Microbiome and Metagenome Analyses of a Closed Habitat During Human Occupation

Abstract

Background: Microbial contamination during the long-term confinements of space exploration present a potential risk for both crew members and spacecraft life support systems. As NASA moves from low Earth orbit further into the solar system, the monitoring of microbial populations within closed human habitation will be necessary to ensure the safety of both the crew and the spacecraft. NASA’s Johnson Space Center has recently developed a microbial swab kit specifically for use during astronaut Extravehicular Activity (EVA). The EVA swab kit is designed to be held in an astronauts’ bulky gloves and or by a robot’s manipulator, and is thus suitable for microbial sample collection in remote and extreme locations. The ability of crew members to successfully use the EVA swab kit to sample the microbial communities of an Analog habitat was tested, resulting in the successful characterization of the microbial communities within this unique habitat. Results: Several samples (floor, dry wall, glass, and metal surfaces) were collected for estimating cultivable, viable, and metabolically active microbial population using the EVA swab kit. The cultivable microbial population ranged from below the detection limit (BDL) to 106 CFU/sample and their identity was characterized using molecular methods. Next-generation sequencing (NGS; both 16S rRNA amplicon and shotgun) were used to characterize the microbial dynamics, community profiles and functional analysis (metabolic, virulence, and antimicrobial resistance). The 16S rRNA amplicon sequencing revealed abundance of viable Actinobacteria (Brevibacterium, Nesternkonia, Mycobacterium, Pseudonocardia and Corynebacterium), Firmicutes (Virgibacillus, Staphylococcus and Oceanobacillus) and Proteobacteria (esp. Acinetobacter) on floor/wall surfaces, while members of Firmicutes (Leuconostocaceae) and Proteobacteria (Enterobacteriaceae) were high on the glass/metal surfaces. Through non-metric multidimensional scaling (NMDS) determined from both 16S rRNA and metagenomic analyses revealed differential microbial speciation between floor/wall surfaces and glass/metal surfaces. Conclusion: This study provides the first assessment of monitoring cultivable and viable microorganisms from a closed spacecraft Analog submerged habitat surfaces. Several statistical treatments suggested that the largest selective pressure on the microbial community structure was the surface type since different kinds of microorganisms were observed in the floor/dry wall surfaces when compared to the metal/glass surfaces, these samples also consistently grouped separately. The metal/glass surfaces had less complex community, lower bio-burden, and more closely resembled the controls. These results indicated that material choice is crucial when building closed habitats, even if they are simply analogs. Despite our results indicating the strong role that surfaces play in selecting for the live/viable microbial communities, our study also shows that there is a shared background community of non-viable microorganisms throughout the Analog habitat. Finally, the microbial ecology of the submerged Analog habitat differs greatly from that of previously studied Analog habitats, while a few species were associated with previously cultivated isolates from the International Space Station and MIR spacecraft.

Microbiomes of air dust collected during the ground-based closed bioregenerative life support experiment "Lunar Palace 365"

“…This may also be the reason for the presence of a large number of unique bacterial OTUs in LP1. Consistent with previous reports [ 79 ], most bacteria in LP1 belong to Proteobacteria, Actinobacteria, Bacteroides, Cyanobacteria, and Firmicutes. Interestingly, compared with other closed environments, the relative abundance of Proteobacteria in the airborne microorganisms is higher in indoor environments with a large number of plants.…”

A Metatranscriptomics Survey of Microbial Diversity on Surfaces Post-Intervention of cleanSURFACES® Technology in an Intensive Care Unit

“…Next-generation sequencing (NGS) technologies have enabled up to billions of DNA fragments to be sequenced in a high-throughput, multiplexed, and parallelized manner. Recently NGS technologies, such as shotgun metagenomics (MG) and metatranscriptomics (MT), have been applied to environmental microbiological testing, which have enabled a comprehensive and less biased approach to pathogen detection ( Ramos et al., 2015 ; Tang et al., 2015 ; Batovska et al., 2019 ; Comar et al., 2019 ; Rampelotto et al., 2019 ; Mohan et al., 2020 ). Comprehensive testing methods like MG and MT randomly sequence DNA and RNA, respectively, from a sample and cast an untargeted net for capturing microbial (prokaryotic and eukaryotic) diversity in complex environments.…”

“…However, it should be noted that 16S rRNA gene amplicon sequencing has several important limitations, including an inability to differentiate between active/inactive cells or viruses, as well as low taxonomic resolution. More recently, a similar study compared 16S rRNA gene amplicon sequencing and shotgun metagenomics, and over twice as many microbial genera were able to be identified through metagenomics ( Mohan et al., 2020 ). Therefore, untargeted methods, such as MG and MT could prove even more valuable in contamination detection in a hospital setting.…”