The world of microbiomes, those tiny yet mighty communities of microorganisms, is a fascinating and complex realm. From our gut to the soil beneath our feet, these microbes play a crucial role in various aspects of life, including human health, soil fertility, and even climate regulation. However, studying them, especially in diverse environments, presents a significant challenge for scientists. How can we ensure that complex data is shared effectively across different disciplines and environments?
Enter STREAMS, a groundbreaking initiative developed by an international team of nearly 250 researchers from 28 countries. STREAMS, or Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies, builds upon the success of STORMS, a widely adopted checklist for human microbiome research, and expands its scope to cover microbes found in soil, water, air, animals, plants, and 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, explains the need for this new framework in a recent paper published in Nature Microbiology.
Kelliher emphasizes that STREAMS is a set of reporting guidelines designed to assist researchers, students, and reviewers in navigating manuscripts related to environmental, non-human host-associated, and synthetic communities. The guidelines are structured around the format of a scientific manuscript, ensuring that crucial details, such as permit information and proper citation of reused data, are not overlooked.
But here's where it gets controversial: STREAMS aims to standardize the reporting of microbiome data, a task that is easier said than done. With so many variables and unique challenges in environmental microbiome research, how can a single set of guidelines capture it all?
Kelliher acknowledges these challenges, stating, "There are so many caveats in environmental microbiome research that just don't translate from the human side. Terminology, data types, even the way samples are collected - it's all different."
And this is the part most people miss: STREAMS is not just about standardization. It's about making the process of sharing and analyzing microbiome data more efficient and accessible. By making the guidelines machine-readable, computers can help analyze and compare studies, streamlining the research process.
The guidelines also align with existing metadata standards and include features that facilitate the submission of data to public databases. This ensures that researchers can easily share their findings with the scientific community, fostering collaboration and accelerating progress in microbiome research.
But the real beauty of STREAMS lies in its inclusivity. The guidelines emerged from a diverse workshop, involving researchers, data repository representatives, journal editors, and funding agencies, ensuring that a wide range of perspectives were considered.
"We were very conscious of making sure that we had diversity in all forms of career stages," 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 is designed to be a "living" resource, regularly updated based on community feedback. The team is already working on a paper that utilizes a large language model to further enhance the guidelines.
Kelliher's journey to leading this initiative is an inspiring one. With a background in neuroscience and costume design, she found herself at Los Alamos National Laboratory after a chance move to New Mexico during her senior year at Skidmore College. Her work on various bioscience projects and her involvement in large Department of Energy programs positioned her perfectly to take on the STREAMS initiative.
"I just want to help some people, especially the students," Kelliher 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."
So, what do you think? Is STREAMS a step towards a more standardized and efficient microbiome research landscape? Or does it fall short in capturing the complexity of environmental microbiome studies? We'd love to hear your thoughts in the comments!
