Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome

Michael D Lee; Aubrie O'Rourke; Hernan Lorenzi; Brad M Bebout; Chris L Dupont; R Craig Everroad

doi:10.1016/j.isci.2021.102114

Reference-guided metagenomics reveals genome-level evidence of potential microbial transmission from the ISS environment to an astronaut's microbiome

iScience. 2021 Jan 29;24(2):102114. doi: 10.1016/j.isci.2021.102114. eCollection 2021 Feb 19.

Authors

Michael D Lee^{1

2}, Aubrie O'Rourke³, Hernan Lorenzi⁴, Brad M Bebout¹, Chris L Dupont⁵, R Craig Everroad¹

Affiliations

¹ Exobiology Branch, NASA Ames Research Center, Mountain View, CA, USA.
² Blue Marble Space Institute of Science, Seattle, WA, USA.
³ Space Life Sciences, NASA Kennedy Space Center, Merritt Island, FL, USA.
⁴ Department of Infectious Diseases, J. Craig Venter Institute, Rockville, MD, USA.
⁵ J. Craig Venter Institute, San Diego, CA, USA.

Abstract

Monitoring microbial communities aboard the International Space Station (ISS) is essential to maintaining astronaut health and the integrity of life-support systems. Using assembled genomes of ISS-derived microbial isolates as references, recruiting metagenomic reads from an astronaut's nasal microbiome revealed no recruitment to a Staphylococcus aureus isolate from samples before launch, yet systematic recruitment across the genome when sampled after 3 months aboard the ISS, with a median percent identity of 100%. This suggests that either a highly similar S. aureus population colonized the astronaut's nasal microbiome while the astronaut was aboard the ISS or that it may have been below detection before spaceflight, instead supporting a shift in community composition. This work highlights the value in generating genomic libraries of microbes from built-environments such as the ISS and demonstrates one way such data can be integrated with metagenomics to facilitate the tracking and monitoring of astronaut microbiomes and health.

Keywords: Microbiology; Space Science.