A roadmap for equitable reuse of public microbiome data

Laura A Hug^#¹, Roland Hatzenpichler^#^{2

3

4}, Cristina Moraru^#⁵, André R Soares^#^{5

6}, Folker Meyer^#^{7

8}, Anke Heyder⁹; Data Reuse Consortium; Alexander J Probst^#^{10

11}

Collaborators, Affiliations

Collaborators

Data Reuse Consortium:
R Z Abdallah, A Abdalrahem, N Abdulkadir, I M Adesiyan, L Alteio, K Anantharaman, R Anderson, A-S Andrei, J A Baeza, F Bak, B Baker, A Bartholomäus, N Bejerman, J Biddle, A Bissett, J A Blakeley-Ruiz, K Block, J Boldt, G Bonilla-Rosso, T L Bornemann, V S Brauer, W Brazelton, A Bremges, E Buelow, Z M Burcham, A Cansdale, J G Caporaso, T Cernava, I Chatzigiannidou, R Costa, C R Currie, A Daebeler, V De Anda, A De Santiago, L M Arake de Tacca, J Debelius, S M Dittami, X Dong, M Džunková, A Edwards, R Edwards, S Egbert, J C Engelmann, S P Esser, T J G Ettema, C L Ettinger, A Petrovic Fabijan, R M W Ferguson, P Ferretti, P Foucault, J A Fuhrman, A M Gada, P Geesink, I R Gerhardt, M O Gessner, D Giovannelli, D Gittins, G B Gloor, R A González-Pech, C Gopalakrishnappa, C Greening, R Gregor, A C Gregory, H-P Grossart, M Groussin, B Valenzuela Guerrero, M Guzel, N Hamamura, T L Hamilton, J N Hamm, L Hart, C Hassenrück, M Hay, R M Hechler, P Hellwig, M Henson, M Herold, P J Hesketh-Best, M Hess, L Hillary, T C Hitch, S S Hivarkar, K J Hoff, E F Hom, S Hou, L W Hugerth, Y Hwang, N Ilott, Z J Jay, S P Jungbluth, E Karimi, Y M Kaspareit, C Keating, M Kellom, E A Kiledal, I Klarenberg, R Knight, A K Koech, E V Koonin, K Kormas, K Kujala, N C Kyrpides, S L La Rosa, C C Laczny, K Lahmers, X Lan, A A Lateef, S H Lau, F Leese, M Á Lezcano, S S Li, R N Lima, S Lücker, A Mahnert, S Majidian, L Malfertheiner, A Marshall, S Meaden, C J Meehan, D V Meier, C Melkonian, D R Mende, J L Meyer, G Michoud, V Mikryukov, S Miravet-Verde, J Muschiol, M K Nata'ala, J D Neufeld, S Neuhauser, O Osuolale, J Osvatic, K M Pappas, D H Parks, R H Parry, P V Pascoal, C Pavloudi, B Peyton, J Plewka, M Poyet, T Priest, E K Quaye, S Ramganesh, T Rattei, P Rausch, E Rech, C Rinke, C Robinson, A Rodríguez-Gijón, L M Rodriguez-R, R R Rohwer, T Roloff, J A Rothman, S Rückert, S E Ruff, J S Saini, M G Santiago-Martínez, L Santoferrara, M S Sarhan, J H Saw, T Sbaffi, R B Schäfer, G Schaible, M Schloter, R A Schmitz, C Schubert, O Schwengers, L Sehnal, A Sekar, J Sekar, M M Seyoum, M B Shah, I Sharon, B Siebers, E T Sieradzki, D Skliros, O L Snoeyenbos-West, A Sorbie, D R Speth, C G Sprehn, P Srivastava, T L Stach, J E Stajich, J Starke, A D Steen, R Stöckl, T Stoikidou, N Stopnisek, R Sukumaran, B Sures, S Suzuki, D Tamarit, P Thieringer, R Y Tito, C B Trivedi, G Trubl, J Truu, M Tsiknia, J Ugalde, L E Valentin-Alvarado, X Vázquez-Campos, J Vierheilig, F A B von Meijenfeldt, M Wagner, C J Walsh, S Wang, Y Wang, C-E Wegner, T Weir, L C Weiss, J L Weissman, A Wichels, C L Williams, T A Williams, A Z Worden, T Woyke, M Wu, W Xiu, Y Zhang, J Zhu, R M Ziels, B Zwirzitz

Affiliations

¹ Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
² Department of Microbiology and Cell Biology, Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
³ Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MO, USA.
⁴ Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
⁵ Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
⁶ Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
⁷ Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
⁸ Department of Computer Science, University of Duisburg-Essen, Essen, Germany.
⁹ Department of Psychology, Ruhr University Bochum, Bochum, Germany.
¹⁰ Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.
¹¹ Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.

^# Contributed equally.

PMID: 41006832
DOI: 10.1038/s41564-025-02116-2

Review

A roadmap for equitable reuse of public microbiome data

Laura A Hug et al. Nat Microbiol. 2025.

. 2025 Sep 26.

doi: 10.1038/s41564-025-02116-2. Online ahead of print.

Authors

Laura A Hug^#¹, Roland Hatzenpichler^#^{2

3

4}, Cristina Moraru^#⁵, André R Soares^#^{5

6}, Folker Meyer^#^{7

8}, Anke Heyder⁹; Data Reuse Consortium; Alexander J Probst^#^{10

11}

Collaborators

Data Reuse Consortium:
R Z Abdallah, A Abdalrahem, N Abdulkadir, I M Adesiyan, L Alteio, K Anantharaman, R Anderson, A-S Andrei, J A Baeza, F Bak, B Baker, A Bartholomäus, N Bejerman, J Biddle, A Bissett, J A Blakeley-Ruiz, K Block, J Boldt, G Bonilla-Rosso, T L Bornemann, V S Brauer, W Brazelton, A Bremges, E Buelow, Z M Burcham, A Cansdale, J G Caporaso, T Cernava, I Chatzigiannidou, R Costa, C R Currie, A Daebeler, V De Anda, A De Santiago, L M Arake de Tacca, J Debelius, S M Dittami, X Dong, M Džunková, A Edwards, R Edwards, S Egbert, J C Engelmann, S P Esser, T J G Ettema, C L Ettinger, A Petrovic Fabijan, R M W Ferguson, P Ferretti, P Foucault, J A Fuhrman, A M Gada, P Geesink, I R Gerhardt, M O Gessner, D Giovannelli, D Gittins, G B Gloor, R A González-Pech, C Gopalakrishnappa, C Greening, R Gregor, A C Gregory, H-P Grossart, M Groussin, B Valenzuela Guerrero, M Guzel, N Hamamura, T L Hamilton, J N Hamm, L Hart, C Hassenrück, M Hay, R M Hechler, P Hellwig, M Henson, M Herold, P J Hesketh-Best, M Hess, L Hillary, T C Hitch, S S Hivarkar, K J Hoff, E F Hom, S Hou, L W Hugerth, Y Hwang, N Ilott, Z J Jay, S P Jungbluth, E Karimi, Y M Kaspareit, C Keating, M Kellom, E A Kiledal, I Klarenberg, R Knight, A K Koech, E V Koonin, K Kormas, K Kujala, N C Kyrpides, S L La Rosa, C C Laczny, K Lahmers, X Lan, A A Lateef, S H Lau, F Leese, M Á Lezcano, S S Li, R N Lima, S Lücker, A Mahnert, S Majidian, L Malfertheiner, A Marshall, S Meaden, C J Meehan, D V Meier, C Melkonian, D R Mende, J L Meyer, G Michoud, V Mikryukov, S Miravet-Verde, J Muschiol, M K Nata'ala, J D Neufeld, S Neuhauser, O Osuolale, J Osvatic, K M Pappas, D H Parks, R H Parry, P V Pascoal, C Pavloudi, B Peyton, J Plewka, M Poyet, T Priest, E K Quaye, S Ramganesh, T Rattei, P Rausch, E Rech, C Rinke, C Robinson, A Rodríguez-Gijón, L M Rodriguez-R, R R Rohwer, T Roloff, J A Rothman, S Rückert, S E Ruff, J S Saini, M G Santiago-Martínez, L Santoferrara, M S Sarhan, J H Saw, T Sbaffi, R B Schäfer, G Schaible, M Schloter, R A Schmitz, C Schubert, O Schwengers, L Sehnal, A Sekar, J Sekar, M M Seyoum, M B Shah, I Sharon, B Siebers, E T Sieradzki, D Skliros, O L Snoeyenbos-West, A Sorbie, D R Speth, C G Sprehn, P Srivastava, T L Stach, J E Stajich, J Starke, A D Steen, R Stöckl, T Stoikidou, N Stopnisek, R Sukumaran, B Sures, S Suzuki, D Tamarit, P Thieringer, R Y Tito, C B Trivedi, G Trubl, J Truu, M Tsiknia, J Ugalde, L E Valentin-Alvarado, X Vázquez-Campos, J Vierheilig, F A B von Meijenfeldt, M Wagner, C J Walsh, S Wang, Y Wang, C-E Wegner, T Weir, L C Weiss, J L Weissman, A Wichels, C L Williams, T A Williams, A Z Worden, T Woyke, M Wu, W Xiu, Y Zhang, J Zhu, R M Ziels, B Zwirzitz

Affiliations

¹ Department of Biology, University of Waterloo, Waterloo, Ontario, Canada.
² Department of Microbiology and Cell Biology, Thermal Biology Institute, Montana State University, Bozeman, MT, USA.
³ Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MO, USA.
⁴ Center for Biofilm Engineering, Montana State University, Bozeman, MT, USA.
⁵ Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany.
⁶ Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany.
⁷ Institute for AI in Medicine, University Hospital Essen, University of Duisburg-Essen, Essen, Germany.
⁸ Department of Computer Science, University of Duisburg-Essen, Essen, Germany.
⁹ Department of Psychology, Ruhr University Bochum, Bochum, Germany.
¹⁰ Environmental Metagenomics, Research Center One Health Ruhr, University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.
¹¹ Centre for Water and Environmental Research (ZWU), University of Duisburg-Essen, Essen, Germany. alexander.probst@uni-due.de.

^# Contributed equally.

PMID: 41006832
DOI: 10.1038/s41564-025-02116-2

Abstract

Science benefits from rapid open data sharing, but current guidelines for data reuse were established two decades ago, when databases were several million times smaller than they are today. These guidelines are largely unfamiliar to the scientific community, and, owing to the rapid increase in biological data generated in the past decade, they are also outdated. As a result, there is a lack of community standards suited to the current landscape and inconsistent implementation of data sharing policies across institutions. Here we discuss current sequence data sharing policies and their benefits and drawbacks, and present a roadmap to establish guidelines for equitable sequence data reuse, developed in consultation with a data consortium of 167 microbiome scientists. We propose the use of a Data Reuse Information (DRI) tag for public sequence data, which will be associated with at least one Open Researcher and Contributor ID (ORCID) account. The machine-readable DRI tag indicates that the data creators prefer to be contacted before data reuse, and simultaneously provides data consumers with a mechanism to get in touch with the data creators. The DRI aims to facilitate and foster collaborations, and serve as a guideline that can be expanded to other data types.

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Conflict of interest statement

Competing interests: R.H. was a member (2021–2024) of the User Executive Committee of the US Department of Energy’s (DOE) Joint Genome Institute. A.P. is an affiliate scientist at JGI and sits on the Prokaryotic Advisory Committee. All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of the DOE. R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He has equity in and acts as a consultant for Cybele. He is a co-founder of Biota, Inc. and has equity. He is a co-founder of Micronoma and has equity and is a scientific advisory board member. He is a board member of Microbiota Vault, Inc. He is a board member of N=1 IBS advisory board and receives income. He is a Senior Visiting Fellow of HKUST Jockey Club Institute for Advanced Study. The terms of these arrangements have been reviewed and approved by the University of California, San Diego in accordance with its conflict of interest policies.

References

1. The Wellcome Trust Sharing Data from Large-Scale Biological Research Projects: A System of Tripartite Responsibility (National Human Genome Research Institute, 2003).
1. Report of the International Strategy Meeting on Human Genome Sequencing held at the Princess Hotel, Southampton, Bermuda, on 25th–28th February 1996 (unpublished manuscript, 1996); http://hdl.handle.net/10161/7715
1. Toronto International Data Release Workshop Authors. Prepublication data sharing. Nature 461, 168–170 (2009). - DOI
1. Parties to the Convention on Biological Diversity. Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity 234–249 (Official Journal of the European Union, 2014); https://eur-lex.europa.eu/eli/agree_prot/2014/283/oj
1. GenBank and WGS Statistics (National Center for Biotechnology Information, accessed February 2024); https://www.ncbi.nlm.nih.gov/genbank/statistics/

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A roadmap for equitable reuse of public microbiome data

Collaborators

Affiliations

A roadmap for equitable reuse of public microbiome data

Authors

Collaborators

Affiliations

Abstract

Conflict of interest statement

References

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