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

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

doi:10.1016/j.isci.2021.102114

Abstract

SummaryMonitoring 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.

Highlights

There is a growing awareness and consideration as to how the microbiome of built-environments affects human health (e.g., National Academies of Sciences and Medicine, 2017)
This work highlights the value in generating genomic libraries of microbes from built-environments such as the International Space Station (ISS) and demonstrates one way such data can be integrated with metagenomics to facilitate the tracking and monitoring of astronaut microbiomes and health
Here we present evidence at the genomic level of either colonization or enrichment of a microbial population at of S. aureus in the nasal microbiome of an astronaut while aboard the ISS—a population that based on read-recruitment is virtually identical to an ISS-derived isolate

Summary

Introduction

There is a growing awareness and consideration as to how the microbiome of built-environments affects human health (e.g., National Academies of Sciences and Medicine, 2017). Microbial surveillance of the ISS environment by NASA has been underway in different respects for some time. These efforts have included culture-based approaches that have allowed the characterization of isolates recovered from surfaces (e.g., Knox et al, 2016; Sielaff et al, 2017; Romsdahl et al, 2018; Blachowicz et al, 2019) and the ISS potable-water system (O’Rourke et al, 2020). A study on astronaut salivary microbiomes revealed an increase in alpha-diversity during spaceflight (Urbaniak et al, 2020). Additional work focusing on different astronaut microbiome sources detected varied alpha-diversity responses during spaceflight for feces (increased), skin (mixed), and nasal (decreased) microbiomes, in addition to identifying

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Results

Conclusion