Advancing microbiome studies with a STREAM-lined approach

Understanding microbiomes can lead to advances in human health, agriculture and more — but as microbiome research expands, data sharing becomes both more important and more difficult. To mitigate this challenge, a multi-institution team of researchers created a set of guidelines that will help microbiome scientists report their data in a uniform, effective way.

The team comprises scientists at Los Alamos National Laboratory along with the New Mexico Consortium who co-led the effort with Lawrence Berkeley National Laboratory; their work was published in Nature Microbiology.

Read the paper 

Why this matters: Microbiome research is the study of communities of microorganisms that live in a specific environment, such as the human skin or gut, a pond, or a wheat field. 

• Environmental microbiomes are complex and varied leading to differences in experimental design and data collection practices.
• It is important to have like-with-like data to share with other researchers to compare results, repeat experiments, or collaborate.

What they did: The STREAMS (Standards for Technical Reporting in Environmental and host-Associated Microbiome Studies) project, co-led by Los Alamos technologist Julia Kelliher who holds a joint-appointment with the New Mexico Consortium, began with a workshop about data management hosted in collaboration with the American Society for Microbiology Microbe Conference and the National Microbiome Data Collaborative.

• Kelliher and senior author Emiley Eloe-Fadrosh of Berkeley Lab reached out to nearly 250 researchers from 28 countries, analyzing more than 1,000 pieces of feedback.

What they learned: Based on the workshop and the community-led input, Kelliher, Eloe-Fadrosh and their colleagues developed a set of 67 guidelines for researchers, students and reviewers.

• Using these guidelines, researchers who are studying environmental, non-human host-associated, and synthetic communities can produce papers that are clear and consistent, and easier to align in public databases or use with artificial intelligence.


Funding: This material is based upon work supported by the National Science Foundation. The work conducted by the National Microbiome Data Collaborative is supported by the Genomic Science Program in the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research.

LA-UR-26-20438