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JPL Researchers Characterize International Space Station Microbiome

NEW YORK (GenomeWeb) – Skin-associated Actinobacteria dominate the microbiome of the International Space Station, according to an analysis performed by a Jet Propulsion Laboratory-led research team.

The team examined dust samples obtained from both the space station and two cleanrooms at JPL where components for spacecraft are assembled. Through a combination of bacterial cultivation, adenosine triphosphate, and propidium monoazide-qPCR assays, the team estimated the viable microbial population, and, using sequencing, gauged the microbial diversity and characterized the microbiomes of the two environments.

As they reported today in Microbiome, the researchers found that skin-associated bacteria like Actinobacteria were more common in the ISS samples as compared to the cleanroom samples.

"By using both traditional and state-of-the-art molecular analysis techniques we can build a clearer picture of the International Space Station's microbial community, helping to spot bacterial agents that may damage equipment or threaten astronaut health, and identify areas in need of more stringent cleaning," senior author Kasthuri Venkateswaran from the California Institute of Technology's JPL said in a statement

Venkateswaran and his colleagues collected particles from one HEPA filter and dust from two vacuum bags from the space station along with three dust samples from vacuum bags from two Earth-bound cleanrooms.

A qPCR-based assay revealed that the ISS HEPA sample had the highest bacterial density than any other sample. But after treatment with propidium monoazide, which eliminates non-viable cells, this difference was no longer noticeable. Some 1.7 percent of ISS HEPA bacteria and 2.7 percent of ISS vacuum dust bacterial were viable, while 4.5 percent of bacteria from one cleanroom, JPL-103, was viable and 66.8 percent of bacteria from the other cleanroom, JPL-SAF, was viable.

Viability estimates as gauged through ATP assays, meanwhile, indicated that the ISS vacuum bag sample contained the highest amount of viable bacteria.

Through their bacterial cultures, the researchers identified 41 bacterial strains, most of which belonged to Firmicutes and a handful to Proteobacteria. They noted that Bacillus was dominant in both ISS samples, though Staphylococcus was only present in the vacuum bag sample.

Both those genera, the researchers added, were absent or underrepresented in the cleanroom samples.

Through pyrosequencing using the Roche-454 FLX-Titanium, Venkateswaran and his colleagues generated some 100,000 bacterial reads greater than 500 basepairs in length. Among the samples treated with PMA to remove non-viable cells, the ISS vacuum sample had the greatest number of reads — just more than 30,000 — while the HEPA filter sample from ISS had the lowest.

Nearly all the viable sequences obtained from the ISS HEPA filter belonged to Corynebacterium, which the researchers pointed out was also present in the ISS vacuum sample. Propionibacterium and Staphylococcus were only present, they noted in the ISS vacuum bag sample.

Sequencing on the Illumina MiSeq further generated some 6.8 million reads. From these reads, the researchers reported that the ISS samples were dominated by Actinobacteria, Bacilli, and Clostridia, while the cleanroom samples had high levels of Alphaproteobacteria and Gammaproteobacteria.

At the family level, the researchers noted that the difference between the space station and JPL samples was pronounced just based on the actinobacterial groups they contained: ISS samples were dominated by Corynebacterium, while JPL samples were dominated by Geodermatophilaceae.

Using pyrosequencing, Venkateswaran and his colleagues also uncovered some 35,000 fungal sequences, most of which belonged to the classes Dothideomycetes, Eurotiomycetes, and Tremellomycetes. They noted that the fungal species richness was location-specific as the dry cleanroom surfaces mostly had Dothideomycetes and Eurotiomycetes, while the ISS samples contained more Eurotiomycetes, Saccharomycetes, and Exobasidiomycetes.

The researchers were unable, they reported, to identify any archaea in their samples, suggesting they are present at low numbers.

Overall, Venkateswaran and his colleagues reported that there is a significant difference in the microbial community profile of ISS and cleanroom microbiomes.

The dominance of the space station samples by Actinobacteria could be due to the presence of the astronauts who live and work there, the researchers said, noting studies of astronauts' skin microbiome would then be warranted.

The number of Actinobacteria in cleanrooms ­— even as up to 50 people may enter a cleanroom versus the six astronauts at ISS — could be kept down by the different gowning procedures needed to enter those facilities, procedures not used on the space station.

The researchers also uncovered a number of bacteria in the ISS samples that are considered opportunistic pathogens, like P. acnes and members of the Corynebacterium genus.

The virulence and effect of these bacteria, the researchers said, needs to be studied to understand their impact on human health in a closed environment.

"The risk of acquiring infection from opportunistic bacterial and fungal pathogens might pose a threat to crewmembers' health and needs to be studied in the future," Venkateswaran and his colleagues said in their paper.