Genomic, Functional, and Metabolic Enhancements in Multidrug-Resistant Enterobacter bugandensis Facilitating its Persistence and Succession in the International Space Station

Background:

The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO₂ levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

Detailed scripts and procedures are given on the Wiki page

Our analysis is distributed into three major parts

1. Comparative genomics of Enterobacter bugandensis between ISS and Earth-bound strains to show their genomics and functional distinctiveness
2. Comprehensive analysis of metagenomics data to estimate the abundance of E. bugandensis in the ISS and identify their co-occurring microorganisms
3. Explore the metabolic interactions of the E. bugandensis in the ISS communities

Here we have the overview of our workflow

Results:

Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorize them within the ESKAPE pathogen group, a collection of pathogens recognized for their formidable resistance to antimicrobial treatments. During the two-year Microbial Tracking 1 mission, 12 strains of multidrug resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonization of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

Conclusions:

Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are two-fold. Firstly, they shed light on microbial behavior, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats.

Cite:

Sengupta, P., Muthamilselvi Sivabalan, S. K., Singh, N. K., Raman, K., & Venkateswaran, K. (2023). Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station. bioRxiv. https://doi.org/10.1101/2023.09.05.556398