Microbiomes, the intricate communities of microorganisms inhabiting various ecosystems, are crucial to human health, soil fertility, and climate regulation. However, the complexity of these tiny life forms, particularly outside the human body, poses significant challenges in data sharing across diverse environments and scientific disciplines. In response, nearly 250 researchers from 28 countries have developed a new set of guidelines named STREAMS, or Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies.
STREAMS builds upon the success of STORMS, a checklist widely adopted in human microbiome research, expanding its scope to encompass microbes found in soil, water, air, animals, plants, and even synthetic environments. Julia Kelliher, the lead author of the STREAMS guidelines and a doctoral student at Michigan State University’s Department of Microbiology, Genetics, & Immunology, elaborated on the necessity of this framework in a paper published in Nature Microbiology.
Addressing a Critical Need in Microbiome Research
The STREAMS guidelines are designed to assist researchers, students, and reviewers in navigating manuscripts related to environmental, non-human host-associated, and synthetic communities. Organized by the structure of a scientific manuscript, these guidelines ensure that critical details, such as permit information or proper citation of reused data, are not overlooked. Kelliher emphasized her straightforward goal: “I just want to help some people, especially the students. 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.”
“Having these reporting guidelines helps everyone—from researchers to reviewers to publishers—work together more effectively,” Kelliher added. The guidelines emerged from a collaborative workshop at the American Society for Microbiology Microbe Conference, where 50 participants, including researchers, data repository representatives, journal editors, and funding agencies, discussed the need for improved reporting standards in environmental microbiome research.
Innovative Features of STREAMS
STREAMS includes 67 checklist items guiding researchers through each section of a scientific paper, facilitating clear and consistent writing. Notably, the guidelines are machine-readable, enabling computers to analyze and compare studies more efficiently. They align with existing metadata standards and include features that simplify data submission to public databases.
One significant distinction between STREAMS and its predecessor, STORMS, is the scope. While STORMS focuses on human microbiomes, STREAMS addresses the unique challenges of environmental and non-human host-associated studies. “There are so many caveats in environmental microbiome research that just don’t translate from the human side,” Kelliher explained. “Terminology, data types, even the way samples are collected—it’s all different.”
The STREAMS team also incorporated new items to reflect emerging practices, such as the use of artificial intelligence in research. “Not all journals are at the same stage of requiring AI usage reporting,” Kelliher noted. “We wanted to make sure STREAMS addressed that.”
A Collaborative and Evolving Resource
Managing input from hundreds of contributors was a formidable task. Kelliher personally reviewed over 1,100 pieces of feedback, compiling a 100-page response document to ensure every comment was considered. “It was definitely a challenge,” she admitted. “We wanted to show the participants that we really cared about every single piece of feedback, and I do think they felt that way.”
STREAMS is designed to be a “living” resource, with plans for regular updates based on community feedback. The team is already working on a paper that employs a large language model to help parse the guidelines. Kelliher’s path to leading the STREAMS initiative was unconventional. Originally trained in neuroscience and costume design, she found herself at Los Alamos National Laboratory after a serendipitous move to New Mexico during her senior year at Skidmore College.
“I was on a hike with a couple of researchers who said they needed an undergrad for a microbiome project,” she recalled. “I interviewed, got the job, and since then I’ve worked on about a dozen bioscience projects.”
Kelliher has been at Los Alamos for eight years, earning a master’s degree from Johns Hopkins University while working part-time at the Laboratory. Now, she continues her work there while pursuing a PhD at Michigan State University. “I still work in addition to the PhD program, which I would not recommend,” she said with a laugh. “I’m certainly very tired all the time.” She also holds a joint appointment with the New Mexico Consortium, a non-profit corporation formed by New Mexico’s three research universities, through which the project receives National Science Foundation funding.
Her experience at Los Alamos, combined with her work on large Department of Energy programs like the National Microbiome Data Collaborative, positioned her to lead the STREAMS initiative. She collaborates with senior author Emiley Eloe-Fadrosh of the Lawrence Berkeley National Lab and Chloe Mirzayi, the lead author of the STORMS guidelines.
Implications for the Future of Microbiome Research
The introduction of STREAMS represents a significant advancement in the field of microbiome research, promising to streamline data sharing and improve the quality of scientific reporting. As the guidelines continue to evolve, they are expected to foster greater collaboration and innovation across disciplines, ultimately enhancing our understanding of the vital roles microbiomes play in various ecosystems.
Looking ahead, the STREAMS team remains committed to refining the guidelines and incorporating new insights from the scientific community. This ongoing effort underscores the importance of adaptability and collaboration in addressing the complex challenges of microbiome research.
