A microbial survey of the International Space Station (ISS)

Abstract

BackgroundModern 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.ResultsSterile 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.ConclusionsWhile 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.

ANCHOR: a 16S rRNA gene amplicon pipeline for microbial analysis of multiple environmental samples

“…The second most abundant Corynebacterium genus annotated OTU in Lang et al . (Lang et al ., ) was equivalent to ANCHOR OTU C. tuberculostearicum_1 at 100% similarity.…”

“…While challenging within unknown systems, the results are briefly interpreted in an attempt to establish whether they are biologically coherent and, if so, whether they can build upon the previous findings reported by Lang et al . (Lang et al ., ) and deepen our knowledge of this unique environment. A total of 1,132,141 amplicons were assembled from the ISS samples, 553,762 of which were unique.…”

“…Each of these genera included highly abundant OTUs, which could be annotated at species level when the data set was analyzed using ANCHOR, such as Finegoldia magna, Haemophilus parainfluenzae and Akkermansia muciniphila ; although some ANCHOR OTUs were highly ambiguous, such as the most abundant OTU Staphylococcus MS_3, where the sequence was conserved at 100% identity to nine species [Table ; Supplementary file 5; Staphylococcus was also the most abundant genera in Lang et al . (Lang et al ., )]. The additional resolution of ANCHOR analysis also yielded original bacterial species, such as Lawsonella clevelandensis (second most abundant OTU at 4.3% of all amplicons), as well as archaeal species, such as Methanobrevibacter smithii , Methanosphaera stadtmaniae and Nitrosopumilus maritimus .…”

“…The additional resolution of ANCHOR analysis also yielded original bacterial species, such as Lawsonella clevelandensis (second most abundant OTU at 4.3% of all amplicons), as well as archaeal species, such as Methanobrevibacter smithii , Methanosphaera stadtmaniae and Nitrosopumilus maritimus . By again comparing results generated by ANCHOR to the analysis of this data by Lang (Lang et al ., ) using Qiime1, it is possible to decipher that the Corynebacterium (genus) reported as dominating the ISS samples was actually constructed from: L. clevelandensis and Corynebacterium tuberculostearicum , two highly abundant species representing 4.3% and 2.2% of the sequences, and annotated by ANCHOR without ambiguity. The two major Qiime1 Corynebacterium sequences (OTU:495067 and OTU:1012948) corresponded to 4.25% and 2.11% of reads, respectively, and were indeed most similar to L. clevelandensis and C. tuberculostearicum (but at only 98% instead of 100% BLASTn identity NCBI nr/nt due to sequence modification).…”

“…The increasing data set complexity is used to assess the challenges of real‐world systems and test the method's potential for biological discovery. The ISS data set [surface swabs were taken on May 9, 2014 (Lang et al ., )] was deliberately selected as technically nonideal and biologically complex: sampling had no replicated biological comparison design. A design was applied a posteriori , predicated on sampling location with unbalanced replication (destiny module = 10n while harmony module = 4n).…”