Low-Shear modeled microgravity alters the Salmonella enterica serovar typhimurium stress response in an RpoS-independent manner

Impact of simulated microgravity on the growth and proteomic profile of Enterobacter cloacae

Previous studies have shown decreased microbial diversity in astronaut gut microbiomes during spaceflight, raising potential health concerns. Enterobacter cloacae, a commensal member of the human gastrointestinal tract microbiota, has the potential to cause opportunistic infections in immunocompromised patients. However, little is known about how E. cloacae cells adapt to extreme environments such as microgravity, and whether this bacterium is of medical concern for astronauts during long-term spaceflight missions, as astronaut immune systems are compromised by microgravity. To this end, E. cloacae growth and proteomic profiles were obtained from high aspect ratio vessel (HARV) cultures grown in the rotary cell culture system (RCCS) in three orientations: low-shear modeled microgravity (LSMMG), normal gravity (NG; oxygenation membrane on bottom), and inverted normal gravity (INV; oxygenation membrane on top). Both NG and INV controls were included to determine if E. cloacae LSMMG and INV HARV cultures overlapped in their growth properties and/or proteomics profiles, as was previously observed for Staphylococcus aureus. Our results revealed significant proteomic changes in E. cloacae that overlapped in LSMMG and INV conditions compared to NG, suggesting that adaptive responses may be driven by both simulated microgravity and orientation of the oxygenation membrane. These findings offer insight into the molecular mechanisms underlying E. cloacae's adaptation to microgravity and its potential health risks for astronauts. This study also underlines the importance of multiple control orientations in ground-based microgravity simulations using the RCCS, guiding future research on microbial behavior in space conditions.IMPORTANCEEnterobacter cloacae can transition from a gut commensal to an opportunistic pathogen in immunocompromised hosts and in closed environments such as hospitals. This danger can be exacerbated by the emergence of multidrug-resistant E. cloacae strains. Astronauts undergo changes in their immune systems during spaceflight that could predispose them to infection and spend extended time in the International Space Station and other closed environments. Therefore, elucidating the impacts of actual spaceflight and simulated microgravity on the biology of E. cloacae and other commensal organisms is vital due to the challenges of antibiotic treatment (such as limited shelf life) during extended spaceflight missions. The findings in this study highlight the importance of using multiple control conditions in ground-based microgravity simulations and lay groundwork for future research into microbial adaptation to space and other extreme environments.

Evaluation of the Salmonella type 3 secretion system (T3SS) as part of a protein production platform for space biology applications

As interest in space exploration and in situ resource utilization grows, the potential to leverage synthetic biology and engineered microorganisms has garnered significant attention. Microorganisms provide a robust and efficient biological chassis to demonstrate the human blueprint for advancing space biology. However, progress toward these applications is hindered by the limited access to space-like environments and a lack of knowledge about how unique environmental factors affect relevant microbial systems. To address these issues, we evaluated the Salmonella Pathogenicity Island 1 (SPI-1) type Ⅲ secretion system (T3SS) as a protein production platform for space applications. Using a NASA-designed microgravity-simulating bioreactor system, we investigated the effects of simulated microgravity on cell growth, stress response, and protein secretion via SPI-1 T3SS. Our results demonstrated increased stress responses in cells grown under simulated microgravity. However, the SPI-1 T3SS maintained its ability to secrete proteins directly into the extracellular space in a single step under simulated microgravity, simplifying downstream purification processes. These findings suggest that the SPI-1 T3SS is a viable candidate for future space biology applications.

Systematic screening of 42 vancomycin-resistant Enterococcus faecium strains for resistance, biofilm, and desiccation in simulated microgravity

Vancomycin-resistant Enterococcus faecium (VRE) presents significant challenges in healthcare, particularly for hospitalized and immunocompromised patients, including astronauts with dysregulated immune function. We investigated 42 clinical E. faecium isolates in simulated microgravity (sim. µg) using a 2-D Clinostat, with standard gravity conditions (1 g) as a control. Isolates were tested against 22 antibiotics and characterized for biofilm formation and desiccation tolerance. Results showed varied responses in minimum inhibitory concentration (MIC) values for seven antibiotics after sim. µg exposure. Additionally, 55% of isolates showed a trend of increased biofilm production, and 59% improved desiccation tolerance. This investigation provides initial insights into E. faecium's changes in response to simulated spaceflight, revealing shifts in antibiotic resistance, biofilm formation, and desiccation tolerance. The observed adaptability emphasizes the need to further understand VRE's resilience to microgravity, which is crucial for preventing infections and ensuring crew health on future long-duration space missions.

Space food production on microbiological safety: Key considerations for the design of Hazard Analysis and Critical Control Points (HACCP) plan

Although diet in space has relied on the sterilized products transported from earth, on-site space food production (e.g., farming, nutritional bioregeneration, bioculture foods, cooking) have been suggested to establish sustainable food supply system. This book chapter describes the key consideration for the design of hazard analysis and critical control points plan optimized for food produced and prepared in outer space. Technical advances in the food production during spaceflight were summarized to categorize the types of on-site space food production. Overall results of previous research regarding microbial monitoring of contaminants onboard the habitat of astronauts (single bacterial isolation and community analysis) and the alteration of physiological characteristics of host-pathogen-food in microgravity were analyzed to suggest information required for hazard analysis. Pathogen control strategies which can be set as critical control points were also designed from raw materials to consumption followed by the waste recycling.

Microbiology of human spaceflight: microbial responses to mechanical forces that impact health and habitat sustainability

SUMMARYUnderstanding the dynamic adaptive plasticity of microorganisms has been advanced by studying their responses to extreme environments. Spaceflight research platforms provide a unique opportunity to study microbial characteristics in new extreme adaptational modes, including sustained exposure to reduced forces of gravity and associated low fluid shear force conditions. Under these conditions, unexpected microbial responses occur, including alterations in virulence, antibiotic and stress resistance, biofilm formation, metabolism, motility, and gene expression, which are not observed using conventional experimental approaches. Here, we review biological and physical mechanisms that regulate microbial responses to spaceflight and spaceflight analog environments from both the microbe and host-microbe perspective that are relevant to human health and habitat sustainability. We highlight instrumentation and technology used in spaceflight microbiology experiments, their limitations, and advances necessary to enable next-generation research. As spaceflight experiments are relatively rare, we discuss ground-based analogs that mimic aspects of microbial responses to reduced gravity in spaceflight, including those that reduce mechanical forces of fluid flow over cell surfaces which also simulate conditions encountered by microorganisms during their terrestrial lifecycles. As spaceflight mission durations increase with traditional astronauts and commercial space programs send civilian crews with underlying health conditions, microorganisms will continue to play increasingly critical roles in health and habitat sustainability, thus defining a new dimension of occupational health. The ability of microorganisms to adapt, survive, and evolve in the spaceflight environment is important for future human space endeavors and provides opportunities for innovative biological and technological advances to benefit life on Earth.

Response of Staphylococcus aureus physiology and Agr quorum sensing to low-shear modeled microgravity

Staphylococcus aureus is commonly isolated from astronauts returning from spaceflight. Previous analysis of omics data from S. aureus low Earth orbit cultures indicated significantly increased expression of the Agr quorum sensing system and its downstream targets in spaceflight samples compared to ground controls. In this current study, the rotary cell culture system (RCCS) was used to investigate the effect of low-shear modeled microgravity (LSMMG) on S. aureus physiology and Agr activity. When cultured in the same growth medium and temperature as the previous spaceflight experiment, S. aureus LSMMG cultures exhibited decreased agr expression and altered growth compared to normal gravity control cultures, which are typically oriented with oxygenation membrane on the bottom of the high aspect rotating vessel (HARV). When S. aureus was grown in an inverted gravity control orientation (oxygenation membrane on top of the HARV), reduced Agr activity was observed relative to both traditional control and LSMMG cultures, signifying that oxygen availability may affect the observed differences in Agr activity. Metabolite assays revealed increased lactate and decreased acetate excretion in both LSMMG and inverted control cultures. Secretomics analysis of LSMMG, control, and inverted control HARV culture supernatants corroborated these results, with inverted and LSMMG cultures exhibiting a decreased abundance of Agr-regulated virulence factors and an increased abundance of proteins expressed in low-oxygen conditions. Collectively, these studies suggest that the orientation of the HARV oxygenation membrane can affect S. aureus physiology and Agr quorum sensing in the RCCS, a variable that should be considered when interpreting data using this ground-based microgravity model.IMPORTANCES. aureus is commonly isolated from astronauts returning from spaceflight and from surfaces within human-inhabited closed environments such as spacecraft. Astronaut health and immune function are significantly altered in spaceflight. Therefore, elucidating the effects of microgravity on S. aureus physiology is critical for assessing its pathogenic potential during long-term human space habitation. These results also highlight the necessity of eliminating potential confounding factors when comparing simulated microgravity model data with actual spaceflight experiments.

Perspectives on the future of host-microbe biology from the Council on Microbial Sciences of the American Society for Microbiology

Host-microbe biology (HMB) stands on the cusp of redefinition, challenging conventional paradigms to instead embrace a more holistic understanding of the microbial sciences. The American Society for Microbiology (ASM) Council on Microbial Sciences hosted a virtual retreat in 2023 to identify the future of the HMB field and innovations needed to advance the microbial sciences. The retreat presentations and discussions collectively emphasized the interconnectedness of microbes and their profound influence on humans, animals, and environmental health, as well as the need to broaden perspectives to fully embrace the complexity of these interactions. To advance HMB research, microbial scientists would benefit from enhancing interdisciplinary and transdisciplinary research to utilize expertise in diverse fields, integrate different disciplines, and promote equity and accessibility within HMB. Data integration will be pivotal in shaping the future of HMB research by bringing together varied scientific perspectives, new and innovative techniques, and 'omics approaches. ASM can empower under-resourced groups with the goal of ensuring that the benefits of cutting-edge research reach every corner of the scientific community. Thus, ASM will be poised to steer HMB toward a future that champions inclusivity, innovation, and accessible scientific progress.

Extremophiles in Space Exploration

In the era of deep space exploration, extremophile research represents a key area of research w.r.t space survival. This review thus delves into the intriguing realm of 'Space and Astro Microbiology', providing insights into microbial survival, resilience, and behavioral adaptations in space-like environments. This discussion encompasses the modified behavior of extremophilic microorganisms, influencing virulence, stress resistance, and gene expression. It then shifts to recent studies on the International Space Station and simulated microgravity, revealing microbial responses that impact drug susceptibility, antibiotic resistance, and its commercial implications. The review then transitions into Astro microbiology, exploring the possibilities of interplanetary transit, lithopanspermia, and terraforming. Debates on life's origin and recent Martian meteorite discoveries are noted. We also discuss Proactive Inoculation Protocols for selecting adaptable microorganisms as terraforming pioneers. The discussion concludes with a note on microbes' role as bioengineers in bioregenerative life support systems, in recycling organic waste for sustainable space travel; and in promoting optimal plant growth to prepare Martian and lunar basalt. This piece emphasizes the transformative impact of microbes on the future of space exploration.

Whole transcriptome analysis highlights nutrient limitation of nitrogen cycle bacteria in simulated microgravity

Regenerative life support systems (RLSS) will play a vital role in achieving self-sufficiency during long-distance space travel. Urine conversion into a liquid nitrate-based fertilizer is a key process in most RLSS. This study describes the effects of simulated microgravity (SMG) on Comamonas testosteroni, Nitrosomonas europaea, Nitrobacter winogradskyi and a tripartite culture of the three, in the context of nitrogen recovery for the Micro-Ecological Life Support System Alternative (MELiSSA). Rotary cell culture systems (RCCS) and random positioning machines (RPM) were used as SMG analogues. The transcriptional responses of the cultures were elucidated. For CO2-producing C. testosteroni and the tripartite culture, a PermaLifeTM PL-70 cell culture bag mounted on an in-house 3D-printed holder was applied to eliminate air bubble formation during SMG cultivation. Gene expression changes indicated that the fluid dynamics in SMG caused nutrient and O2 limitation. Genes involved in urea hydrolysis and nitrification were minimally affected, while denitrification-related gene expression was increased. The findings highlight potential challenges for nitrogen recovery in space.

Incremental increases in physiological fluid shear progressively alter pathogenic phenotypes and gene expression in multidrug resistant Salmonella

The ability of bacteria to sense and respond to mechanical forces has important implications for pathogens during infection, as they experience wide fluid shear fluctuations in the host. However, little is known about how mechanical forces encountered in the infected host drive microbial pathogenesis. Herein, we combined mathematical modeling with hydrodynamic bacterial culture to profile transcriptomic and pathogenesis-related phenotypes of multidrug resistant S. Typhimurium (ST313 D23580) under different fluid shear conditions relevant to its transition from the intestinal tract to the bloodstream. We report that D23580 exhibited incremental changes in transcriptomic profiles that correlated with its pathogenic phenotypes in response to these progressive increases in fluid shear. This is the first demonstration that incremental changes in fluid shear forces alter stress responses and gene expression in any ST313 strain and offers mechanistic insight into how forces encountered by bacteria during infection might impact their disease-causing ability in unexpected ways.

Biofilm reactors for the treatment of used water in space:potential, challenges, and future perspectives

Water is not only essential to sustain life on Earth, but also is a crucial resource for long-duration deep space exploration and habitation. Current systems in space rely on the resupply of water from Earth, however, as missions get longer and move farther away from Earth, resupply will no longer be a sustainable option. Thus, the development of regenerative reclamation water systems through which useable water can be recovered from "waste streams" (i.e., used waters) is sorely needed to further close the loop in space life support systems. This review presents the origin and characteristics of different used waters generated in space and discusses the intrinsic challenges of developing suitable technologies to treat such streams given the unique constrains of space exploration and habitation (e.g., different gravity conditions, size and weight limitations, compatibility with other systems, etc.). In this review, we discuss the potential use of biological systems, particularly biofilms, as possible alternatives or additions to current technologies for water reclamation and waste treatment in space. The fundamentals of biofilm reactors, their advantages and disadvantages, as well as different reactor configurations and their potential for use and challenges to be incorporated in self-sustaining and regenerative life support systems in long-duration space missions are also discussed. Furthermore, we discuss the possibility to recover value-added products (e.g., biomass, nutrients, water) from used waters and the opportunity to recycle and reuse such products as resources in other life support subsystems (e.g., habitation, waste, air, etc.).

Effects of short-term exposure to simulated microgravity on the physiology of Bacillus subtilis and multiomic analysis

In our study, Bacillus subtilis was disposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14 days, while the control group was disposed to the same bioreactors in a normal gravity (NG) environment for 14 days. The B. subtilis strain exposed to the SMG (labeled BSS) showed an enhanced growth ability, increased biofilm formation ability, increased sensitivity to ampicillin sulbactam and cefotaxime, and some metabolic alterations compared with the B. subtilis strain under NG conditions (labeled BSN) and the original strain of B. subtilis (labeled BSO). The differentially expressed proteins (DEPs) associated with an increased growth rate, such as DNA strand exchange activity, oxidoreductase activity, proton-transporting ATP synthase complex, and biosynthetic process, were significantly upregulated in BSS. The enhanced biofilm formation ability may be related with the DEPs of spore germination and protein processing in BSS, and differentially expressed genes involved in protein localization and peptide secretion were also significantly enriched. The results revealed that SMG may increase the level of related functional proteins by upregulating or downregulating affiliated genes to change physiological characteristics and modulate growth ability, biofilm formation ability (epsB, epsC, epsN), antibiotic sensitivity (penP) and metabolism. Our experiment may gives new ideas for the study of space microbiology.

Migration of surface-associated microbial communities in spaceflight habitats

Astronauts are spending longer periods locked up in ships or stations for scientific and exploration spatial missions. The International Space Station (ISS) has been inhabited continuously for more than 20 years and the duration of space stays by crews could lengthen with the objectives of human presence on the moon and Mars. If the environment of these space habitats is designed for the comfort of astronauts, it is also conducive to other forms of life such as embarked microorganisms. The latter, most often associated with surfaces in the form of biofilm, have been implicated in significant degradation of the functionality of pieces of equipment in space habitats. The most recent research suggests that microgravity could increase the persistence, resistance and virulence of pathogenic microorganisms detected in these communities, endangering the health of astronauts and potentially jeopardizing long-duration manned missions. In this review, we describe the mechanisms and dynamics of installation and propagation of these microbial communities associated with surfaces (spatial migration), as well as long-term processes of adaptation and evolution in these extreme environments (phenotypic and genetic migration), with special reference to human health. We also discuss the means of control envisaged to allow a lasting cohabitation between these vibrant microscopic passengers and the astronauts.

Microgravity and evasion of plant innate immunity by human bacterial pathogens

Spaceflight microgravity and modeled-microgravity analogs (MMA) broadly alter gene expression and physiology in both pathogens and plants. Research elucidating plant and bacterial responses to normal gravity or microgravity has shown the involvement of both physiological and molecular mechanisms. Under true and simulated microgravity, plants display differential expression of pathogen-defense genes while human bacterial pathogens exhibit increased virulence, antibiotic resistance, stress tolerance, and reduced LD50 in animal hosts. Human bacterial pathogens including Salmonella enterica and E. coli act as cross-kingdom foodborne pathogens by evading and suppressing the innate immunity of plants for colonization of intracellular spaces. It is unknown if evasion and colonization of plants by human pathogens occurs under microgravity and if there is increased infection capability as demonstrated using animal hosts. Understanding the relationship between microgravity, plant immunity, and human pathogens could prevent potentially deadly outbreaks of foodborne disease during spaceflight. This review will summarize (1) alterations to the virulency of human pathogens under microgravity and MMA, (2) alterations to plant physiology and gene expression under microgravity and MMA, (3) suppression and evasion of plant immunity by human pathogens under normal gravity, (4) studies of plant-microbe interactions under microgravity and MMA. A conclusion suggests future study of interactions between plants and human pathogens under microgravity is beneficial to human safety, and an investment in humanity's long and short-term space travel goals.

Impact of simulated microgravity on bioremoval of heavy-metals by Lactobacillus acidophilus ATCC 4356 from water

There are several reports about the effect of gravity removal on some characteristics of microorganisms due to possible change in surface layer thickness and adherence properties. In this study, bioremoval efficiency of Lactobacillus acidophilus ATCC 4356 from water under simulated microgravity conditions was investigated. Furthermore, pretreatment effects (untreated, NaOH, and heat pretreated) of L. acidophilus ATCC 4356 on heavy metal removal was evaluated on microgravity, as our previous research showed impact of pretreatment on adherence properties of probiotics to environmental metals. The results showed that ability of L. acidophilus for arsenic adsorption enhanced following heat-pretreatment in simulated and normal gravity. Moreover, in both conditions of simulated microgravity and normal gravity NaOH-treated L. acidophilus increased the removal of cadmium and lead. In none of the conditions, pretreatment of lactobacillus affects mercury removal. Evaluation of stability of binding of L. acidophilus-heavy metal was investigated to check irreversibility of complex formation between microorganisms and metals in simulated gastrointestinal conditions. Data showed release of heavy metals from complex in normal gravity. Obtained results of this research show the favorable potential of simulated microgravity condition to increase bioremoval capacity of L. acidophilus for heavy metals.

Role of RpoS in Regulating Stationary Phase Salmonella Typhimurium Pathogenesis-Related Stress Responses under Physiological Low Fluid Shear Force Conditions

The discovery that biomechanical forces regulate microbial virulence was established with the finding that physiological low fluid shear (LFS) forces altered gene expression, stress responses, and virulence of the enteric pathogen Salmonella enterica serovar Typhimurium during the log phase. These log phase LFS-induced phenotypes were independent of the master stress response regulator, RpoS (σ^S). Given the central importance of RpoS in regulating stationary-phase stress responses of S. Typhimurium cultured under conventional shake flask and static conditions, we examined its role in stationary-phase cultures grown under physiological LFS. We constructed an isogenic rpoS mutant derivative of wild-type S. Typhimurium and compared the ability of these strains to survive in vitro pathogenesis-related stresses that mimic those encountered in the infected host and environment. We also compared the ability of these strains to colonize (adhere, invade, and survive within) human intestinal epithelial cell cultures. Unexpectedly, LFS-induced resistance of stationary-phase S. Typhimurium cultures to acid and bile salts stresses did not rely on RpoS. Likewise, RpoS was dispensable for stationary-phase LFS cultures to adhere to and survive within intestinal epithelial cells. In contrast, the resistance of these cultures to challenges of oxidative and thermal stresses, and their invasion into intestinal epithelial cells was influenced by RpoS. These findings expand our mechanistic understanding of how physiological fluid shear forces modulate stationary-phase S. Typhimurium physiology in unexpected ways and provide clues into microbial mechanobiology and nuances of Salmonella responses to microenvironmental niches in the infected host.

IMPORTANCE Bacterial pathogens respond dynamically to a variety of stresses in the infected host, including physical forces of fluid flow (fluid shear) across their surfaces. While pathogens experience wide fluctuations in fluid shear during infection, little is known about how these forces regulate microbial pathogenesis. This is especially important for stationary-phase bacterial growth, which is a critical period to understand microbial resistance, survival, and infection potential, and is regulated in many bacteria by the general stationary-phase stress response protein RpoS. Here, we showed that, unlike conventional culture conditions, several stationary-phase Salmonella pathogenic stress responses were not impacted by RpoS when bacteria were cultured under fluid shear conditions relevant to those encountered in the intestine of the infected host. These findings offer new insight into how physiological fluid shear forces encountered by Salmonella during infection might impact pathogenic responses in unexpected ways that are relevant to their disease-causing ability.

"A designer diet layout for astronauts using a microbiome mediated approach."

Astronauts undergo space travel to bring scientific information to benefit humanity under various missions of space agencies such as NASA, European Space Agency, Indian Space Research Organization etc. During space missions, they encounter several stressors namely microgravity, fluid shifts, cosmic radiation, sleep deprivation and alteration in the circadian rhythm perturbing the quality of sleep. In addition, confined spaces makes pathogen interaction more likely if a pathobiont gets introduced into spacecraft. Microbiota is the first line оf resistаnсe tо vаriоus disorders and diseаses. It direсtly influenсes the biосhemiсаl, рhysiоlоgiсаl, аnd immunоlоgiсаl раthwаys. 'Gut microbiota' is essential for maintenance of healthy gut barrier functions. 'Dysbiosis' refers to perturbation of microbiota which is correlated with several metabolic and psychological disorders. Microbial metabolites are implicated in maintenance of human health. Investigations conducted on astronauts in international space missions and on analog terrestrial models have indicated a 'dysbiosis' of the gut microbiota associated with spaceflights. 'Dysbiosis' of the gut microbiome observed in astronauts has been implicated in immune dysregulation and a probiotic enriched diet is proposed to restore immune homeostasis. This article not just summarizes the state of art research on dysbiosis of the gut microbiome of astronauts, but also a diet mediated correction plan to restore their health especially during long term space missions. A characterization of microbial metabolites of the gut to enable administration of astronaut specific probiotic, postbiotic or synbiotic to alleviate space associated dysbiosis is proposed. It is also recommended that astronauts maintain a balanced nutritious diet throughout life to promote a resilient microbiota that is not perturbed by space missions. Further, a bioregenerative life support system wherein a probiotic may be produced in space station is proposed.

Spaceflight Analogue Culture Enhances the Host-Pathogen Interaction Between Salmonella and a 3-D Biomimetic Intestinal Co-Culture Model

Physical forces associated with spaceflight and spaceflight analogue culture regulate a wide range of physiological responses by both bacterial and mammalian cells that can impact infection. However, our mechanistic understanding of how these environments regulate host-pathogen interactions in humans is poorly understood. Using a spaceflight analogue low fluid shear culture system, we investigated the effect of Low Shear Modeled Microgravity (LSMMG) culture on the colonization of Salmonella Typhimurium in a 3-D biomimetic model of human colonic epithelium containing macrophages. RNA-seq profiling of stationary phase wild type and Δhfq mutant bacteria alone indicated that LSMMG culture induced global changes in gene expression in both strains and that the RNA binding protein Hfq played a significant role in regulating the transcriptional response of the pathogen to LSMMG culture. However, a core set of genes important for adhesion, invasion, and motility were commonly induced in both strains. LSMMG culture enhanced the colonization (adherence, invasion and intracellular survival) of Salmonella in this advanced model of intestinal epithelium using a mechanism that was independent of Hfq. Although S. Typhimurium Δhfq mutants are normally defective for invasion when grown as conventional shaking cultures, LSMMG conditions unexpectedly enabled high levels of colonization by an isogenic Δhfq mutant. In response to infection with either the wild type or mutant, host cells upregulated transcripts involved in inflammation, tissue remodeling, and wound healing during intracellular survival. Interestingly, infection by the Δhfq mutant led to fewer transcriptional differences between LSMMG- and control-infected host cells relative to infection with the wild type strain. This is the first study to investigate the effect of LSMMG culture on the interaction between S. Typhimurium and a 3-D model of human intestinal tissue. These findings advance our understanding of how physical forces can impact the early stages of human enteric salmonellosis.

The rising dominance of microbiology: what to expect in the next 15 years?

What microbiology beholds after a decade and a half in the future requires a vision based on the facts and ongoing trends in research and technological advancements. While the latter, assisted by microbial dark matter, presents a greater potential of creating an upsurge in in-situ and ex-situ rapid microbial detection techniques, this anticipated change will also set forth a revolution in microbial cultivation and diversity analyses. The availability of a microbial genetic toolbox at the expanse will help complement the current understanding of the microbiome and assist in real-time monitoring of the dynamics for detecting the health status of the host with utmost precision. Alongside, in light of the emerging infectious diseases, antimicrobial resistance (AMR) and social demands for safer and better health care alternatives, microbiology laboratories are prospected to drift in terms of the volume and nature of research and outcomes. With today's microbiological lens, one can predict with certainty that in the years to come, microbes will play a significant role in therapeutic treatment and the designing of novel diagnostic techniques. Another area where the scope of microbial application seems to be promising is the use of novel probiotics as a method to offer health benefits whilst promoting metabolic outputs specific for microbiome replenishment. Nonetheless, the evolution of extraterrestrial microbes or the adaptation of earth microbes as extraterrestrial residents are also yet another prominent microbial event one may witness in the upcoming years. But like the two sides of the coin, there is also an urgent need to dampen the bloom of urbanization, overpopulation and global trade and adopting sustainable approaches to control the recurrence of epidemics and pandemics.

Effects of Simulated Microgravity on the Physiology of Stenotrophomonas maltophilia and Multiomic Analysis

Many studies have shown that the space environment plays a pivotal role in changing the characteristics of conditional pathogens, especially their pathogenicity and virulence. However, Stenotrophomonas maltophilia, a type of conditional pathogen that has shown to a gradual increase in clinical morbidity in recent years, has rarely been reported for its impact in space. In this study, S. maltophilia was exposed to a simulated microgravity (SMG) environment in high-aspect ratio rotating-wall vessel bioreactors for 14days, while the control group was exposed to the same bioreactors in a normal gravity (NG) environment. Then, combined phenotypic, genomic, transcriptomic, and proteomic analyses were conducted to compare the influence of the SMG and NG on S. maltophilia. The results showed that S. maltophilia in simulated microgravity displayed an increased growth rate, enhanced biofilm formation ability, increased swimming motility, and metabolic alterations compared with those of S. maltophilia in normal gravity and the original strain of S. maltophilia. Clusters of Orthologous Groups (COG) annotation analysis indicated that the increased growth rate might be related to the upregulation of differentially expressed genes (DEGs) involved in energy metabolism and conversion, secondary metabolite biosynthesis, transport and catabolism, intracellular trafficking, secretion, and vesicular transport. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that the increased motility might be associated the upregulation of differentially expressed proteins (DEPs) involved in locomotion, localization, biological adhesion, and binding, in accordance with the upregulated DEGs in cell motility according to COG classification, including pilP, pilM, flgE, flgG, and ronN. Additionally, the increased biofilm formation ability might be associated with the upregulation of DEPs involved in biofilm formation, the bacterial secretion system, biological adhesion, and cell adhesion, which were shown to be regulated by the differentially expressed genes (chpB, chpC, rpoN, pilA, pilG, pilH, and pilJ) through the integration of transcriptomic and proteomic analyses. These results suggested that simulated microgravity might increase the level of corresponding functional proteins by upregulating related genes to alter physiological characteristics and modulate growth rate, motility, biofilm formation, and metabolism. In conclusion, this study is the first general analysis of the phenotypic, genomic, transcriptomic, and proteomic changes in S. maltophilia under simulated microgravity and provides some suggestions for future studies of space microbiology.

Advances in space microbiology

Microbial research in space is being conducted for almost 50 years now. The closed system of the International Space Station (ISS) has acted as a microbial observatory for the past 10 years, conducting research on adaptation and survivability of microorganisms exposed to space conditions. This adaptation can be either beneficial or detrimental to crew members and spacecraft. Therefore, it becomes crucial to identify the impact of two primary stress conditions, namely, radiation and microgravity, on microbial life aboard the ISS. Elucidating the mechanistic basis of microbial adaptation to space conditions aids in the development of countermeasures against their potentially detrimental effects and allows us to harness their biotechnologically important properties. Several microbial processes have been studied, either in spaceflight or using devices that can simulate space conditions. However, at present, research is limited to only a few microorganisms, and extensive research on biotechnologically important microorganisms is required to make long-term space missions self-sustainable.

Evaluating the effect of spaceflight on the host-pathogen interaction between human intestinal epithelial cells and Salmonella Typhimurium

Spaceflight uniquely alters the physiology of both human cells and microbial pathogens, stimulating cellular and molecular changes directly relevant to infectious disease. However, the influence of this environment on host-pathogen interactions remains poorly understood. Here we report our results from the STL-IMMUNE study flown aboard Space Shuttle mission STS-131, which investigated multi-omic responses (transcriptomic, proteomic) of human intestinal epithelial cells to infection with Salmonella Typhimurium when both host and pathogen were simultaneously exposed to spaceflight. To our knowledge, this was the first in-flight infection and dual RNA-seq analysis using human cells.

Modeled microgravity alters lipopolysaccharide and outer membrane vesicle production of the beneficial symbiont Vibrio fischeri

Reduced gravity, or microgravity, can have a pronounced impact on the physiology of animals, but the effects on their associated microbiomes are not well understood. Here, the impact of modeled microgravity on the shedding of Gram-negative lipopolysaccharides (LPS) by the symbiotic bacterium Vibrio fischeri was examined using high-aspect ratio vessels. LPS from V. fischeri is known to induce developmental apoptosis within its symbiotic tissues, which is accelerated under modeled microgravity conditions. In this study, we provide evidence that exposure to modeled microgravity increases the amount of LPS released by the bacterial symbiont in vitro. The higher rates of shedding under modeled microgravity conditions are associated with increased production of outer-membrane vesicles (OMV), which has been previously correlated to flagellar motility. Mutants of V. fischeri defective in the production and rotation of their flagella show significant decreases in LPS shedding in all treatments, but levels of LPS are higher under modeled microgravity despite loss of motility. Modeled microgravity also appears to affect the outer-membrane integrity of V. fischeri, as cells incubated under modeled microgravity conditions are more susceptible to cell-membrane-disrupting agents. These results suggest that, like their animal hosts, the physiology of symbiotic microbes can be altered under microgravity-like conditions, which may have important implications for host health during spaceflight.

Immunity in Space: Prokaryote Adaptations and Immune Response in Microgravity

Immune dysfunction has long been reported by medical professionals regarding astronauts suffering from opportunistic infections both during their time in space and a short period afterwards once back on Earth. Various species of prokaryotes onboard these space missions or cultured in a microgravity analogue exhibit increased virulence, enhanced formation of biofilms, and in some cases develop specific resistance for specific antibiotics. This poses a substantial health hazard to the astronauts confined in constant proximity to any present bacterial pathogens on long space missions with a finite number of resources including antibiotics. Furthermore, some bacteria cultured in microgravity develop phenotypes not seen in Earth gravity conditions, providing novel insights into bacterial evolution and avenues for research. Immune dysfunction caused by exposure to microgravity may increase the chance of bacterial infection. Immune cell stimulation, toll-like receptors and pathogen-associated molecular patterns can all be altered in microgravity and affect immunological crosstalk and response. Production of interleukins and other cytokines can also be altered leading to immune dysfunction when responding to bacterial infection. Stem cell differentiation and immune cell activation and proliferation can also be impaired and altered by the microgravity environment once more adding to immune dysfunction in microgravity. This review elaborates on and contextualises these findings relating to how bacteria can adapt to microgravity and how the immune system subsequently responds to infection.

Exploration of space to achieve scientific breakthroughs

Living organisms adapt to changing environments using their amazing flexibility to remodel themselves by a process called evolution. Environmental stress causes selective pressure and is associated with genetic and phenotypic shifts for better modifications, maintenance, and functioning of organismal systems. The natural evolution process can be used in complement to rational strain engineering for the development of desired traits or phenotypes as well as for the production of novel biomaterials through the imposition of one or more selective pressures. Space provides a unique environment of stressors (e.g., weightlessness and high radiation) that organisms have never experienced on Earth. Cells in the outer space reorganize and develop or activate a range of molecular responses that lead to changes in cellular properties. Exposure of cells to the outer space will lead to the development of novel variants more efficiently than on Earth. For instance, natural crop varieties can be generated with higher nutrition value, yield, and improved features, such as resistance against high and low temperatures, salt stress, and microbial and pest attacks. The review summarizes the literature on the parameters of outer space that affect the growth and behavior of cells and organisms as well as complex colloidal systems. We illustrate an understanding of gravity-related basic biological mechanisms and enlighten the possibility to explore the outer space environment for application-oriented aspects. This will stimulate biological research in the pursuit of innovative approaches for the future of agriculture and health on Earth.

Transcriptional Profiling of the Probiotic Escherichia coli Nissle 1917 Strain under Simulated Microgravity

Long-term space missions affect the gut microbiome of astronauts, especially the viability of some pathogens. Probiotics may be an effective solution for the management of gut microbiomes, but there is a lack of studies regarding the physiology of probiotics in microgravity. Here, we investigated the effects of microgravity on the probiotic Escherichia coli Nissle 1917 (EcN) by comparing transcriptomic data during exponential and stationary growth phases under simulated microgravity and normal gravity. Microgravity conditions affected several physiological features of EcN, including its growth profile, biofilm formation, stress responses, metal ion transport/utilization, and response to carbon starvation. We found that some changes, such as decreased adhesion ability and acid resistance, may be disadvantageous to EcN relative to gut pathogens under microgravity, indicating the need to develop probiotics optimized for space flight.

Omics Analysis Reveals the Mechanism of Enhanced Recombinant Protein Production Under Simulated Microgravity

Simulated microgravity (SMG) is regarded as a suitable environment to produce recombinant proteins. This study showed that β-glucuronidase expressing Escherichia coli had higher productivity of recombinant protein and higher plasmid copy number under SMG compared with the normal gravity condition. The cellular changes were analyzed at both transcriptomic and proteomic levels. The upregulation of a group of ribosome/RNA polymerase genes and a cluster of genes involving energy metabolism at transcriptomic level stood out for improved production of recombinant protein under SMG. The protein folding modulators such as chaperones were upregulated at proteomic level, which could be a result of the increased activity of protein synthesis and can help recombinant protein production. Protein export was also strengthened, which was revealed at both transcriptomic and proteomic levels. The results demonstrated that SMG is a favorable environment for recombinant protein production arousing the upregulation of protein synthesis, protein folding, and protein export.

Spaceflight and simulated microgravity conditions increase virulence of Serratia marcescens in the Drosophila melanogaster infection model

While it has been shown that astronauts suffer immune disorders after spaceflight, the underlying causes are still poorly understood and there are many variables to consider when investigating the immune system in a complex environment. Additionally, there is growing evidence that suggests that not only is the immune system being altered, but the pathogens that infect the host are significantly influenced by spaceflight and ground-based spaceflight conditions. In this study, we demonstrate that Serratia marcescens (strain Db11) was significantly more lethal to Drosophila melanogaster after growth on the International Space Station than ground-based controls, but the increased virulence phenotype of S. marcescens did not persist after the bacterial cultures were passaged on the ground. Increased virulence was also observed in bacteria that were grown in simulated microgravity conditions on the ground using the rotating wall vessel. Increased virulence of the space-flown bacteria was similar in magnitude between wild-type flies and those that were mutants for the well-characterized immune pathways Imd and Toll, suggesting that changes to the host immune system after infection are likely not a major factor contributing towards increased susceptibility of ground-reared flies infected with space-flown bacteria. Characterization of the bacteria shows that at later timepoints spaceflight bacteria grew at a greater rate than ground controls in vitro, and in the host. These results suggest complex physiological changes occurring in pathogenic bacteria in space environments, and there may be novel mechanisms mediating these physiological effects that need to be characterized.

EcAMSat spaceflight measurements of the role of σs in antibiotic resistance of stationary phase Escherichia coli in microgravity

We report the results of the EcAMSat (Escherichia coli Antimicrobial Satellite) autonomous space flight experiment, investigating the role of σs in the development of antibiotic resistance in uropathogenic E. coli (UPEC) in microgravity (µ-g). The presence of σs, encoded by the rpoS gene, has been shown to increase antibiotic resistance in Earth gravity, but it was unknown if this effect occurs in µ-g. Two strains, wildtype (WT) UPEC and its isogenic ΔrpoS mutant, were grown to stationary phase aboard EcAMSat, an 11-kg small satellite, and in a parallel ground-based control experiment; cell growth rates for the two strains were found to be unaltered by µ-g. After starvation for over 24 h, stationary-phase cells were incubated with three doses of gentamicin (Gm), a common treatment for urinary tract infections (which have been reported in astronauts). Cellular metabolic activity was measured optically using the redox-based indicator alamarBlue (aB): both strains exhibited slower metabolism in µ-g, consistent with results from previous smallsat missions. The results also showed that µ-g did not enhance UPEC resistance to Gm; in fact, both strains were more susceptible to Gm in µ-g. It was also found, via a second ground-control experiment, that multi-week storage in the payload hardware stressed the cells, potentially obscuring small differential effects of the antibiotic between WT and mutant and/or between µ-g and ground. Overall, results showed that the ∆rpoS mutant was 34-37% less metabolically active than the WT for four different sets of conditions: ground without Gm, ground with Gm; µ-g without Gm, µ-g with Gm. We conclude therefore that the rpoS gene and its downstream products are important therapeutic targets for treating bacterial infections in space, much as they are on the ground.

Modulatory effect of low-shear modeled microgravity on stress resistance, membrane lipid composition, virulence, and relevant gene expression in the food-borne pathogen Listeria monocytogenes

The present study investigated the influence of low-shear modeled microgravity (LSMMG) conditions on Listeria monocytogenes stress response (heat, cold, and acid), membrane fatty acid composition, and virulence potential as well as stress-/virulence-associated gene expression. The results showed that LSMMG-cultivated cells had lower survival rate and lower D-values under heat and acid stress conditions compared to cells grown under normal gravity (NG). Interestingly, the cold resistance was elevated in cells cultivated under LSMMG conditions when compared to NG conditions. A higher amount of anteiso-branched chain fatty acids and lower ratio of iso/anteiso were observed in LSMMG cultured cells, which would contribute to increased membrane fluidity. Under LSMMG conditions, upregulated expression of cold stress-related genes (cspA, cspB, and cspD) was noticed but no change in expression was observed for heat (dnaK, groES, clpC, clpP, and clpE) and acid stress-related genes (sigB). The LSMMG-grown cells showed inferior virulence capacity in terms of infection, cell cycle arrest, and apoptosis induction in Caco-2 cells compared to those grown under NG conditions. Approximately 3.65, 2.13, 4.02, and 2.65-fold downregulation of prfA, hly, inlA, and bsh genes, respectively, in LSMMG-cultured cells might be the reason for reduced virulence. In conclusion, these findings suggest that growth under LSMMG conditions stimulates alterations in L. monocytogenes stress/virulence response, perhaps due to changes in lipid composition and related genes expression.

Transcriptional profiling of the mutualistic bacterium Vibrio fischeri and an hfq mutant under modeled microgravity

For long-duration space missions, it is critical to maintain health-associated homeostasis between astronauts and their microbiome. To achieve this goal it is important to more fully understand the host–symbiont relationship under the physiological stress conditions of spaceflight. To address this issue we examined the impact of a spaceflight analog, low-shear-modeled microgravity (LSMMG), on the transcriptome of the mutualistic bacterium Vibrio fischeri. Cultures of V. fischeri and a mutant defective in the global regulator Hfq (∆hfq) were exposed to either LSMMG or gravity conditions for 12 h (exponential growth) and 24 h (stationary phase growth). Comparative transcriptomic analysis revealed few to no significant differentially expressed genes between gravity and the LSMMG conditions in the wild type or mutant V. fischeri at exponential or stationary phase. There was, however, a pronounced change in transcriptomic profiles during the transition between exponential and stationary phase growth in both V. fischeri cultures including an overall decrease in gene expression associated with translational activity and an increase in stress response. There were also several upregulated stress genes specific to the LSMMG condition during the transition to stationary phase growth. The ∆hfq mutants exhibited a distinctive transcriptome profile with a significant increase in transcripts associated with flagellar synthesis and transcriptional regulators under LSMMG conditions compared to gravity controls. These results indicate the loss of Hfq significantly influences gene expression under LSMMG conditions in a bacterial symbiont. Together, these results improve our understanding of the mechanisms by which microgravity alters the physiology of beneficial host-associated microbes.

Insight into Pseudomonas aeruginosa pyocyanin production under low-shear modeled microgravity

Long-term space flight impairs the immune system of astronauts, rendering them vulnerable to opportunistic infections. Pseudomonas aeruginosa causes opportunistic infections, particularly in individuals with a compromised immune system; it can be a major health hazard for astronauts during space flight missions. Hence, the production of the most abundant redox active virulence factor, pyocyanin by P. aeruginosa, was assessed under low-shear modeled microgravity (LSMMG) conditions, simulated using a high aspect ratio vessel. Moreover, we evaluated changes in the expression of genes involved in pyocyanin biosynthesis and genes involved in the MexGHI-OpmD operon quorum sensing. Extracellular DNA and H₂O₂ production were measured, and their correlation with pyocyanin production was examined. Interestingly, the pyocyanin quantity was 2.58-fold lower in the LSMMG conditions compared to the normal gravity. LSMMG caused downregulation of the genes associated with pyocyanin biosynthesis. Interestingly, extracellular DNA and H₂O₂ release were significantly high in the normal gravity environment. Scanning electron microscopy revealed aggregation and elongated cells under LSMMG. Taken together, these findings suggest that LSMMG did not induce pyocyanin secretion in P. aeruginosa.

Modeling Host-Pathogen Interactions in the Context of the Microenvironment: Three-Dimensional Cell Culture Comes of Age

Tissues and organs provide the structural and biochemical landscapes upon which microbial pathogens and commensals function to regulate health and disease. While flat two-dimensional (2-D) monolayers composed of a single cell type have provided important insight into understanding host-pathogen interactions and infectious disease mechanisms, these reductionist models lack many essential features present in the native host microenvironment that are known to regulate infection, including three-dimensional (3-D) architecture, multicellular complexity, commensal microbiota, gas exchange and nutrient gradients, and physiologically relevant biomechanical forces (e.g., fluid shear, stretch, compression). A major challenge in tissue engineering for infectious disease research is recreating this dynamic 3-D microenvironment (biological, chemical, and physical/mechanical) to more accurately model the initiation and progression of host-pathogen interactions in the laboratory. Here we review selected 3-D models of human intestinal mucosa, which represent a major portal of entry for infectious pathogens and an important niche for commensal microbiota. We highlight seminal studies that have used these models to interrogate host-pathogen interactions and infectious disease mechanisms, and we present this literature in the appropriate historical context. Models discussed include 3-D organotypic cultures engineered in the rotating wall vessel (RWV) bioreactor, extracellular matrix (ECM)-embedded/organoid models, and organ-on-a-chip (OAC) models. Collectively, these technologies provide a more physiologically relevant and predictive framework for investigating infectious disease mechanisms and antimicrobial therapies at the intersection of the host, microbe, and their local microenvironments.

Simulated microgravity triggers characteristic morphology and stress response in Saccharomyces cerevisiae

Reduction of gravity results in changes in gene expression and morphology in the budding yeast Saccharomyces cerevisiae. We studied the genes responsible for the morphological changes induced by simulated microgravity (SMG) using the yeast morphology data. We comprehensively captured the features of the morphological changes in yeast cells cultured in SMG with CalMorph, a high-throughput image-processing system. Statistical analysis revealed that 95 of 501 morphological traits were significantly affected, which included changes in bud direction, the ratio of daughter to mother cell size, the random daughter cell shape, the large mother cell size, bright nuclei in the M phase, and the decrease in angle between two nuclei. We identified downregulated genes that impacted the morphological changes in conditions of SMG by focusing on each of the morphological features individually. Gene Ontology (GO)-enrichment analysis indicated that morphological changes under conditions of SMG were caused by cooperative downregulation of 103 genes annotated to six GO terms, which included cytoplasmic ribonucleoprotein granule, RNA elongation, mitotic cell cycle phase transition, nucleocytoplasmic transport, protein-DNA complex subunit organization, and RNA localization. P-body formation was also promoted under conditions of SMG. These results suggest that cooperative downregulation of multiple genes occurs in conditions of SMG.

Cytoskeleton structure and total methylation of mouse cardiac and lung tissue during space flight

The purpose of this work was to evaluate the protein and mRNA expression levels of multiple cytoskeletal proteins in the cardiac and lung tissue of mice that were euthanized onboard the United States Orbital Segment of the International Space Station 37 days after the start of the SpaceX-4 mission (September 2014, USA). The results showed no changes in the cytoskeletal protein content in the cardiac and lung tissue of the mice, but there were significant changes in the mRNA expression levels of the associated genes, which may be due to an increase in total genome methylation. The mRNA expression levels of DNA methylases, the cytosine demethylases Tet1 and Tet3, histone acetylase and histone deacetylase did not change, and the mRNA expression level of cytosine demethylase Tet2 was significantly decreased.

Effects of spaceflight and simulated microgravity on microbial growth and secondary metabolism

Spaceflight and ground-based microgravity analog experiments have suggested that microgravity can affect microbial growth and metabolism. Although the effects of microgravity and its analogs on microorganisms have been studied for more than 50 years, plausible conflicting and diverse results have frequently been reported in different experiments, especially regarding microbial growth and secondary metabolism. Until now, only the responses of a few typical microbes to microgravity have been investigated; systematic studies of the genetic and phenotypic responses of these microorganisms to microgravity in space are still insufficient due to technological and logistical hurdles. The use of different test strains and secondary metabolites in these studies appears to have caused diverse and conflicting results. Moreover, subtle changes in the extracellular microenvironments around microbial cells play a key role in the diverse responses of microbial growth and secondary metabolisms. Therefore, "indirect" effects represent a reasonable pathway to explain the occurrence of these phenomena in microorganisms. This review summarizes current knowledge on the changes in microbial growth and secondary metabolism in response to spaceflight and its analogs and discusses the diverse and conflicting results. In addition, recommendations are given for future studies on the effects of microgravity in space on microbial growth and secondary metabolism.

Spaceflight Modifies Escherichia coli Gene Expression in Response to Antibiotic Exposure and Reveals Role of Oxidative Stress Response

Bacteria grown in space experiments under microgravity conditions have been found to undergo unique physiological responses, ranging from modified cell morphology and growth dynamics to a putative increased tolerance to antibiotics. A common theory for this behavior is the loss of gravity-driven convection processes in the orbital environment, resulting in both reduction of extracellular nutrient availability and the accumulation of bacterial byproducts near the cell. To further characterize the responses, this study investigated the transcriptomic response of Escherichia coli to both microgravity and antibiotic concentration. E. coli was grown aboard International Space Station in the presence of increasing concentrations of the antibiotic gentamicin with identical ground controls conducted on Earth. Here we show that within 49 h of being cultured, E. coli adapted to grow at higher antibiotic concentrations in space compared to Earth, and demonstrated consistent changes in expression of 63 genes in response to an increase in drug concentration in both environments, including specific responses related to oxidative stress and starvation response. Additionally, we find 50 stress-response genes upregulated in response to the microgravity when compared directly to the equivalent concentration in the ground control. We conclude that the increased antibiotic tolerance in microgravity may be attributed not only to diminished transport processes, but also to a resultant antibiotic cross-resistance response conferred by an overlapping effect of stress response genes. Our data suggest that direct stresses of nutrient starvation and acid-shock conveyed by the microgravity environment can incidentally upregulate stress response pathways related to antibiotic stress and in doing so contribute to the increased antibiotic stress tolerance observed for bacteria in space experiments. These results provide insights into the ability of bacteria to adapt under extreme stress conditions and potential strategies to prevent antimicrobial-resistance in space and on Earth.

Payload hardware and experimental protocol development to enable future testing of the effect of space microgravity on the resistance to gentamicin of uropathogenic Escherichia coli and its σs-deficient mutant

Human immune response is compromised and bacteria can become more antibiotic resistant in space microgravity (MG). We report that under low-shear modeled microgravity (LSMMG), stationary-phase uropathogenic Escherichia coli (UPEC) become more resistant to gentamicin (Gm), and that this increase is dependent on the presence of σs (a transcription regulator encoded by the rpoS gene). UPEC causes urinary tract infections (UTIs), reported to afflict astronauts; Gm is a standard treatment, so these findings could impact astronaut health. Because LSMMG findings can differ from MG, we report preparations to examine UPEC's Gm sensitivity during spaceflight using the E. coli Anti-Microbial Satellite (EcAMSat) as a free-flying "nanosatellite" in low Earth orbit. Within EcAMSat's payload, a 48-microwell fluidic card contains and supports study of bacterial cultures at constant temperature; optical absorbance changes in cell suspensions are made at three wavelengths for each microwell and a fluid-delivery system provides growth medium and predefined Gm concentrations. Performance characterization is reported here for spaceflight prototypes of this payload system. Using conventional microtiter plates, we show that Alamar Blue (AB) absorbance changes can assess the Gm effect on E. coli viability, permitting telemetric transfer of the spaceflight data to Earth. Laboratory results using payload prototypes are consistent with wellplate and flask findings of differential sensitivity of UPEC and its ∆rpoS strain to Gm. if σs plays the same role in space MG as in LSMMG and Earth gravity, countermeasures discovered in recent Earth studies (aimed at weakening the UPEC antioxidant defense) to control UPEC infections would prove useful also in space flights. Further, EcAMSat results should clarify inconsistencies from previous space experiments on bacterial antibiotic sensitivity and other issues.

The adaptation of Escherichia coli cells grown in simulated microgravity for an extended period is both phenotypic and genomic

Microorganisms impact spaceflight in a variety of ways. They play a positive role in biological systems, such as waste water treatment but can be problematic through buildups of biofilms that can affect advanced life support. Of special concern is the possibility that during extended missions, the microgravity environment will provide positive selection for undesirable genomic changes. Such changes could affect microbial antibiotic sensitivity and possibly pathogenicity. To evaluate this possibility, Escherichia coli (lac plus) cells were grown for over 1000 generations on Luria Broth medium under low-shear modeled microgravity conditions in a high aspect rotating vessel. This is the first study of its kind to grow bacteria for multiple generations over an extended period under low-shear modeled microgravity. Comparisons were made to a non-adaptive control strain using growth competitions. After 1000 generations, the final low-shear modeled microgravity-adapted strain readily outcompeted the unadapted lac minus strain. A portion of this advantage was maintained when the low-shear modeled microgravity strain was first grown in a shake flask environment for 10, 20, or 30 generations of growth. Genomic sequencing of the 1000 generation strain revealed 16 mutations. Of the five changes affecting codons, none were neutral. It is not clear how significant these mutations are as individual changes or as a group. It is concluded that part of the long-term adaptation to low-shear modeled microgravity is likely genomic. The strain was monitored for acquisition of antibiotic resistance by VITEK analysis throughout the adaptation period. Despite the evidence of genomic adaptation, resistance to a variety of antibiotics was never observed.

Investigation of simulated microgravity effects on Streptococcus mutans physiology and global gene expression

Astronauts have been previously shown to exhibit decreased salivary lysozyme and increased dental calculus and gingival inflammation in response to space flight, host factors that could contribute to oral diseases such as caries and periodontitis. However, the specific physiological response of caries-causing bacteria such as Streptococcus mutans to space flight and/or ground-based simulated microgravity has not been extensively investigated. In this study, high aspect ratio vessel S. mutans simulated microgravity and normal gravity cultures were assessed for changes in metabolite and transcriptome profiles, H₂O₂ resistance, and competence in sucrose-containing biofilm media. Stationary phase S. mutans simulated microgravity cultures displayed increased killing by H₂O₂ compared to normal gravity control cultures, but competence was not affected. RNA-seq analysis revealed that expression of 153 genes was up-regulated ≥2-fold and 94 genes down-regulated ≥2-fold during simulated microgravity high aspect ratio vessel growth. These included a number of genes located on extrachromosomal elements, as well as genes involved in carbohydrate metabolism, translation, and stress responses. Collectively, these results suggest that growth under microgravity analog conditions promotes changes in S. mutans gene expression and physiology that may translate to an altered cariogenic potential of this organism during space flight missions.

The gene expression patterns, metabolism and physiology of tooth cavities-causing microbes change in a space-like gravity environment. These findings could help explain why astronauts are at a greater risk for dental diseases when in space. Kelly Rice and colleagues from the University of Florida, Gainesville, USA, cultured Streptococcus mutans bacteria under simulated microgravity and normal gravity conditions. The bacteria grown in microgravity were more susceptible to killing with hydrogen peroxide, tended to aggregate in more compact cellular structures, showed changes in their metabolite profile and expressed around 250 genes at levels that were either much higher or lower than normal gravity control cultures. These genes included many involved in carbohydrate metabolism, protein production and stress responses. The observed changes collectively suggest that space flight and microgravity could alter the cavities-causing potential of S. mutans.

Mechanotransduction as an Adaptation to Gravity

Gravity has played a critical role in the development of terrestrial life. A key event in evolution has been the development of mechanisms to sense and transduce gravitational force into biological signals. The objective of this manuscript is to review how living organisms on Earth use mechanotransduction as an adaptation to gravity. Certain cells have evolved specialized structures, such as otoliths in hair cells of the inner ear and statoliths in plants, to respond directly to the force of gravity. By conducting studies in the reduced gravity of spaceflight (microgravity) or simulating microgravity in the laboratory, we have gained insights into how gravity might have changed life on Earth. We review how microgravity affects prokaryotic and eukaryotic cells at the cellular and molecular levels. Genomic studies in yeast have identified changes in genes involved in budding, cell polarity, and cell separation regulated by Ras, PI3K, and TOR signaling pathways. Moreover, transcriptomic analysis of late pregnant rats have revealed that microgravity affects genes that regulate circadian clocks, activate mechanotransduction pathways, and induce changes in immune response, metabolism, and cells proliferation. Importantly, these studies identified genes that modify chromatin structure and methylation, suggesting that long-term adaptation to gravity may be mediated by epigenetic modifications. Given that gravity represents a modification in mechanical stresses encounter by the cells, the tensegrity model of cytoskeletal architecture provides an excellent paradigm to explain how changes in the balance of forces, which are transmitted across transmembrane receptors and cytoskeleton, can influence intracellular signaling pathways and gene expression.

Exposure of Mycobacterium marinum to low-shear modeled microgravity: effect on growth, the transcriptome and survival under stress

Waterborne pathogenic mycobacteria can form biofilms, and certain species can cause hard-to-treat human lung infections. Astronaut health could therefore be compromised if the spacecraft environment or water becomes contaminated with pathogenic mycobacteria. This work uses Mycobacterium marinum to determine the physiological changes in a pathogenic mycobacteria grown under low-shear modeled microgravity (LSMMG). M. marinum were grown in high aspect ratio vessels (HARVs) using a rotary cell culture system subjected to LSMMG or the control orientation (normal gravity, NG) and the cultures used to determine bacterial growth, bacterium size, transcriptome changes, and resistance to stress. Two exposure times to LSMMG and NG were examined: bacteria were grown for ~40 h (short), or 4 days followed by re-dilution and growth for ~35 h (long). M. marinum exposed to LSMMG transitioned from exponential phase earlier than the NG culture. They were more sensitive to hydrogen peroxide but showed no change in resistance to gamma radiation or pH 3.5. RNA-Seq detected significantly altered transcript levels for 562 and 328 genes under LSMMG after short and long exposure times, respectively. Results suggest that LSMMG induced a reduction in translation, a downregulation of metabolism, an increase in lipid degradation, and increased chaperone and mycobactin expression. Sigma factor H (sigH) was the only sigma factor transcript induced by LSMMG after both short and long exposure times. In summary, transcriptome studies suggest that LSMMG may simulate a nutrient-deprived environment similar to that found within macrophage during infection. SigH is also implicated in the M. marinum LSMMG transcriptome response.

Microgravity as a biological tool to examine host-pathogen interactions and to guide development of therapeutics and preventatives that target pathogenic bacteria

Space exploration programs have long been interested in the effects of spaceflight on biology. This research is important not only in its relevance to future deep space exploration, but also because it has allowed investigators to ask questions about how gravity impacts cell behavior here on Earth. In the 1980s, scientists designed and built the first rotating wall vessel, capable of mimicking the low shear environment found in space. This vessel has since been used to investigate growth of both microorganisms and human tissue cells in low shear modeled microgravity conditions. Bacterial behavior has been shown to be altered both in space and under simulated microgravity conditions. In some cases, bacteria appear attenuated, whereas in others virulence is enhanced. This has consequences not only for manned spaceflight, but poses larger questions about the ability of bacteria to sense the world around them. By using the microgravity environment as a tool, we can exploit this phenomenon in the search for new therapeutics and preventatives against pathogenic bacteria for use both in space and on Earth.

The Bacterial iprA Gene Is Conserved across Enterobacteriaceae, Is Involved in Oxidative Stress Resistance, and Influences Gene Expression in Salmonella enterica Serovar Typhimurium

The iprA gene (formerly known as yaiV or STM0374) is located in a two-gene operon in the Salmonella enterica serovar Typhimurium genome and is associated with altered expression during spaceflight and rotating-wall-vessel culture conditions that increase virulence. However, iprA is uncharacterized in the literature. In this report, we present the first targeted characterization of this gene, which revealed that iprA is highly conserved across Enterobacteriaceae We found that S Typhimurium, Escherichia coli, and Enterobacter cloacae ΔiprA mutant strains display a multi-log-fold increase in oxidative stress resistance that is complemented using a plasmid-borne wild-type (WT) copy of the S Typhimurium iprA gene. This observation was also associated with increased catalase activity, increased S Typhimurium survival in macrophages, and partial dependence on the katE gene and full dependence on the rpoS gene. Our results indicate that IprA protein activity is sensitive to deletion of the N- and C-terminal 10 amino acids, while a region that includes amino acids 56 to 80 is dispensable for activity. RNA sequencing (RNA-Seq) analysis revealed several genes altered in expression in the S Typhimurium ΔiprA mutant strain compared to the WT, including those involved in fimbria formation, spvABCD-mediated virulence, ethanolamine utilization, the phosphotransferase system (PTS) transport, and flagellin phase switching from FlgB to FliC (likely a stochastic event) and several genes of hypothetical or putative function.

IMPORTANCE

Overall, this work reveals that the conserved iprA gene measurably influences bacterial biology and highlights the pool of currently uncharacterized genes that are conserved across bacterial genomes. These genes represent potentially useful targets for bacterial engineering, vaccine design, and other possible applications.

Increased biofilm formation ability in Klebsiella pneumoniae after short-term exposure to a simulated microgravity environment

Biofilm formation is closely related to the pathogenetic processes of Klebsiella pneumoniae, which frequently causes infections in immunocompromised individuals. The immune system of astronauts is compromised in spaceflight. Accordingly, K. pneumoniae, which used to be isolated from orbiting spacecraft and astronauts, poses potential threats to the health of astronauts and mission security. Microgravity is a key environmental cue during spaceflight. Therefore, determining its effects on bacterial biofilm formation is necessary. In this study, K. pneumoniae ATCC BAA-1705 was exposed to a simulated microgravity (SMG) environment. K. pneumoniae grown under SMG formed thicker biofilms compared with those under normal gravity (NG) control after 2 weeks of subculture. Two indicative dyes (i.e., Congo red and calcofluor) specifically binding to cellulose fibers and/or fimbriae were utilized to reconfirm the enhanced biofilm formation ability of K. pneumoniae grown under SMG. Further analysis showed that the biofilms formed by SMG-treated K. pneumoniae were susceptible to cellulase digestion. Yeast cells mannose-resistant agglutination by K. pneumoniae type 3 fimbriae was more obvious in the SMG group, which suggests that cellulose production and type 3 fimbriae expression in K. pneumoniae were both enhanced under the SMG condition. Transcriptomic analysis showed that 171 genes belonging to 15 functional categories were dysregulated in this organism exposed to the SMG conditions compared with those in the NG group, where the genes responsible for the type 3 fimbriae (mrkABCDF) and its regulator (mrkH) were upregulated.

Influence of Low-Shear Modeled Microgravity on Heat Resistance, Membrane Fatty Acid Composition, and Heat Stress-Related Gene Expression in Escherichia coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895

We previously showed that modeled microgravity conditions alter the physiological characteristics of Escherichia coli O157:H7. To examine how microgravity conditions affect bacterial heat stress responses, D values, membrane fatty acid composition, and heat stress-related gene expression (clpB, dnaK, grpE, groES, htpG, htpX, ibpB, and rpoH), E. coli O157:H7 ATCC 35150, ATCC 43889, ATCC 43890, and ATCC 43895 were cultured under two different conditions: low-shear modeled microgravity (LSMMG, an analog of spaceflight conditions) and normal gravity (NG, Earth-like conditions). When 24-h cultures were heated to 55°C, cells cultured under LSMMG conditions showed reduced survival compared with cells cultured under NG conditions at all time points (P < 0.05). D values of all tested strains were lower after LSMMG culture than after NG culture. Fourteen of 37 fatty acids examined were present in the bacterial membrane: nine saturated fatty acids (SFA) and five unsaturated fatty acids (USFA). The USFA/SFA ratio, a measure of membrane fluidity, was higher under LSMMG conditions than under NG conditions. Compared with control cells grown under NG conditions, cells cultured under LSMMG conditions showed downregulation of eight heat stress-related genes (average, -1.9- to -3.7-fold). The results of this study indicate that in a simulated space environment, heat resistance of E. coli O157:H7 decreased, and this might be due to the synergistic effects of the increases in membrane fluidity and downregulated relevant heat stress genes.

IMPORTANCE

Microgravity is a major factor that represents the environmental conditions in space. Since infectious diseases are difficult to deal with in a space environment, comprehensive studies on the behavior of pathogenic bacteria under microgravity conditions are warranted. This study reports the changes in heat stress resistance of E. coli O157:H7, the severe foodborne pathogen, under conditions that mimic microgravity. The results provide scientific clues for further understanding of the bacterial response under the simulated microgravity conditions. It will contribute not only to the improvement of scientific knowledge in the academic fields but also ultimately to the development of a prevention strategy for bacterial disease in the space environment.