Investigation of Spaceflight Induced Changes to Astronaut Microbiomes.

Michael D Morrison,David J Smith,Kasthuri Venkateswaran,Fathi Karouia,Satish Mehta,James B Thissen,Crystal Jaing,Camilla Urbaniak

doi:10.3389/fmicb.2021.659179

Abstract

The International Space Station (ISS) is a uniquely enclosed environment that has been continuously occupied for the last two decades. Throughout its operation, protecting the health of the astronauts on-board has been a high priority. The human microbiome plays a significant role in maintaining human health, and disruptions in the microbiome have been linked to various diseases. To evaluate the effects of spaceflight on the human microbiome, body swabs and saliva samples were collected from four ISS astronauts on consecutive expeditions. Astronaut samples were analyzed using shotgun metagenomic sequencing and microarrays to characterize the microbial biodiversity before, during, and after the astronauts’ time onboard the ISS. Samples were evaluated at an individual and population level to identify changes in microbial diversity and abundance. No significant changes in the number or relative abundance of taxa were observed between collection time points when samples from all four astronauts were analyzed together. When the astronauts’ saliva samples were analyzed individually, the saliva samples of some astronauts showed significant changes in the relative abundance of taxa during and after spaceflight. The relative abundance of Prevotella in saliva samples increased during two astronauts’ time onboard the ISS while the relative abundance of other commensal taxa such as Neisseria, Rothia, and Haemophilus decreased. The abundance of some antimicrobial resistance genes within the saliva samples also showed significant changes. Most notably, elfamycin resistance gene significantly increased in all four astronauts post-flight and a CfxA6 beta-lactam marker significantly increased during spaceflight but returned to normal levels post-flight. The combination of both shotgun metagenomic sequencing and microarrays showed the benefit of both technologies in monitoring microbes on board the ISS. There were some changes in each astronaut’s microbiome during spaceflight, but these changes were not universal for all four astronauts. Two antimicrobial resistance gene markers did show a significant change in abundance in the saliva samples of all four astronauts across their collection times. These results provide insight for future ISS microbial monitoring studies and targets for antimicrobial resistance screenings.

Highlights

Decades of research has revealed the important role of microorganisms in maintaining human health
The number of mapped reads and the Livermore Metagenomic Analysis Toolkit (LMAT) taxonomic classification results for all control and astronaut samples are shown in Supplementary Data Sheet 1, and the relative abundance of species in each control samples is shown in Supplementary Figure 1
The development of highthroughput sequencing technologies and subsequent research into the human microbiome has revealed the important role these microbial communities play in maintaining human health

Summary

Introduction

Decades of research has revealed the important role of microorganisms in maintaining human health. Maintaining a healthy “core” microbiome is widely considered essential for maintaining a healthy lifestyle. Both government and private space organizations have shown great interest in increasing human access to space with plans of returning to the Moon and landing humans on Mars in the coming decades. One major challenge with renewed long-term spaceflight is the potential risk for human health. Medical treatments during these missions will be limited to the supplies in the on board pharmacy. Several early Apollo missions had astronauts experience upper respiratory infections, viral gastroenteritis, and urinary tract infections linked to pre-flight exposures (Berry, 1974). It has been shown that some bacteria are affected by spaceflight and exhibit increased virulence (Wilson et al, 2007, 2008) and antibiotic resistance (Tixador et al, 1985; Moatti et al, 1986; Klaus and Howard, 2006)

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