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

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

Linking Microbial Community, Environmental Variables, and Methanogenesis in Anaerobic Biogas Digesters of Chemically Enhanced Primary Treatment Sludge

(2017) Feng Ju et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

Bacillus sp. strains to produce bio-hydrogen from the organic fraction of municipal solid waste

(2016) A.T. Shah et al.   APPLIED ENERGY

In-situ biogas upgrading in thermophilic granular UASB reactor: key factors affecting the hydrogen mass transfer rate

(2016) Ilaria Bassani et al.   BIORESOURCE TECHNOLOGY

Deeper insight into the structure of the anaerobic digestion microbial community; the biogas microbiome database is expanded with 157 new genomes

(2016) Laura Treu et al.   BIORESOURCE TECHNOLOGY

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

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

Untangling the Effect of Fatty Acid Addition at Species Level Revealed Different Transcriptional Responses of the Biogas Microbial Community Members

(2016) Laura Treu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Dramatic performance ofClostridium thermocellumexplained by its wide range of cellulase modalities

(2016) Qi Xu et al.   Science Advances

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

Dispersing misconceptions and identifying opportunities for the use of 'omics' in soil microbial ecology

(2015) James I. Prosser   NATURE REVIEWS MICROBIOLOGY

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

(2015) Dongwan D. Kang et al.   PeerJ

Bacillus cereus ATCC 14579 RpoN (Sigma 54) Is a Pleiotropic Regulator of Growth, Carbohydrate Metabolism, Motility, Biofilm Formation and Toxin Production

(2015) Hasmik Hayrapetyan et al.   PLoS One

Oxidative stress response and nitrogen utilization are strongly variable in Saccharomyces cerevisiae wine strains with different fermentation performances

(2014) Laura Treu et al.   APPLIED MICROBIOLOGY AND 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

Expanded microbial genome coverage and improved protein family annotation in the COG database

(2014) Michael Y. Galperin et al.   NUCLEIC ACIDS RESEARCH

Do Rumen Bacteroidetes Utilize an Alternative Mechanism for Cellulose Degradation?

(2014) A. E. Naas et al.   mBio

Thermophilic microbial cellulose decomposition and methanogenesis pathways recharacterized by metatranscriptomic and metagenomic analysis

(2014) Yu Xia et al.   Scientific Reports

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

Insights into cellulosome assembly and dynamics: from dissection to reconstruction of the supramolecular enzyme complex

(2013) Steven P Smith et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2013) Mads Albertsen 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

Pfam: the protein families database

(2013) Robert D. Finn 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

Gene and translation initiation site prediction in metagenomic sequences

(2012) Doug Hyatt et al.   BIOINFORMATICS

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Metagenomics of the Svalbard Reindeer Rumen Microbiome Reveals Abundance of Polysaccharide Utilization Loci

(2012) Phillip B. Pope et al.   PLoS One

Mesophilic and Thermophilic Conditions Select for Unique but Highly Parallel Microbial Communities to Perform Carboxylate Platform Biomass Conversion

(2012) Emily B. Hollister et al.   PLoS One

Metabolic and microbial community dynamics during the hydrolytic and acidogenic fermentation in a leach-bed process

(2012) Heike Sträuber et al.   Energy Sustainability and Society

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

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

(2011) M. Hess et al.   SCIENCE

Development of microbial populations in the anaerobic hydrolysis of grass silage for methane production

(2010) Hong Wang et al.   FEMS MICROBIOLOGY ECOLOGY

Complex Glycan Catabolism by the Human Gut Microbiota: The Bacteroidetes Sus-like Paradigm

(2009) Eric C. Martens et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Metagenomics: Read Length Matters

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

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

(2008) Harry J. Flint et al.   NATURE REVIEWS MICROBIOLOGY