Cleanrooms and other oligotrophic environments represent unique ecosystems that may expedite microbial speciation. These environments select microorganisms that can survive in nutrient-deficient conditions, potentially giving rise to new species. Understanding the genomes of these unique microorganisms within cleanroom habitats is pivotal for unfolding microbial dark matter, and it holds significant implications for broader applications in controlled terrestrial settings, such as hospital ICUs and surgical theatres. In this regard, we present a comprehensive method leveraging whole-genome sequences and phylogenomics advancements for identifying novel species. Our study has successfully identified six microbial species, including a previously unknown genus, isolated from various spacecraft-associated cleanrooms. Notably, these organisms exhibit many genes associated with virulence, disease, and defence mechanisms.

While exploring clinically relevant microbes in cleanrooms, we focused on Enterobacter bugandensis, a nosocomial BSL-2 pathogen, assessing its survival and adaptation within the extreme conditions of the International Space Station—a hermetically sealed cleanroom. Our investigation uncovered substantial genomic and functional modifications in response to these stresses, underscoring its adaptive capabilities. Additionally, we conducted predictive analyses of metabolic interactions within the cleanroom microbial community, elucidating how these interactions shape community structure and potentially initiate succession processes. Further, I plan to delve into microbial interactions across various cleanroom environments, including hospitals, and compare their community structures with those of other built environments like offices and metro stations. This comparative analysis is essential for unravelling the complexities of microbial survival and adaptation in oligotrophic environments. By contributing to the intersection of public health and cleanroom facilities, our research will provide valuable insights that can guide strategies to mitigate the spread of pathogens and foster a balanced microbiome in diverse environments.