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STREAMS guidelines: standards for technical reporting in environmental and host-associated microbiome studies
Julia M. Kelliher, Chloe Mirzayi, Sarah R. Bordenstein, Aaron Oliver, Christina A. Kellogg, Eneida Hatcher, Maureen Berg, Petr Baldrián, Mashael R. Aljumaah, Christina A. Miller, Chris Mungall, Vlastimil Novák, Alexis Palucki, Ethan Smith, Nazifa Tabassum, Gregory Bonito, J. Rodney Brister, Patrick Chain, Mingfei Chen, Samuel Degregori, José Pablo Dundore-Arias, Joanne Emerson, Vanessa Fernandes, Roberto Flores, Antonio G. González, 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 Thompson, Scott Tighe, Ethell Vereen, Aaron Robinson, Abdoul Razck 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 E. Murray, Alla Lapidus, Andreas Bremges, Archana Anand, Ashvini Chauhan, Avishek Dutta, Bablu Kumar, Bela Hausmann, Benoit Chassaing, Braden Tierney, Brian P. Hedlund, Bridget Chalifour, Buck Hanson, Carly R. Muletz‐Wolz, Cassandra L. Ettinger, Chongle Pan, Chris Robinson, Christine Moissl-Eichinger, Chris Hunter, Christopher W. Schadt, Christos Ouzounis, Craig W. Herbold, Cristal Zúñiga, 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, Elisha M. Wood‐Charlson, Elliott P. Barnhart, Emanuele Chisari, Emilie J. Skoog, Emily Graham, Emily Wissel, Emily Davenport, Emily St. John, Eric Cavanna, Erica B. 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, J. R. Saunders, Jack A. Gilbert, James R. Henriksen, Janani Hariharan, Jason A. Rothman, Jaume Puig, Jeffrey A. Kimbrel, Jesús Mercado‐Blanco, Jiarong Guo, João Carlos Setúbal, Joel F. Swift, Johannes R. Krause, Jonathan L. Klassen, Jordan E. Bisanz, Jorge L. Mazza Rodrigues, José Luís Balcázar, Josh D. Neufeld, B.A. E. R. SYKES, Joy E. M. Watts, Judson Van Wyk, Justine W. Debelius, Kaelan Prime, Karthik Anantharaman, K. S. Raman, Katherine D. McMahon, Kelly D. Goodwin, Kent Pham, Keren Yanuka‐Golub, Kevin S. Myers, Krista Ryon, Kristen Peach, Kunal Jain, Lewis M. Ward, L. Johnson, Leandro Nascimento Lemos, Lee Ann McCue, Lennel A. Camuy‐Vélez, Levi Waldron, Lílian Caesar, Liping Zhao, Lisa Karstens, Lorena Rodríguez‐Rubio, Maite Muniesa, Maneesh Dave, Marc W. Van Goethem, Maria Pachiadaki, Mariana Lozada, Marie Kroeger, Mark McCauley, Mark A. Miller, Matthew Grisnik, Matthew Kellom, Melissa A. Cregger, Mia M. Howard, Michael Poulsen, Michelle A. Allen, Mireia Valles‐Colomer, Mitiku Mihiret Seyoum, Moamen M. Elmassry, Montana Smith, Mostafa S. Elshahed, Natascha S. Varona, Neslihan Taş, Nicholas J. B. Brereton, Nicola G. Kriefall, Nicola Segata, Noha H. Youssef, Özge Eyice, Paul D. Cotter, Peter J. Turnbaugh, Petra Pjevac, Phillip B. Pope, Pilar Junier, Pratyay Sengupta, Pubudu Handakumbura, Rebecca A. Reiss, Reese J Saho, Reid Longley, Renato Augusto Corrêa dos Santos, Rhiannon Mondav, Richard White, Robert J. Knight, Robert J. Gruninger, Roland C. Wilhelm, Rosanna A. Alegado, Samantha Miller, Sara L. Jackrel, Sarahi L. Garcia, Sarai S. Finks, Sean P. Jungbluth, Sehyun Oh, Sergio E. Baranzini, Sergio Sánchez-Carrillo, Shane Roesemann, Sierra Moxon, Sigmund Jensen, Sneha Couvillion, Stephania L. Tsola, Stephanie A. Yarwood, Sunil Mundra, Susan H. Brawley, Suzanne B. Hodgkins, Tanja Woyke, Theodore M. Nelson, Thomas Möck, Tyler Myers, W. Judson Hervey, William Boulton, William Nelson, Winston Anthony, Xiao‐Jun Allen Liu, Xuefeng Peng, Yaqi You, Ying Zhang, Yun Kit Yeoh, Zachary M. Burcham, Emiley A. Eloe‐Fadrosh
Bibliographic record
VenueNature Microbiology · 2025
Typearticle
Languageen
FieldBiochemistry, Genetics and Molecular Biology
TopicGut microbiota and health
Canadian institutionsAgriculture and Agri-Food CanadaUniversity of WaterlooLaurentian UniversityUniversity of Calgary
FundersNational Institute of General Medical Sciences
KeywordsMicrobiomeChecklistResource (disambiguation)Human microbiomeHuman Microbiome ProjectData sharing
Abstract
No abstract in any covered source. Its absence is recorded, not treated as a negative.
No abstract. This is not a gap in this database; OpenAlex has none either. 23.3% of the frame is in this state, and the screen finds HALF as much metaresearch here, so the absence is a measured bias rather than a missing field.
How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
metaresearch head score (Codex)0.001
metaresearch head score (Gemma)0.001
Version: codex-gemma-dda1882f352aValidation status: machine_predicted_unvalidated
Candidate categoriesnone
Consensus categoriesnone
DomainCandidate signal: none · Consensus signal: none
Study designCandidate signal: Bench or experimental · Consensus signal: Bench or experimental
GenreCandidate signal: Empirical · Consensus signal: Empirical
Teacher disagreement score0.418
Threshold uncertainty score0.820
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.001 | 0.001 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.000 |
| Insufficient payload (model declined to judge) | 0.000 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
Opus teacher head0.015
GPT teacher head0.374
Teacher spread0.359 · how far apart the two teachers sit on this one work
Validation status
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
The models applied no category: nothing in the taxonomy fit this work.
Study designBench or experimental
Domainnot available
GenreEmpirical
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".
Quick stats
Citations6
Published2025
Admission routes1
Has abstractno