Whole metagenome profiles of particulates collected from the International Space Station

Abstract

BackgroundThe built environment of the International Space Station (ISS) is a highly specialized space in terms of both physical characteristics and habitation requirements. It is unique with respect to conditions of microgravity, exposure to space radiation, and increased carbon dioxide concentrations. Additionally, astronauts inhabit a large proportion of this environment. The microbial composition of ISS particulates has been reported; however, its functional genomics, which are pertinent due to potential impact of its constituents on human health and operational mission success, are not yet characterized.MethodsThis study examined the whole metagenome of ISS microbes at both species- and gene-level resolution. Air filter and dust samples from the ISS were analyzed and compared to samples collected in a terrestrial cleanroom environment. Furthermore, metagenome mining was carried out to characterize dominant, virulent, and novel microorganisms. The whole genome sequences of select cultivable strains isolated from these samples were extracted from the metagenome and compared.ResultsSpecies-level composition in the ISS was found to be largely dominated by Corynebacterium ihumii GD7, with overall microbial diversity being lower in the ISS relative to the cleanroom samples. When examining detection of microbial genes relevant to human health such as antimicrobial resistance and virulence genes, it was found that a larger number of relevant gene categories were observed in the ISS relative to the cleanroom. Strain-level cross-sample comparisons were made for Corynebacterium, Bacillus, and Aspergillus showing possible distinctions in the dominant strain between samples.ConclusionSpecies-level analyses demonstrated distinct differences between the ISS and cleanroom samples, indicating that the cleanroom population is not necessarily reflective of space habitation environments. The overall population of viable microorganisms and the functional diversity inherent to this unique closed environment are of critical interest with respect to future space habitation. Observations and studies such as these will be important to evaluating the conditions required for long-term health of human occupants in such environments.Electronic supplementary materialThe online version of this article (doi:10.1186/s40168-017-0292-4) contains supplementary material, which is available to authorized users.

Succession and persistence of microbial communities and antimicrobial resistance genes associated with International Space Station environmental surfaces

“…Microbiome monitoring experiments conducted on the ISS were the microbial diversity analyses of the Kibo module [ 32 ], vacuum filter debris [ 33 ], HEPA (High Efficiency Particulate Air) filters [ 34 , 35 ], ISS environmental surfaces [ 36 ], astronaut’s skin mycobiome [ 37 ], and Russian filter debris [ 38 ]. All of these studies were carried out using amplicon-targeted sequencing and were focused on microbial identification only; functional analyses were not performed.…”

The influence of bioregenerative life‐support system dietary structure and lifestyle on the gut microbiota: a 105‐day ground‐based space simulation in Lunar Palace 1

“…Hence, one of the major challenges in manned space exploration is protecting astronauts from microbiota dysbiosis. In recent years, with the development of high‐throughput sequencing technology for complex microbial communities, both host‐derived and environmental microbiome have frequently been studied, either in space stations (Checinska et al ., ; Moissleichinger et al ., ; Mora et al ., ; Be et al ., ) or ground‐based space simulations (Li et al ., ; Mayer et al ., ; Sun et al ., ; Blachowicz et al ., ; Schwendner et al ., ; Turroni et al ., ).…”

“…For example, several microbiota monitoring experiments on the ISS have been launched (i.e., NASA's ‘Microbial Observatory’ project (Venkateswaran et al ., ), JAXA's ‘Microbe’ experiment series (Kazuo et al ., ) and ESA's ARBEX/Extremophiles project (Moissleichinger et al ., ). Mora and Checinska (Mora et al ., ; Be et al ., ) found that specific human skin‐associated microorganisms make a substantial contribution to the ISS microbiome, which is not the case in Earth‐based cleanrooms. During the Mars500 project, despite substantial fluctuation with respect to microbial diversity and abundance throughout the experiment, the location within the facility and the confinement duration were identified as factors significantly shaping the microbial diversity and composition, with the crew representing the main source for microbial dispersal (Schwendner et al ., ).…”

Bioaerosols and Transmission, a Diverse and Growing Community of Practice

“…Finally, the collection of nucleic acid may be leveraged to obtain more sophisticated information than is available by PCR and Sanger sequencing. Metagenomics on environmental samples has been well-described in other spheres and is currently being explored for air samples (54)(55)(56)(57).…”