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George E Fox - One of the best experts on this subject based on the ideXlab platform.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis. The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. Pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. Pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. Pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. Pumilus likely belong to the B. safensis group.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from clean rooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061 T . In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis . The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061 T . The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all B. safensis/B. Pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061 T , and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. Pumilus while the other houses all the B. safensis strains. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism9s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. Pumilus actually belong to the B. safensis group. Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide resistance, genome comparison, phage insertions
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bacillus Pumilus safr 032 genome revisited sequence update and re annotation
2016Co-Authors: Victor G Stepanov, Madhan R Tirumalai, Saied Montazari, Aleksandra Checinska, Kasthuri Venkateswaran, George E FoxAbstract:Bacillus Pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. Pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. Pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. Pumilus strains revealed indications of misassembly in the B. Pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
Kasthuri Venkateswaran - One of the best experts on this subject based on the ideXlab platform.
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bacillus Pumilus safr 032 genome revisited sequence update and re annotation
2016Co-Authors: Victor G Stepanov, Madhan R Tirumalai, Saied Montazari, Aleksandra Checinska, Kasthuri Venkateswaran, George E FoxAbstract:Bacillus Pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. Pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. Pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. Pumilus strains revealed indications of misassembly in the B. Pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
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recurrent isolation of hydrogen peroxide resistant spores of bacillus Pumilus from a spacecraft assembly facility
2005Co-Authors: Michael Kempf, Fei Chen, Roger Kern, Kasthuri VenkateswaranAbstract:While the microbial diversity of a spacecraft assembly facility at the Jet Propulsion Laboratory (Pasadena, CA) was being monitored, H2O2-resistant bacterial strains were repeatedly isolated from various surface locations. H2O2 is a possible sterilant for spacecraft hardware because it is a low-temperature process and compatible with various modern-day spacecraft materials, electronics, and components. Both conventional biochemical testing and molecular analyses identified these strains as Bacillus Pumilus. This Bacillus species was found in both unclassified (entrance floors, anteroom, and air-lock) and classified (floors, cabinet tops, and air) locations. Both vegetative cells and spores of several B. Pumilus isolates were exposed to 5% liquid H2O2 for 60 min. Spores of each strain exhibited higher resistance than their respective vegetative cells to liquid H2O2. Results indicate that the H2O2 resistance observed in both vegetative cells and spores is strain-specific, as certain B. Pumilus strains were ...
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recurrent isolation of hydrogen peroxide resistant spores of bacillus Pumilus from a spacecraft assembly facility
2005Co-Authors: Michael Kempf, Fei Chen, Roger Kern, Kasthuri VenkateswaranAbstract:While the microbial diversity of a spacecraft assembly facility at the Jet Propulsion Laboratory (Pasadena, CA) was being monitored, H2O2-resistant bacterial strains were repeatedly isolated from various surface locations. H2O2 is a possible sterilant for spacecraft hardware because it is a low-temperature process and compatible with various modern-day spacecraft materials, electronics, and components. Both conventional biochemical testing and molecular analyses identified these strains as Bacillus Pumilus. This Bacillus species was found in both unclassified (entrance floors, anteroom, and air-lock) and classified (floors, cabinet tops, and air) locations. Both vegetative cells and spores of several B. Pumilus isolates were exposed to 5% liquid H2O2 for 60 min. Spores of each strain exhibited higher resistance than their respective vegetative cells to liquid H2O2. Results indicate that the H2O2 resistance observed in both vegetative cells and spores is strain-specific, as certain B. Pumilus strains were two to three times more resistant than a standard Bacillus subtilis dosimetry strain. An example of this trend was observed when the type strain of B. Pumilus, ATCC 7061, proved sensitive, whereas several environmental strains exhibited varying degrees of resistance, to H2O2. Repeated isolation of H2O2-resistant strains of B. Pumilus in a clean-room is a concern because their persistence might potentially compromise life-detection missions, which have very strict cleanliness and sterility requirements for spacecraft hardware.
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maldi tofms compared with other polyphasic taxonomy approaches for the identification and classification of bacillus Pumilus spores
2004Co-Authors: Danielle N Dickinson, Masataka Satomi, James D Winefordner, David H Powell, Kasthuri VenkateswaranAbstract:Abstract To verify the efficacy of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS) protein profiling for identifying and differentiating bacterial species, several strains of Bacillus Pumilus were examined in a thorough taxonomic study incorporating a polyphasic approach. Sixteen isolates of putative B. Pumilus isolated from spacecraft assembly facilities, the Mars Odyssey spacecraft, and the International Space Station, were characterized for their biochemical and molecular profiles using the Biolog system, DNA techniques, and MALDI-TOFMS protein profiling. MALDI-TOFMS protein profiling was more accurate than Biolog metabolic profiling, more discriminating than 16S rDNA sequence analysis, and complemented the results of gyrB sequence analysis and DNA–DNA hybridization for the identification of the B. Pumilus spores. This is the first report whereby MALDI-TOFMS generated protein profiles from a set of microbes is compared directly with DNA–DNA hybridization yielding a positive correlation. Unique, cluster-specific biomarker peaks have been identified in the spores of the B. Pumilus examined in this study. MALDI-TOFMS protein profiling is a rapid and simple analysis and has been demonstrated as a useful taxonomic tool for differentiating spores of the genus Bacillus . For practical purposes, it would be ideal (and necessary) to have a publicly available, standardized MALDI profile database, to facilitate the use of the technique as a diagnostic method to differentiate bacterial species.
Madhan R Tirumalai - One of the best experts on this subject based on the ideXlab platform.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis. The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. Pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. Pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. Pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. Pumilus likely belong to the B. safensis group.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from clean rooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061 T . In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis . The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061 T . The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all B. safensis/B. Pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061 T , and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. Pumilus while the other houses all the B. safensis strains. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism9s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. Pumilus actually belong to the B. safensis group. Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide resistance, genome comparison, phage insertions
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bacillus Pumilus safr 032 genome revisited sequence update and re annotation
2016Co-Authors: Victor G Stepanov, Madhan R Tirumalai, Saied Montazari, Aleksandra Checinska, Kasthuri Venkateswaran, George E FoxAbstract:Bacillus Pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. Pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. Pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. Pumilus strains revealed indications of misassembly in the B. Pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
Victor G Stepanov - One of the best experts on this subject based on the ideXlab platform.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis. The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. Pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. Pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. Pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. Pumilus likely belong to the B. safensis group.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from clean rooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061 T . In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis . The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061 T . The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all B. safensis/B. Pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061 T , and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. Pumilus while the other houses all the B. safensis strains. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism9s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. Pumilus actually belong to the B. safensis group. Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide resistance, genome comparison, phage insertions
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bacillus Pumilus safr 032 genome revisited sequence update and re annotation
2016Co-Authors: Victor G Stepanov, Madhan R Tirumalai, Saied Montazari, Aleksandra Checinska, Kasthuri Venkateswaran, George E FoxAbstract:Bacillus Pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. Pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. Pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. Pumilus strains revealed indications of misassembly in the B. Pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
Saied Montazari - One of the best experts on this subject based on the ideXlab platform.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from cleanrooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spores resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, and the draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061T. Additional comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis. The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by MERTA and ATCC7061T. The FO-36b genome has ten unique open reading frames and two phage-like regions, homologous to the Bacillus bacteriophage SPP1 and Brevibacillus phage Jimmer1. Differing remnants of the Jimmer1 phage are found in essentially all B. safensis / B. Pumilus strains. Seven unique genes are part of these phage elements. Whole Genome Phylogenetic Analysis of the B. Pumilus, B. safensis and other Firmicutes genomes, separate them into three distinct clusters. Two clusters are subgroups of B. Pumilus while one houses all the B. safensis strains. The Genome-genome distance analysis and a phylogenetic analysis of gyrA sequences corroborated these results. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can alter the expression levels of key proteins thereby changing the organism’s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. Multiple genome comparison indicates that many strains named as B. Pumilus likely belong to the B. safensis group.
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bacillus safensis fo 36b and bacillus Pumilus safr 032 a whole genome comparison of two spacecraft assembly facility isolates
2018Co-Authors: Madhan R Tirumalai, Victor G Stepanov, Saied Montazari, Andrea Wunsche, Racquel O Gonzalez, Kasturi Venkateswaran, George E FoxAbstract:Bacillus strains producing highly resistant spores have been isolated from clean rooms and space craft assembly facilities. Organisms that can survive such conditions merit planetary protection concern and if that resistance can be transferred to other organisms, a health concern too. To further efforts to understand these resistances, the complete genome of Bacillus safensis strain FO-36b, which produces spore resistant to peroxide and radiation was determined. The genome was compared to the complete genome of B. Pumilus SAFR-032, as well as draft genomes of B. safensis JPL-MERTA-8-2 and the type strain B. Pumilus ATCC7061 T . In addition, comparisons were made to 61 draft genomes that have been mostly identified as strains of B. Pumilus or B. safensis . The FO-36b gene order is essentially the same as that in SAFR-032 and other B. Pumilus strains [1]. The annotated genome has 3850 open reading frames and 40 noncoding RNAs and riboswitches. Of these, 307 are not shared by SAFR-032, and 65 are also not shared by either MERTA or ATCC7061 T . The FO-36b genome was found to have ten unique reading frames and two phage-like regions, which have homology with the Bacillus bacteriophage SPP1 (NC_004166) and Brevibacillus phage Jimmer1 (NC_029104). Differing remnants of the Jimmer1 phage are found in essentially all B. safensis/B. Pumilus strains. Seven unique genes are part of these phage elements. Comparison of gyrA sequences from FO-36b, SAFR-032, ATCC7061 T , and 61 other draft genomes separate the various strains into three distinct clusters. Two of these are subgroups of B. Pumilus while the other houses all the B. safensis strains. It is not immediately obvious that the presence or absence of any specific gene or combination of genes is responsible for the variations in resistance seen. It is quite possible that distinctions in gene regulation can change the level of expression of key proteins thereby changing the organism9s resistance properties without gain or loss of a particular gene. What is clear is that phage elements contribute significantly to genome variability. The larger comparison of multiple strains indicates that many strains named as B. Pumilus actually belong to the B. safensis group. Keywords: Planetary protection, Bacillus endospores, extreme radiation resistance, peroxide resistance, genome comparison, phage insertions
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bacillus Pumilus safr 032 genome revisited sequence update and re annotation
2016Co-Authors: Victor G Stepanov, Madhan R Tirumalai, Saied Montazari, Aleksandra Checinska, Kasthuri Venkateswaran, George E FoxAbstract:Bacillus Pumilus strain SAFR-032 is a non-pathogenic spore-forming bacterium exhibiting an anomalously high persistence in bactericidal environments. In its dormant state, it is capable of withstanding doses of ultraviolet (UV) radiation or hydrogen peroxide, which are lethal for the vast majority of microorganisms. This unusual resistance profile has made SAFR-032 a reference strain for studies of bacterial spore resistance. The complete genome sequence of B. Pumilus SAFR-032 was published in 2007 early in the genomics era. Since then, the SAFR-032 strain has frequently been used as a source of genetic/genomic information that was regarded as representative of the entire B. Pumilus species group. Recently, our ongoing studies of conservation of gene distribution patterns in the complete genomes of various B. Pumilus strains revealed indications of misassembly in the B. Pumilus SAFR-032 genome. Synteny-driven local genome resequencing confirmed that the original SAFR-032 sequence contained assembly errors associated with long sequence repeats. The genome sequence was corrected according to the new findings. In addition, a significantly improved annotation is now available. Gene orders were compared and portions of the genome arrangement were found to be similar in a wide spectrum of Bacillus strains.
