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STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies

Julia Kelliher·Chloe Mirzayi·Sarah R. Bordenstein·Aaron Oliver·Christina A. Kellogg·Eneida L. Hatcher·Maureen Berg·Petr Baldrian·Mashael Aljumaah·Cassandra Maria Miller·Christopher Mungall·Vlastimil Novak·Alexis Palucki·Ethan Smith·Nazifa Tabassum·Gregory Bonito·J. Rodney Brister·Patrick S. Chain·Jose Pablo Dundore-Arias·Joanne B. Emerson·Vanessa Moreira Fernandes·Roberto Flores·Antonio Gonzalez·Zoe A. Hansen·Scott A. Jackson·Ahmed M. Moustafa·Trent R. Northen·Nonia Pariente·Jennifer Pett-Ridge·Sydne Record·Linta Reji·Anna-Louise Reysenbach·Virginia I. Rich·Lorna Richardson·Simon Roux·Lynn M. Schriml·Reed S. Shabman·Maria A. Sierra·Matthew B. Sullivan·Punithavathi Sundaramurthy·Katherine M. Thibault·Luke R. Thompson·Scott W. Tighe·Ethell Vereen·STREAMS Consortium·Emiley A. Eloe-Fadrosh
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Abstract

The interdisciplinary nature of microbiome research, coupled with the generation of complex multi-omics data, makes knowledge sharing challenging. The Strengthening the Organization and Reporting of Microbiome Studies (STORMS) guidelines provide a checklist for the reporting of study information, experimental design and analytical methods within a scientific manuscript on human microbiome research. Here, in this Consensus Statement, we present the standards for technical reporting in environmental and host-associated microbiome studies (STREAMS) guidelines. The guidelines expand on STORMS and include 67 items to support the reporting and review of environmental (for example, terrestrial, aquatic, atmospheric and engineered), synthetic and non-human host-associated microbiome studies in a standardized and machine-actionable manner. Based on input from 248 researchers spanning 28 countries, we provide detailed guidance, including comparisons with STORMS, and case studies that demonstrate the usage of the STREAMS guidelines. STREAMS, like STORMS, will be a living community resource updated by the Consortium with consensus-building input of the broader community.

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Julia Kelliher, Chloe Mirzayi, Sarah R. Bordenstein, Aaron Oliver, Christina A. Kellogg, Eneida L. Hatcher, Maureen Berg, Petr Baldrian, Mashael Aljumaah, Cassandra Maria Miller, Christopher Mungall, Vlastimil Novak, Alexis Palucki, Ethan Smith, Nazifa Tabassum, Gregory Bonito, J. Rodney Brister, Patrick S. Chain, Jose Pablo Dundore-Arias, Joanne B. Emerson, Vanessa Moreira Fernandes, Roberto Flores, Antonio Gonzalez, Zoe A. Hansen, Scott A. Jackson, Ahmed M. Moustafa, Trent R. Northen, Nonia Pariente, Jennifer Pett-Ridge, Sydne Record, Linta Reji, Anna-Louise Reysenbach, Virginia I. Rich, Lorna Richardson, Simon Roux, Lynn M. Schriml, Reed S. Shabman, Maria A. Sierra, Matthew B. Sullivan, Punithavathi Sundaramurthy, Katherine M. Thibault, Luke R. Thompson, Scott W. Tighe, Ethell Vereen, STREAMS Consortium, Emiley A. Eloe-Fadrosh. 2025-12-01. STREAMS guidelines: Standards for technical reporting in environmental and host-associated microbiome studies. https://doi.org/10.1038/s41564-025-02186-2

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