Metagenomic analysis and functional characterization of the biogas microbiome using high throughput shotgun sequencing and a novel binning strategy

A balanced microbiota efficiently produces methane in a novel high-rate horizontal anaerobic reactor for the treatment of swine wastewater

(2015) Rose Maria Duda et al.   BIORESOURCE TECHNOLOGY

Microbial diversity and dynamicity of biogas reactors due to radical changes of feedstock composition

(2015) Davide De Francisci et al.   BIORESOURCE TECHNOLOGY

New steady-state microbial community compositions and process performances in biogas reactors induced by temperature disturbances

(2015) Gang Luo et al.   Biotechnology for Biofuels

Eubacteria and archaea communities in seven mesophile anaerobic digester plants in Germany

(2015) Christian Abendroth et al.   Biotechnology for Biofuels

Microbial community dynamics in replicate anaerobic digesters exposed sequentially to increasing organic loading rate, acidosis, and process recovery

(2015) Xavier Goux et al.   Biotechnology for Biofuels

Anaerobic Mono- and Co-digestion of Mechanically Pretreated Meadow Grass for Biogas Production

(2015) Panagiotis Tsapekos et al.   ENERGY & FUELS

Biogas Upgrading via Hydrogenotrophic Methanogenesis in Two-Stage Continuous Stirred Tank Reactors at Mesophilic and Thermophilic Conditions

(2015) Ilaria Bassani et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Complete genome sequence of the strain Defluviitoga tunisiensis L3, isolated from a thermophilic, production-scale biogas plant

(2015) Irena Maus et al.   JOURNAL OF BIOTECHNOLOGY

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Deeply sequenced metagenome and metatranscriptome of a biogas-producing microbial community from an agricultural production-scale biogas plant

(2015) Andreas Bremges et al.   GigaScience

Functionally redundant but dissimilar microbial communities within biogas reactors treating maize silage in co-fermentation with sugar beet silage

(2015) Susanne G. Langer et al.   Microbial Biotechnology

Towards molecular biomarkers for biogas production from lignocellulose-rich substrates

(2014) Michael Lebuhn et al.   ANAEROBE

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

(2014) Kristina Lang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Microbial analysis in biogas reactors suffering by foaming incidents

(2014) Panagiotis G. Kougias et al.   BIORESOURCE TECHNOLOGY

A metagenomic study of the microbial communities in four parallel biogas reactors

(2014) Linn Solli et al.   Biotechnology for Biofuels

Performance and bacterial enrichment of bioelectrochemical systems during methane and acetate production

(2014) Nikolaos Xafenias et al.   INTERNATIONAL JOURNAL OF HYDROGEN ENERGY

Complete genome sequence of the cellulolytic thermophile Ruminoclostridium cellulosi wild-type strain DG5 isolated from a thermophilic biogas plant

(2014) Daniela E. Koeck et al.   JOURNAL OF BIOTECHNOLOGY

Identification and assembly of genomes and genetic elements in complex metagenomic samples without using reference genomes

(2014) H Bjørn Nielsen et al.   NATURE BIOTECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Tackling soil diversity with the assembly of large, complex metagenomes

(2014) Adina Chuang Howe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Performance and microbial community analysis of the anaerobic reactor with coke oven gas biomethanation and in situ biogas upgrading

(2013) Wen Wang et al.   BIORESOURCE TECHNOLOGY

Detailed analysis of metagenome datasets obtained from biogas-producing microbial communities residing in biogas reactors does not indicate the presence of putative pathogenic microorganisms

(2013) Felix G Eikmeyer et al.   Biotechnology for Biofuels

The impact of genomic variability on gene expression in environmentalSaccharomyces cerevisiaestrains

(2013) Laura Treu et al.   ENVIRONMENTAL MICROBIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

MetaCluster 5.0: a two-round binning approach for metagenomic data for low-abundance species in a noisy sample

(2012) Y. Wang et al.   BIOINFORMATICS

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing

(2012) Roland Wirth et al.   Biotechnology for Biofuels

Effect of ammonium and acetate on methanogenic pathway and methanogenic community composition

(2012) Ioannis A. Fotidis et al.   FEMS MICROBIOLOGY ECOLOGY

High-density PhyloChip profiling of stimulated aquifer microbial communities reveals a complex response to acetate amendment

(2012) Kim M. Handley et al.   FEMS MICROBIOLOGY ECOLOGY

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing

(2012) Martha Zakrzewski et al.   JOURNAL OF BIOTECHNOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Untangling Genomes from Metagenomes: Revealing an Uncultured Class of Marine Euryarchaeota

(2012) V. Iverson et al.   SCIENCE

Microbial community structure in a biogas digester utilizing the marine energy crop Saccharina latissima

(2012) Phillip B. Pope et al.   3 Biotech

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Potential impact of process parameters upon the bacterial diversity in the mesophilic anaerobic digestion of beet silage

(2011) Niclas Krakat et al.   BIORESOURCE TECHNOLOGY

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Characterization of microbial biofilms in a thermophilic biogas system by high-throughput metagenome sequencing

(2011) Antje Rademacher et al.   FEMS MICROBIOLOGY ECOLOGY

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

(2011) Chris L Dupont et al.   ISME Journal

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Bacterial community structures are unique and resilient in full-scale bioenergy systems

(2011) J. J. Werner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The microcosm of a biogas fermenter: Comparison of moderate hyperthermophilic (60°C) with thermophilic (55°C) conditions

(2010) Niclas Krakat et al.   ENGINEERING IN LIFE SCIENCES

The future of anaerobic digestion and biogas utilization

(2009) J.B. Holm-Nielsen et al.   BIORESOURCE TECHNOLOGY

Ecophysiology of syntrophic communities that degrade saturated and unsaturated long-chain fatty acids

(2009) Diana Z. Sousa et al.   FEMS MICROBIOLOGY ECOLOGY

Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge

(2009) Delphine Rivière et al.   ISME Journal

Phylogenetic characterization of a biogas plant microbial community integrating clone library 16S-rDNA sequences and metagenome sequence data obtained by 454-pyrosequencing

(2009) Magdalena Kröber et al.   JOURNAL OF BIOTECHNOLOGY

Complete genome sequence of Thermanaerovibrio acidaminovorans type strain (Su883T)

(2009) Mansi Chovatia et al.   Standards in Genomic Sciences

Metagenomics: Read Length Matters

(2008) K. E. Wommack et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Diversity of the resident microbiota in a thermophilic municipal biogas plant

(2008) Agnes Weiss et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Effect of sulfate on methanogenic communities that degrade unsaturated and saturated long-chain fatty acids (LCFA)

(2008) Diana Z. Sousa et al.   ENVIRONMENTAL MICROBIOLOGY

The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology

(2008) Andreas Schlüter et al.   JOURNAL OF BIOTECHNOLOGY

Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor

(2008) Lutz Krause et al.   JOURNAL OF BIOTECHNOLOGY