Comparative genomic analysis of Cohnella hashimotonis sp. nov. isolated from the International Space Station
Year: 2023
Type: article
Abstract: A single strain from the family Paenibacillaceae was isolated from the wall behind the Waste Hygiene Compartment aboard the International Space Station (ISS) in April 2018, as part of the Microbial Tracking mission series. This strain was identified as a gram-positive, rod-shaped, oxidase-positive, catalase-negative motile bacterium in the genus Cohnella, designated as F6_2S_P_1T. The 16S sequence of the F6_2S_P_1T strain places it in a clade with C. rhizosphaerae and C. ginsengisoli, which were originally isolated from plant tissue or rhizosphere environments. The closest 16S and gyrB matches to strain F6_2S_P_1T are to C. rhizosphaerae with 98.84 and 93.99% sequence similarity, while a core single-copy gene phylogeny from all publicly available Cohnella genomes places it as more closely related to C. ginsengisoli. Average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values to any described Cohnella species are <89 and <22%, respectively. The major fatty acids for strain F6_2S_P_1T are anteiso-C15:0 (51.7%), iso-C16:0 (23.1%), and iso-C15:0 (10.5%), and it is able to metabolize a wide range of carbon compounds. Given the results of the ANI and dDDH analyses, this ISS strain is a novel species within the genus Cohnella for which we propose the name Cohnella hashimotonis, with the type strain F6_2S_P_1T (=NRRL B-65657T and DSMZ 115098T). Because no closely related Cohnella genomes were available, this study generated the whole-genome sequences (WGSs) of the type strains for C. rhizosphaerae and C. ginsengisoli. Phylogenetic and pangenomic analysis reveals that F6_2S_P_1T, C. rhizosphaerae, and C. ginsengisoli, along with two uncharacterized Cohnella strains, possess a shared set of 332 gene clusters which are not shared with any other WGS of Cohnella species, and form a distinct clade branching off from C. nanjingensis. Functional traits were predicted for the genomes of strain F6_2S_P_1T and other members of this clade.
Source: Frontiers in Microbiology
Language: English
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: gold
Estimated APC paid: $3,295
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, 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, G2884980164, G3399367771, 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
OpenAlex ID: W4380680943