Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost

Brumm, Phillip; Land, Miriam L.; Mead, David

doi:10.1186/s40793-016-0153-y

Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost

Journal Article · Wed Apr 27 00:00:00 EDT 2016 · Standards in Genomic Sciences

DOI:https://doi.org/10.1186/s40793-016-0153-y· OSTI ID:1261376

Brumm, Phillip ^[1]; Land, Miriam L. ^[2]; Mead, David ^[1]

Univ. of Wisconsin, Madison, WI (United States)
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Geobacillus sp. WCH70 was one of several thermophilic organisms isolated from hot composts in the Middleton, WI area. Comparison of 16 S rRNA sequences showed the strain may be a new species, and is most closely related to G. galactosidasius and G. toebii. The genome was sequenced, assembled, and annotated by the DOE Joint Genome Institute and deposited at the NCBI in December 2009 (CP001638). The genome of Geobacillus species WCH70 consists of one circular chromosome of 3,893,306 bp with an average G + C content of 43 %, and two circular plasmids of 33,899 and 10,287 bp with an average G + C content of 40 %. Among sequenced organisms, Geobacillus sp. WCH70 shares highest Average Nucleotide Identity (86 %) with G. thermoglucosidasius strains, as well as similar genome organization. Geobacillus sp. WCH70 appears to be a highly adaptable organism, with an exceptionally high 125 annotated transposons in the genome. The organism also possesses four predicted restriction-modification systems not found in other Geobacillus species.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE

Grant/Contract Number:: AC05-00OR22725

OSTI ID:: 1261376

Journal Information:: Standards in Genomic Sciences, Journal Name: Standards in Genomic Sciences Journal Issue: 33 Vol. 11; ISSN 1944-3277

Publisher:: BioMed CentralCopyright Statement

Country of Publication:: United States

Language:: English

References (46)

Predicting transmembrane protein topology with a hidden markov model: application to complete genomes11Edited by F. Cohen Krogh, Anders; Larsson, Björn; von Heijne, Gunnar Journal of Molecular Biology, Vol. 305, Issue 3 https://doi.org/10.1006/jmbi.2000.4315	journal	January 2001
Genome-wide identification, structural analysis and expression profiles of GRAS gene family in orchardgrass Xu, Xiaoheng; Feng, Guangyan; Huang, Linkai Molecular Biology Reports, Vol. 47, Issue 3 https://doi.org/10.1007/s11033-020-05279-9	journal	February 2020
Variations of culturable thermophilic microbe numbers and bacterial communities during the thermophilic phase of composting Li, Rong; Li, Linzhi; Huang, Rong World Journal of Microbiology and Biotechnology, Vol. 30, Issue 6 https://doi.org/10.1007/s11274-013-1593-9	journal	January 2014
Complete Genome Sequence of Geobacillus strain Y4.1MC1, a Novel CO-Utilizing Geobacillus thermoglucosidasius Strain Isolated from Bath Hot Spring in Yellowstone National Park Brumm, Phillip; Land, Miriam L.; Hauser, Loren J. BioEnergy Research, Vol. 8, Issue 3 https://doi.org/10.1007/s12155-015-9585-2	journal	February 2015
Genome sequencing in microfabricated high-density picolitre reactors Margulies, Marcel; Egholm, Michael; Altman, William E. Nature, Vol. 437, Issue 7057, p. 376-380 https://doi.org/10.1038/nature03959	journal	July 2005
The minimum information about a genome sequence (MIGS) specification Field, Dawn; Garrity, George; Gray, Tanya Nature Biotechnology, Vol. 26, Issue 5 https://doi.org/10.1038/nbt1360	journal	May 2008
Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments Pérez Castro, Sherlynette; Borton, Mikayla A.; Regan, Kathleen The ISME Journal, Vol. 15, Issue 12 https://doi.org/10.1038/s41396-021-01026-5	journal	June 2021
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Multiplex profiling of serum proteins in solution using barcoded antibody fragments and next generation sequencing Brofelth, Mattias; Ekstrand, Anna Isinger; Gour, Shashank Communications Biology, Vol. 3, Issue 1 https://doi.org/10.1038/s42003-020-1068-0	journal	July 2020
Three novel halotolerant and thermophilic Geobacillus strains from shallow marine vents Maugeri, Teresa L.; Gugliandolo, Concetta; Caccamo, Daniela Systematic and Applied Microbiology, Vol. 25, Issue 3 https://doi.org/10.1078/0723-2020-00119	journal	January 2002
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.955	journal	March 1997
Rfam: an RNA family database Griffiths-Jones, S. Nucleic Acids Research, Vol. 31, Issue 1 https://doi.org/10.1093/nar/gkg006	journal	January 2003
MUSCLE: multiple sequence alignment with high accuracy and high throughput Edgar, R. C. Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797 https://doi.org/10.1093/nar/gkh340	journal	March 2004
The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide Liolios, K. Nucleic Acids Research, Vol. 34, Issue 90001 https://doi.org/10.1093/nar/gkj145	journal	January 2006
The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata Liolios, Konstantinos; Chen, I-Min A.; Mavromatis, Konstantinos Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp848	journal	November 2009
IMG 4 version of the integrated microbial genomes comparative analysis system Markowitz, Victor M.; Chen, I-Min A.; Palaniappan, Krishna Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt963	journal	October 2013
Proposals Concerning the Higher Taxa of Bacteria Gibbons, N. E.; Murray, R. G. E. International Journal of Systematic Bacteriology, Vol. 28, Issue 1 https://doi.org/10.1099/00207713-28-1-1	journal	January 1978
Approved Lists of Bacterial Names Sneath, P. H. A.; McGOWAN, Vicki; Skerman, V. B. D. International Journal of Systematic and Evolutionary Microbiology, Vol. 30, Issue 1 https://doi.org/10.1099/00207713-30-1-225	journal	January 1980
Taxonomic study of aerobic thermophilic bacilli: descriptions of Geobacillus subterraneus gen. nov., sp. nov. and Geobacillus uzenensis sp. nov. from petroleum reservoirs and transfer of Bacillus stearothermophilus, Bacillus thermocatenulatus, Bacillus thermoleovorans, Bacillus kaustophilus, Bacillus thermodenitrificans to Geobacillus as the new combinations G. stearothermophilus, G. th. Ivanov, M. V.; Lysenko, A. M.; Petrunyaka, V. V. International Journal of Systematic and Evolutionary Microbiology, Vol. 51, Issue 2 https://doi.org/10.1099/00207713-51-2-433	journal	March 2001
Geobacillus toebii sp. nov., a novel thermophilic bacterium isolated from hay compost. Sung, M. H.; Kim, H.; Bae, J. W. International Journal of Systematic and Evolutionary Microbiology, Vol. 52, Issue 6 https://doi.org/10.1099/00207713-52-6-2251	journal	November 2002
Geobacillus lituanicus sp. nov. Kuisiene, N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 6 https://doi.org/10.1099/ijs.0.02976-0	journal	November 2004
Base-Calling of Automated Sequencer Traces Using Phred. II. Error Probabilities Ewing, Brent; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.186	journal	March 1998
Consed: A Graphical Tool for Sequence Finishing Gordon, David; Abajian, Chris; Green, Phil Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.195	journal	March 1998
Prodigal: prokaryotic gene recognition and translation initiation site identification Hyatt, Doug; Chen, Gwo-Liang; LoCascio, Philip F. BMC Bioinformatics, Vol. 11, Issue 1 https://doi.org/10.1186/1471-2105-11-119	journal	March 2010
Industrial Applications of Hyperthermophilic Enzymes: A Review de Miguel Bouzas, Trinidad; Barros-Velazquez, Jorge; Gonzalez Villa, Tomas Protein & Peptide Letters, Vol. 13, Issue 7 https://doi.org/10.2174/092986606777790548	journal	July 2006
Selected Enzymes from Extreme Thermophiles with Applications in Biotechnology Bergquist, Peter; Morgan, Hugh; Saul, David Current Biotechnology, Vol. 3, Issue 1 https://doi.org/10.2174/2211550102999131230150918	journal	March 2014
Genomic analysis of six new Geobacillus strains reveals highly conserved carbohydrate degradation architectures and strategies Brumm, Phillip J.; De Maayer, Pieter; Mead, David A. Frontiers in Microbiology, Vol. 6 https://doi.org/10.3389/fmicb.2015.00430	journal	May 2015
Thermophilic Protease-Producing Geobacillus from Buranga Hot Springs in Western Uganda Hawumba, Joseph F.; Theron, Jacques; Brözel, Volker S. Current Microbiology, Vol. 45, Issue 2 https://doi.org/10.1007/s00284-001-0116-3	journal	August 2002
Genomic characterization of thermophilic Geobacillus species isolated from the deepest sea mud of the Mariana Trench Takami, Hideto; Nishi, Shinro; Lu, Jei Extremophiles, Vol. 8, Issue 5 https://doi.org/10.1007/s00792-004-0394-3	journal	May 2004
Geobacillus galactosidasius sp. nov., a new thermophilic galactosidase-producing bacterium isolated from compost Poli, Annarita; Laezza, Giusi; Gul-Guven, Reyhan Systematic and Applied Microbiology, Vol. 34, Issue 6 https://doi.org/10.1016/j.syapm.2011.03.009	journal	September 2011
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
Alcohol pretreatment of stools effect on culturomics Afouda, Pamela; Hocquart, Marie; Pham, Thi-Phuong-Thao Scientific Reports, Vol. 10, Issue 1 https://doi.org/10.1038/s41598-020-62068-x	journal	March 2020
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Woese, C. R.; Kandler, O.; Wheelis, M. L. Proceedings of the National Academy of Sciences, Vol. 87, Issue 12 https://doi.org/10.1073/pnas.87.12.4576	journal	June 1990
MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods Tamura, K.; Peterson, D.; Peterson, N. Molecular Biology and Evolution, Vol. 28, Issue 10 https://doi.org/10.1093/molbev/msr121	journal	May 2011
tRNAscan-SE: A Program for Improved Detection of Transfer RNA Genes in Genomic Sequence Lowe, Todd M.; Eddy, Sean R. Nucleic Acids Research, Vol. 25, Issue 5 https://doi.org/10.1093/nar/25.5.0955	journal	March 1997
RNAmmer: consistent and rapid annotation of ribosomal RNA genes Lagesen, Karin; Hallin, Peter; Rødland, Einar Andreas Nucleic Acids Research, Vol. 35, Issue 9 https://doi.org/10.1093/nar/gkm160	journal	April 2007
List of new names and new combinations previously effectively, but not validly, published Oren, Aharon; Garrity, George M. International Journal of Systematic and Evolutionary Microbiology, Vol. 65, Issue Pt_4 https://doi.org/10.1099/ijs.0.000178	journal	April 2015
Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Nazina, T. N. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 54, Issue 6 https://doi.org/10.1099/ijs.0.02932-0	journal	November 2004
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes Kim, M.; Oh, H. -S.; Park, S. -C. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 2 https://doi.org/10.1099/ijs.0.059774-0	journal	February 2014
Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes Kim, M.; Oh, H. -S.; Park, S. -C. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, Vol. 64, Issue Pt 5 https://doi.org/10.1099/ijs.0.064931-0	journal	May 2014
List of new names and new combinations previously effectively, but not validly, published Oren, Aharon; Garrity, George M. International Journal of Systematic and Evolutionary Microbiology, Vol. 67, Issue 11 https://doi.org/10.1099/ijsem.0.002415	journal	November 2017
List of new names and new combinations previously effectively, but not validly, published Oren, Aharon; Garrity, George International Journal of Systematic and Evolutionary Microbiology, Vol. 70, Issue 3 https://doi.org/10.1099/ijsem.0.003991	journal	March 2020
Base-Calling of Automated Sequencer Traces Using Phred. I. Accuracy Assessment Ewing, Brent; Hillier, LaDeana; Wendl, Michael C. Genome Research, Vol. 8, Issue 3 https://doi.org/10.1101/gr.8.3.175	journal	March 1998
Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1 Bhalla, A.; Kainth, A. S.; Sani, R. K. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomeA.00595-13	journal	June 2013
Draft Genome Sequence of Lignocellulose-Degrading Thermophilic Bacterium Geobacillus sp. Strain WSUCF1 Bhalla, A.; Kainth, A. S.; Sani, R. K. Genome Announcements, Vol. 1, Issue 4 https://doi.org/10.1128/genomea.00595-13	journal	June 2013
Comparative analysis of the Geobacillus hemicellulose utilization locus reveals a highly variable target for improved hemicellulolysis De Maayer, Pieter; Brumm, Phillip J.; Mead, David A. BMC Genomics, Vol. 15, Issue 1 https://doi.org/10.1186/1471-2164-15-836	journal	January 2014

Cited By (3)

Coexistence of Heavy Metal Tolerance and Antibiotic Resistance in Thermophilic Bacteria Belonging to Genus Geobacillus Najar, Ishfaq Nabi; Das, Sayak; Kumar, Santosh Frontiers in Microbiology, Vol. 13 https://doi.org/10.3389/fmicb.2022.914037	journal	August 2022
Peculiarities and biotechnological potential of environmental adaptation by Geobacillus species Suzuki, Hirokazu Applied Microbiology and Biotechnology, Vol. 102, Issue 24 https://doi.org/10.1007/s00253-018-9422-6	journal	October 2018
Geobacillus yumthangensis sp. nov., a thermophilic bacterium isolated from a north-east Indian hot spring Najar, Ishfaq Nabi; Sherpa, Mingma Thundu; Das, Sayak International Journal of Systematic and Evolutionary Microbiology, Vol. 68, Issue 11 https://doi.org/10.1099/ijsem.0.003002	journal	November 2018

Similar Records

Complete genome sequence of Geobacillus thermoglucosidasius C56-YS93, a novel biomass degrader isolated from obsidian hot spring in Yellowstone National Park

Journal Article · Mon Oct 05 00:00:00 EDT 2015 · Standards in Genomic Sciences · OSTI ID:1260598

Complete genome sequences of Geobacillus sp. Y412MC52, a xylan-degrading strain isolated from obsidian hot spring in Yellowstone National Park

Journal Article · Mon Oct 19 00:00:00 EDT 2015 · Standards in Genomic Sciences · OSTI ID:1259497

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
Geobacillus sp. WCH70
Restriction-modification
Thermophile
Transposons
Wood compost

Complete genome sequences of Geobacillus sp. WCH70, a thermophilic strain isolated from wood compost

Citation Formats

References (46)

Cited By (3)

Similar Records

Related Subjects