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

Summary 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 prior to 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.