A novel archaeal species belonging to Methanoculleus genus identified via de-novo assembly and metagenomic binning process in biogas reactors.

[1]  S. Campanaro,et al.  Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes. , 2016, Bioresource technology.

[2]  G. Tyson,et al.  Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion. , 2016, Environmental microbiology.

[3]  Taha,et al.  Single TRAM domain RNA-binding proteins in Archaea: functional insight from Ctr3 from the Antarctic methanogen Methanococcoides burtonii. , 2016, Environmental microbiology.

[4]  A. Pühler,et al.  Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants , 2016, Biotechnology for Biofuels.

[5]  Irini Angelidaki,et al.  Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors , 2016, Scientific Reports.

[6]  S. Campanaro,et al.  Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members. , 2016, Environmental science & technology.

[7]  K. Konstantinidis,et al.  The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes , 2016 .

[8]  I. Angelidaki,et al.  Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis , 2016, Biotechnology for Biofuels.

[9]  M. Kanehisa,et al.  BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences. , 2016, Journal of molecular biology.

[10]  S. Campanaro,et al.  Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy , 2016, Biotechnology for Biofuels.

[11]  I. Angelidaki,et al.  Biogas Upgrading via Hydrogenotrophic Methanogenesis in Two-Stage Continuous Stirred Tank Reactors at Mesophilic and Thermophilic Conditions. , 2015, Environmental science & technology.

[12]  Dongwan D. Kang,et al.  MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities , 2015, PeerJ.

[13]  Alexander Sczyrba,et al.  Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant , 2015, GigaScience.

[14]  Natalia N. Ivanova,et al.  Microbial species delineation using whole genome sequences , 2015, Nucleic acids research.

[15]  Connor T. Skennerton,et al.  CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes , 2015, Genome research.

[16]  Brian C. Thomas,et al.  Unusual biology across a group comprising more than 15% of domain Bacteria , 2015, Nature.

[17]  Ramon Rosselló-Móra,et al.  Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal. , 2015, Systematic and applied microbiology.

[18]  J. Blom,et al.  Insights into the annotated genome sequence of Methanoculleus bourgensis MS2(T), related to dominant methanogens in biogas-producing plants. , 2015, Journal of biotechnology.

[19]  Kenneth H. Williams,et al.  Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling , 2015, Current Biology.

[20]  Michael Y. Galperin,et al.  Expanded microbial genome coverage and improved protein family annotation in the COG database , 2014, Nucleic Acids Res..

[21]  Donovan Parks,et al.  GroopM: an automated tool for the recovery of population genomes from related metagenomes , 2014, PeerJ.

[22]  Fangfang Xia,et al.  The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST) , 2013, Nucleic Acids Res..

[23]  C. Huttenhower,et al.  PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes , 2013, Nature Communications.

[24]  Shihu Hu,et al.  Anaerobic oxidation of methane coupled to nitrate reduction in a novel archaeal lineage , 2013, Nature.

[25]  P. Hugenholtz,et al.  Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes , 2013, Nature Biotechnology.

[26]  S. Campanaro,et al.  The transcriptional landscape of the deep-sea bacterium Photobacterium profundum in both a toxR mutant and its parental strain , 2012, BMC Genomics.

[27]  Brian C. Thomas,et al.  Fermentation, Hydrogen, and Sulfur Metabolism in Multiple Uncultivated Bacterial Phyla , 2012, Science.

[28]  J. Blom,et al.  Complete Genome Sequence of the Hydrogenotrophic, Methanogenic Archaeon Methanoculleus bourgensis Strain MS2T, Isolated from a Sewage Sludge Digester , 2012, Journal of bacteriology.

[29]  N. Sang,et al.  Microorganisms in landfill bioreactors for accelerated stabilization of solid wastes. , 2012, Journal of bioscience and bioengineering.

[30]  Edward C. Uberbacher,et al.  Gene and translation initiation site prediction in metagenomic sequences , 2012, Bioinform..

[31]  S. Sørensen,et al.  Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing. , 2012, Journal of biotechnology.

[32]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[33]  A. Goesmann,et al.  Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing. , 2012, FEMS microbiology ecology.

[34]  Ruben E. Valas,et al.  Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage , 2011, The ISME Journal.

[35]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[36]  D. Higgins,et al.  Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega , 2011, Molecular systems biology.

[37]  S. Campanaro,et al.  Temperature-dependent global gene expression in the Antarctic archaeon Methanococcoides burtonii. , 2011, Environmental microbiology.

[38]  Alessio Mengoni,et al.  CONTIGuator: a bacterial genomes finishing tool for structural insights on draft genomes , 2011, Source Code for Biology and Medicine.

[39]  Folker Meyer,et al.  37. The Metagenomics RAST Server: A Public Resource for the Automatic Phylogenetic and Functional Analysis of Metagenomes , 2011 .

[40]  Alexander Goesmann,et al.  Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing , 2011, PloS one.

[41]  L. S. Yilmaz,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.

[42]  Yanfen Wang,et al.  Methanoculleus hydrogenitrophicus sp. nov., a methanogenic archaeon isolated from wetland soil. , 2010, International journal of systematic and evolutionary microbiology.

[43]  L. Rohlin,et al.  Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A , 2010, BMC Microbiology.

[44]  M. Klocke,et al.  Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants , 2010, Applied and Environmental Microbiology.

[45]  Christian M. Zmasek,et al.  phyloXML: XML for evolutionary biology and comparative genomics , 2009, BMC Bioinformatics.

[46]  Naryttza N. Diaz,et al.  The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. , 2008, Journal of biotechnology.

[47]  Anne-Kristin Kaster,et al.  Methanogenic archaea: ecologically relevant differences in energy conservation , 2008, Nature Reviews Microbiology.

[48]  Yuki Moriya,et al.  KAAS: an automatic genome annotation and pathway reconstruction server , 2007, Nucleic Acids Res..

[49]  Mike S. M. Jetten,et al.  A microbial consortium couples anaerobic methane oxidation to denitrification , 2006, Nature.

[50]  K. Konstantinidis,et al.  Genomic insights that advance the species definition for prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[51]  Rudolf Amann,et al.  Simultaneous Fluorescence In Situ Hybridization of mRNA and rRNA in Environmental Bacteria , 2004, Applied and Environmental Microbiology.

[52]  D. Boone,et al.  Isolation of a Methanogen from Deep Marine Sediments That Contain Methane Hydrates, and Description of Methanoculleus submarinus sp. nov , 2003, Applied and Environmental Microbiology.

[53]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[54]  Kim Rutherford,et al.  Artemis: sequence visualization and annotation , 2000, Bioinform..

[55]  B. Svensson,et al.  Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors , 1999 .

[56]  Hideki Harada,et al.  Fluorescence In Situ Hybridization Using 16S rRNA-Targeted Oligonucleotides Reveals Localization of Methanogens and Selected Uncultured Bacteria in Mesophilic and Thermophilic Sludge Granules , 1999, Applied and Environmental Microbiology.

[57]  Jan Dolfing,et al.  Comparison of Methane Production Rate and Coenzyme F420 Content of Methanogenic Consortia in Anaerobic Granular Sludge , 1985, Applied and environmental microbiology.

[58]  G. Vogels,et al.  Proposed structure for coenzyme F420 from Methanobacterium. , 1978, Biochemistry.

[59]  B. Simmons,et al.  A single-base resolution map of an archaeal transcriptome. , 2010, Genome research.

[60]  E. Stackebrandt Taxonomic parameters revisited : tarnished gold standards , 2006 .

[61]  P. Hugenholtz,et al.  Design and evaluation of 16S rRNA-targeted oligonucleotide probes for fluorescence in situ hybridization. , 2002, Methods in molecular biology.

[62]  David A. Stahl,et al.  Development and application of nucleic acid probes , 1991 .

[63]  Andreas Wilke,et al.  phylogenetic and functional analysis of metagenomes , 2022 .

[64]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .