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MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data

Nature Microbiology volume 9, pages 1152–1156 (2024)Cite this article

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Here we present the establishment of an open-access web-based repository for microbiological Raman spectroscopy data. The data collection, called ‘MicrobioRaman’ (https://www.ebi.ac.uk/biostudies/MicrobioRaman/studies), was inspired by the great success and usefulness of research databases such as GenBank and UniProt. This centralized repository, residing within the BioStudies database1 — which is maintained by a public institution, the European Bioinformatics Institute — minimizes the risk of data loss or eventual abandonment, offering a long-term common reference for analysis with advantages in accessibility and transparency over commercial data analysis tools. We feel that MicrobioRaman will provide a foundation for this growing field by serving as an open-access repository for sharing microbiological Raman data and through the codification of a set of reporting standards.

Despite the potential of Raman spectroscopy in microbiology, the reporting of analytical methods and data for microbiological systems has evolved in a haphazard manner, and progress in the field is hindered by the lack of both a set of standards for data reporting and a common database to deposit microbiological Raman data. Raman data from microorganisms is relatively complex to analyse because proper interpretation is dependent on biological context, experimental conditions and data processing.

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Fig. 1: Overview of Raman technologies and their applications in microbiology.

References

  1. Sarkans, U. et al. Nucleic Acids Res. 46, D1266–D1270 (2018).

    Article  CAS  PubMed  Google Scholar 

  2. Huang, W. E., Griffiths, R. I., Thompson, I. P., Bailey, M. J. & Whiteley, A. Anal. Chem. 76, 4452–4458 (2004).

    Article  CAS  PubMed  Google Scholar 

  3. Alcolombri, U., Pioli, R., Stocker, R. & Berry, D. ISME Commun. 2, 55 (2022).

    Article  PubMed  PubMed Central  Google Scholar 

  4. Wagner, M. & Haider, S. Curr. Opin. Biotechnol. 23, 96–102 (2012).

    Article  CAS  PubMed  Google Scholar 

  5. Pereira, F. C. et al. Nat. Commun. 11, 5104 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Lee, K. S. et al. Nat. Rev. Methods Primers 1, 80 (2021).

    Article  CAS  Google Scholar 

  7. Hatzenpichler, R., Krukenberg, V., Spietz, R. L. & Jay, Z. J. Nat. Rev. Microbiol. 18, 241–256 (2020).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  8. Wang, Y., Huang, W. E., Cui, L. & Wagner, M. Curr. Opin. Biotechnol. 41, 34–42 (2016).

    Article  CAS  PubMed  Google Scholar 

  9. Gala de Pablo, J., Lindley, M., Hiramatsu, K. & Goda, K. Acc. Chem. Res. 54, 2132–2143 (2021).

    Article  CAS  PubMed  Google Scholar 

  10. Guo, S., Popp, J. & Bocklitz, T. Nat. Protoc. 16, 5426–5459 (2021).

    Article  CAS  PubMed  Google Scholar 

Download references

Acknowledgements

We gratefully acknowledge funding from a Gordon and Betty Moore Foundation Symbiosis in Aquatic Systems Initiative Investigator Award (GBMF9197 to R.S.; https://doi.org/10.37807/GBMF9197) and the Simons Foundation through the Principles of Microbial Ecosystems (PriME) collaboration (grant no. 542395 to R.S.). Development of BioStudies is supported by the European Molecular Biology Laboratory member states. A.J.P. was supported by the German Research Foundation (DFG)—CRC 1439/1, project number 426547801. The Stocker group thanks R. Naisbit for scientific editing.

Author information

Authors and Affiliations

  1. Institute for Environmental Engineering, Department of Civil, Environmental and Geomatic Engineering, ETH Zurich, Zurich, Switzerland

    Kang Soo Lee, Zachary Landry, Pratchaya Pramoj Na Ayutthaya, Richard J. Henshaw, Clara Martínez-Pérez, Oliver Müller, Jing Wang, Yang Yue & Roman Stocker

  2. Department of Marine and Environmental Biology, University of Southern California, Los Angeles, CA, USA

    Zachary Landry

  3. European Molecular Biology Laboratory, European Bioinformatics Institute, EMBL-EBI, Cambridge, UK

    Awais Athar & Ugis Sarkans

  4. Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel

    Uria Alcolombri

  5. Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria

    David Berry, Márton Palatinszky, Fátima C. Pereira, Alessandra Riva & Michael Wagner

  6. Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria

    David Berry

  7. HORIBA France SAS, Palaiseau, France

    Philippe de Bettignies

  8. Department of Electrical and Computer Engineering and Department of Biomedical Engineering, Boston University, Boston, MA, USA

    Ji-Xin Cheng

  9. Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zurich, Switzerland

    Gabor Csucs & Sung Sik Lee

  10. Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China

    Li Cui

  11. Institute of Physical Chemistry (IPC) and Abbe Center of Photonics (ACP), Friedrich Schiller University Jena, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany

    Volker Deckert & Jürgen Popp

  12. Leibniz Institute of Photonic Technology e.V. Jena, member of Leibniz Health Technology, member of the Leibniz Centre for Photonics in Infection Research (LPI), Jena, Germany

    Volker Deckert & Jürgen Popp

  13. WITec GmbH, Ulm, Germany

    Thomas Dieing & Ievgeniia Iermak

  14. Department of Materials Science and Engineering, and Department of Radiology, Stanford University, Stanford, CA, USA

    Jennifer Dionne

  15. Institute of Scientific Instruments of the Czech Academy of Sciences, v.v.i, Brno, Czech Republic

    Ondrej Doskocil, Zdenek Pilat, Filip Plesinger & Ota Samek

  16. Department of Environmental Microbiology, Eawag, Dübendorf, Switzerland

    Glen D’Souza, Olga T. Schubert & Astrid K. M. Stubbusch

  17. Institute of Biogeochemistry and Pollutant Dynamics, Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland

    Glen D’Souza, Olga T. Schubert & Astrid K. M. Stubbusch

  18. CMET, Center for Microbial Technology and Ecology, Department of Biotechnology, Ghent University, Gent, Belgium

    Cristina García-Timermans

  19. Institute of Biophysics, Department of Bionanosciences, University of Natural Resources and Life Sciences (BOKU), Vienna, Austria

    Notburga Gierlinger

  20. Department of Chemistry, The University of Tokyo, Tokyo, Japan

    Keisuke Goda

  21. Institute of Technological Sciences, Wuhan University, Wuhan, China

    Keisuke Goda

  22. Department of Bioengineering, University of California, Los Angeles, CA, USA

    Keisuke Goda

  23. Department of Chemistry and Biochemistry, Department of Microbiology and Cell Biology, Center for Biofilm Engineering, and Thermal Biology Institute, Montana State University, Bozeman, MT, USA

    Roland Hatzenpichler

  24. Department of Engineering Science, University of Oxford, Oxford, UK

    Wei E. Huang

  25. Chair of Analytical Chemistry and Water Chemistry, Institute of Water Chemistry, TUM School of Natural Sciences (Dep. Chemistry), Technical University of Munich, Garching, Germany

    Natalia P. Ivleva

  26. Department of Chemistry, Humboldt- Universität zu Berlin, Berlin, Germany

    Janina Kneipp

  27. Renishaw GmbH, Pliezhausen, Germany

    Patrick Kubryk

  28. Institute of Biodiversity, Aquatic Geomicrobiology, Friedrich Schiller University Jena, Jena, Germany

    Kirsten Küsel

  29. Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany

    Kirsten Küsel

  30. Department of Environmental and Energy Engineering, Yonsei University, Wonju, Republic of Korea

    Tae Kwon Lee

  31. Institute of Biochemistry, Department of Biology, ETH Zurich, Zurich, Switzerland

    Sung Sik Lee

  32. Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of Bioengineering and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China

    Bo Ma

  33. Central Laser Facility, Research Complex at Harwell, STFC Rutherford Appleton Laboratory, UKRI, Harwell, UK

    Pavel Matousek

  34. Environmental Microbiology and Biotechnology (EMB), University of Duisburg-Essen, Essen, Germany

    Rainer U. Meckenstock

  35. Department of Chemistry, Columbia University, New York, NY, USA

    Wei Min

  36. Kavli Institute for Brain Science, Columbia University, New York, NY, USA

    Wei Min

  37. Institute of Physics, Faculty of Mathematics and Physics, Charles University, Prague, Czech Republic

    Peter Mojzeš

  38. Department of Chemistry and Applied Biosciences, ETH Zurich, Zurich, Switzerland

    Naresh Kumar & Renato Zenobi

  39. Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark

    Per Halkjær Nielsen & Michael Wagner

  40. School of Physics and Astronomy, University of Nottingham, Nottingham, UK

    Ioan Notingher

  41. School of Biological Sciences, University of Southampton, Southampton, UK

    Fátima C. Pereira

  42. Ceramic Physics Laboratory, Kyoto Institute of Technology, Kyoto, Japan

    Giuseppe Pezzotti

  43. Department of Molecular Genetics, Institute of Biomedical Science, Kansai Medical University, Osaka, Japan

    Giuseppe Pezzotti

  44. Department of Immunology, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan

    Giuseppe Pezzotti

  45. Environmental Metagenomics, Research Center One Health Ruhr of the University Alliance Ruhr, Faculty of Chemistry, University of Duisburg-Essen, Essen, Germany

    Alexander J. Probst

  46. School of Life Sciences, Technical University of Munich, Freising-Weihenstephan, Germany

    Alessandra Riva

  47. Department of Engineering Mathematics and Physics, Faculty of Engineering, Cairo University, Giza, Egypt

    Amr. A. E. Saleh

  48. Centre for Research in Earth and Space Sciences, York University, Toronto, Ontario, Canada

    Haley M. Sapers

  49. Geological Institute, Department of Earth Sciences, ETH Zurich, Zurich, Switzerland

    Astrid K. M. Stubbusch

  50. Department of Mechanical Engineering, MIT, Cambridge, MA, USA

    Loza F. Tadesse

  51. Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA

    Loza F. Tadesse

  52. Jameel Clinic for AI & Healthcare, MIT, Cambridge, MA, USA

    Loza F. Tadesse

  53. School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA

    Gordon T. Taylor

  54. Advanced Analytical Technologies, Empa, Dübendorf, Switzerland

    Jing Wang & Yang Yue

  55. Division of Biomedical Engineering, James Watt School of Engineering, University of Glasgow, Glasgow, UK

    Huabing Yin

  56. Timegate Instruments Oy, Oulu, Finland

    Jacopo Zini

  57. Drug Research Program, Division of Pharmaceutical Biosciences, Faculty of Pharmacy, University of Helsinki, Helsinki, Finland

    Jacopo Zini

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  1. Kang Soo Lee
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Contributions

K.S.L., Z.L., A.A., U.S. and R.S. wrote the paper. All authors reviewed and approved the paper.

Corresponding authors

Correspondence to Kang Soo Lee, Ugis Sarkans or Roman Stocker.

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Lee, K.S., Landry, Z., Athar, A. et al. MicrobioRaman: an open-access web repository for microbiological Raman spectroscopy data. Nat Microbiol 9, 1152–1156 (2024). https://doi.org/10.1038/s41564-024-01656-3

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