PUB - Publikationen an der Universität Bielefeld

Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery.
Goux X, Calusinska M, Lemaigre S, Marynowska M, Klocke M, Udelhoven T, Benizri E, Delfosse P., Biotechnol Biofuels 8(), 2015
PMID: 26288654

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions.
Stolze Y, Zakrzewski M, Maus I, Eikmeyer F, Jaenicke S, Rottmann N, Siebner C, Puhler A, Schluter A., Biotechnol Biofuels 8(), 2015
PMID: 25688290

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates.
Maus I, Koeck DE, Cibis KG, Hahnke S, Kim YS, Langer T, Kreubel J, Erhard M, Bremges A, Off S, Stolze Y, Jaenicke S, Goesmann A, Sczyrba A, Scherer P, Konig H, Schwarz WH, Zverlov VV, Liebl W, Puhler A, Schluter A, Klocke M., Biotechnol Biofuels 9(), 2016
PMID: 27525040

Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants.
Nettmann E, Bergmann I, Pramschufer S, Mundt K, Plogsties V, Herrmann C, Klocke M., Appl. Environ. Microbiol. 76(8), 2010
PMID: 20154117

Microbial community analysis of a biogas-producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate.
Klocke M, Mahnert P, Mundt K, Souidi K, Linke B., Syst. Appl. Microbiol. 30(2), 2006
PMID: 16697135

An integrated metagenome and -proteome analysis of the microbial community residing in a biogas production plant.
Ortseifen V, Stolze Y, Maus I, Sczyrba A, Bremges A, Albaum SP, Jaenicke S, Fracowiak J, Puhler A, Schluter A., J. Biotechnol. 231(), 2016
PMID: 27312700

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants.
Stolze Y, Bremges A, Rumming M, Henke C, Maus I, Puhler A, Sczyrba A, Schluter A., Biotechnol Biofuels 9(), 2016
PMID: 27462367

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes.
Treu L, Kougias PG, Campanaro S, Bassani I, Angelidaki I., Bioresour. Technol. 216(), 2016
PMID: 27243603

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics.
Evans PN, Parks DH, Chadwick GL, Robbins SJ, Orphan VJ, Golding SD, Tyson GW., Science 350(6259), 2015
PMID: 26494757

Novel cultivation-based approach to understanding the miscellaneous crenarchaeotic group (MCG) archaea from sedimentary ecosystems.
Gagen EJ, Huber H, Meador T, Hinrichs KU, Thomm M., Appl. Environ. Microbiol. 79(20), 2013
PMID: 23934495

Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA).
Lazar CS, Biddle JF, Meador TB, Blair N, Hinrichs KU, Teske AP., Environ. Microbiol. 17(7), 2015
PMID: 25331558

Occurrence and expression of novel methyl-coenzyme M reductase gene (mcrA) variants in hot spring sediments.
McKay LJ, Hatzenpichler R, Inskeep WP, Fields MW., Sci Rep 7(1), 2017
PMID: 28775334

Environmental evidence for net methane production and oxidation in putative ANaerobic MEthanotrophic (ANME) archaea.
Lloyd KG, Alperin MJ, Teske A., Environ. Microbiol. 13(9), 2011
PMID: 21806748

Archaea of the Miscellaneous Crenarchaeotal Group are abundant, diverse and widespread in marine sediments.
Kubo K, Lloyd KG, F Biddle J, Amann R, Teske A, Knittel K., ISME J 6(10), 2012
PMID: 22551871

Crenarchaeal heterotrophy in salt marsh sediments.
Seyler LM, McGuinness LM, Kerkhof LJ., ISME J 8(7), 2014
PMID: 24553469

Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments.
He Y, Li M, Perumal V, Feng X, Fang J, Xie J, Sievert SM, Wang F., Nat Microbiol 1(6), 2016
PMID: 27572832

Anaerobic digestion of wheat straw--performance of continuous solid-state digestion.
Pohl M, Heeg K, Mumme J., Bioresour. Technol. 146(), 2013
PMID: 23954246

Biofilms in biogas fermenters—community structure, influence on biogas yields and optimization of technical solutions for retaining the microbial biomass (BIOGAS-BIOFILM)
Bergmann I, Klocke M., 2015

MEGAHIT v1.0: A fast and scalable metagenome assembler driven by advanced methodologies and community practices.
Li D, Luo R, Liu CM, Leung CM, Ting HF, Sadakane K, Yamashita H, Lam TW., Methods 102(), 2016
PMID: 27012178

AUTHOR UNKNOWN, 0

The Sequence Alignment/Map format and SAMtools.
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R; 1000 Genome Project Data Processing Subgroup., Bioinformatics 25(16), 2009
PMID: 19505943

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data.
Huson DH, Beier S, Flade I, Gorska A, El-Hadidi M, Mitra S, Ruscheweyh HJ, Tappu R., PLoS Comput. Biol. 12(6), 2016
PMID: 27327495

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities.
Kang DD, Froula J, Egan R, Wang Z., PeerJ 3(), 2015
PMID: 26336640

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW., Genome Res. 25(7), 2015
PMID: 25977477

acdc - Automated Contamination Detection and Confidence estimation for single-cell genome data.
Lux M, Kruger J, Rinke C, Maus I, Schluter A, Woyke T, Sczyrba A, Hammer B., BMC Bioinformatics 17(1), 2016
PMID: 27998267

Prokka: rapid prokaryotic genome annotation.
Seemann T., Bioinformatics 30(14), 2014
PMID: 24642063

GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369

IMG/M 4 version of the integrated metagenome comparative analysis system.
Markowitz VM, Chen IM, Chu K, Szeto E, Palaniappan K, Pillay M, Ratner A, Huang J, Pagani I, Tringe S, Huntemann M, Billis K, Varghese N, Tennessen K, Mavromatis K, Pati A, Ivanova NN, Kyrpides NC., Nucleic Acids Res. 42(Database issue), 2013
PMID: 24136997

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies.
Stamatakis A., Bioinformatics 30(9), 2014
PMID: 24451623

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web.
Robinson O, Dylus D, Dessimoz C., Mol. Biol. Evol. 33(8), 2016
PMID: 27189561

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing.
Rademacher A, Zakrzewski M, Schluter A, Schonberg M, Szczepanowski R, Goesmann A, Puhler A, Klocke M., FEMS Microbiol. Ecol. 79(3), 2011
PMID: 22126587

Genomic insights that advance the species definition for prokaryotes.
Konstantinidis KT, Tiedje JM., Proc. Natl. Acad. Sci. U.S.A. 102(7), 2005
PMID: 15701695

Genomic evidence for distinct carbon substrate preferences and ecological niches of Bathyarchaeota in estuarine sediments.
Lazar CS, Baker BJ, Seitz K, Hyde AS, Dick GJ, Hinrichs KU, Teske AP., Environ. Microbiol. 18(4), 2016
PMID: 26626228

Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system.
Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF., Nat Commun 7(), 2016
PMID: 27774985

EDGAR 2.0: an enhanced software platform for comparative gene content analyses.
Blom J, Kreis J, Spanig S, Juhre T, Bertelli C, Ernst C, Goesmann A., Nucleic Acids Res. 44(W1), 2016
PMID: 27098043

dbCAN: a web resource for automated carbohydrate-active enzyme annotation.
Yin Y, Mao X, Yang J, Chen X, Mao F, Xu Y., Nucleic Acids Res. 40(Web Server issue), 2012
PMID: 22645317

Predominant archaea in marine sediments degrade detrital proteins.
Lloyd KG, Schreiber L, Petersen DG, Kjeldsen KU, Lever MA, Steen AD, Stepanauskas R, Richter M, Kleindienst S, Lenk S, Schramm A, Jorgensen BB., Nature 496(7444), 2013
PMID: 23535597

Enzymology of the wood-Ljungdahl pathway of acetogenesis.
Ragsdale SW., Ann. N. Y. Acad. Sci. 1125(), 2008
PMID: 18378591

Methanogenesis and the Wood-Ljungdahl Pathway: An Ancient, Versatile, and Fragile Association.
Borrel G, Adam PS, Gribaldo S., Genome Biol Evol 8(6), 2016
PMID: 27189979

WebMGA: a customizable web server for fast metagenomic sequence analysis.
Wu S, Zhu Z, Fu L, Niu B, Li W., BMC Genomics 12(), 2011
PMID: 21899761

Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants.
Maus I, Wibberg D, Stantscheff R, Stolze Y, Blom J, Eikmeyer FG, Fracowiak J, Konig H, Puhler A, Schluter A., J. Biotechnol. 201(), 2014
PMID: 25455016

Trace element requirements of agricultural biogas digesters during biological conversion of renewable biomass to methane
Demirel B, Scherer P., 2009

Expression, purification and crystallization of the ammonium transporter Amt-1 from Archaeoglobus fulgidus.
Andrade SL, Dickmanns A, Ficner R, Einsle O., Acta Crystallogr. Sect. F Struct. Biol. Cryst. Commun. 61(Pt 9), 2005
PMID: 16511180

A comparative study of methylglyoxal metabolism in trypanosomatids.
Greig N, Wyllie S, Patterson S, Fairlamb AH., FEBS J. 276(2), 2008
PMID: 19076214

PhyloSift: phylogenetic analysis of genomes and metagenomes.
Darling AE, Jospin G, Lowe E, Matsen FA 4th, Bik HM, Eisen JA., PeerJ 2(), 2014
PMID: 24482762

MUSCLE: multiple sequence alignment with high accuracy and high throughput.
Edgar RC., Nucleic Acids Res. 32(5), 2004
PMID: 15034147

Culture Independent Genomic Comparisons Reveal Environmental Adaptations for Altiarchaeales.
Bird JT, Baker BJ, Probst AJ, Podar M, Lloyd KG., Front Microbiol 7(), 2016
PMID: 27547202

Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction.
Seitz KW, Lazar CS, Hinrichs KU, Teske AP, Baker BJ., ISME J 10(7), 2016
PMID: 26824177

Asgard archaea illuminate the origin of eukaryotic cellular complexity.
Zaremba-Niedzwiedzka K, Caceres EF, Saw JH, Backstrom D, Juzokaite L, Vancaester E, Seitz KW, Anantharaman K, Starnawski P, Kjeldsen KU, Stott MB, Nunoura T, Banfield JF, Schramm A, Baker BJ, Spang A, Ettema TJ., Nature 541(7637), 2017
PMID: 28077874

Trimmomatic: a flexible trimmer for Illumina sequence data.
Bolger AM, Lohse M, Usadel B., Bioinformatics 30(15), 2014
PMID: 24695404

Prodigal: prokaryotic gene recognition and translation initiation site identification.
Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ., BMC Bioinformatics 11(), 2010
PMID: 20211023

Fast and sensitive protein alignment using DIAMOND.
Buchfink B, Xie C, Huson DH., Nat. Methods 12(1), 2014
PMID: 25402007

Database resources of the National Center for Biotechnology Information.
NCBI Resource Coordinators, Agarwala R, Barrett T, Beck J, Benson DA, Bollin C, Bolton E, Bourexis D, Brister JR, Bryant SH, Canese K, Charowhas C, Clark K, DiCuccio M, Dondoshansky I, Federhen S, Feolo M, Funk K, Geer LY, Gorelenkov V, Hoeppner M, Holmes B, Johnson M, Khotomlianski V, Kimchi A, Kimelman M, Kitts P, Klimke W, Krasnov S, Kuznetsov A, Landrum MJ, Landsman D, Lee JM, Lipman DJ, Lu Z, Madden TL, Madej T, Marchler-Bauer A, Karsch-Mizrachi I, Murphy T, Orris R, Ostell J, O'Sullivan C, Panchenko A, Phan L, Preuss D, Pruitt KD, Rodarmer K, Rubinstein W, Sayers EW, Schneider V, Schuler GD, Sherry ST, Sirotkin K, Siyan K, Slotta D, Soboleva A, Soussov V, Starchenko G, Tatusova TA, Todorov K, Trawick BW, Vakatov D, Wang Y, Ward M, Wilbur WJ, Yaschenko E, Zbicz K., Nucleic Acids Res. 44(D1), 2015
PMID: 26615191

SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA., J. Comput. Biol. 19(5), 2012
PMID: 22506599

QUAST: quality assessment tool for genome assemblies.
Gurevich A, Saveliev V, Vyahhi N, Tesler G., Bioinformatics 29(8), 2013
PMID: 23422339

RNAmmer: consistent and rapid annotation of ribosomal RNA genes.
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW., Nucleic Acids Res. 35(9), 2007
PMID: 17452365

The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL, Galperin MY, Natale DA, Koonin EV., Nucleic Acids Res. 28(1), 2000
PMID: 10592175

The COG database: new developments in phylogenetic classification of proteins from complete genomes.
Tatusov RL, Natale DA, Garkavtsev IV, Tatusova TA, Shankavaram UT, Rao BS, Kiryutin B, Galperin MY, Fedorova ND, Koonin EV., Nucleic Acids Res. 29(1), 2001
PMID: 11125040

The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats.
Grissa I, Vergnaud G, Pourcel C., BMC Bioinformatics 8(), 2007
PMID: 17521438

Complete genome analysis of Clostridium bornimense strain M2/40(T): A new acidogenic Clostridium species isolated from a mesophilic two-phase laboratory-scale biogas reactor.
Tomazetto G, Hahnke S, Koeck DE, Wibberg D, Maus I, Puhler A, Klocke M, Schluter A., J. Biotechnol. 232(), 2015
PMID: 26256097