Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight

Tierney, Braden T, Kim, JangKeun, Overbey, Eliah G, Ryon, Krista A, Foox, Jonathan, Sierra, Maria A, Bhattacharya, Chandrima, Damle, Namita, Najjar, Deena, Park, Jiwoon, Garcia Medina, J Sebastian, Houerbi, Nadia, Meydan, Cem, Wain Hirschberg, Jeremy, Qiu, Jake, Kleinman, Ashley S, Al-Ghalith, Gabriel A, MacKay, Matthew, Afshin, Evan E, Dhir, Raja, Borg, Joseph, Gatt, Christine, Brereton, Nicholas, Readhead, Benjamin P, Beyaz, Semir, Venkateswaran, Kasthuri J, Wiseman, Kelly, Moreno, Juan, Boddicker, Andrew M, Zhao, Junhua, Lajoie, Bryan R, Scott, Ryan T, Altomare, Andrew, Kruglyak, Semyon, Levy, Shawn, Church, George M, Mason, Christopher E (June 2024) Longitudinal multi-omics analysis of host microbiome architecture and immune responses during short-term spaceflight. Nature Microbiology. ISSN 2058-5276

PDF 10.1038.s41564-024-01635-8.pdf - Published Version Available under License Creative Commons Attribution. Download (9MB)

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.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
CSHL Authors:	Beyaz, Semir
Communities:	CSHL labs > Beyaz lab
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	11 June 2024
Date Deposited:	17 Jun 2024 13:04
Last Modified:	17 Jun 2024 13:04
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/41583

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