The theory and application of space microbiology: China's experiences in space experiments and beyond

Infections in long-duration space missions

As government space agencies and private companies announce plans for deep space exploration and colonisation, prioritisation of medical preparedness is becoming crucial. Among all medical conditions, infections pose one of the biggest threats to astronaut health and mission success. To gain a comprehensive understanding of these risks, we review the measured and estimated incidence of infections in space, effect of space environment on the human immune system and microbial behaviour, current preventive and management strategies for infections, and future perspectives for diagnosis and treatment. This information will enable space agencies to enhance their comprehension of the risk of infection in space, highlight gaps in knowledge, aid better crew preparation, and potentially contribute to sepsis management in terrestrial settings, including not only isolated or austere environments but also conventional clinical settings.

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.

Exopolysaccharide-Producing Lacticaseibacillus rhamnosus Space Mutant Improves the Techno-Functional Characteristics of Fermented Cow and Goat Milks

Lacticaseibacillus rhamnosus Probio-M9 (Probio-M9) is increasingly used as a co-fermentation culture in fermented milk production. Recently, a capsular polysaccharide (CPS)- and exopolysaccharide (EPS)-producing mutant of Probio-M9, HG-R7970-3, was generated by space mutagenesis. This study compared the performance of cow and goat milk fermentation between the non-CPS/-EPS-producing parental strain (Probio-M9) and the CPS/EPS producer (HG-R7970-3), and the stability of products fermented by the two bacteria. Our results showed that using HG-R7970-3 as the fermentative culture could improve the probiotic viable counts, physico-chemical, texture, and rheological properties in both cow and goat milk fermentation. Substantial differences were also observed in the metabolomics profiles between fermented cow and goat milks produced by the two bacteria. Comparing with Probio-M9-fermented cow and goat milks, those fermented by HG-R7970-3 were enriched in a number of flavor compounds and potential functional components, particularly acids, esters, peptides, and intermediate metabolites. Moreover, HG-R7970-3 could improve the post-fermentation flavor retention capacity. These new and added features are of potential to improve the techno-functional qualities of conventional fermented milks produced by Probio-M9, and these differences are likely imparted by the acquired CPS-/EPS-producing ability of the mutant. It merits further investigation into the sensory quality and in vivo function of HG-R7970-3-fermented milks.

The Space Environment Activates Capsular Polysaccharide Production in Lacticaseibacillus rhamnosus Probio-M9 by Mutating the wze (ywqD) Gene

The study of microorganisms in outer space has focused mainly on investigating phenotypic changes in microbial pathogens induced by factors encountered in space. This study aimed to investigate the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Probio-M9 cells were exposed to space in a spaceflight. Interestingly, our results showed that a substantial proportion of space-exposed mutants (35/100) exhibited a ropy phenotype, characterized by their larger colony sizes and an acquired ability to produce capsular polysaccharide (CPS), compared with the original Probio-M9 or the ground control isolates without space exposure. Whole-genome sequencing analyses on both the Illumina and PacBio platforms revealed a skewed distribution of single nucleotide polymorphisms (12/89 [13.5%]) toward the CPS gene cluster, particularly in the wze (ywqD) gene. The wze gene encodes a putative tyrosine-protein kinase that regulates CPS expression through substrate phosphorylation. Transcriptomics analysis of two space-exposed ropy mutants revealed increased expression in the wze gene relative to a ground control isolate. Finally, we showed that the acquired ropy phenotype (CPS-producing ability) and space-induced genomic changes could be stably inherited. Our findings confirmed that the wze gene directly influences the capacity for CPS production in Probio-M9, and space mutagenesis is a potential strategy for inducing stable physiological changes in probiotics. IMPORTANCE This work investigated the effect of space exposure on a probiotic bacterium, Lacticaseibacillus rhamnosus Probio-M9. Interestingly, the space-exposed bacteria became capable of producing capsular polysaccharide (CPS). Some probiotic-derived CPSs have nutraceutical potential and bioactive properties. They also enhance the survival of probiotics through the gastrointestinal transit and ultimately strengthen the probiotic effects. Space mutagenesis seems to be a promising strategy for inducing stable changes in probiotics, and the obtained high-CPS-yielding mutants are valuable resources for future applications.

Comparative analysis of aroma components and quality of Geotrichum candidum after space mutation breeding

Aim

The aroma-producing strain of Geotrichum candidum GDMCC60675 was taken as the research object, the composition of aroma-producing substances of G. candidum was studied, and the target strains of G. candidum suitable for food additives were screened out by mutagenesis.

Methods

Mutants were obtained by space breeding. The colony morphology and cell morphology of the mutant strain were identified, the phylogenetic tree of the two strains was constructed, and the whole-genome sequences of the wild strain and the mutant strain were compared. The aroma components and key odor compounds of the two strains were analyzed and compared by HS-SPME-GC-MS and E-nose detection, and the data were processed by using the relative odor activity value (ROAV) analysis method.

Results

A mutant strain of G. candidum was found with different characteristics of aroma production compared with wild-type G. candidum. It was found that its colony morphology and cell morphology were similar. However, it was found that the aroma-producing substances produced by the two strains were different, and the key difference compound was phenyl ethyl alcohol, which also proved that the two strains were different, and the main aroma note was different.

Wound Healing Effects of Dracontomelon dao on Bacterial Infection Wounds in Rats and Its Potential Mechanisms under Simulated Space Environment

Dracontomelon dao (D. dao) is the leaves of Dracontomelon duperreanum Pierre (D. dao auct. non (Blanco) Merr. and Rolfe; D. sinense Stopf.). As a valuable traditional Chinese medicine from Anacardiaceae, D. dao has a long history of treating bedsores, skin ulcers, and other infection diseases. In addition, the volatile oil from D. dao leaves exhibits antitumor effects. However, these reported studies only focused on evaluating the antimicrobial efficacy on model strains in vitro, without paying attention to the antimicrobial activity and anti-inflammatory effects in vivo. This study was aimed to provide evidence of antimicrobial activity and anti-inflammatory and proangiogenesis activities of Dracontomelon dao (D. dao) on the skin of rats under simulated space environment. The weightlessness model of rats in space environment was established. Then, rats were given D. dao for 15 days. Wound healing effects of D. dao on histopathology and inflammatory cytokines in E. coli-induced wound infection in weightless rats were analyzed. Furthermore, the molecular biology technology was performed to evaluate the wound healing effects of D. dao on the relative protein level of NF-κB as well as PI3K/Akt signaling pathways. Immunohistochemistry was used for the protein expression of VEGFA. The wound healing effects of D. dao on bacterially infected wounds in rats were manifested by lowering the size of the wound and significantly increasing the shrinkage rate of the wound. D. dao had effect on alleviating histological damage of skin tissue and downregulation inflammatory cytokines level. In addition, the results indicated that D. dao has a regulatory effect on inflammation and angiogenesis and could regulate the relative protein level of MAPK/NF-κB as well as PI3K/AKT signaling pathways. The current study highlighted the crucial role of D. dao in relieving skin tissue injury in E. coli-induced wound infection in weightless rats by regulating the MAPK/NF-κB as well as PI3K/AKT signaling pathways. This study could provide a new agent for the treatment of bacterial infected wounds in simulated space environment.

Phenotypic, genomic, and transcriptomic changes in an Acinetobacter baumannii strain after spaceflight in China's Tiangong-2 space laboratory

Acinetobacter baumannii is an opportunistic pathogen often found in patients with low immunity. It causes nosocomial infections, which are difficult to treat. This bacterium can rapidly mutate, developing resistance to antimicrobials and adapting to environmental stress, thereby increasing its survival. Understanding such adaptive mechanisms will be beneficial for controlling the spread of A. baumannii. Astrobiology studies have demonstrated that microbiomes from astronauts and manned spaceflight environments show resistance to stress and antibiotics. Astronauts also encounter low immunity during spaceflight missions. The extreme conditions of spaceflight provide a unique research platform for studying how opportunistic pathogens such as A. baumannii adapt to conditions such as microgravity and mutate during spaceflight. In this study, we compared phenotypic variations and analyzed genomic and transcriptomic variations in A. baumannii strains exposed to three different conditions: ST1 (64 days on Tiangong-2 space laboratory), GT1 (ground control), and Aba (original strain). Biofilm formation ability of the ST1 strain increased after 64 days of spaceflight. In addition, high-throughput sequencing revealed that some differentially expressed genes were upregulated in the ST1 strain compared to the GT1 strain. These results provide insights into the environmental adaptation of this widespread pathogen.

Growth Behavior and Transcriptome Profile Analysis of Proteus mirabilis Strain Under Long- versus Short-Term Simulated Microgravity Environment

Spaceflight missions affect the behavior of microbes that are inevitably introduced into space environments and may impact astronauts’ health. Current studies have mainly focused on the biological characteristics and molecular mechanisms of microbes after short-term or long-term spaceflight, but few have compared the impact of various lengths of spaceflight missions on the characteristics of microbes. Researchers generally agree that microgravity (MG) is the most critical factor influencing microbial physiology in space capsules during flight missions. This study compared the growth behavior and transcriptome profile of Proteus mirabilis cells exposed to long-term simulated microgravity (SMG) with those exposed to short-term SMG. The results showed that long-term SMG decreased the growth rate, depressed biofilm formation ability, and affected several transcriptomic profiles, including stress response, membrane transportation, metal ion transportation, biological adhesion, carbohydrate metabolism, and lipid metabolism in contrast to short-term SMG. This study improved the understanding of long-term versus short-term SMG effects on P. mirabilis behavior and provided relevant references for analyzing the influence of P. mirabilis on astronaut health during spaceflights.

Aerospace Technology Improves Fermentation Potential of Microorganisms

It is highly possible to obtain high-quality microbial products in appreciable amounts, as aerospace technology is advancing continuously. Genome-wide genetic variations in microorganisms can be triggered by space microgravity and radiation. Mutation rate is high, mutant range is wide, and final mutant character is stable. Therefore, space microorganism breeding is growing to be a new and promising area in microbial science and has greatly propelled the development of fermentation technology. Numerous studies have discovered the following improvements of fermentation potential in microorganisms after exposure to space: (1) reduction in fermentation cycle and increase in growth rate; (2) improvement of mixed fermentation species; (3) increase in bacterial conjugation efficiency and motility; (4) improvement of the bioactivity of various key enzymes and product quality; (5) enhancement of multiple adverse stress resistance; (6) improvement of fermentation metabolites, flavor, appearance, and stability. Aerospace fermentation technology predominantly contributes to bioprocessing in a microgravity environment. Unlike terrestrial fermentation, aerospace fermentation keeps cells suspended in the fluid medium without significant shear forces. Space radiation and microgravity have physical, chemical, and biological effects on mutant microorganisms by causing alternation in fluid dynamics and genome, transcriptome, proteome, and metabolome levels.

Decreased Biofilm Formation Ability of a Multidrug-Resistant Pseudomonas aeruginosa Strain After Exposure to a Simulated Microgravity Environment

Background: The refractory infection induced by multidrug-resistant (MDR) Pseudomonas aeruginosa has become one of the most urgent problems in hospitals. The biofilms formed by P. aeruginosa increase its resistance to antibiotics. A simulated microgravity (SMG) environment provides a platform to understand the factors affecting biofilm formation in bacteria. Objectives: This study aimed to investigate the SMG effects on MDR P. aeruginosa biofilm formation and explore the relevant mechanisms. Methods: In this study, a clinostat was used to simulate a microgravity (MG) environment. The motility and biofilm formation ability of MDR P. aeruginosa were observed using the swimming test and the crystal violet staining method, respectively. The underlying mechanism of phenotypic changes was further investigated by comparative transcriptomic analysis. Results: Multidrug-resistant P. aeruginosa grown under the SMG condition exhibited decreased swimming motility and biofilm formation ability compared to those under the normal gravity (NG) condition. Further analysis revealed that the decreased swimming motility and biofilm formation ability could be attributed to the downregulated expression of genes responsible for flagellar synthesis (flhB, fliQ, and fliR) and type IV pili biogenesis (pilDEXY1Y2VW). Conclusions: This is the first study to perform experiments on MDR P. aeruginosa under the SMG condition. It will be beneficial to understand the mechanism of MDR P. aeruginosa biofilm formation and develop new treatment strategies for infectious diseases induced by MDR P. aeruginosa in the future.

Survey and Evaluation of Spacecraft-Associated Aluminum-Degrading Microbes and Their Rapid Identification Methods

Aluminum corrosion has become a major obstacle in spacecraft construction given that aluminum is used extensively throughout the construction process. Despite its many attributes in strength and durability, aluminum is susceptible to corrosion, in particular, corrosion due to microbial contamination. Scientists have encountered a number of problems with microbial aluminum corrosion within spacecraft components. Here, we summarize recent findings with regard to the phenomenon of microbiologically influenced corrosion (MIC) on space stations in the context of microbial strains isolated from the Mir space station (Mir) and the International Space Station (ISS). Given that strains found on spacecraft are of terrestrial origin, an understanding of the contribution of Al-corrosive microbes to corrosion and related risks to space travel and astronaut health is essential for implementation of prevention strategies. Accordingly, an efficient rapid identification method of microbes with the capability to degrade aluminum is proposed. In particular, onboard implementation of a matrix-assisted laser desorption/ionization-time of flight mass spectrometer (MALDI-TOF MS) is addressed. The use of a MALDI-TOF MS on board spacecraft will be crucial to future successes in space travel given that traditional methods of identifying corrosive species are far more time-consuming. Identification of microbes by way of a MALDI-TOF MS may also aid in the study of microbial corrosion and be a valuable asset for MIC prevention.

Simulated Weightlessness Perturbs the Intestinal Metabolomic Profile of Rats

Recently, disorders of intestinal homeostasis in the space environment have been extensively demonstrated. Accumulating evidence have suggested microgravity and simulated weightlessness could induce dysbiosis of intestinal microbiota, which may contribute to the bowel symptoms during spaceflight. However, the specific responses of intestinal metabolome under simulated weightlessness and its relationship with the intestinal microbiome and immune characteristics remain largely unknown. In the current study, 20 adult Sprague-Dawley (SD) rats were randomly divided into the control group and the simulated weightlessness group using a hindlimb unloading model. The metabolomic profiling of cecal contents from eight rats of each group was investigated by gas chromatography-time of flight/mass spectrometry. The significantly different metabolites, biomarkers, and related pathways were identified. Multivariate analysis, such as principal component analysis and orthogonal projections to latent structures-discriminant analysis, demonstrated an obvious separation between the control group and the simulated weightlessness group. Significantly different metabolites, such as xylose, sinapinic acid, indolelactate, and digalacturonic acid, were identified, which participate in mainly pyrimidine metabolism, pentose and glucuronate interconversions, and valine, leucine and isoleucine metabolism. Cytidine-5'-monophosphate, 4-hydroxypyridine, and phloretic acid were determined as pivotal biomarkers under simulated weightlessness. Moreover, the significantly different metabolites were remarkably correlated with dysbiosis of the intestinal microbiota and disturbance of immunological characteristics induced by simulated weightlessness. These metabolic features provide crucial candidates for therapeutic targets for metabolic disorders under weightlessness.

Increased growth rate and amikacin resistance of Salmonella enteritidis after one-month spaceflight on China's Shenzhou-11 spacecraft

China launched the Tiangong-2 space laboratory in 2016 and will eventually build a basic space station by the early 2020s. These spaceflight missions require astronauts to stay on the space station for more than 6 months, and they inevitably carry microbes into the space environment. It is known that the space environment affects microbial behavior, including growth rate, biofilm formation, virulence, drug resistance, and metabolism. However, the mechanisms of these alternations have not been fully elucidated. Therefore, it is beneficial to monitor microorganisms for preventing infections among astronauts in a space environment. Salmonella enteritidis is a Gram-negative bacterial pathogen that commonly causes acute gastroenteritis in humans. In this study, to better understand the effects of the space environment on S. enteritidis, a S. enteritidis strain was taken into space by the Shenzhou-11 spacecraft from 17 October 2016 to 18 November 2016, and a ground simulation with similar temperature conditions was simultaneously performed as a control. It was found that the flight strain displayed an increased growth rate, enhanced amikacin resistance, and some metabolism alterations compared with the ground strain. Enrichment analysis of proteome revealed that the increased growth rate might be associated with differentially expressed proteins involved in transmembrane transport and energy production and conversion assembly. A combined transcriptome and proteome analysis showed that the amikacin resistance was due to the downregulation of the oppA gene and oligopeptide transporter protein OppA. In conclusion, this study is the first systematic analysis of the phenotypic, genomic, transcriptomic, and proteomic variations in S. enteritidis during spaceflight and will provide beneficial insights for future studies on space microbiology.

Decreased biofilm formation ability of Acinetobacter baumannii after spaceflight on China's Shenzhou 11 spacecraft

China has prepared for construction of a space station by the early 2020s. The mission will require astronauts to stay on the space station for at least 180 days. Microbes isolated from the International Space Station (ISS) have shown profound resistance to clinical antibiotics and environmental stresses. Previous studies have demonstrated that the space environment could affect microbial survival, growth, virulence, biofilms, metabolism, as well as their antibiotic‐resistant phenotypes. Furthermore, several studies have reported that astronauts experience a decline in their immunity during long‐duration spaceflights. Monitoring microbiomes in the ISS or the spacecraft will be beneficial for the prevention of infection among the astronauts during spaceflight. The development of a manned space program worldwide not only provides an opportunity to investigate the impact of this extreme environment on opportunistic pathogenic microbes, but also offers a unique platform to detect mutations in pathogenic bacteria. Various microorganisms have been carried on a spacecraft for academic purposes. Acinetobacter baumannii is a common multidrug‐resistant bacterium often prevalent in hospitals. Variations in the ability to cope with environmental hazards increase the chances of microbial survival. Our study aimed to compare phenotypic variations and analyze genomic and transcriptomic variations in A. baumannii among three different groups: SS1 (33 days on the Shenzhou 11 spacecraft), GS1 (ground control), and Aba (reference strain). Consequently, the biofilm formation ability of the SS1 strain decreased after 33 days of spaceflight. Furthermore, high‐throughput sequencing revealed that some differentially expressed genes were downregulated in the SS1 strain compared with those in the GS1 strain. In conclusion, this present study provides insights into the environmental adaptation of A. baumannii and might be useful for understanding changes in the opportunistic pathogenic microbes on our spacecraft and on China's future ISS.

Responses of Intestinal Mucosal Barrier Functions of Rats to Simulated Weightlessness

Exposure to microgravity or weightlessness leads to various adaptive and pathophysiological alterations in digestive structures and physiology. The current study was carried out to investigate responses of intestinal mucosal barrier functions to simulated weightlessness, by using the hindlimb unloading rats model. Compared with normal controls, simulated weightlessness damaged the intestinal villi and structural integrity of tight junctions, up-regulated the expression of pro-apoptotic protein Bax while down-regulated the expression of anti-apoptotic protein Bcl-2, thus improved the intestinal permeability. It could also influence intestinal microbiota composition with the expansion of Bacteroidetes and decrease of Firmicutes. The predicted metagenomic analysis emphasized significant dysbiosis associated differences in genes involved in membrane transport, cofactors and vitamins metabolism, energy metabolism, and genetic information processing. Moreover, simulated weightlessness could modify the intestinal immune status characterized by the increase of proinflammatory cytokines, decrease of secretory immunoglobulin A, and activation of TLR4/MyD88/NF-κB signaling pathway in ileum. These results indicate the simulated weightlessness disrupts intestinal mucosal barrier functions in animal model. The data also emphasize the necessity of monitoring and regulating astronauts’ intestinal health during real space flights to prevent breakdowns in intestinal homeostasis of crewmembers.

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.