Microbiomes, the diverse communities of microorganisms that inhabit various environments, are crucial to understanding human health, soil fertility, and climate regulation. However, the complexity of studying these microscopic life forms across different settings has posed significant challenges for scientists. To address this, nearly 250 researchers from 28 countries have developed a groundbreaking set of guidelines known as STREAMS, or Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies.
STREAMS builds upon the success of STORMS, a checklist previously used in human microbiome research, expanding its scope to include microbes found in soil, water, air, animals, plants, and synthetic environments. This development aims to streamline data sharing and improve research consistency across various disciplines.
Streamlining Microbiome Research
Julia Kelliher, the lead author of the STREAMS guidelines and a doctoral student at Michigan State University’s Department of Microbiology, Genetics, & Immunology, highlighted the need for this new framework in a paper published in Nature Microbiology. Kelliher explained that STREAMS offers a structured approach to reporting, ensuring that critical details such as permit information and data citation are not overlooked.
“I just want to help some people,” Kelliher stated, emphasizing the accessibility of the guidelines through tutorials, user guides, and a list of acronyms. “Having these reporting guidelines helps everyone—from researchers to reviewers to publishers—work together more effectively,” she added.
Collaborative Efforts and Diverse Input
The guidelines were developed during a workshop held in conjunction with the American Society for Microbiology Microbe Conference. This event brought together 50 participants, including researchers, data repository representatives, journal editors, and funding agencies, to discuss the need for improved reporting standards in environmental microbiome research.
“We were very conscious of making sure that we had diversity in all forms of career stage,” Kelliher noted. “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 comprises 67 checklist items that guide researchers through each section of a scientific paper, facilitating clear and consistent writing. It is also designed to be machine-readable, allowing computers to analyze and compare studies more efficiently. The guidelines align with existing metadata standards and include features that simplify data submission to public databases.
Expanding the Scope Beyond STORMS
One significant distinction between STREAMS and its predecessor, STORMS, is the expanded scope. While STORMS focused 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 Living Resource for the Scientific Community
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, with plans for regular updates based on community feedback. The team is already working on a paper that uses a large language model to help parse the guidelines.
From Neuroscience to Microbiome Research
Kelliher’s journey to leading the STREAMS initiative was anything but conventional. Initially trained in neuroscience and costume design, she found herself working at Los Alamos National Laboratory after a chance encounter 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.
Since then, Kelliher has worked on numerous bioscience projects, earning her master’s degree from Johns Hopkins University while working part-time at Los Alamos. Now, she continues her work at the laboratory 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.”
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.
The STREAMS guidelines represent a significant advancement in microbiome research, offering a comprehensive framework for scientists worldwide. As the scientific community continues to embrace these standards, the potential for groundbreaking discoveries in microbiome studies grows ever more promising.
