A microbial survey of the International Space Station (ISS)

Abstract

Background: Modern advances in sequencing technology have enabled the census of microbial members of many natural ecosystems. Recently, attention is increasingly being paid to the microbial residents of human-made, built ecosystems, both private (homes) and public (subways, office buildings, and hospitals). Here, we report results of the characterization of the microbial ecology of a singular built environment, the International Space Station (ISS). This ISS sampling involved the collection and microbial analysis (via 16S rDNA PCR) of 15 surfaces sampled by swabs onboard the ISS. This sampling was a component of Project MERCCURI (Microbial Ecology Research Combining Citizen and University Researchers on ISS). Learning more about the microbial inhabitants of the "buildings" in which we travel through space will take on increasing importance, as plans for human exploration continue, with the possibility of colonization of other planets and moons.

Results: Sterile swabs were used to sample 15 surfaces onboard the ISS. The sites sampled were designed to be analogous to samples collected for (1) the Wildlife of Our Homes project and (2) a study of cell phones and shoes that were concurrently being collected for another component of Project MERCCURI. Sequencing of the 16S rDNA genes amplified from DNA extracted from each swab was used to produce a census of the microbes present on each surface sampled. We compared the microbes found on the ISS swabs to those from both homes on Earth and data from the Human Microbiome Project.

Conclusions: While significantly different from homes on Earth and the Human Microbiome Project samples analyzed here, the microbial community composition on the ISS was more similar to home surfaces than to the human microbiome samples. The ISS surfaces are species-rich with 1,036-4,294 operational taxonomic units (OTUs per sample). There was no discernible biogeography of microbes on the 15 ISS surfaces, although this may be a reflection of the small sample size we were able to obtain.

Keywords: 16S; International space station; Microbial ecology; Microbiology of the built environment; Microbiome.

Figure 1. Relative abundances of the most common bacterial families found on surfaces of the ISS.

Pie chart showing the relative abundances of the most common bacterial families found on the 15 surfaces of the International Space Station. This graph was produced using METAGENassist (Arndt et al., 2012).

Figure 2. Non-metric multidimensional scaling (NMDS) ordination plots of 15 ISS surface samples.

Non-metric multidimensional scaling (NMDS) ordination plots, based on Bray–Curtis (A) or Unweighted Unifrac (B) distances between the samples obtained from the International Space Station. In these plots, points that are closer together have more similar microbial communities. Note, there is a (starboard) crew vent sample that does not cluster with the other ISS samples in (A) and in (B), a second sample (aft lab vent) appears closer to it. This graph was produced using the Phyloseq package (McMurdie & Susan, 2013) in R (R Core Team, 2014).

Figure 3. Most abundant bacterial families found in each of the two “outlier” samples on the ISS.

Bar chart showing the distribution across all samples of the 3 most abun- dant bacterial families found in each of the two samples (starboard crew vent and aft lab vent) that do not cluster with the others in Fig. 2. All six of these families are known to be found in association with human (or animal) gastrointestinal tract.

Figure 4. Non-metric multidimensional scaling (NMDS) ordination plots of ISS surface samples.

Non-metric multidimensional scaling (NMDS) ordination plots, based on Bray–Curtis (A) or Unweighted Unifrac (B) distances between samples obtained from the International Space Station and samples obtained from homes on Earth. In these plots, points that are closer together have more similar microbial communities. We found that the ISS samples and Earth home samples were significantly different from each other, both based on the Bray–Curtis dissimilarity (adonis, R² = 0.0666, P = 0.001) and the Unifrac distance (adonis, R² = 0.04189, P = 0.001). Note, the crew and lab vent samples that are distinct from the other ISS samples Fig. 2, do not cluster with any of the Earth home surfaces. This graph was produced using the Phyloseq package (McMurdie & Susan, 2013) in R (R Core Team, 2014).

Figure 5. NMDS plots showing clustering of ISS, Earth homes, and Human Microbiome Project body sites.

Non-metric multidimensional scaling (NMDS) ordination plots, based on Bray–Curtis (A and C) or Unweighted Unifrac (B and D) distances between samples obtained from the International Space Station, from homes on Earth, and from 13 body site from the Human Microbiome Project. The plots in (A) and (B) show identical data, as do the plots in (C) and (D). The points in (A) vs. (B) and (C) vs. (D) are colored differently as an aid for visualization. In these plots, points that are closer together have more similar microbial communities. The microbial communities associated with the ISS, homes on Earth, and the HMP samples were significantly different from each other (adonis, R² = 0.08, P < 0.001). Note: the crew and lab vent samples that are distinct from the other ISS samples in Fig. 2 are more similar to the human gastrointestinal tract samples from the HMP. This graph was produced using the Phyloseq package (McMurdie & Susan, 2013) in R (R Core Team, 2014).

Figure 6. Comparison of Shannon diversity among the ISS, Earth homes, and HMP body sites.

Shannon diversity, a measure of how many species there are as well as how evenly the counts of individuals are distributed across species is plotted for every sample. There is wide variation among the HMP samples, with the oral (blue) and gastrointestinal (green) samples typically having more diversity than the skin (pink) or airway (coral) samples. Surfaces on the International Space Station have relatively high Shannon diversity, on par with that of the most diverse HMP samples, and the average home sample. This graph was produced using the Phyloseq package (McMurdie & Susan, 2013) in R (R Core Team, 2014).

Figure 7. Proportion of OTUs found in the ISS samples that were closely related (97% sequence similarity) to human pathogens versus the phylogenetic diversity of those samples.

This figure was modified from Fig. 4A of (Kembel et al., 2012). The pink star represents the ISS samples. The plot shows the proportion of OTUs that were closely related (97% sequence similarity) to human pathogens versus the phylogenetic diversity of those samples.