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

Comparative metagenomics of biogas-producing microbial communities from production-scale biogas plants operating under wet or dry fermentation conditions

(2015) Yvonne Stolze et al.   Biotechnology for Biofuels

Elviz – exploration of metagenome assemblies with an interactive visualization tool

(2015) Michael Cantor et al.   BMC BIOINFORMATICS

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

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

Herbinix hemicellulosilytica gen. nov., sp. nov., a thermophilic cellulose-degrading bacterium isolated from a thermophilic biogas reactor

(2015) Daniela E. Koeck et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Draft genome sequence of Herbinix hemicellulosilytica T3/55T, a new thermophilic cellulose degrading bacterium isolated from a thermophilic biogas reactor

(2015) Daniela E. Koeck et al.   JOURNAL OF BIOTECHNOLOGY

The bacterial communities associated with fecal types and body weight of rex rabbits

(2015) Bo Zeng et al.   Scientific Reports

VizBin - an application for reference-independent visualization and human-augmented binning of metagenomic data

(2015) Cedric C Laczny et al.   Microbiome

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Linn Solli et al.   Biotechnology for Biofuels

The giraffe (Giraffa camelopardalis) rumen microbiome

(2014) Michael Roggenbuck et al.   FEMS MICROBIOLOGY ECOLOGY

The chicken gastrointestinal microbiome

(2014) Brian B. Oakley et al.   FEMS MICROBIOLOGY LETTERS

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

A Comparative Metagenome Survey of the Fecal Microbiota of a Breast- and a Plant-Fed Asian Elephant Reveals an Unexpectedly High Diversity of Glycoside Hydrolase Family Enzymes

(2014) Nele Ilmberger et al.   PLoS One

A pyrosequencing-based metagenomic study of methane-producing microbial community in solid-state biogas reactor

(2013) An Li et al.   Biotechnology for Biofuels

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Comparative Metagenomic and Metatranscriptomic Analysis of Hindgut Paunch Microbiota in Wood- and Dung-Feeding Higher Termites

(2013) Shaomei He et al.   PLoS One

Phylogenetic Analysis of a Microbialite-Forming Microbial Mat from a Hypersaline Lake of the Kiritimati Atoll, Central Pacific

(2013) Dominik Schneider et al.   PLoS One

The Microbial Community in the Feces of the White Rhinoceros (Ceratotherium simum) as Determined by Barcoded Pyrosequencing Analysis

(2013) Gaorui Bian et al.   PLoS One

Effect of DNA Extraction Methods and Sampling Techniques on the Apparent Structure of Cow and Sheep Rumen Microbial Communities

(2013) Gemma Henderson et al.   PLoS One

Microbial Diversity and Biochemical Potential Encoded by Thermal Spring Metagenomes Derived from the Kamchatka Peninsula

(2013) Bernd Wemheuer et al.   ARCHAEA-AN INTERNATIONAL MICROBIOLOGICAL JOURNAL

Two SusD-Like Proteins Encoded within a Polysaccharide Utilization Locus of an Uncultured Ruminant Bacteroidetes Phylotype Bind Strongly to Cellulose

(2012) A. K. Mackenzie et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng 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

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, accurate error-correction of amplicon pyrosequences using Acacia

(2012) Lauren Bragg et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Assessment of Metagenomic Assembly Using Simulated Next Generation Sequencing Data

(2012) Daniel R. Mende et al.   PLoS One

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

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

The hydrolysis and biogas production of complex cellulosic substrates using three anaerobic biomass sources

(2012) C. Keating et al.   WATER SCIENCE AND TECHNOLOGY

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

The role of acetyl xylan esterase in the solubilization of xylan and enzymatic hydrolysis of wheat straw and giant reed

(2011) Junhua Zhang et al.   Biotechnology for Biofuels

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Chemolithotrophic acetogenic H2/CO2 utilization in Italian rice field soil

(2011) Fanghua Liu et al.   ISME Journal

Comparative and Joint Analysis of Two Metagenomic Datasets from a Biogas Fermenter Obtained by 454-Pyrosequencing

(2011) Sebastian Jaenicke et al.   PLoS One

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

(2011) M. Hess et al.   SCIENCE

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Cellulosomes: Highly Efficient Nanomachines Designed to Deconstruct Plant Cell Wall Complex Carbohydrates

(2010) Carlos M.G.A. Fontes et al.   Annual Review of Biochemistry

Polyphasic Analyses of Methanogenic Archaeal Communities in Agricultural Biogas Plants

(2010) E. Nettmann et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Determination of methanogenic Archaea abundance in a mesophilic biogas plant based on 16S rRNA gene sequence analysis

(2010) I. Bergmann et al.   CANADIAN JOURNAL OF MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Biogas production: current state and perspectives

(2009) Peter Weiland   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Plant biomass degradation by gut microbiomes: more of the same or something new?

(2009) Mark Morrison et al.   CURRENT OPINION IN BIOTECHNOLOGY

Evaluation of the bacterial diversity in the feces of cattle using 16S rDNA bacterial tag-encoded FLX amplicon pyrosequencing (bTEFAP)

(2008) Scot E Dowd et al.   BMC MICROBIOLOGY

From cellulosomes to cellulosomics

(2008) Edward A. Bayer et al.   CHEMICAL RECORD

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