New insights from the biogas microbiome by comprehensive genome-resolved metagenomics of nearly 1600 species originating from multiple anaerobic digesters

Effects of thermal hydrolytic pre-treatment on biogas process efficiency and microbial community structure in industrial- and laboratory-scale digesters

(2019) M. Westerholm et al.   WASTE MANAGEMENT

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants

(2018) Julia Hassa et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion

(2018) Susanne Theuerl et al.   BIORESOURCE TECHNOLOGY

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion

(2018) Yangyang Jia et al.   Biotechnology for Biofuels

Characterization of Bathyarchaeota genomes assembled from metagenomes of biofilms residing in mesophilic and thermophilic biogas reactors

(2018) Irena Maus et al.   Biotechnology for Biofuels

A year of monitoring 20 mesophilic full-scale bioreactors reveals the existence of stable but different core microbiomes in bio-waste and wastewater anaerobic digestion systems

(2018) Magdalena Calusinska et al.   Biotechnology for Biofuels

The Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level

(2018) Luis M Rodriguez-R et al.   NUCLEIC ACIDS RESEARCH

Performance and genome-centric metagenomics of thermophilic single and two-stage anaerobic digesters treating cheese wastes

(2018) Alessandra Fontana et al.   WATER RESEARCH

Metagenomic binning reveals the functional roles of core abundant microorganisms in twelve full-scale biogas plants

(2018) Stefano Campanaro et al.   WATER RESEARCH

Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics

(2018) Laura Treu et al.   Frontiers in Microbiology

Microbial rRNA gene expression and co-occurrence profiles associate with biokinetics and elemental composition in full-scale anaerobic digesters

(2018) Ryan M. Ziels et al.   Microbial Biotechnology

Spatial Distribution and Diverse Metabolic Functions of Lignocellulose-Degrading Uncultured Bacteria as Revealed by Genome-Centric Metagenomics

(2018) Panagiotis G. Kougias et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial activity response to hydrogen injection in thermophilic anaerobic digesters revealed by genome-centric metatranscriptomics

(2018) Alessandra Fontana et al.   Microbiome

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

(2017) Robert M Bowers et al.   NATURE BIOTECHNOLOGY

Anaerobic granular sludge for simultaneous biomethanation of synthetic wastewater and CO with focus on the identification of CO-converting microorganisms

(2017) Yuhang Jing et al.   WATER RESEARCH

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

(2017) Donovan H. Parks et al.   Nature Microbiology

Non-autotrophic methanogens dominate in anaerobic digesters

(2017) Atsushi Kouzuma et al.   Scientific Reports

Deep metagenome and metatranscriptome analyses of microbial communities affiliated with an industrial biogas fermenter, a cow rumen, and elephant feces reveal major differences in carbohydrate hydrolysis strategies

(2016) Simon Güllert et al.   Biotechnology for Biofuels

Unraveling the microbiome of a thermophilic biogas plant by metagenome and metatranscriptome analysis complemented by characterization of bacterial and archaeal isolates

(2016) Irena Maus et al.   Biotechnology for Biofuels

Identification and genome reconstruction of abundant distinct taxa in microbiomes from one thermophilic and three mesophilic production-scale biogas plants

(2016) Yvonne Stolze et al.   Biotechnology for Biofuels

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis

(2016) Gang Luo et al.   Biotechnology for Biofuels

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

(2016) Stefano Campanaro et al.   Biotechnology for Biofuels

Genome-centric resolution of microbial diversity, metabolism and interactions in anaerobic digestion

(2016) Inka Vanwonterghem et al.   ENVIRONMENTAL MICROBIOLOGY

Identification of syntrophic acetate-oxidizing bacteria in anaerobic digesters by combined protein-based stable isotope probing and metagenomics

(2016) Freya Mosbæk et al.   ISME Journal

Genomic characterization of Defluviitoga tunisiensis L3, a key hydrolytic bacterium in a thermophilic biogas plant and its abundance as determined by metagenome fragment recruitment

(2016) Irena Maus et al.   JOURNAL OF BIOTECHNOLOGY

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

Comparative Analysis of Methanogenic Communities in Different Laboratory-Scale Anaerobic Digesters

(2016) Ayrat M. Ziganshin et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Methylotrophic methanogenesis discovered in the archaeal phylum Verstraetearchaeota

(2016) Inka Vanwonterghem et al.   Nature Microbiology

Novel Syntrophic Populations Dominate an Ammonia-Tolerant Methanogenic Microbiome

(2016) J. A. Frank et al.   mSystems

Dynamic functional characterization and phylogenetic changes due to Long Chain Fatty Acids pulses in biogas reactors

(2016) Panagiotis G. Kougias et al.   Scientific Reports

Cellulose and hemicellulose decomposition by forest soil bacteria proceeds by the action of structurally variable enzymatic systems

(2016) Rubén López-Mondéjar et al.   Scientific Reports

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

Anaerobic digestion of lignocellulosic biomass: Challenges and opportunities

(2015) Chayanon Sawatdeenarunat et al.   BIORESOURCE TECHNOLOGY

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

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

Metagenome changes in the mesophilic biogas-producing community during fermentation of the green alga Scenedesmus obliquus

(2015) Roland Wirth et al.   JOURNAL OF BIOTECHNOLOGY

Microbial species delineation using whole genome sequences

(2015) Neha J. Varghese et al.   NUCLEIC ACIDS RESEARCH

Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics

(2015) P. N. Evans et al.   SCIENCE

Ammonia and temperature determine potential clustering in the anaerobic digestion microbiome

(2015) Jo De Vrieze et al.   WATER RESEARCH

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

Inoculum selection is crucial to ensure operational stability in anaerobic digestion

(2014) Jo De Vrieze et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Phylogeny, culturing, and metagenomics of the human gut microbiota

(2014) Alan W. Walker et al.   TRENDS IN MICROBIOLOGY

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

454 pyrosequencing analyses of bacterial and archaeal richness in 21 full-scale biogas digesters

(2013) Carina Sundberg et al.   FEMS MICROBIOLOGY ECOLOGY

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

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Roland Wirth et al.   Biotechnology for Biofuels

Measures of phylogenetic differentiation provide robust and complementary insights into microbial communities

(2012) Donovan H Parks et al.   ISME Journal

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Syntrophorhabdus aromaticivorans gen. nov., sp. nov., the First Cultured Anaerobe Capable of Degrading Phenol to Acetate in Obligate Syntrophic Associations with a Hydrogenotrophic Methanogen

(2008) Y.-L. Qiu et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY