Confined built environments reveal surprising dynamics of their microbiome and resistome

摘要

During space simulation experiments the crew's safety and health are challenged by an extreme confinement from the surrounding hostile environment with specific implications and exposures for the human microbiome. To better understand microbial dynamics in isolated and confined built environments (ICE), front torso skin of 6 crewmembers and frequently interacted surfaces of the furniture in an only 11-meter-in-diameter dome located on the barren slopes of the Mauna-Loa volcano in Hawaii were sampled for a whole year (HI-SEAS IV). The crew was isolated and confined, and hygiene practices were restricted. 181 microbiome samples were analyzed by 16S rRNA gene profiling and qPCR as well as the antimicrobial resistance profile (covering detergents and multidrug resistances e.g. qacE-deltal, intl, bla and tetM). In contrast to our previous study (Schwendner et al. 2017) the microbial diversity increased slightly in the built environment, and even stronger and significantly (P = 8.7 × 10E-19) on the skin of the crew members. Metadata predictions showed high model accuracy (97%) for different sampling categories and the day of sampling (R = 0.8, P = 2.3 × 10E-8). Differential abundance analysis indicated a discriminative pattern for microbial communities at the beginning (Gardnerella) and end (Kocuria, Dermacoccaceae, Brevundimonas) of the isolation period. Important microbial and metabolic features to predict sample states were identified by a supervised learning regressor. Hence, detected microbes faced their exposure to this ICE by many detoxification mechanisms against stress inducing factors from the environment or its maintenance by the crew (e.g. mycothiol and ectoine biosynthesis). Overall the interaction of the skin microbiome and the microbiome of the built environment seems to be highly dynamic especially in this confined habitat. Our attempts to understand the dynamics of the microbiome and resistome could present a first step to manage such built environments more expedient in the future.