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Weill Cornell Medicine

Nat. Microbiol., Jun 11 2024, | https://doi.org/10.1038/s41564-024-01635-8 Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Braden T. Tierney ^1,2,18, JangKeun Kim ^1,2,18, Eliah G. Overbey ^1,2,3,4, Krista A. Ryon ¹, Jonathan Foox¹, Maria A. Sierra ⁵, Chandrima Bhattacharya ⁵, Namita Damle ¹, Deena Najjar ^1,6, Jiwoon Park ^1,2, J. Sebastian Garcia Medina ^1,2,5, Nadia Houerbi ^1,2, Cem Meydan ^1,2, Jeremy Wain Hirschberg ¹, Jake Qiu ¹, Ashley S. Kleinman ¹, Gabriel A. Al-Ghalith ⁷, Matthew MacKay ⁵, Evan E. Afshin ^1,2, Raja Dhir ^7,8, Joseph Borg ⁹, Christine Gatt ⁹, Nicholas Brereton¹⁰, Benjamin P. Readhead¹¹, Semir Beyaz¹², Kasthuri J. Venkateswaran ¹³, Kelly Wiseman ¹⁴, Juan Moreno¹⁴, Andrew M. Boddicker¹⁴, Junhua Zhao ¹⁴, Bryan R. Lajoie ¹⁴, Ryan T. Scott ¹⁵, Andrew Altomare ¹⁴, Semyon Kruglyak ¹⁴, Shawn Levy ¹⁴, George M. Church ¹⁶ & Christopher E. Mason ^1,2,3,17,*

¹Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA.
²The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
³BioAstra, Inc., New York, NY, USA.
⁴Center for STEM, University of Austin, Austin, TX, USA.
⁵Tri-Institutional Biology and Medicine program, Weill Cornell Medicine, New York, NY, USA.
⁶Albert Einstein College of Medicine, Bronx, NY, USA.
⁷Seed Health, Inc., Venice, CA, USA.
⁸Swiss Institute of Allergy and Asthma Research (SIAF), University of Zurich, Davos, Switzerland.
⁹Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, Malta.
¹⁰School of Biology and Environmental Science, University College Dublin, Dublin, Ireland.
¹¹ASU-Banner Neurodegenerative Disease Research Center, Arizona State University, Tempe, AZ, USA.
¹²Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
¹³Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA, USA.
¹⁴Element Biosciences, San Diego, CA, USA.
¹⁵KBR; Space Biosciences Division, NASA Ames Research Center, Moffett Field, CA, USA.
¹⁶Harvard Medical School and the Wyss Institute, Boston, MA, USA.
¹⁷The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
¹⁸These authors contributed equally: Braden T. Tierney, JangKeun Kim.

^*Corresponding author: correspondence to Christopher E. Mason

Abstract

Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes. However, documenting microbial shifts during spaceflight has been difficult due to mission constraints that lead to limited sampling and profiling. Here we executed a six-month longitudinal study to quantify the high-resolution human microbiome response to three days in orbit for four individuals. Using paired metagenomics and metatranscriptomics alongside single-nuclei immune cell profiling, we characterized time-dependent, multikingdom microbiome changes across 750 samples and 10 body sites before, during and after spaceflight at eight timepoints. We found that most alterations were transient across body sites; for example, viruses increased in skin sites mostly during flight. However, longer-term shifts were observed in the oral microbiome, including increased plaque-associated bacteria (for example, Fusobacteriota), which correlated with immune cell gene expression. Further, microbial genes associated with phage activity, toxin-antitoxin systems and stress response were enriched across multiple body sites. In total, this study reveals in-depth characterization of microbiome and immune response shifts experienced by astronauts during short-term spaceflight and the associated changes to the living environment, which can help guide future missions, spacecraft design and space habitat planning.

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형식Research article
게재일2024년 06월 (BRIC 등록일 2024-06-13)
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