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

Julia M Kelliher^{1

2

3}, Chloe Mirzayi⁴, Sarah R Bordenstein^{5

6}, Aaron Oliver⁷, Christina A Kellogg⁸, Eneida L Hatcher⁹, Maureen Berg¹⁰, Petr Baldrian¹¹, Mashael Aljumaah^{12

13}, Cassandra Maria Luz Miller¹⁴, Christopher Mungall¹⁵, Vlastimil Novak¹⁵, Alexis Palucki¹⁶, Ethan Smith¹⁷, Nazifa Tabassum¹⁸, Gregory Bonito¹⁹, J Rodney Brister⁹, Patrick S G Chain²⁰, Mingfei Chen¹⁵, Samuel Degregori²¹, Jose Pablo Dundore-Arias²², Joanne B Emerson²³, Vanessa Moreira C Fernandes²⁴, Roberto Flores²⁵, Antonio Gonzalez²¹, Zoe A Hansen²⁶, Scott A Jackson²⁷, Ahmed M Moustafa^{28

29

30}, Trent R Northen¹⁵, Nonia Pariente^{31

32}, Jennifer Pett-Ridge^{33

34

35}, Sydne Record^{36

37}, Linta Reji³⁸, Anna-Louise Reysenbach³⁹, Virginia I Rich^{40

41}, Lorna Richardson⁴², Simon Roux¹⁵, Lynn M Schriml⁴³, Reed S Shabman⁴⁴, Maria A Sierra⁴⁵, Matthew B Sullivan^{40

41}, Punithavathi Sundaramurthy⁴⁶, Katherine M Thibault⁴⁷, Luke R Thompson^{48

49}, Scott Tighe⁵⁰, Ethell Vereen⁵¹; STREAMS Consortium; Emiley A Eloe-Fadrosh⁵²

Collaborators, Affiliations

Collaborators

STREAMS Consortium:
Aaron Robinson, Abdoul R Sare, Abdulmalik A Oladipupo, Adrien Vigneron, Ahmed A Shibl, Alejandro De Santiago, Alexander J Probst, Ali Navid, Alice C McHardy, Alicia Clum, Alison Buchan, Alison Murray, Alla Lapidus, Amanda Araujo Serrao de Andrade, Andreas Bremges, Archana Anand, Ashvini Chauhan, Avishek Dutta, Bablu Kumar, Bela Hausmann, Benoit Chassaing, Braden T Tierney, Brian P Hedlund, Bridget Chalifour, Buck T Hanson, Carly Muletz Wolz, Cassandra L Ettinger, Chongle Pan, Chris Robinson, Christian Hodar Quiroga, Christine Moissl-Eichinger, Christopher Hunter, Christopher Schadt, Christos Ouzounis, Craig W Herbold, Cristal Zuniga, Cruz Mercedes Cecilia, Curtis Huttenhower, D Lee Taylor, Daniel McDonald, Daniel D Sprockett, Daniel P Schachtman, Dennis J Zhang, Dennis Metze, Devin Coleman-Derr, Dominik Merges, Donald M Walker, Donovan H Parks, Durgesh Kumar Jaiswal, E Anders Kiledal, Edoardo Pasolli, Eduardo Vinicius Kuhn, Elisha Wood-Charlson, Elliott Barnhart, Emanuele Chisari, Emilie J Skoog, Emily B Graham, Emily F Wissel, Emily R Davenport, Emily St John, Eric Cavanna, Erica Young, Erika Ganda, Federico M Lauro, Francesco Asnicar, Francisca E Rodriguez, Francisco Dini-Andreote, Frederik Artz, Frederik Bak, Frederik Schulz, Gabriela Canto-Encalada, Gareth Trubl, Grace Pold, Gregorio Iraola, Hanareia Ehau-Taumaunu, Heather R Skeen, Hermes Hernan Bolivar-Torres, Hinsby Cadillo-Quiroz, Holly M Bik, Imelda Forteza, Ishi Keenum, Iyanu Oduwole, Jaci Saunders, Jack A Gilbert, Jada Daniels, James R Henriksen, Janani Hariharan, Jason A Rothman, Jaume Puig, Jeffrey Kimbrel, Jesús Mercado-Blanco, Jiarong Guo, Joao Carlos Setubal, Joel F Swift, Johannes R Krause, Jonathan L Klassen, Jordan E Bisanz, Jorge L Mazza Rodrigues, Jose L Balcazar, Josh D Neufeld, Brooke E Sykes, Joy Watts, Judson Van Wyk, Justine Debelius, Kaelan J Prime, Karthik Anantharaman, Karthik Raman, Katherine D McMahon, Kelly Goodwin, Kent Pham, Keren Yanuka-Golub, Kevin S Myers, Krista A Ryon, Kristen Peach, Kunal R Jain, L M Ward, Leah Johnson, Leandro Nascimento Lemos, Lee Ann McCue, Lennel A Camuy-Vélez, Levi Waldron, Lilian Caesar, Liping Zhao, Lisa Karstens, Lorena Rodriguez-Rubio, Maite Muniesa, Maneesh Dave, Marc W Van Goethem, María Dolores Ramos Barbero, Maria Pachiadaki, Mariana Lozada, Marie Kroeger, Mark McCauley, Mark A Miller, Matthew Grisnik, Matthew Kellom, Melissa A Cregger, Mia Howard, Michael Poulsen, Michelle A Allen, Mireia Valles-Colomer, Mitiku Mihiret Seyoum, Moamen M Elmassry, Montana Smith, Mostafa S Elshahed, Natascha Varona, Neslihan Tas, Nicholas J B Brereton, Nicola G Kriefall, Nicola Segata, Noha H Youssef, Ozge Eyice, Paul D Cotter, Peter J Turnbaugh, Petra Pjevac, Phillip B Pope, Pilar Junier, Pratyay Sengupta, Pubudu P Handakumbura, Rebecca A Reiss, Reese Saho, Reid Longley, Renato Augusto Corrêa Dos Santos, Rhiannon Mondav, Richard Allen White 3rd, Rob Knight, Robert J Gruninger, Roland C Wilhelm, Rosanna ʻAnolani Alegado, Samantha N Miller, Sara L Jackrel, Sarahi L Garcia, Sarai S Finks, Sean P Jungbluth, Sehyun Oh, Sergio E Baranzini, Sergio Sanchez-Carrillo, Shane Roesemann, Sierra Moxon, Sigmund Jensen, Sneha Couvillion, Stephania L Tsola, Stephanie A Yarwood, Sunil Mundra, Susan H Brawley, Suzanne Hodgkins, Sydney Chen, Tanja Woyke, Theodore M Nelson, Thomas Mock, Tyler Myers, W Judson Hervey, William Boulton, William Nelson, Winston E Anthony, Xiao Jun A Liu, Xuefeng Peng, Yaqi You, Ying Zhang, Yun Kit Yeoh, Zachary M Burcham

Affiliations

¹ New Mexico Consortium, Los Alamos, NM, USA. jkelliher@lanl.gov.
² Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA. jkelliher@lanl.gov.
³ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. jkelliher@lanl.gov.
⁴ Institute for Implementation Science in Public Health, CUNY Graduate School of Public Health and Health Policy, New York, NY, USA.
⁵ Departments of Biology and Entomology, Pennsylvania State University, University Park, PA, USA.
⁶ One Health Microbiome Center, Pennsylvania State University, University Park, PA, USA.
⁷ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁸ US Geological Survey, St. Petersburg, FL, USA.
⁹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
¹⁰ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹¹ Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
¹² UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
¹³ Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.
¹⁴ Department of Biology, University of New Mexico, Sevilleta LTER, Albuquerque, NM, USA.
¹⁵ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁶ MCIBS, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁷ Department of Animal Science, Pennsylvania State University, University Park, PA, USA.
¹⁸ Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁹ Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA.
²⁰ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
²¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
²² Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, USA.
²³ University of California, Davis, Davis, CA, USA.
²⁴ Department of Biological Sciences, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, USA.
²⁵ National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
²⁶ Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.
²⁷ National Institute of Standards and Technology, Gaithersburg, MD, USA.
²⁸ Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
²⁹ Center for Microbial Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
³⁰ Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
³¹ Public Library of Science, San Francisco, CA, USA.
³² Public Library of Science, Cambridge, UK.
³³ Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
³⁴ Life and Environmental Sciences Department, University of California, Merced, Merced, CA, USA.
³⁵ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
³⁶ University of Maine, Orono, ME, USA.
³⁷ Maine Agricultural and Forest Experiment Station, Orono, ME, USA.
³⁸ University of Chicago, Chicago, IL, USA.
³⁹ Center for Life in Extreme Environments, Portland State University, Portland, OR, USA.
⁴⁰ Department of Microbiology, The Ohio State University, Columbus, OH, USA.
⁴¹ The Ohio State University Center of Microbiome Science, Columbus, OH, USA.
⁴² EMBL-European Bioinformatics Institute, Hinxton, UK.
⁴³ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
⁴⁴ Office of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
⁴⁵ Tri-Institutional Computational Biology, Weill Cornell Medicine, New York, NY, USA.
⁴⁶ University of California, San Francisco, San Francisco, CA, USA.
⁴⁷ National Ecological Observatory Network, Battelle, Boulder, CO, USA.
⁴⁸ Northern Gulf Institute, Mississippi State University, Starkville, MS, USA.
⁴⁹ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
⁵⁰ University of Vermont, Burlington, VT, USA.
⁵¹ Morehouse College, Atlanta, GA, USA.
⁵² Lawrence Berkeley National Laboratory, Berkeley, CA, USA. eaeloefadrosh@lbl.gov.

PMID: 41326814
DOI: 10.1038/s41564-025-02186-2

Review

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

Julia M Kelliher et al. Nat Microbiol. 2025 Dec.

. 2025 Dec;10(12):3059-3068.

doi: 10.1038/s41564-025-02186-2. Epub 2025 Dec 1.

Authors

Collaborators

STREAMS Consortium:
Aaron Robinson, Abdoul R Sare, Abdulmalik A Oladipupo, Adrien Vigneron, Ahmed A Shibl, Alejandro De Santiago, Alexander J Probst, Ali Navid, Alice C McHardy, Alicia Clum, Alison Buchan, Alison Murray, Alla Lapidus, Amanda Araujo Serrao de Andrade, Andreas Bremges, Archana Anand, Ashvini Chauhan, Avishek Dutta, Bablu Kumar, Bela Hausmann, Benoit Chassaing, Braden T Tierney, Brian P Hedlund, Bridget Chalifour, Buck T Hanson, Carly Muletz Wolz, Cassandra L Ettinger, Chongle Pan, Chris Robinson, Christian Hodar Quiroga, Christine Moissl-Eichinger, Christopher Hunter, Christopher Schadt, Christos Ouzounis, Craig W Herbold, Cristal Zuniga, Cruz Mercedes Cecilia, Curtis Huttenhower, D Lee Taylor, Daniel McDonald, Daniel D Sprockett, Daniel P Schachtman, Dennis J Zhang, Dennis Metze, Devin Coleman-Derr, Dominik Merges, Donald M Walker, Donovan H Parks, Durgesh Kumar Jaiswal, E Anders Kiledal, Edoardo Pasolli, Eduardo Vinicius Kuhn, Elisha Wood-Charlson, Elliott Barnhart, Emanuele Chisari, Emilie J Skoog, Emily B Graham, Emily F Wissel, Emily R Davenport, Emily St John, Eric Cavanna, Erica Young, Erika Ganda, Federico M Lauro, Francesco Asnicar, Francisca E Rodriguez, Francisco Dini-Andreote, Frederik Artz, Frederik Bak, Frederik Schulz, Gabriela Canto-Encalada, Gareth Trubl, Grace Pold, Gregorio Iraola, Hanareia Ehau-Taumaunu, Heather R Skeen, Hermes Hernan Bolivar-Torres, Hinsby Cadillo-Quiroz, Holly M Bik, Imelda Forteza, Ishi Keenum, Iyanu Oduwole, Jaci Saunders, Jack A Gilbert, Jada Daniels, James R Henriksen, Janani Hariharan, Jason A Rothman, Jaume Puig, Jeffrey Kimbrel, Jesús Mercado-Blanco, Jiarong Guo, Joao Carlos Setubal, Joel F Swift, Johannes R Krause, Jonathan L Klassen, Jordan E Bisanz, Jorge L Mazza Rodrigues, Jose L Balcazar, Josh D Neufeld, Brooke E Sykes, Joy Watts, Judson Van Wyk, Justine Debelius, Kaelan J Prime, Karthik Anantharaman, Karthik Raman, Katherine D McMahon, Kelly Goodwin, Kent Pham, Keren Yanuka-Golub, Kevin S Myers, Krista A Ryon, Kristen Peach, Kunal R Jain, L M Ward, Leah Johnson, Leandro Nascimento Lemos, Lee Ann McCue, Lennel A Camuy-Vélez, Levi Waldron, Lilian Caesar, Liping Zhao, Lisa Karstens, Lorena Rodriguez-Rubio, Maite Muniesa, Maneesh Dave, Marc W Van Goethem, María Dolores Ramos Barbero, Maria Pachiadaki, Mariana Lozada, Marie Kroeger, Mark McCauley, Mark A Miller, Matthew Grisnik, Matthew Kellom, Melissa A Cregger, Mia Howard, Michael Poulsen, Michelle A Allen, Mireia Valles-Colomer, Mitiku Mihiret Seyoum, Moamen M Elmassry, Montana Smith, Mostafa S Elshahed, Natascha Varona, Neslihan Tas, Nicholas J B Brereton, Nicola G Kriefall, Nicola Segata, Noha H Youssef, Ozge Eyice, Paul D Cotter, Peter J Turnbaugh, Petra Pjevac, Phillip B Pope, Pilar Junier, Pratyay Sengupta, Pubudu P Handakumbura, Rebecca A Reiss, Reese Saho, Reid Longley, Renato Augusto Corrêa Dos Santos, Rhiannon Mondav, Richard Allen White 3rd, Rob Knight, Robert J Gruninger, Roland C Wilhelm, Rosanna ʻAnolani Alegado, Samantha N Miller, Sara L Jackrel, Sarahi L Garcia, Sarai S Finks, Sean P Jungbluth, Sehyun Oh, Sergio E Baranzini, Sergio Sanchez-Carrillo, Shane Roesemann, Sierra Moxon, Sigmund Jensen, Sneha Couvillion, Stephania L Tsola, Stephanie A Yarwood, Sunil Mundra, Susan H Brawley, Suzanne Hodgkins, Sydney Chen, Tanja Woyke, Theodore M Nelson, Thomas Mock, Tyler Myers, W Judson Hervey, William Boulton, William Nelson, Winston E Anthony, Xiao Jun A Liu, Xuefeng Peng, Yaqi You, Ying Zhang, Yun Kit Yeoh, Zachary M Burcham

Affiliations

¹ New Mexico Consortium, Los Alamos, NM, USA. jkelliher@lanl.gov.
² Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA. jkelliher@lanl.gov.
³ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA. jkelliher@lanl.gov.
⁴ Institute for Implementation Science in Public Health, CUNY Graduate School of Public Health and Health Policy, New York, NY, USA.
⁵ Departments of Biology and Entomology, Pennsylvania State University, University Park, PA, USA.
⁶ One Health Microbiome Center, Pennsylvania State University, University Park, PA, USA.
⁷ Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, La Jolla, CA, USA.
⁸ US Geological Survey, St. Petersburg, FL, USA.
⁹ National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
¹⁰ DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹¹ Laboratory of Environmental Microbiology, Institute of Microbiology of the Czech Academy of Sciences, Prague, Czech Republic.
¹² UNC Microbiome Core, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA.
¹³ Department of Botany and Microbiology, College of Science, King Saud University, Riyadh, Saudi Arabia.
¹⁴ Department of Biology, University of New Mexico, Sevilleta LTER, Albuquerque, NM, USA.
¹⁵ Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
¹⁶ MCIBS, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁷ Department of Animal Science, Pennsylvania State University, University Park, PA, USA.
¹⁸ Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA, USA.
¹⁹ Department of Microbiology, Genetics, and Immunology, Michigan State University, East Lansing, MI, USA.
²⁰ Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
²¹ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
²² Department of Biology and Chemistry, California State University, Monterey Bay, Seaside, CA, USA.
²³ University of California, Davis, Davis, CA, USA.
²⁴ Department of Biological Sciences, Charles E. Schmidt College of Science, Florida Atlantic University, Boca Raton, FL, USA.
²⁵ National Institute on Aging, National Institutes of Health, Bethesda, MD, USA.
²⁶ Department of Plant Pathology, University of Minnesota, Saint Paul, MN, USA.
²⁷ National Institute of Standards and Technology, Gaithersburg, MD, USA.
²⁸ Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
²⁹ Center for Microbial Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, USA.
³⁰ Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
³¹ Public Library of Science, San Francisco, CA, USA.
³² Public Library of Science, Cambridge, UK.
³³ Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
³⁴ Life and Environmental Sciences Department, University of California, Merced, Merced, CA, USA.
³⁵ Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.
³⁶ University of Maine, Orono, ME, USA.
³⁷ Maine Agricultural and Forest Experiment Station, Orono, ME, USA.
³⁸ University of Chicago, Chicago, IL, USA.
³⁹ Center for Life in Extreme Environments, Portland State University, Portland, OR, USA.
⁴⁰ Department of Microbiology, The Ohio State University, Columbus, OH, USA.
⁴¹ The Ohio State University Center of Microbiome Science, Columbus, OH, USA.
⁴² EMBL-European Bioinformatics Institute, Hinxton, UK.
⁴³ Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD, USA.
⁴⁴ Office of Data Science and Emerging Technologies, National Institute of Allergy and Infectious Diseases, Bethesda, MD, USA.
⁴⁵ Tri-Institutional Computational Biology, Weill Cornell Medicine, New York, NY, USA.
⁴⁶ University of California, San Francisco, San Francisco, CA, USA.
⁴⁷ National Ecological Observatory Network, Battelle, Boulder, CO, USA.
⁴⁸ Northern Gulf Institute, Mississippi State University, Starkville, MS, USA.
⁴⁹ Ocean Chemistry and Ecosystems Division, Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, USA.
⁵⁰ University of Vermont, Burlington, VT, USA.
⁵¹ Morehouse College, Atlanta, GA, USA.
⁵² Lawrence Berkeley National Laboratory, Berkeley, CA, USA. eaeloefadrosh@lbl.gov.

PMID: 41326814
DOI: 10.1038/s41564-025-02186-2

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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Conflict of interest statement

Competing interests: The authors declare no competing interests.

References

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

Collaborators

Affiliations

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

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

References

Publication types

MeSH terms

LinkOut - more resources

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