trends in microbiome Research
The STREAMS guidelines also address emerging practices in the field,such as the increasing use of artificial intelligence (AI). Recognizing that not all journals currently require reporting on AI usage, the team proactively included items to address this evolving landscape.
The team is committed to maintaining STREAMS as a “living” resource, planning regular updates based on community feedback. They are even exploring the use of a large language model to assist in parsing and interpreting the guidelines.
An Unconventional Path to Leadership
Kelliher’s journey to leading the STREAMS initiative was anything but conventional. Her background spans neuroscience, costume design, and extensive experience at los Alamos National Laboratory, where she has worked on numerous bioscience projects for the past eight years. Her work on large Department of Energy programs, including the national Microbiome Data Collaborative, provided a strong foundation for this leadership role. She is collaborating with Emiley Eloe-Fadrosh of the Lawrence Berkeley National Lab and Chloe Mirzayi, the lead author of the STORMS guidelines.
The development of STREAMS represents a meaningful step forward in microbiome research, promising to foster greater collaboration, clarity, and ultimately, a deeper understanding of the vital role these microscopic communities play in our world.
Source: Michigan State University
Journal reference: Kelliher, J. M., et al. (2025). STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies. Nature Microbiology. doi:10.1038/s41564-025-02186-2. https://www.nature.com/articles/s41564-025-02186-2.
