Microbiome dynamics during the HI-SEAS IV mission, and implications for future crewed missions beyond Earth

Abstract

Background Human health is closely interconnected with its microbiome. Resilient microbiomes in, on and around the human body will be key for safe and successful long-term space travel. However, longitudinal dynamics of microbiomes inside confined built environments are still poorly understood. Herein we used the Hawaii Space Exploration Analog and Simulation IV (HI-SEAS IV) mission, a one year-long isolation study, to investigate microbial transfer between crew and habitat, in order to understand adverse developments which may occur in a future outpost on the Moon or Mars. Results Longitudinal 16S rRNA gene profiles, as well as quantitative observations, revealed significant differences in microbial diversity, abundance and composition between samples of the built environment and its crew. The microbiome composition and diversity associated with abiotic surfaces was found to be rather stable, whereas the microbial skin profiles of individual crewmembers were highly dynamic, resulting in an increased microbiome diversity at the end of the isolation period. The skin microbiome dynamics were especially pronounced by a regular transfer of the indicator species Methanobrevibacter between crewmembers within the first 200 days. Quantitative information was used to track the propagation of antimicrobial resistance in the habitat. Together with functional and phenotypic predictions, quantitative and qualitative data supported the observation of a delayed longitudinal microbial homogenization between crew and habitat surfaces which was mainly caused by a malfunctioning sanitary facility. Conclusions This study highlights main routes of microbial transfer, interaction of the crew and origins of microbial dynamics in an isolated environment. We identify key targets of microbial monitoring, and emphasize the need for defined baselines of microbiome diversity and abundance on surfaces and crew skin. Targeted manipulation to counteract adverse developments of the microbiome could be a highly important strategy to ensure safety during future space endeavors.

The indoor environment - a potential source for intact human-associated anaerobes

“…The fastq data analysis was performed using QIIME2 (Bolyen et al, 2019) as described previously (Mahnert et al, 2020). After quality filtering, the DADA2 algorithm (Callahan et al, 2016) was used to denoise truncated reads and generate amplicon sequence variants (ASVs).…”

Microbial Pathogenicity in Space

“…All necessary security and safety measurements need to be considered beforehand because any occurring mission improvements will have to happen on board, with all the limitations of space vehicles [ 2 ]. Such advances should focus on detection and control of microbes and microbial diversity on astronauts and spacecraft [ 7 ], as well as on monitoring of spacecraft water systems and ensuring the identification and counteract measures of any waterborne microbial contamination [ 3 ]. Linked to both of these aspects, some authors suggest microbiome manipulation as a way to guarantee and improve astronauts’ health [ 7 ].…”

“…Most microorganisms found in the ISS are normally perceived as not relevant nor causing disease; however, with long exposure to microgravity, the astronauts’ immune systems tend to be less responsive and might struggle to fight these microorganisms, which would then become pathogenic [ 3 ]. As an additional factor, the risk of becoming infected with a pathogenic microorganism is increased in confined spacecraft environments and with the close proximity of astronauts [ 7 , 11 , 12 ]. Further risks and restrictions include access to treatment options, drugs, and resources, as well as the ability to perform proper hygiene [ 7 ].…”

“…As an additional factor, the risk of becoming infected with a pathogenic microorganism is increased in confined spacecraft environments and with the close proximity of astronauts [ 7 , 11 , 12 ]. Further risks and restrictions include access to treatment options, drugs, and resources, as well as the ability to perform proper hygiene [ 7 ].…”

“…Another approach to fully understand the existing microbes and their dynamics, inside spacecrafts, on astronauts, and on anything going in or out of the spacecrafts, is the use of molecular biology and sequencing experiments. For this, swabbing of the surfaces and the astronauts’ bodies, over a defined period of time, followed with direct DNA extraction, or microbial isolation and DNA extraction, and sequencing for identification of the microbiomes is the most common method, which is what was done for example by Mahnert et al [ 7 ] and Sielaff et al [ 16 ]. Although frequently neglected, morphological and physiological characterization of the isolates also helps to understand any phenotypic changes after isolation and provides very important insights and material for further investigations.…”