GeneBites

A new study published the largest dataset yet of microbial and chemical presence on the International Space Station, revealing composition differences across physical areas influenced by human activities.

Our living environments on Earth contain all sorts of microbes and ecological interactions. But with the possibility of one day living elsewhere in the universe, what kinds of microbes will we have to interact with in space? Since some microbes have the potential to cause disease while others can benefit human health, scientists are interested in figuring out which types we’ll have to co-exist with off-world. Previous research studies have found that many of the microbes on the International Space Station (ISS) are associated with human skin. These ISS bacteria have unique genetic traits that could potentially help them survive stress and extreme environments. Additionally, studies have also found that the microorganisms that live within and on the bodies of astronauts, otherwise known as their microbiomes, seem to change while at the ISS, and that astronauts in space often suffer immune reactions or dysfunctions, possibly as a result of these changes. In order to better understand the microbial and environmental health risks of living in space, scientists have been working to develop better and easier ways to profile ISS microbes. To attain these microbial profiles, researchers developed a way to sequence their DNA without needing to grow the microbes first, in a process called culture-independent profiling.

Microbes can be identified by variations in a gene called the 16S rRNA gene, which encodes a vital part of the protein-manufacturing ribosome. All bacteria and archaea (another type of microorganism) have this gene, so scientists can learn about the diversity of microbes by sequencing 16S without needing to sequence all the DNA from the microbes. In a recent study, researchers took hundreds of swab samples from different modules of the United States Orbital Segment of the ISS and sequenced the 16S genes in a culture-independent manner. They found that even though the whole ISS has a controlled atmosphere, there were differences in the number of microbe species identified and the types of microbes present between modules. Notably, modules right next to each other sometimes had more distinct microbe profiles than some physically-distant modules.

Instead of proximity determining the types of microbes present, the researchers found that the way the modules were used had a major impact. Notably, the module where food was handled had a high presence of food-associated microbes, and microbes that come from human waste were high in the module with the Waste and Hygiene Compartment. The scientists also compared their findings with public microbial datasets from Earth to try to determine the likely sources of the microbes on the ISS; most of the microbial presence was likely derived from human skin, whereas environmental-associated microbes (e.g. those found in Earth soil or water) were much less prevalent. 

Additionally, when comparing these findings with Earth data, the scientists found that the microbe diversity on the ISS is lower than the diversity in other human-constructed environments, such as homes and hospitals, as well as lower than free-living Earth environments; this low diversity could potentially be related to the immune problems astronauts face.

In addition to identifying microbes, the researchers also analyzed surface chemicals, finding traces originating from plants and food, animal metabolism, environmental microbes, microbes from the digestive tract, and industrial chemicals. The chemical profiles of the compartments differed from each other, and some of the chemicals identified matched the modules’ known human uses. Interestingly, high signals of cleaning product chemicals were associated with a higher measure of microbial diversity based on evolutionary distance.

In order to determine whether the microbes on the ISS carried genes that are relevant for human health, the researchers used a different sequencing technique that surveys genes more broadly than the 16S sequencing. They found genetic evidence of some common viruses that infect humans; previous research has shown that some viruses that stay dormant in humans long-term can reactivate and release virus particles from the host during spaceflight. They also found genes from bacteria that are known to cause disease. When looking at antimicrobial resistance genes in another bacteria species that was detected, the researchers discovered that the samples from the ISS had more diversity in the antimicrobial resistance genes than some sequenced strains from Earth samples. This could be important for scientists to watch out for, since more genetic diversity could mean more potential for sub-populations of microbes to survive antimicrobial treatments, although that was not directly tested in this study.

Altogether, this study provides insights into potential astronaut health concerns associated with life aboard the ISS, from low overall microbe diversity to presence of potential pathogens and more diverse antimicrobial resistance genes. While this study does not directly test the impacts of the sequenced microbes on human health, it does demonstrate that the way humans use the spaces in the ISS impacts the microbes that live there. Furthermore, the genomic and chemical data were put into publicly-available databases, meaning that other researchers can continue to reference the information in exploring additional questions about the ISS environment. For example, scientists could try to see whether the antimicrobial resistance genes found in ISS bacteria have also been associated with clinical outcomes in Earth bacterial infections. Additionally, future studies could investigate whether astronaut microbiomes acquire the higher diversity of antimicrobial resistance genes found in ISS samples, and the corresponding health implications.

Much about life in space remains unknown, but scientists are beginning to learn about the microbial companions that astronauts have when they leave Earth behind. Yet with so much of the universe still unexplored, we have yet to see how much even our closest microbial co-travelers will change and adapt with enough time off-world.

Edited by Saadia Bhatti and Jameson Blount