Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes
Year: 2023
Type: article
Abstract: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA–DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows:Arthrobacter burdickiiIIF3SC-B10T(= NRRL B-65660T= DSM 115933T),Leifsonia virtsiiF6_8S_P_1AT(= NRRL B-65661T= DSM 115931T),Leifsonia williamsiiF6_8S_P_1BT(= NRRL B-65662T= DSM 115932T),Paenibacillus vandeheiiF6_3S_P_1CT(= NRRL B-65663T= DSM 115940T), andSporosarcina highlanderaeF6_3S_P_2T(= NRRL B-65664T= DSM 115943T). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.
Source: Scientific Reports
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $2,390
Funders: National Aeronautics and Space Administration, California Institute of Technology, WorldQuant Foundation, Nuclear Safety and Security Commission, National Institutes of Health, Ames Research Center, Jet Propulsion Laboratory, Kavli Nanoscience Institute, California Institute of Technology, Japan Aerospace Exploration Agency, National Institute of Mental Health
Awards: G1284901464, (1) SUMMARYMASSIVELY PARALLEL DNA SEQUENCING CONTINUES TO PROVIDE ASTONISHING INSIGHTS INTO THE REGULATORY COMPLEXITY OF THE MAMMALIAN GENOME REVEALING HERITABLE AND DE NOVO OCCURRING RISK FACTORS PREDISPOSING HUMANS TO A WIDE VARIETY OF DISEASES AND DISORDERS. NOTABLY MEMBERS OF THE ENCYCLOPEDIA OF DNA ELEMENTS (ENCODE) CONSORTIUM INCLUDING CO-INVESTIGATORS DRS. MASON AND SNYDER HAVE RECENTLY MAPPED THOUSANDS OF NON-CODING REGULATORY ELEMENTS IN THE HUMAN GENOME THAT SPECIFY RISK AND PROTECTIVE SITES FOR MANY DISEASE. THESE NONCODING GENETIC VARIATIONS ALSO SHOW DIFFERENTIAL IMPACT DEPENDING ON THE EPIGENETIC CHANGES OF THE GENOME INCLUDING METHYLATION OF DNA AND CHROMATIN STATES INSIDE CELLS. YET THESE QUESTIONS HAVE NOT BEEN COMPREHENSIVELY EXAMINED IN HUMAN ASTRONAUTS DUE TO THE FACT THAT THE VERY FIRST DATA SETS THAT CAN DELINEATE THE PUTATIVE IMPACT OF GENOME-WIDE NONCODING VARIATION AND EPIGENETIC CHANGES FROM SPACE TRAVEL ARE ONLY NOW BEING GENERATED IN THE NASA TWINS STUDY.HOWEVER WITH THIS DATA FROM NASA TWINS STUDY THERE IS A UNIQUE OPPORTUNITY TO BOTH GENERATE NEW COMPUTATIONAL TOOLS FOR THE INTEGRATION OF THE DATA FROM THESE SAMPLES AND ALSO TO UTILIZE NOVEL SINGLE-CELL APPROACHES FOR EPIGENETIC STATES IN THE HUMAN CELLS TAKEN FROM SPACE. WE PROPOSE TO EXPAND AND FURTHER INTEGRATE OUR TOOLS FOR EXAMINING THE REGULATORY CHANGES TO DNA AND RNA TOGETHER CALLED "EPISUITE " WHICH WILL PROVIDE LONG-SOUGHT SOLUTIONS TO PROBLEMS IN INTEGRATIVE GENOMICS AND ESTABLISH A MORE SYSTEMS-LEVEL VIEW OF HUMAN PHYSIOLOGY DURING SPACE TRAVEL. SPECIFICALLY WE WILL OPTIMIZE AND INTEGRATE OPEN-SOURCE AND PUBLISHED BIOINFORMATICS TOOLS BETWEEN BOTH LABORATORIES (HUGE-SEQ METHYLKIT EDMR R-MAKE) EXPAND OUR CODE BASE WITH TWO NEW TOOLS (METHCLONE AND CEMBASE) AND THEN CREATE A WEB-INTERFACE FOR USERS TO UPLOAD ORGANIZE AND ANALYZE THESE DATA RELATIVE TO ENCODE PUBLIC DATA. THEN WE WILL USE NOVEL SINGLE-CELL EXPERIMENTAL METHODS (SCATAC-SEQ) TO CONFIRM AND CHARACTERIZE THE IMPACT AND SCOPE OF SUCH NONCODING AND EPIGENETIC CHANGES. TOGETHER THE DATA AND TOOLS IN EPISUITE CONCOMITANT WITH THE NEW SINGLE-CELL CHROMATIN DATA WILL ENABLE DISCOVERY AND VALIDATION OF SPECIFIC LOCI THAT REPRESENT THE GENETIC AND EPIGENETIC RISKS FACED BY ASTRONAUTS AND ALSO AN IMPROVED UNDERSTANDING OF THE REGULATORY AND GENETIC IMPACT (BMED5) OF THESE MOLECULAR CHANGES.(2) HYPOTHESISWE HYPOTHESIZE THAT SPECIFIC AREAS OF THE GENOME ARE EPIGENETICALLY DYSREGULATED AS A RESULT OF SPACE TRAVEL AND THAT SOME OF THESE AREAS DIFFER BETWEEN ASTRONAUTS. MOREOVER WE HYPOTHESIZE THAT THE ENRICHMENT OF NON-CODING VARIANTS IN DISTINCT BIOLOGICAL PATHWAYS WILL ALSO DIFFER BETWEEN ASTRONAUTS AND ANALYSIS AND INTEGRATION OF THESE DATA WILL REVEAL THE FIRST REGIONS OF "EPIGENETIC SPACE RISK" FOR THE ASTRONAUTS DELINEATED IN BMED5. TO VALIDATE THESE PREDICTIONS WE WILL PERFORM SINGLE-CELL ATAC-SEQ (ASSAY FOR TRANSPOSASE ACCESSIBLE CHROMATIN) ON CELL FRACTIONS FROM EARTH-BASED CONTROL SAMPLES AND THOSE TAKEN FROM SPACE.(3) SPECIFIC AIMSAIM 1. CREATE A WEB-BASED FRAMEWORK FOR INTEGRATING NON-CODING GENOMIC VARIATION AND DIFFERENTIAL EPIGENETIC STATES. THIS EPISUITE INTERFACE AND SET OF MACHINE-LEARNING ALGORITHMS WILL HELP ONGOING WORK WITH THE NASA TWINS STUDY AND AID FUTURE INVESTIGATIONS THAT LEVERAGE MULTI-OMICS DATA SETS FROM ASTRONAUTS. THESE DATA WILL ALSO BE LINKED TO GENE EXPRESSION DATA TO GAUGE THE IMPACT OF GENETIC AND EPIGENETIC CHANGES ON SPECIFIC BIOLOGICAL NETWORKS.AIM 2. VALIDATE THE ALTERED CHROMATIN STATES IN CELLS FROM SPACE TRAVEL AND MEASURE THE PROPORTION OF CELLS CHANGED WITH SINGLE-CELL ATAC-SEQ. WE WILL USE AN ASSAY CALLED SINGLE CELL (SCATAC-SEQ) WHICH CAN MEASURE THE SITES OF OPEN AND CLOSED CHROMATIN ON A CELL-BY-CELL BASIS. THIS WILL VALIDATE THE SITES WHERE WE OBSERVE EPIGENETIC CHANGES AND ALSO PROVIDE THE FIRST ESTIMATE OF THE PROPORTION OF CELLS EPIGENETICALLY IMPACTED BY SPACE TRAVEL., G2632102402, G2676722403, G2884980164, G3152186863, G3399367771, G3648211085, NEXT-GENERATION SEQUENCING (NGS) TECHNOLOGIES HAVE RECENTLY BEEN USED TO DETECT AND CLASSIFY EPIGENETIC CHANGES AT AN UNPRECEDENTED LEVEL. EPIGENETIC, THIS PROPOSAL FOR A TRANSLATIONAL RESEARCH INSTITUTE IS SUBMITTED ON BEHALF OF A CONSORTIUM OF NON-PROFIT ACADEMIC INSTITUTIONS IN RESPONSE TO NASA C, The Spatiotemporal Landscape of the Human Brain Epitranscriptome, G6978705394, G7034034363, G7222129478, G830101876
OpenAlex ID: W4388409390