Metagenomics reveals functional synergy and novel polysaccharide utilization loci in the Castor canadensis fecal microbiome

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

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

Molecular Mechanism by which Prominent Human Gut Bacteroidetes Utilize Mixed-Linkage Beta-Glucans, Major Health-Promoting Cereal Polysaccharides

(2017) Kazune Tamura et al.   Cell Reports

Biosynthesis of the Plant Cell Wall Matrix Polysaccharide Xyloglucan

(2016) Markus Pauly et al.   Annual Review of Plant Biology

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

(2016) Keith Mewis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

LCA*: an entropy-based measure for taxonomic assignment within assembled metagenomes

(2016) Niels W. Hanson et al.   BIOINFORMATICS

Synthesis and evaluation of a series of 6-chloro-4-methylumbelliferyl glycosides as fluorogenic reagents for screening metagenomic libraries for glycosidase activity

(2016) Hong-Ming Chen et al.   CARBOHYDRATE RESEARCH

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

Substrate-Driven Convergence of the Microbial Community in Lignocellulose-Amended Enrichments of Gut Microflora from the Canadian Beaver (Castor canadensis) and North American Moose (Alces americanus)

(2016) Mabel T. Wong et al.   Frontiers in Microbiology

Bacterial and Archaeal Diversity in the Gastrointestinal Tract of the North American Beaver (Castor canadensis)

(2016) Robert J. Gruninger et al.   PLoS One

Bacteroides intestinalis DSM 17393, a member of the human colonic microbiome, upregulates multiple endoxylanases during growth on xylan

(2016) Kui Wang et al.   Scientific Reports

MetaPathways v2.5: quantitative functional, taxonomic and usability improvements: Fig. 1.

(2015) Kishori M. Konwar et al.   BIOINFORMATICS

Biocatalysts for biomass deconstruction from environmental genomics

(2015) Zachary Armstrong et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

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

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

Marked seasonal variation in the wild mouse gut microbiota

(2015) Corinne F Maurice et al.   ISME Journal

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

Baleen whales host a unique gut microbiome with similarities to both carnivores and herbivores

(2015) Jon G. Sanders et al.   Nature Communications

Anvi’o: an advanced analysis and visualization platform for ‘omics data

(2015) A. Murat Eren et al.   PeerJ

The Gut Microbiota of Wild Mice

(2015) Laura Weldon et al.   PLoS One

Automatic prediction of polysaccharide utilization loci in Bacteroidetes species

(2014) Nicolas Terrapon et al.   BIOINFORMATICS

The Devil Lies in the Details: How Variations in Polysaccharide Fine-Structure Impact the Physiology and Evolution of Gut Microbes

(2014) Eric C. Martens et al.   JOURNAL OF MOLECULAR BIOLOGY

A complex gene locus enables xyloglucan utilization in the model saprophyteCellvibrio japonicus

(2014) Johan Larsbrink et al.   MOLECULAR MICROBIOLOGY

A discrete genetic locus confers xyloglucan metabolism in select human gut Bacteroidetes

(2014) Johan Larsbrink et al.   NATURE

Gill bacteria enable a novel digestive strategy in a wood-feeding mollusk

(2014) Roberta M. O’Connor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

PhyloSift: phylogenetic analysis of genomes and metagenomes

(2014) Aaron E. Darling et al.   PeerJ

Mining for hemicellulases in the fungus-growing termite Pseudacanthotermes militaris using functional metagenomics

(2013) Géraldine Bastien et al.   Biotechnology for Biofuels

Biomining active cellulases from a mining bioremediation system

(2013) Keith Mewis et al.   JOURNAL OF BIOTECHNOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle

(2013) Erin D. Scully et al.   PLoS One

Revealing Nature's Cellulase Diversity: The Digestion Mechanism of Caldicellulosiruptor bescii CelA

(2013) R. Brunecky et al.   SCIENCE

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Structures of xyloglucans in primary cell walls of gymnosperms, monilophytes (ferns sensu lato) and lycophytes

(2012) Yves S.Y. Hsieh et al.   PHYTOCHEMISTRY

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

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

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

(2011) R. Caspi et al.   NUCLEIC ACIDS RESEARCH

Mitochondrial Genomes Reveal Slow Rates of Molecular Evolution and the Timing of Speciation in Beavers (Castor), One of the Largest Rodent Species

(2011) Susanne Horn et al.   PLoS One

Target Region Selection Is a Critical Determinant of Community Fingerprints Generated by 16S Pyrosequencing

(2011) Purnima S. Kumar et al.   PLoS One

Evidence of cellulose metabolism by the giant panda gut microbiome

(2011) L. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

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

(2011) M. Hess et al.   SCIENCE

A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries

(2011) Keith Mewis et al.   Jove-Journal of Visualized Experiments

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

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

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice

(2010) Kelly S Swanson et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Adaptation to herbivory by the Tammar wallaby includes bacterial and glycoside hydrolase profiles different from other herbivores

(2010) P. B. Pope et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

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

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

Large Insert Environmental Genomic Library Production

(2009) Marcus Taupp et al.   Jove-Journal of Visualized Experiments

Extraction of High Molecular Weight Genomic DNA from Soils and Sediments

(2009) Sangwon Lee et al.   Jove-Journal of Visualized Experiments

DNA Extraction from 0.22 μM Sterivex Filters and Cesium Chloride Density Gradient Centrifugation

(2009) Jody J. Wright et al.   Jove-Journal of Visualized Experiments

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE