New global guidelines streamline environmental microbiome research

Microbiomes, the communities of microorganisms that live in and around us, play a vital role in everything from human health to soil fertility and climate regulation. But studying these tiny life forms, especially outside the human body, presents a major challenge: how do scientists share complex data across such a wide range of environments and disciplines?

To help solve this problem, a team of nearly 250 researchers from 28 countries has developed a new set of guidelines called STREAMS, short for Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies. STREAMS builds on the success of STORMS, a widely adopted checklist used in human microbiome research, and expands it to cover microbes found in soil, water, air, animals, plants and even synthetic environments.

Julia Kelliher, lead author of the STREAMS guidelines and a doctoral student in Michigan State University’s department of Microbiology, Genetics, & Immunology, explained the need for the new framework in a new paper published in Nature Microbiology.

Kelliher explained that STREAMS is a set of reporting guidelines that helps researchers, students, and reviewers go through manuscripts about environmental, non-human host-associated, and synthetic communities. The guidelines are organized by the structure of a scientific manuscript and help ensure that important details—like permit information or proper citation of reused data—aren’t overlooked.

Kelliher’s hope for STREAMS is simple: “I just want to help some people,” she said, “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,” said Kelliher.

The guidelines emerged from a workshop hosted in collaboration with the American Society for Microbiology Microbe Conference, where 50 participants, including researchers, data repository representatives, journal editors and funding agencies discussed the need for better reporting standards in environmental microbiome research.

“We were very conscious of making sure that we had diversity in all forms of career stage,” Kelliher said. “Some of the best ideas came from early-career researchers who are out there collecting metadata, and they were happy to be included, too.”

STREAMS includes 67 checklist items that guide researchers through each section of a scientific paper, making it easier to write clearly and consistently. It’s also designed to be machine-readable, which means computers can help analyze and compare studies more efficiently. The guidelines align with existing metadata standards and include features that make it easier for researchers to submit their data to public databases.

One major difference between STREAMS and its predecessor, STORMS, is the scope. While STORMS focuses on human microbiomes, STREAMS tackles 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 said. “Terminology, data types, even the way samples are collected—it’s all different.”

The STREAMS team also added 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,” she said. “We wanted to make sure STREAMS addressed that.”

Managing input from hundreds of contributors was no small feat. 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 said. “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. The team plans to update it regularly based on community feedback, and they’re already working on a paper that uses a large language model to help parse the guidelines.

Kelliher’s path to STREAMS was anything but traditional. Originally trained in neuroscience and costume design, she found herself working at Los Alamos National Laboratory after a chance 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 8 years. After completing undergrad, she earned her master’s degree from Johns Hopkins University while working part-time at the Laboratory. Now, she is continuing her work at Los Alamos while pursuing her 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 is collaborating on the work with senior author Emiley Eloe-Fadrosh of the Lawrence Berkeley National Lab and Chloe Mirzayi, the lead author of the STORMS guidelines.