Genomic and Applied Microbiology

Former Publications (2011-2001)

2011

Becker K, Mutter W, Daniel R, Rudack C, Peschel A, Pieper DH (2011) Bakterielle Untermieter in der menschlichen Nase. GENOMXPRESS 1.11:8-10.

Bijtenhoorn P, Mayerhofer H, Müller-Dieckmann J, Utpatel C, Schipper C, Hornung C, Szesny M, Grond S, Thürmer A, Brzuszkiewicz E, Daniel R, Dierking K, Schulenburg H, Streit WR (2011) A novel metagenomic short-chain dehydrogenase/reductase attenuates Pseudomonas aeruginosa biofilm formation and virulence on Caenorhabditis elegans. PLoS One 6(10):e26278 (abstract).

Bletz S, Schuldes J, Brzuszkiewicz E, Daniel R, Gottschalk G, Karch H, Mellmann A (2011) Evolutionary events in Enterohemorrhagic Escherichia coli (EHEC) O26:H11. International Journal of Medical Microbiology 301(Supplement 47):115.

Brzuszkiewicz E, Thürmer A, Schuldes J, Leimbach A, Liesegang H, Meyer FD, Boelter J, Petersen H, Gottschalk G, Daniel R (2011) Genome sequence analyses of two isolates from the recent Escherichia coli outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic Escherichia coli (EAHEC). Arch Microbiol 193(12):883-891 (abstract).

Brzuszkiewicz E, Weiner J, Wollherr A, Thürmer A, Hüpeden J, Lomholt HB, Kilian M, Gottschalk G, Daniel R, Mollenkopf HJ, Meyer TF, Brüggemann H (2011) Comparative genomics and transcriptomics of Propionibacterium acnes. PLoS One 6(6):e21581 (abstract).

Daniel R (2011) Soil-based metagenomics, in Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats (de Bruijn FJ, Ed.), pp. 83-92, John Wiley & Sons, Inc.

Djukic M, Poehlein A, Thürmer A, Daniel R (2011) Genome sequence of Brevibacillus laterosporus LMG 15441, a pathogen of invertebrates. J Bacteriol 193(19):5535-5536 (abstract).

Duda KA, Lindner B, Brade H, Leimbach A, Brzuszkiewicz E, Dobrindt U, Holst O (2011) The lipopolysaccharide of the mastitis isolate Escherichia coli strain 1303 comprises a novel O-antigen and the rare K-12 core type. Microbiology 157(Pt 6):1750-1760 (abstract).

Fekete PZ, Brzuszkiewicz E, Blum-Oehler G, Olasz F, Szabo M, Gottschalk G, Hacker J, Nagy B (2011) DNA sequence analysis of the composite plasmid pTC conferring virulence and antimicrobial resistance for porcine enterotoxigenic Escherichia coli. Int J Med Microbiol 302(1):4-9 (abstract).

Gounder K, Brzuszkiewicz E, Liesegang H, Wolherr A, Daniel R, Gottschalk G, Reva O, Kumwenda B, Srivastava M, Bricio C, Berenguer J, van Heerden E, Litthauer D (2011) Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01. BMC Genomics 12(1):577 (abstract).

Hoff KH, Tech M, Lingner T, Daniel R, Morgenstern B, Meinicke P (2011) Gene prediction in metagenomic fragments with Orphelia: a large scale machine learning approach, in Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches (de Bruijn FJ, Ed.), pp. 359-368, John Wiley & Sons, Inc.

Kadlec K, Brenner Michael G, Sweeney MT, Brzuszkiewicz E, Liesegang H, Daniel R, Watts JL, Schwarz S (2011) Molecular basis of macrolide, triamilide, and lincosamide resistance in Pasteurella multocida from bovine respiratory disease. Antimicrob Agents Chemother 55(5):2475-2477 (abstract).

Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H, Wollher A, Daniel R, Simon M, Brinkhoff T (2011) Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics 12:324 (abstract).

Kaster AK, Goenrich M, Seedorf H, Liesegang H, Wollherr A, Gottschalk G, Thauer RK (2011) More than 200 genes required for methane formation from H(2) and CO(2) and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus. Archaea 2011973848 (abstract).

Markert S, Gardebrecht A, Felbeck H, Sievert SM, Klose J, Becher D, Albrecht D, Thürmer A, Daniel R, Kleiner M, Hecker M, Schweder T (2011) Status quo in physiological proteomics of the uncultured Riftia pachyptila endosymbiont. Proteomics 11(15):3106-3117 (abstract).

Nacke H, Thürmer A, Wollherr A, Will C, Hodac L, Herold N, Schoning I, Schrumpf M, Daniel R (2011) Pyrosequencing-based assessment of bacterial community structure along different management types in German forest and grassland soils. PLoS One 6(2):e17000 (abstract).

Nacke H, Will C, Herzog S, Nowka B, Engelhaupt M, Daniel R (2011) Identification of novel lipolytic genes and gene families by screening of metagenomic libraries derived from soil samples of the German Biodiversity Exploratories. FEMS Microbiol Ecol 78(1):188-201 (abstract).

Poehlein A, Kusian B, Friedrich B, Daniel R, Bowien B (2011) Complete genome sequence of the type strain Cupriavidus necator N-1. J Bacteriol 193(18):5017 (abstract).

Rechnitzer H, Brzuszkiewicz E, Strittmatter A, Liesegang H, Lysnyansky I, Daniel R, Gottschalk G, Rottem S (2011) Genomic features and insights into the biology of Mycoplasma fermentans. Microbiology 157(Pt 3):760-773 (abstract).

Schallmey M, Ly A, Wang C, Meglei G, Voget S, Streit WR, Driscoll BT, Charles TC (2011) Harvesting of novel polyhydroxyalkanaote (PHA) synthase encoding genes from a soil metagenome library using phenotypic screening. FEMS Microbiol Lett 321(2):150-156 (abstract).

Simon C, Daniel R (2011) Metagenomic analyses: past and future trends. Appl Environ Microbiol 77(4):1153-1161 (abstract).

Thürmer A, Voigt B, Angelov A, Albrecht D, Hecker M, Liebl W (2011) Proteomic analysis of the extremely thermoacidophilic archaeon Picrophilus torridus at pH and temperature values close to its growth limit. Proteomics 11(23):4559-4568 (abstract).

Vockenhuber MP, Sharma CM, Statt MG, Schmidt D, Xu Z, Dietrich S, Liesegang H, Mathews DH, Suess B (2011) Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 8(3):468-477 (abstract).

Vogel RF, Pavlovic M, Ehrmann MA, Wiezer A, Liesegang H, Offschanka S, Voget S, Angelov A, Bocker G, Liebl W (2011) Genomic analysis reveals Lactobacillus sanfranciscensis as stable element in traditional sourdoughs. Microb Cell Fact 10 Suppl 1S6 (abstract).

Voget S, Klippel B, Daniel R, Antranikian G (2011) Complete genome sequence of Carnobacterium sp. 17-4. J Bacteriol 193(13):3403-3404 (abstract).

Volland S, Rachinger M, Strittmatter A, Daniel R, Gottschalk G, Meyer O (2011) Complete genome sequences of the chemolithoautotrophic Oligotropha carboxidovorans strains OM4 and OM5. J Bacteriol 193(18):5043 (abstract).

Zedelius J, Rabus R, Grundmann O, Werner I, Brodkorb D, Schreiber F, Ehrenreich P, Behrends A, Wilkes H, Kube M, Reinhardt R, Widdel F (2011) Alkane degradation under anoxic conditions by a nitrate-reducing bacterium with possible involvement of the electron acceptor in substrate activation. Environ Microbiol Rep 3(1):125-135 (abstract).

2010

Angelov A, Liebl S, Ballschmiter M, Bomeke M, Lehmann R, Liesegang H, Daniel R, Liebl W (2010) Genome sequence of the polysaccharide-degrading, thermophilic anaerobe Spirochaeta thermophila DSM 6192. J Bacteriol 192(24):6492-6493 (abstract).

Farnbacher M, Jahns T, Willrodt D, Daniel R, Haas R, Goesmann A, Kurtz S, Rieder G (2010) Sequencing, annotation, and comparative genome analysis of the gerbil-adapted Helicobacter pylori strain B8. BMC Genomics 11:335 (abstract).

Hoffmann K, Wollherr A, Larsen M, Rachinger M, Liesegang H, Ehrenreich A, Meinhardt F (2010) Facilitation of direct conditional knockout of essential genes in Bacillus licheniformis DSM13 by comparative genetic analysis and manipulation of genetic competence. Appl Environ Microbiol 76(15):5046-5057 (abstract).

Klee SR, Brzuszkiewicz EB, Nattermann H, Brüggemann H, Dupke S, Wollherr A, Franz T, Pauli G, Appel B, Liebl W, Couacy-Hymann E, Boesch C, Meyer FD, Leendertz FH, Ellerbrok H, Gottschalk G, Grunow R, Liesegang H (2010) The genome of a Bacillus isolate causing anthrax in chimpanzees combines chromosomal properties of B. cereus with B. anthracis virulence plasmids. PLoS One 5(7):e10986 (abstract).

Köpke M, Held C, Hujer S, Liesegang H, Wiezer A, Wollherr A, Ehrenreich A, Liebl W, Gottschalk G, Dürre P (2010) Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci U S A 107(29):13087-13092 (abstract).

Kuenne C, Voget S, Pischimarov J, Oehm S, Goesmann A, Daniel R, Hain T, Chakraborty T (2010) Comparative analysis of plasmids in the genus Listeria. PLoS One 5(9):e12511 (abstract).

Leimbach A, Brzuszkiewicz E, Thürmer A, Daniel R, Gottschalk G, Dobrindt U (2010) Elucidation of the complete genome sequence of Escherichia coli acute bovine mastitis isolate 1303: implications for host-pathogen interactions. Reproduction in Domestic Animals 45 (Supplement 1):29.

Liesegang H, Kaster AK, Wiezer A, Goenrich M, Wollherr A, Seedorf H, Gottschalk G, Thauer RK (2010) Complete genome sequence of Methanothermobacter marburgensis, a methanoarchaeon model organism. J Bacteriol 192(21):5850-5851 (abstract).

Schreiber F, Gumrich P, Daniel R, Meinicke P (2010) Treephyler: fast taxonomic profiling of metagenomes. Bioinformatics 26(7):960-1 (abstract).

Simon C, Daniel R (2010) Construction of small-insert and large-insert metagenomic libraries. Methods Mol Biol 668:39-50 (abstract).

Streit WR, Daniel R (2010) Metagenomics: Methods and Protocols (Methods in Molecular Biology, Vol. 668) W. Streit, R. Daniel (eds.) Humana Press, Springer Verlag.

Wagenknecht M, Dib JR, Thürmer A, Daniel R, Farias ME, Meinhardt F (2010) Structural peculiarities of linear megaplasmid, pLMA1, from Micrococcus luteus interfere with pyrosequencing reads assembly. Biotechnol Lett 32(12):1853-1862 (abstract).

Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I, Bunk B, Cypionka H, Daniel R, Drepper T, Gerdts G, Hahnke S, Han C, Jahn D, Kalhoefer D, Kiss H, Klenk HP, Kyrpides N, Liebl W, Liesegang H, Meincke L, Pati A, Petersen J, Piekarski T, Pommerenke C, Pradella S, Pukall R, Rabus R, Stackebrandt E, Thole S, Thompson L, Tielen P, Tomasch J, von Jan M, Wanphrut N, Wichels A, Zech H, Simon M (2010) The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 4(1):61-77 (abstract).

Will C, Nacke H, Thürmer A, Daniel R (2010) Schlaglicht Biodiversität / Charakterisierung und Nutzung der bakteriellen Diversität in Bodenmetagenomen. GENOMXPRESS 1.10:9-11.

Will C, Thürmer A, Wollherr A, Nacke H, Herold N, Schrumpf M, Gutknecht J, Wubet T, Buscot F, Daniel R (2010) Horizon-specific bacterial community composition of German grassland soils, as revealed by pyrosequencing-based analysis of 16S rRNA genes. Appl Environ Microbiol 76(20):6751-6759 (abstract).

Zdziarski J, Brzuszkiewicz E, Wullt B, Liesegang H, Biran D, Voigt B, Gronberg-Hernandez J, Ragnarsdottir B, Hecker M, Ron EZ, Daniel R, Gottschalk G, Hacker J, Svanborg C, Dobrindt U (2010) Host imprints on bacterial genomes--rapid, divergent evolution in individual patients. PLoS Pathog 6(8):e1001078 (abstract).

2009

Brzuszkiewicz E, Gottschalk G, Ron E, Hacker J, Dobrindt U (2009) Adaptation of pathogenic E. coli to various niches: genome flexibility is the key. Genome Dyn 6:110-125 (abstract).

Ducka P, Eckhard U, Schönauer E, Kofler S, Gottschalk G, Brandstetter H, Nüss D (2009) A universal strategy for high-yield production of soluble and functional clostridial collagenases in E. coli. Appl. Microbiol. Biotechnol. 83(6):1155-65 (abstract).

Ferguson T, Soares JA, Lienard T, Gottschalk G, Krzycki JA (2009) RamA, a protein required for reductive activation of corrinoid-dependent methylamine methyltransferase reactions in methanogenic archaea. J. Biol. Chem. 284(4):2285-2295 (abstract).

Schmeisser C, Liesegang H, Krysciak D, Bakkou N, Le Quere A, Wollherr A, Heinemeyer I, Morgenstern B, Pommerening-Roser A, Flores M, Palacios R, Brenner S, Gottschalk G, Schmitz RA, Broughton WJ, Perret X, Strittmatter AW, Streit WR (2009) Rhizobium sp. strain NGR234 possesses a remarkable number of secretion systems. Appl Environ Microbiol 75(12):4035-4045 (abstract).

Simon C, Daniel R (2009) Achievements and new knowledge unraveled by metagenomic approaches. Appl Microbiol Biotechnol 85(2):265-276 (abstract).

Simon C, Daniel R (2009) Mikrobielles Leben im Eis. GENOMXPRESS 1.09:4-6.

Simon C, Herath J, Rockstroh S, Daniel R (2009) Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 75(9):2964-2968 (abstract).

Simon C, Wiezer A, Strittmatter AW, Daniel R (2009) Phylogenetic diversity and metabolic potential revealed in a glacier ice metagenome. Appl Environ Microbiol 75(23):7519-7526 (abstract).

Staron A, Sofia HJ, Dietrich S, Ulrich LE, Liesegang H, Mascher T (2009) The third pillar of bacterial signal transduction: classification of the extracytoplasmic function (ECF) sigma factor protein family. Mol Microbiol 74(3):557-581 (abstract).

Steele HL, Jaeger KE, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16(1-2):25-37 (abstract).

Strittmatter AW, Liesegang H, Rabus R, Decker I, Amann J, Andres S, Henne A, Fricke WF, Martinez-Arias R, Bartels D, Goesmann A, Krause L, Pühler A, Klenk HP, Richter M, Schuler M, Glöckner FO, Meyerdierks A, Gottschalk G, Amann R (2009) Genome sequence of Desulfobacterium autotrophicum HRM2, a marine sulfate reducer oxidizing organic carbon completely to carbon dioxide. Environ. Microbiol. 11(5):1038-1055 (abstract).

Voigt B, Antelmann H, Albrecht D, Ehrenreich A, Maurer KH, Evers S, Gottschalk G, van Dijl JM, Schweder T, Hecker M (2009) Cell physiology and protein secretion of Bacillus licheniformis compared to Bacillus subtilis. J Mol Microbiol Biotechnol 16(1-2):53-68 (abstract).

Waschkowitz T, Rockstroh S, Daniel R (2009) Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl Environ Microbiol 75(8):2506-2516 (abstract).

Zech H, Thole S, Schreiber K, Kalhofer D, Voget S, Brinkhoff T, Simon M, Schomburg D, Rabus R (2009) Growth phase-dependent global protein and metabolite profiles of Phaeobacter gallaeciensis strain DSM 17395, a member of the marine Roseobacter-clade. Proteomics 9(14):3677-3697 (abstract).

2008

Brüggemann H, Gottschalk G (2008) Comparative genomics of clostridia: link between the ecological niche and cell surface properties. Ann N Y Acad Sci 1125: 73-81 (abstract).

Hoff KJ, Tech M, Lingner T, Daniel R, Morgenstern B, Meinicke P (2008) Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics 9(1): 217 (abstract).

Liebl W, Winterhalter C, Baumeister W, Armbrecht M, Valdez M (2008) Xylanase attachment to the cell wall of the hyperthermophilic bacterium Thermotoga maritima. J Bacteriol 190(4): 1350-1358 (abstract).

Seedorf H, Fricke WF, Veith B, Brüggemann H, Liesegang H, Strittmatter A, Miethke M, Buckel W, Hinderberger J, Li F, Hagemeier C, Thauer RK, Gottschalk G (2008) The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA 105(6): 2128-2133 (abstract).

Tzvetkov MV, Liebl W (2008) Phytate utilization by genetically engineered lysine-producing Corynebacterium glutamicum. J Biotechnol 134(3-4): 211-217 (abstract).

Weidenbach K, Ehlers C, Kock J, Ehrenreich A, Schmitz RA (2008) Insights into the NrpR regulon in Methanosarcina mazei Gö1. Arch Microbiol 190(3): 319-332 (abstract).

2007

Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O, Junge H, Voigt B, Jungblut PR, Vater J, Süssmuth R, Liesegang H, Strittmatter A, Gottschalk G, Borriss R (2007) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25(9): 1007-1014 (abstract).

Li F, Hagemeier CH, Seedorf H, Gottschalk G, Thauer RK (2007) Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase. J Bacteriol 189(11): 4299-4304 (abstract).

Mahapatra A, Srinivasan G, Richter KB, Meyer A, Lienard T, Zhang JK, Zhao G, Kang PT, Chan M, Gottschalk G, Metcalf WW, Krzycki JA (2007) Class I and class II lysyl-tRNA synthetase mutants and the genetic encoding of pyrrolysine in Methanosarcina spp. Mol Microbiol 64(5): 1306-1318 (abstract).

Martin-Cuadrado AB, Lopez-Garcia P, Alba JC, Moreira D, Monticelli L, Strittmatter A, Gottschalk G, Rodriguez-Valera F (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS One 2(9): e914 (abstract).

Parschat K, Overhage J, Strittmatter AW, Henne A, Gottschalk G, Fetzner S (2007) Complete nucleotide sequence of the 113-kilobase linear catabolic plasmid pAL1 of Arthrobacter nitroguajacolicus Ru61a and transcriptional analysis of genes involved in quinaldine degradation. J Bacteriol 189(10): 3855-3867 (abstract).

Pflueger K, Ehrenreich A, Salmon K, Gunsalus RP, Deppenmeier U, Gottschalk G, Müller V (2007) Identification of genes involved in salt adaptation in the archaeon Methanosarcina mazei Gö1 using genome-wide gene expression profiling. FEMS Microbiol Lett 277(1): 79-89 (abstract).

Voigt B, Hoi le T, Jürgen B, Albrecht D, Ehrenreich A, Veith B, Evers S, Maurer KH, Hecker M, Schweder T (2007) The glucose and nitrogen starvation response of Bacillus licheniformis. Proteomics 7(3): 413-423 (abstract).

2006

Angelov A, Liebl W (2006) Insights into extreme thermoacidophily based on genome analysis of Picrophilus torridus and other thermoacidophilic archaea. J Biotechnol 126: 3-10 (abstract).

Angelov A, Putyrski M, Liebl W (2006) Molecular and biochemical characterization of alpha-glucosidase and alpha-mannosidase and their clustered genes from the thermoacidophilic archaeon Picrophilus torridus. J Bacteriol 188(20): 7123-7131 (abstract).

Ballschmiter M, Fütterer O, Liebl W (2006) Identification and characterization of a novel intracellular alkaline alpha-amylase from the hyperthermophilic bacterium Thermotoga maritima MSB8. Appl Environ Microbiol 72(3): 2206-2211 (abstract).

Brzuszkiewicz E, Brüggemann H, Liesegang H, Emmerth M, Olschlager T, Nagy G, Albermann K, Wagner C, Buchrieser C, Emody L, Gottschalk G, Hacker J, Dobrindt U (2006) How to become a uropathogen: Comparative genomic analysis of extraintestinal pathogenic Escherichia coli strains. Proc Natl Acad Sci USA 103(34): 12879-12884 (abstract).

Chen XH, Vater J, Piel J, Franke P, Scholz R, Schneider K, Koumoutsi A, Hitzeroth G, Grammel N, Strittmatter AW, Gottschalk G, Süssmuth RD, Borriss R (2006) Structural and functional characterization of three polyketide synthase gene clusters in Bacillus amyloliquefaciens FZB 42. J Bacteriol 188(11): 4024-4036 (abstract).

Dickmanns A, Ballschmiter M, Liebl W, Ficner R (2006) Structure of the novel alpha-amylase AmyC from Thermotoga maritima. Acta Crystallogr. D. Biol. Crystallogr. 62(Pt 3): 262-270 (abstract).

Ehrenreich A (2006) DNA microarray technology for the microbiologist: an overview. Appl Microbiol Biotechnol 73(2): 255-273 (abstract).

Ehrenreich A, Gottschalk G, Brüggemann H (2006) Genomics of pathogenic clostridia and bacilli, in Pathogenomics: Genome analysis of pathogenic microbes (Hacker J, and Dobrindt U, Eds.), pp. 257-280, Wiley-VCH Verlag, Weinheim.

Fricke WF, Seedorf H, Henne A, Kruer M, Liesegang H, Hedderich R, Gottschalk G, Thauer RK (2006) The genome sequence of Methanosphaera stadtmanae reveals why this human intestinal archaeon is restricted to methanol and H2 for methane formation and ATP synthesis. J Bacteriol 188(2): 642-658 (abstract).

Hochhut B, Wilde C, Balling G, Middendorf B, Dobrindt U, Brzuszkiewicz E, Gottschalk G, Carniel E, Hacker J (2006) Role of pathogenicity island-associated integrases in the genome plasticity of uropathogenic Escherichia coli strain 536. Mol Microbiol 61(3): 584-595 (abstract).

Hoi LT, Voigt B, Jürgen B, Ehrenreich A, Gottschalk G, Evers S, Feesche J, Maurer KH, Hecker M, Schweder T (2006) The phosphate-starvation response of Bacillus licheniformis. Proteomics 6(12): 3582-3601 (abstract).

Kleine J, Liebl W (2006) Comparative characterization of deletion derivatives of the modular xylanase XynA of Thermotoga maritima. Extremophiles 10(5): 373-81 (abstract).

Medalia N, Sharon M, Martinez-Arias R, Mihalache O, Robinson CV, Medalia O, Zwickl P (2006) Functional and structural characterization of the Methanosarcina mazei proteasome and PAN complexes. J Struct Biol 156(1): 84-92 (abstract).

Nougayrede JP, Homburg S, Taieb F, Boury M, Brzuszkiewicz E, Gottschalk G, Buchrieser C, Hacker J, Dobrindt U, Oswald E (2006) Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313(5788): 848-851 (abstract).

Petersen M, Daniel R (2006) Purification and characterization of an extracellular lipase from Clostridium tetanomorphum. W J Microbiol Biotechnol 22(5): 431-435 (abstract).

Pohlmann A, Fricke WF, Reinecke F, Kusian B, Liesegang H, Cramm R, Eitinger T, Ewering C, Potter M, Schwartz E, Strittmatter A, Voss I, Gottschalk G, Steinbüchel A, Friedrich B, Bowien B (2006) Genome sequence of the bioplastic-producing "Knallgas" bacterium Ralstonia eutropha H16. Nat Biotechnol 24(10): 1257-1262 (abstract).

Schwarz S, Waschkowitz T, Daniel R- (2006) Enhancement of gene detection frequencies by combining DNA-based stable-isotope probing with the construction of metagenomic DNA libraries. W J Microbiol Biotechnol 22(4): 363-368 (abstract).

Veit K, Ehlers C, Ehrenreich A, Salmon K, Hovey R, Gunsalus RP, Deppenmeier U, Schmitz RA (2006) Global transcriptional analysis of Methanosarcina mazei strain Gö1 under different nitrogen availabilities. Mol Genet Genomics 276(1): 41-55 (abstract).

Voget S, Steele HL, Streit WR (2006) Characterization of a metagenome-derived halotolerant cellulase. J Biotechnol 126(1): 26-36 (abstract).

Voigt B, Schweder T, Sibbald MJ, Albrecht D, Ehrenreich A, Bernhardt J, Feesche J, Maurer KH, Gottschalk G, van Dijl JM, Hecker M (2006) The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions. Proteomics 6(1): 268-281 (abstract).

Wyszynska A, Pawlowski M, Bujnicki J, Pawelec D, Van Putten JP, Brzuszkiewicz E, Jagusztyn-Krynicka EK (2006) Genetic characterisation of the cjaAB operon of Campylobacter coli. Pol J Microbiol 55(2): 85-94 (abstract).

2005

Angelov A, Fütterer O, Valerius O, Braus GH, Liebl W (2005) Properties of the recombinant glucose/galactose dehydrogenase from the extreme thermoacidophile, Picrophilus torridus. Febs J. 272(4): 1054-1062 (abstract).

Ballschmiter M, Armbrecht M, Ivanova K, Antranikian G, Liebl W (2005) AmyA, an alpha-amylase with beta-cyclodextrin-forming activity, and AmyB from the thermoalkaliphilic organism Anaerobranca gottschalkii: two alpha-amylases adapted to their different cellular localizations. Appl Environ Microbiol 71(7): 3709-3715 (abstract).

Daniel R (2005) The metagenomics of soil. Nat Rev Microbiol 3(6): 470-478 (abstract).

Hoster F, Schmitz JE, Daniel R (2005) Enrichment of chitinolytic microorganisms: isolation and characterization of a chitinase exhibiting antifungal activity against phytopathogenic fungi from a novel Streptomyces strain. Appl Microbiol Biotechnol 66(4): 434-442 (abstract).

Hovey R, Lentes S, Ehrenreich A, Salmon K, Saba K, Gottschalk G, Gunsalus RP, Deppenmeier U (2005) DNA microarray analysis of Methanosarcina mazei Gö1 reveals adaptation to different methanogenic substrates. Mol Genet Genomics 273(3): 225-239 (abstract).

Liebl W (2005) Corynebacterium Taxonomy, in Handbook of Corynebacterium glutamicum (Eggeling L, and Bott M, Eds.), pp. 9-34, CRC Press.

Prust C, Hoffmeister M, Liesegang H, Wiezer A, Fricke WF, Ehrenreich A, Gottschalk G, Deppenmeier U (2005) Complete genome sequence of the acetic acid bacterium Gluconobacter oxydans. Nat Biotechnol 23(2): 195-200 (abstract).

Schuster SC, Gottschalk G (2005) Microbial genomics in its second decade. Curr. Opin. Microbiol. 8(5): 561-563 (abstract).

Streit W, Jaeger KE, Daniel R (2005) Umweltgenomik (Metagenomik) als nahezu unerschöpfliche Quelle für neue Biokatalysatoren, Stoffwechselwege und Wirkstoffe. GENOMXPRESS 3.05: 32-33.

Wiezer A, Merkl R (2005) A comparative categorization of gene flux in diverse microbial species. Genomics 86(4): 462-475 (abstract).

2004

Andres S, Wiezer A, Bendfeldt H, Waschkowitz T, Toeche-Mittler C, Daniel R (2004) Insights into the genome of the enteric bacterium Escherichia blattae: cobalamin (B12) biosynthesis, B12-dependent reactions, and inactivation of the gene region encoding B12-dependent glycerol dehydratase by a new mu-like prophage. J Mol Microbiol Biotechnol 8(3): 150-168 (abstract).

Patent: Angelov A, Fütterer O, Liebl W (2004) Cloning, expression and characterisation of a glucose-1-dehydrogenase of the thermoacidophilic archaeon Picrophilus torridus.

Bertoldo C, Armbrecht M, Becker F, Schäfer T, Antranikian G, Liebl W (2004) Cloning, sequencing, and characterization of a heat- and alkali-stable type I pullulanase from Anaerobranca gottschalkii. Appl Environ Microbiol 70(6): 3407-3416 (abstract).

Brüggemann H, Bauer R, Raffestin S, Gottschalk G (2004) Characterization of a heme oxygenase of Clostridium tetani and its possible role in oxygen tolerance. Arch Microbiol 182: 259-263 (abstract).

Brüggemann H, Gottschalk G (2004) Insights in metabolism and toxin production from the complete genome sequence of Clostridium tetani. Anaerobe 1053-68.

Brüggemann H, Henne A, Hoster F, Liesegang H, Wiezer A, Strittmatter A, Hujer S, Dürre P, Gottschalk G (2004) The complete genome sequence of Propionibacterium acnes, a commensal of human skin. Science 305(5684): 671-673 (abstract).

Daniel R (2004) The soil metagenome--a rich resource for the discovery of novel natural products. Curr Opin Biotechnol 15(3): 199-204 (abstract).

Daniel R, Streit WR (2004) Metagenomik, mehr als nur die Suche nach neuen Biokatalysatoren. Biospektrum (1): 39-41.

Fütterer O, Angelov A, Liesegang H, Gottschalk G, Schleper C, Schepers B, Dock C, Antranikian G, Liebl W (2004) Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci USA 101(24): 9091-9096 (abstract).

Grozdanov L, Raasch C, Schulze J, Sonnenborn U, Gottschalk G, Hacker J, Dobrindt U (2004) Analysis of the genome structure of the nonpathogenic probiotic Escherichia coli strain Nissle 1917. J Bacteriol 186(16): 5432-5441 (abstract).

Hacker J, Hochhut B, Middendorf B, Schneider G, Buchrieser C, Gottschalk G, Dobrindt U (2004) Pathogenomics of mobile genetic elements of toxigenic bacteria. Int J Med Microbiol 293(7-8): 453-461 (abstract).

Helmstaedt K, Heinrich G, Merkl R, Braus GH (2004) Chorismate mutase of Thermus thermophilus is a monofunctional AroH class enzyme inhibited by tyrosine. Arch Microbiol 181(3): 195-203 (abstract).

Henne A, Brüggemann H, Raasch C, Wiezer A, Hartsch T, Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, Merkl R, Gottschalk G, Fritz HJ (2004) The genome sequence of the extreme thermophile Thermus thermophilus. Nat Biotechnol 22(5): 547-553 (abstract).

Liebl W (2004) Genomics taken to the extreme. Nat Biotechnol 22(5): 524-525 (abstract).

Merkl R (2004) SIGI: score-based identification of genomic islands. BMC Bioinformatics 5(1): 22 (abstract).

Schneider G, Dobrindt U, Brüggemann H, Nagy G, Janke B, Blum-Oehler G, Buchrieser C, Gottschalk G, Emody L, Hacker J (2004) The pathogenicity island-associated K15 capsule determinant exhibits a novel genetic structure and correlates with virulence in uropathogenic Escherichia coli strain 536. Infect Immun 72(10): 5993-6001 (abstract).

Streit WR, Daniel R, Jaeger KE (2004) Prospecting for biocatalysts and drugs in the genomes of non-cultured microorganisms. Curr Opin Biotechnol 15(4): 285-290 (abstract).

Sun J, Daniel R, Wagner-Döbler I, Zeng AP (2004) Is autoinducer-2 a universal signal for interspecies communication: a comparative genomic and phylogenetic analysis of the synthesis and signal transduction pathways. BMC Evol Biol 436 (abstract).

Veith B, Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Bäumer S, Henne A, Liesegang H, Merkl R, Ehrenreich A, Gottschalk G (2004) The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microbiol Biotechnol 7(4): 204-211 (abstract).

Voigt B, Schweder T, Becher D, Ehrenreich A, Gottschalk G, Feesche J, Maurer KH, Hecker M (2004) A proteomic view of cell physiology of Bacillus licheniformis. Proteomics 4(5): 1465-1490 (abstract).

2003

Brüggemann H, Bäumer S, Fricke WF, Wiezer A, Liesegang H, Decker I, Herzberg C, Martinez-Arias R, Merkl R, Henne A, Gottschalk G (2003) The genome sequence of Clostridium tetani, the causative agent of tetanus disease. Proc Natl Acad Sci USA 100(3): 1316-1321 (abstract).

Patent: Brüggemann H, Bäumer S, Gottschalk G, Hartsch T (2003) Clostridium tetani collagenase and uses thereof.

Daniel R (2003) Die mikrobielle Diversität als Quelle für neuartige Biokatalysatoren: Konstruktion und Durchmusterung von Metagenombanken. Biospektrum 9605-606.

Dobrindt U, Agerer F, Michaelis K, Janka A, Buchrieser C, Samuelson M, Svanborg C, Gottschalk G, Karch H, Hacker J (2003) Analysis of genome plasticity in pathogenic and commensal Escherichia coli isolates by use of DNA arrays. J Bacteriol 185(6): 1831-1840 (abstract).

Droogmans L, Roovers M, Bujnicki JM, Tricot C, Hartsch T, Stalon V, Grosjean H (2003) Cloning and characterization of tRNA (m1A58) methyltransferase (TrmI) from Thermus thermophilus HB27, a protein required for cell growth at extreme temperatures. Nucleic Acids Res. 31(8): 2148-2156 (abstract).

Empadinhas N, Albuquerque L, Henne A, Santos H, da Costa MS (2003) The bacterium Thermus thermophilus, like hyperthermophilic archaea, uses a two-step pathway for the synthesis of mannosylglycerate. Appl Environ Microbiol 69(6): 3272-3279 (abstract).

Friedrich A, Rumszauer J, Henne A, Averhoff B (2003) Pilin-like proteins in the extremely thermophilic bacterium Thermus thermophilus HB27: implication in competence for natural transformation and links to type IV pilus biogenesis. Appl Environ Microbiol 69(7): 3695-3700 (abstract).

Fuhrmann S, Ferner M, Jeffke T, Henne A, Gottschalk G, Meyer O (2003) Complete nucleotide sequence of the circular megaplasmid pHCG3 of Oligotropha carboxidovorans: function in the chemolithoautotrophic utilization of CO, H2 and CO2. Gene 32267-75 (abstract).

Klunker D, Haas B, Hirtreiter A, Figueiredo L, Naylor DJ, Pfeifer G, Müller V, Deppenmeier U, Gottschalk G, Hartl FU, Hayer-Hartl M (2003) Coexistence of group I and group II chaperonins in the archaeon Methanosarcina mazei. J. Biol. Chem. 278(35): 33256-33267 (abstract).

Knietsch A, Bowien S, Whited G, Gottschalk G, Daniel R (2003) Identification and characterization of coenzyme B12-dependent glycerol dehydratase- and diol dehydratase-encoding genes from metagenomic DNA libraries derived from enrichment cultures. Appl Environ Microbiol 69(6): 3048-3060 (abstract).

Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Construction and screening of metagenomic libraries derived from enrichment cultures: generation of a gene bank for genes conferring alcohol oxidoreductase activity on Escherichia coli. Appl Environ Microbiol 69(3): 1408-1416 (abstract).

Knietsch A, Waschkowitz T, Bowien S, Henne A, Daniel R (2003) Metagenomes of complex microbial consortia derived from different soils as sources for novel genes conferring formation of carbonyls from short-chain polyols on Escherichia coli. J Mol Microbiol Biotechnol 5(1): 46-56 (abstract).

Kollas AK, Duin EC, Eberl M, Altincicek B, Hintz M, Reichenberg A, Henschker D, Henne A, Steinbrecher I, Ostrovsky DN, Hedderich R, Beck E, Jomaa H, Wiesner J (2003) Functional characterization of GcpE, an essential enzyme of the non-mevalonate pathway of isoprenoid biosynthesis. FEBS Lett. 532432-436.

Lodge JA, Maier T, Liebl W, Hoffmann V, Strater N (2003) Crystal structure of Thermotoga maritima alpha-glucosidase AglA defines a new clan of NAD+-dependent glycosidases. J. Biol. Chem. 278(21): 19151-19158 (abstract).

Merkl R (2003) A survey of codon and amino acid frequency bias in microbial genomes focusing on translational efficiency. J. Mol. Evol. 57(4): 453-466 (abstract).

Pflüger K, Baumann S, Gottschalk G, Lin W, Santos H, Müller V (2003) Lysine-2,3-aminomutase and beta-lysine acetyltransferase genes of methanogenic archaea are salt induced and are essential for the biosynthesis of Nepsilon-acetyl-beta-lysine and growth at high salinity. Appl Environ Microbiol 69(10): 6047-6055 (abstract).

Schwartz E, Henne A, Cramm R, Eitinger T, Friedrich B, Gottschalk G (2003) Complete nucleotide sequence of pHG1: a Ralstonia eutropha H16 megaplasmid encoding key enzymes of H2-based lithoautotrophy and anaerobiosis. J. Mol. Biol. 332(2): 369-383 (abstract).

Stecker C, Johann A, Herzberg C, Averhoff B, Gottschalk G (2003) Complete nucleotide sequence and genetic organization of the 210-kilobase linear plasmid of Rhodococcus erythropolis BD2. J Bacteriol 185(17): 5269-5274 (abstract).

Tech M, Merkl R (2003) YACOP: Enhanced gene prediction obtained by a combination of existing methods. In Silico Biol. 3(4): 0037 (abstract).

Tzvetkov M, Klopprogge C, Zelder O, Liebl W (2003) Genetic dissection of trehalose biosynthesis in Corynebacterium glutamicum: inactivation of trehalose production leads to impaired growth and an altered cell wall lipid composition. Microbiology 149(Pt 7): 1659-1673 (abstract).

Valle M, Gillet R, Kaur S, Henne A, Ramakrishnan V, Frank J (2003) Visualizing tmRNA entry into a stalled ribosome. Science 300(5616): 127-130 (abstract).

Voget S, Leggewie C, Uesbeck A, Raasch C, Jaeger KE, Streit WR (2003) Prospecting for novel biocatalysts in a soil metagenome. Appl Environ Microbiol 69(10): 6235-6242 (abstract).

Wiezer A, Merkl R (2003) secureBLAST. In Silico Biol. 3(4): 405-409 (abstract).

Yano JK, Blasco F, Li H, Schmid RD, Henne A, Poulos TL (2003) Preliminary characterization and crystal structure of a thermostable cytochrome P450 from Thermus thermophilus. J. Biol. Chem. 278(1): 608-616 (abstract).

2002

Ahel I, Stathopoulos C, Ambrogelly A, Sauerwald A, Toogood H, Hartsch T, Soll D (2002) Cysteine activation is an inherent in vitro property of prolyl-tRNA synthetases. J. Biol. Chem. 277(38): 34743-34748 (abstract).

Bäumer S, Lentes S, Gottschalk G, Deppenmeier U (2002) Identification and analysis of proton-translocating pyrophosphatases in the methanogenic archaeon Methanosarcina mazei. Archaea 11-7.

Bullard JM, Williams JC, Acker WK, Jacobi C, Janjic N, McHenry CS (2002) DNA polymerase III holoenzyme from Thermus thermophilus identification, expression, purification of components, and use to reconstitute a processive replicase. J. Biol. Chem. 277(16): 13401-13408 (abstract).

Daniel R (2002) Construction of environmental libraries for functional screening of enzyme acitivity, in Directed molecular evolution of proteins (Johnson K, and Brakmann S, Eds.), pp. 63-78, Wiley-VCH Verlag, Weinheim.

Daniel R, Schmitz RA, Streit W (2002) Aus Wattenmeer und Wüstensand - Mikrobielle Diversität als Quelle für neuartige Biokatalysatoren und Wirkstoffe. Georgia Augusta 1111-115.

Deppenmeier U, Johann A, Hartsch T, Merkl R, Schmitz RA, Martinez-Arias R, Henne A, Wiezer A, Bäumer S, Jacobi C, Brüggemann H, Lienard T, Christmann A, Bömeke M, Steckel S, Bhattacharyya A, Lykidis A, Overbeek R, Klenk HP, Gunsalus RP, Fritz HJ, Gottschalk G (2002) The genome of Methanosarcina mazei: evidence for lateral gene transfer between bacteria and archaea. J Mol Microbiol Biotechnol 4(4): 453-461 (abstract).

Dobrindt U, Blum-Oehler G, Nagy G, Schneider G, Johann A, Gottschalk G, Hacker J (2002) Genetic structure and distribution of four pathogenicity islands (PAI I536 to PAI IV536) of uropathogenic Escherichia coli strain 536. Infect Immun 70(11): 6365-6372 (abstract).

Feng L, Stathopoulos C, Ahel I, Mitra A, Tumbula-Hansen D, Hartsch T, Soll D (2002) Aminoacyl-tRNA formation in the extreme thermophile Thermus thermophilus. Extremophiles 6(2): 167-174 (abstract).

Friedrich A, Prust C, Hartsch T, Henne A, Averhoff B (2002) Molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium Thermus thermophilus strain HB27. Appl Environ Microbiol 68(2): 745-755 (abstract).

Grozdanov L, Zahringer U, Blum-Oehler G, Brade L, Henne A, Knirel YA, Schombel U, Schulze J, Sonnenborn U, Gottschalk G, Hacker J, Rietschel ET, Dobrindt U (2002) A single nucleotide exchange in the wzy gene is responsible for the semirough O6 lipopolysaccharide phenotype and serum sensitivity of Escherichia coli strain Nissle 1917. J Bacteriol 184(21): 5912-5925 (abstract).

Patent: Hauer B, Schmid RD, Merkl R, Blasco F (2002) Cytochrome P450 Monooxygenase consisting of thermophilic bacteria. Patent WO 02/33057 A2.

Hogan BP, Hartsch T, Erie DA (2002) Transcript cleavage by Thermus thermophilus RNA polymerase. Effects of GreA and anti-GreA factors. J. Biol. Chem. 277(2): 967-975 (abstract).

Larbig KD, Christmann A, Johann A, Klockgether J, Hartsch T, Merkl R, Wiehlmann L, Fritz HJ, Tümmler B (2002) Gene islands integrated into tRNA(Gly) genes confer genome diversity on a Pseudomonas aeruginosa clone. J Bacteriol 184(23): 6665-6680 (abstract).

Liebl W, Kloos WE, Ludwig W (2002) Plasmid-borne macrolide resistance in Micrococcus luteus. Microbiology 148(Pt 8): 2479-2487 (abstract).

Merkl R, Waack S (2002) Bioinformatik Interaktiv. Wiley-VCH, Weinheim.

Raasch C, Armbrecht M, Streit W, Hocker B, Strater N, Liebl W (2002) Identification of residues important for NAD+ binding by the Thermotoga maritima alpha-glucosidase AglA, a member of glycoside hydrolase family 4. FEBS Lett. 517(1-3): 267-271 (abstract).

Roessler M, Pflueger K, Flach H, Lienard T, Gottschalk G, Müller V (2002) Identification of a salt-induced primary transporter for glycine betaine in the methanogen Methanosarcina mazei Gö1. Appl Environ Microbiol 68(5): 2133-2139 (abstract).

Shiryaev VM, Selivanova OM, Hartsch T, Nazimov IV, Spirin AS (2002) Ribosomal protein S1 from Thermus thermophilus: its detection, identification and overproduction. FEBS Lett. 525(1-3): 88 (abstract).

2001

Antranikian G, Klenk HP, Freudl R, Sterner R, Liebl W (2001) Extremophile Mikroorganismen als Quelle stabiler Biokatalysatoren, in Biokatalyse (Heiden S, and Erb RW, Eds.), Spektrum Verlag, Heidelberg.

Carter AP, Clemons WM, Jr., Brodersen DE, Morgan-Warren RJ, Hartsch T, Wimberly BT, Ramakrishnan V (2001) Crystal structure of an initiation factor bound to the 30S ribosomal subunit. Science 291(5503): 498-501 (abstract).

Dobrindt U, Blum-Oehler G, Hartsch T, Gottschalk G, Ron EZ, Fünfstück R, Hacker J (2001) S-Fimbria-encoding determinant sfaI is located on pathogenicity island III536 of uropathogenic Escherichia coli strain 536. Infect Immun 69(7): 4248-4256 (abstract).

Entcheva P, Liebl W, Johann A, Hartsch T, Streit WR (2001) Direct cloning from enrichment cultures, a reliable strategy for isolation of complete operons and genes from microbial consortia. Appl Environ Microbiol 67(1): 89-99 (abstract).

Friedrich A, Hartsch T, Averhoff B (2001) Natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in Acinetobacter sp. strain BD413 and Thermus thermophilus HB27. Appl Environ Microbiol 67(7): 3140-3148 (abstract).

Gottschalk G, Thauer RK (2001) The Na(+)-translocating methyltransferase complex from methanogenic archaea. Biochim Biophys Acta 1505(1): 28-36 (abstract).

Hoster F, Daniel R, Gottschalk G (2001) Isolation of a new Thermoanaerobacterium thermosaccharolyticum strain (FH1) producing a thermostable dextranase. J Gen Appl Microbiol 47(4): 187-192 (abstract).

Majernik A, Gottschalk G, Daniel R (2001) Screening of environmental DNA libraries for the presence of genes conferring Na(+)(Li(+))/H(+) antiporter activity on Escherichia coli: characterization of the recovered genes and the corresponding gene products. J Bacteriol 183(22): 6645-6653 (abstract).

Pioletti M, Schlunzen F, Harms J, Zarivach R, Gluhmann M, Avila H, Bashan A, Bartels H, Auerbach T, Jacobi C, Hartsch T, Yonath A, Franceschi F (2001) Crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and IF3. EMBO J. 20(8): 1829-1839 (abstract).

Roujeinikova A, Raasch C, Burke J, Baker PJ, Liebl W, Rice DW (2001) The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity. J. Mol. Biol. 312(1): 119-131 (abstract).

Schmitz RA, Daniel R, Deppenmeier U, Gottschalk G (2001) The anaerobic way of life, in: The Prokaryotes, third edition (Balows B, Trüper HG, Dworkin M, Harder W, and Schleifer KH, Eds.), Springer Verlag, New York.

Seifert C, Bowien S, Gottschalk G, Daniel R (2001) Identification and expression of the genes and purification and characterization of the gene products involved in reactivation of coenzyme B12-dependent glycerol dehydratase of Citrobacter freundii. Eur J Biochem 268(8): 2369-2378 (abstract).

Sterner R, Liebl W (2001) Thermophilic adaptation of proteins. Crit. Rev. Biochem. Mol. Biol. 36(1): 39-106 (abstract).