The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns

Rodolfo A Salido¹, Haoqi Nina Zhao², Daniel McDonald³, Helena Mannochio-Russo², Simone Zuffa², Renee E Oles⁴, Allegra T Aron⁵, Yasin El Abiead², Sawyer Farmer³, Antonio González³, Cameron Martino³, Ipsita Mohanty², Ceth W Parker⁶, Lucas Patel⁷, Paulo Wender Portal Gomes², Robin Schmid², Tara Schwartz³, Jennifer Zhu², Michael R Barratt⁸, Kathleen H Rubins⁸, Hiutung Chu⁹, Fathi Karouia¹⁰, Kasthuri Venkateswaran⁶, Pieter C Dorrestein¹¹, Rob Knight¹²

Affiliations

¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
³ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
⁴ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA.
⁶ Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
⁷ Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA.
⁸ Astronaut Office, NASA Johnson Space Center, Houston, TX, USA.
⁹ Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA; Space Research Within Reach, San Francisco, CA, USA; Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA.
¹¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. Electronic address: pdorrestein@health.ucsd.edu.
¹² Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA. Electronic address: rknight@ucsd.edu.

PMID: 40020666
PMCID: PMC12068931 (available on 2026-04-03)
DOI: 10.1016/j.cell.2025.01.039

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns

Rodolfo A Salido et al. Cell. 2025.

. 2025 Apr 3;188(7):2022-2041.e23.

doi: 10.1016/j.cell.2025.01.039. Epub 2025 Feb 27.

Authors

Affiliations

¹ Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA.
² Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA.
³ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
⁴ Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Department of Pathology, University of California, San Diego, La Jolla, CA, USA.
⁵ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Department of Chemistry and Biochemistry, University of Denver, Denver, CO, USA.
⁶ Biotechnology and Planetary Protection Group, Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
⁷ Bioinformatics and Systems Biology Program, University of California, San Diego, La Jolla, CA, USA; Medical Scientist Training Program, University of California, San Diego, La Jolla, CA, USA.
⁸ Astronaut Office, NASA Johnson Space Center, Houston, TX, USA.
⁹ Department of Pathology, University of California, San Diego, La Jolla, CA, USA; Chiba University-UC San Diego Center for Mucosal Immunology, Allergy and Vaccines (CU-UCSD cMAV), La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA.
¹⁰ Blue Marble Space Institute of Science, Exobiology Branch, NASA Ames Research Center, Moffett Field, CA, USA; Space Research Within Reach, San Francisco, CA, USA; Center for Space Medicine, Baylor College of Medicine, Houston, TX, USA.
¹¹ Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Pharmacology, University of California, San Diego, La Jolla, CA, USA; Collaborative Mass Spectrometry Innovation Center, University of California, San Diego, La Jolla, CA, USA. Electronic address: pdorrestein@health.ucsd.edu.
¹² Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Center for Microbiome Innovation, University of California, San Diego, La Jolla, CA, USA; Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA; Halıcıoğlu Data Science Institute, University of California, San Diego, La Jolla, CA, USA. Electronic address: rknight@ucsd.edu.

PMID: 40020666
PMCID: PMC12068931 (available on 2026-04-03)
DOI: 10.1016/j.cell.2025.01.039

Abstract

Space habitation provides unique challenges in built environments isolated from Earth. We produced a 3D map of the microbes and metabolites throughout the United States Orbital Segment (USOS) of the International Space Station (ISS) with 803 samples collected during space flight, including controls. We find that the use of each of the nine sampled modules within the ISS strongly drives the microbiology and chemistry of the habitat. Relating the microbiology to other Earth habitats, we find that, as with human microbiota, built environment microbiota also align naturally along an axis of industrialization, with the ISS providing an extreme example of an industrialized environment. We demonstrate the utility of culture-independent sequencing for microbial risk monitoring, especially as the location of sequencing moves to space. The resulting resource of chemistry and microbiology in the space-built environment will guide long-term efforts to maintain human health in space for longer durations.

Keywords: 3D mapping; International Space Station; built environment; culture independent; extraterrestrial habitat; indoor environment; metabolome; metabolomics; microbiome; surface swab.

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Conflict of interest statement

Declaration of interests R.K. is a scientific advisory board member and consultant for BiomeSense, Inc., and has equity and receives income. He is a scientific advisory board member and has equity in GenCirq. He is a consultant and scientific advisory board member for DayTwo and receives income. 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, has equity, and is a scientific advisory board member. D.M. is a consultant for and has equity in BiomeSense, Inc. 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. P.C.D. is the scientific advisor to and holds equity in Sirenas and Cybele Microbiome and is scientific co-founder and scientific advisor of and has equity in Ometa Labs, Arome, and Enveda (with approval by UC San Diego). C.M. is the founder of, has equity in, and receives income from Leaven Foods Inc.

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The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns

Affiliations

The International Space Station has a unique and extreme microbial and chemical environment driven by use patterns

Authors

Affiliations

Abstract

Conflict of interest statement

References

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources