Investigation of Spaceflight Induced Changes to Astronaut Microbiomes

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.

Keywords: astronaut; international space station; metagenomics; microarray; microbiome; spaceflight.

FIGURE 1

Overall experimental and data analysis workflow and sample collection timeline.

FIGURE 2

Genera with an average relative abundance of at least 1% across all body locations from all four astronauts. The bars in each column represent the average relative abundance of that genus across all samples from that body location.

FIGURE 3

The top 12 genera with the highest relative abundance across all astronaut samples pre-, during and post-flight. The body locations are separated into individual columns and each astronaut is represented as a row. The samples in each cell are arranged in chronological order to display the change in the microbiomes over time.

FIGURE 4

The observed species richness and evenness of astronaut saliva samples. The species richness (top row), Shannon index (middle row), and Simpson index (bottom row) are displayed by astronaut (s1 in the first column, s2 in the second column, s3 in the third column, and s4 in the fourth column) and samples are grouped by collection timepoints. The flight status of each sample is indicated by shape (pre-flight are triangles, during-flight are circles, and post-flight are squares).

FIGURE 5

Heatmaps showing the relative abundance of genera identified as differentially abundant in Astronaut 1 (A), Astronaut 3 (B), and Astronaut 4 (C).

FIGURE 6

NMDS plots depicting the Jaccard distance between samples. Ear (A), nostril (B), mouth (C), saliva (D), and skin (E) samples are shown grouped by astronaut (Astronaut 1 or s1, red; s2, green; s3, blue; s4, purple) and flight status (pre, circle; during, square; post, triangle).

FIGURE 7

PCoA plots depicting the Euclidean distance between samples. Ear (A), nostril (B), mouth (C), saliva (D), and skin (E) samples are shown grouping by astronaut (s1, red; s2, green; s3, blue; s4, purple) and flight status (pre, circle; during, square; post triangle).