Global metagenomic survey reveals a new bacterial candidate phylum in geothermal springs
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Amrita Pati | Tanja Woyke | Natalia N. Ivanova | Jennifer Pett-Ridge | David Paez-Espino | N. Kyrpides | E. Rubin | R. Malmstrom | S. Grasby | T. Woyke | Amrita Pati | Wenjun Li | P. Dunfield | E. Eloe-Fadrosh | B. Hedlund | Hailiang Dong | A. Brady | J. Pett‐Ridge | A. Dekas | J. Jarett | David Páez-Espino | B. Briggs | Wen-Jun Li | D. Goudeau | Jessica Jarett | Hailiang Dong | Rex Malmstrom | Danielle Goudeau | Emiley A. Eloe-Fadrosh | Peter F. Dunfield | Brian P. Hedlund | Anne E. Dekas | Stephen E. Grasby | Allyson L. Brady | Brandon R. Briggs | Edward M. Rubin | Nikos C. Kyrpides | Natalia N. Ivanova
[1] H. Mori,et al. Bmc Molecular Biology the Yfhq Gene of Escherichia Coli Encodes a Trna:cm32/um32 Methyltransferase , 2022 .
[2] N. Moran,et al. Parallel genomic evolution and metabolic interdependence in an ancient symbiosis , 2007, Proceedings of the National Academy of Sciences.
[3] K. Schleifer,et al. ARB: a software environment for sequence data. , 2004, Nucleic acids research.
[4] Lorenzo Segovia,et al. The hidden universal distribution of amino acid biosynthetic networks: a genomic perspective on their origins and evolution , 2008, Genome Biology.
[5] H. Santos,et al. Comparative study of the thermostabilizing properties of mannosylglycerate and other compatible solutes on model enzymes , 2002, Extremophiles.
[6] C. Gustafsson,et al. The spoU gene of Escherichia coli, the fourth gene of the spoT operon, is essential for tRNA (Gm18) 2'-O-methyltransferase activity. , 1997, Nucleic acids research.
[7] F. Avilés,et al. Amyloid Formation by Human Carboxypeptidase D Transthyretin-like Domain under Physiological Conditions* , 2014, The Journal of Biological Chemistry.
[8] D. Holmes,et al. Anaerobic degradation of aromatic amino acids by the hyperthermophilic archaeon Ferroglobus placidus. , 2014, Microbiology.
[9] K. Schleifer,et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences , 2014, Nature Reviews Microbiology.
[10] M. Lynch,et al. Ecology and exploration of the rare biosphere , 2015, Nature Reviews Microbiology.
[11] Nuno Empadinhas,et al. Diversity and biosynthesis of compatible solutes in hyper/thermophiles. , 2006, International microbiology : the official journal of the Spanish Society for Microbiology.
[12] Radhey S. Gupta,et al. The Phylogeny and Signature Sequences Characteristics of Fibrobacteres, Chlorobi, and Bacteroidetes , 2004, Critical reviews in microbiology.
[13] Holly M. Bik,et al. PhyloSift: phylogenetic analysis of genomes and metagenomes , 2014, PeerJ.
[14] P. Christensen,et al. Sediment mineralization, nutrient fluxes, denitrification and dissimilatory nitrate reduction to ammonium in an estuarine fjord with sea cage trout farms , 2000 .
[15] Natalia N. Ivanova,et al. Insights into the phylogeny and coding potential of microbial dark matter , 2013, Nature.
[16] R. Cavicchioli,et al. Influence of Temperature on tRNA Modification in Archaea: Methanococcoides burtonii (Optimum Growth Temperature [Topt], 23°C) and Stetteria hydrogenophila (Topt, 95°C) , 2003 .
[17] S. Douthwaite,et al. YibK is the 2'-O-methyltransferase TrmL that modifies the wobble nucleotide in Escherichia coli tRNA(Leu) isoacceptors. , 2010, RNA.
[18] J. Oost,et al. Unravelling the structural and mechanistic basis of CRISPR–Cas systems , 2014, Nature Reviews Microbiology.
[19] D. Noguera,et al. mathFISH, a Web Tool That Uses Thermodynamics-Based Mathematical Models for In Silico Evaluation of Oligonucleotide Probes for Fluorescence In Situ Hybridization , 2010, Applied and Environmental Microbiology.
[20] Toni Gabaldón,et al. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses , 2009, Bioinform..
[21] Yihua Huang,et al. Structure of the nonameric bacterial amyloid secretion channel , 2014, Proceedings of the National Academy of Sciences.
[22] Rolf Backofen,et al. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems , 2013, Nucleic acids research.
[23] Hiroyuki Kimura,et al. Selective Phylogenetic Analysis Targeted at 16S rRNA Genes of Thermophiles and Hyperthermophiles in Deep-Subsurface Geothermal Environments , 2006, Applied and Environmental Microbiology.
[24] Evan Andersen,et al. ProDeGe: a computational protocol for fully automated decontamination of genomes , 2015, The ISME Journal.
[25] J. Wagner,et al. Structural and biochemical analysis of sliding clamp/ligand interactions suggest a competition between replicative and translesion DNA polymerases. , 2004, Journal of molecular biology.
[26] S. Harayama,et al. Ignavibacterium album gen. nov., sp. nov., a moderately thermophilic anaerobic bacterium isolated from microbial mats at a terrestrial hot spring and proposal of Ignavibacteria classis nov., for a novel lineage at the periphery of green sulfur bacteria. , 2010, International journal of systematic and evolutionary microbiology.
[27] Pelin Yilmaz,et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..
[28] T. Nishino,et al. Fusion-type lycopene beta-cyclase from a thermoacidophilic archaeon Sulfolobus solfataricus. , 2003, Biochemical and biophysical research communications.
[29] J. Kuriyan,et al. Crystal Structure of the Processivity Clamp Loader Gamma (γ) Complex of E. coli DNA Polymerase III , 2001, Cell.
[30] D. Schüler,et al. The Periplasmic Nitrate Reductase Nap Is Required for Anaerobic Growth and Involved in Redox Control of Magnetite Biomineralization in Magnetospirillum gryphiswaldense , 2012, Journal of bacteriology.
[31] Lynne A. Goodwin,et al. Thermus oshimai JL-2 and T. thermophilus JL-18 genome analysis illuminates pathways for carbon, nitrogen, and sulfur cycling , 2013, Standards in genomic sciences.
[32] Brian C. Thomas,et al. Community-wide analysis of microbial genome sequence signatures , 2009, Genome Biology.
[33] N. Pace,et al. Remarkable archaeal diversity detected in a Yellowstone National Park hot spring environment. , 1994, Proceedings of the National Academy of Sciences of the United States of America.
[34] Daniel H. Huson,et al. Dendroscope: An interactive viewer for large phylogenetic trees , 2007, BMC Bioinformatics.
[35] Elmar Pruesse,et al. SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes , 2012, Bioinform..
[36] Daniel H. Haft,et al. A Guild of 45 CRISPR-Associated (Cas) Protein Families and Multiple CRISPR/Cas Subtypes Exist in Prokaryotic Genomes , 2005, PLoS Comput. Biol..
[37] D. Bolam,et al. Glycan recognition by the Bacteroidetes Sus-like systems. , 2012, Current opinion in structural biology.
[38] H. Hori. Methylated nucleosides in tRNA and tRNA methyltransferases , 2014, Front. Genet..
[39] P. François,et al. Importance of Bacillithiol in the Oxidative Stress Response of Staphylococcus aureus , 2013, Infection and Immunity.
[40] Yuzhen Ye,et al. Expanding the catalog of cas genes with metagenomes , 2013, Nucleic acids research.
[41] Nikos Kyrpides,et al. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats , 2007, BMC Bioinformatics.
[42] Robert C. Edgar,et al. BIOINFORMATICS APPLICATIONS NOTE , 2001 .
[43] Janusz M. Bujnicki,et al. Molecular evolution of dihydrouridine synthases , 2012, BMC Bioinformatics.
[44] J. Dodsworth,et al. Pyrosequencing Reveals High-Temperature Cellulolytic Microbial Consortia in Great Boiling Spring after In Situ Lignocellulose Enrichment , 2013, PloS one.
[45] S. Cianchetta,et al. Proteolysis of the proofreading subunit controls the assembly of Escherichia coli DNA polymerase III catalytic core. , 2009, Biochimica et biophysica acta.
[46] E. Shock,et al. Microbiology and geochemistry of great boiling and mud hot springs in the United States Great Basin , 2009, Extremophiles.
[47] Č. Venclovas,et al. Comprehensive analysis of DNA polymerase III α subunits and their homologs in bacterial genomes , 2013, Nucleic acids research.
[48] R. Huber,et al. Crystal structure of gingipain R: an Arg‐specific bacterial cysteine proteinase with a caspase‐like fold , 1999, The EMBO journal.
[49] Thijs J. G. Ettema,et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes , 2015, Nature.
[50] Susannah G. Tringe,et al. The YNP Metagenome Project: Environmental Parameters Responsible for Microbial Distribution in the Yellowstone Geothermal Ecosystem , 2013, Front. Microbiol..
[51] Alexandros Stamatakis,et al. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..
[52] Brian C. Thomas,et al. Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.
[53] Kenneth H. Williams,et al. Extraordinary phylogenetic diversity and metabolic versatility in aquifer sediment , 2013, Nature Communications.
[54] B. Hungate,et al. A Comprehensive Census of Microbial Diversity in Hot Springs of Tengchong, Yunnan Province China Using 16S rRNA Gene Pyrosequencing , 2013, PloS one.
[55] Ruben E. Valas,et al. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage , 2011, The ISME Journal.
[56] Kenneth H. Williams,et al. Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling , 2015, Current Biology.
[57] Sathees B. C. Chandra,et al. The linkage between reverse gyrase and hyperthermophiles: A review of their invariable association , 2009, The Journal of Microbiology.
[58] B. Hungate,et al. Potential role of Thermus thermophilus and T. oshimai in high rates of nitrous oxide (N2O) production in ∼80 °C hot springs in the US Great Basin , 2011, Geobiology.
[59] Derek R Lovley,et al. Genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon Ferroglobus placidus , 2011, The ISME Journal.
[60] S. Giovannoni,et al. Implications of streamlining theory for microbial ecology , 2014, The ISME Journal.
[61] D. M. Ward,et al. Complete genome of Candidatus Chloracidobacterium thermophilum, a chlorophyll-based photoheterotroph belonging to the phylum Acidobacteria. , 2012, Environmental microbiology.
[62] N. Moran,et al. Extreme genome reduction in symbiotic bacteria , 2011, Nature Reviews Microbiology.
[63] H. Hirakawa,et al. A protein secretion system linked to bacteroidete gliding motility and pathogenesis , 2009, Proceedings of the National Academy of Sciences.
[64] N. Pace,et al. Novel Division Level Bacterial Diversity in a Yellowstone Hot Spring , 1998, Journal of bacteriology.
[65] Sean R. Eddy,et al. Rfam 11.0: 10 years of RNA families , 2012, Nucleic Acids Res..
[66] Dmitry Antipov,et al. Assembling Single-Cell Genomes and Mini-Metagenomes From Chimeric MDA Products , 2013, J. Comput. Biol..
[67] Rudolf Amann,et al. Fluorescence In Situ Hybridization and Catalyzed Reporter Deposition for the Identification of Marine Bacteria , 2002, Applied and Environmental Microbiology.
[68] Eugene V Koonin,et al. The basic building blocks and evolution of CRISPR-CAS systems. , 2013, Biochemical Society transactions.
[69] Edward M. Rubin,et al. Searching for new branches on the tree of life , 2014, Science.
[70] Sean R. Eddy,et al. Infernal 1.1: 100-fold faster RNA homology searches , 2013, Bioinform..
[71] Robert D. Finn,et al. HMMER web server: interactive sequence similarity searching , 2011, Nucleic Acids Res..
[72] S. Grasby,et al. Humboldt’s spa: microbial diversity is controlled by temperature in geothermal environments , 2014, The ISME Journal.
[73] M. Chapman,et al. Curli biogenesis: order out of disorder. , 2014, Biochimica et biophysica acta.
[74] Andrew Robinson,et al. Architecture and Conservation of the Bacterial DNA Replication Machinery, an Underexploited Drug Target , 2012, Current drug targets.
[75] I-Min A. Chen,et al. IMG/M 4 version of the integrated metagenome comparative analysis system , 2013, Nucleic Acids Res..
[76] David Posada,et al. ProtTest: selection of best-fit models of protein evolution , 2005, Bioinform..
[77] S. Gavrilov,et al. Characterization of Melioribacter roseus gen. nov., sp. nov., a novel facultatively anaerobic thermophilic cellulolytic bacterium from the class Ignavibacteria, and a proposal of a novel bacterial phylum Ignavibacteriae. , 2013, Environmental microbiology.
[78] Brian C. Thomas,et al. Small Genomes and Sparse Metabolisms of Sediment-Associated Bacteria from Four Candidate Phyla , 2013, mBio.
[79] D. Bryant,et al. Prokaryotic photosynthesis and phototrophy illuminated. , 2006, Trends in microbiology.
[80] K. Weber,et al. Microorganisms pumping iron: anaerobic microbial iron oxidation and reduction , 2006, Nature Reviews Microbiology.
[81] M. Noordewier,et al. Genome Streamlining in a Cosmopolitan Oceanic Bacterium , 2005, Science.
[82] James R. Knight,et al. Genome sequencing in microfabricated high-density picolitre reactors , 2005, Nature.
[83] G. Michel,et al. Environmental and Gut Bacteroidetes: The Food Connection , 2011, Front. Microbio..
[84] H. Brüssow,et al. Comparative Genomics of Streptococcus thermophilus Phage Species Supports a Modular Evolution Theory , 1999, Journal of Virology.
[85] Natalia N. Ivanova,et al. Microbial species delineation using whole genome sequences , 2015, Nucleic acids research.
[86] Pedro M. Coutinho,et al. The carbohydrate-active enzymes database (CAZy) in 2013 , 2013, Nucleic Acids Res..
[87] John P. Huelsenbeck,et al. MrBayes 3: Bayesian phylogenetic inference under mixed models , 2003, Bioinform..
[88] Stan J. J. Brouns,et al. Evolution and classification of the CRISPR–Cas systems , 2011, Nature Reviews Microbiology.
[89] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[90] N. Pace. Mapping the Tree of Life: Progress and Prospects , 2009, Microbiology and Molecular Biology Reviews.
[91] J. Dodsworth,et al. Sediment microbial communities in Great Boiling Spring are controlled by temperature and distinct from water communities , 2012, The ISME Journal.
[92] Donovan H. Parks,et al. First genomic insights into members of a candidate bacterial phylum responsible for wastewater bulking , 2015, PeerJ.
[93] Connor T. Skennerton,et al. Crass: identification and reconstruction of CRISPR from unassembled metagenomic data , 2013, Nucleic acids research.
[94] Brian C. Thomas,et al. Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.
[95] P. Forterre,et al. Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. , 2007, Archaea.
[96] M. Wagner,et al. Modeling Formamide Denaturation of Probe-Target Hybrids for Improved Microarray Probe Design in Microbial Diagnostics , 2012, PloS one.
[97] K. Katoh,et al. MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.
[98] J. Helmann,et al. Biosynthesis and functions of bacillithiol, a major low-molecular-weight thiol in Bacilli , 2010, Proceedings of the National Academy of Sciences.
[99] Rolf Backofen,et al. CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci , 2014, Bioinform..
[100] R. Wierenga,et al. A comprehensive analysis of the geranylgeranylglyceryl phosphate synthase enzyme family identifies novel members and reveals mechanisms of substrate specificity and quaternary structure organization , 2014, Molecular microbiology.
[101] M. Strous,et al. Microbial nitrate respiration--genes, enzymes and environmental distribution. , 2011, Journal of biotechnology.
[102] Natalia N. Ivanova,et al. The DOE-JGI Standard Operating Procedure for the Annotations of Microbial Genomes , 2009, Standards in genomic sciences.