Polysaccharide utilization loci in Bacteroides determine population fitness and community-level interactions

Design of synthetic human gut microbiome assembly and butyrate production

(2021) Ryan L. Clark et al.   Nature Communications

Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus

(2020) Didier Ndeh et al.   Nature Communications

Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

(2020) Guillaume Déjean et al.   mBio

A unified catalog of 204,938 reference genomes from the human gut microbiome

(2020) Alexandre Almeida et al.   NATURE BIOTECHNOLOGY

Metabolism of Glycosphingolipids and Their Role in the Pathophysiology of Lysosomal Storage Disorders

(2020) Alex E. Ryckman et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Gut microbiota in human metabolic health and disease

(2020) Yong Fan et al.   NATURE REVIEWS MICROBIOLOGY

Bacteroides thetaiotaomicron Fosters the Growth of Butyrate-Producing Anaerostipes caccae in the Presence of Lactose and Total Human Milk Carbohydrates

(2020) Loo Wee Chia et al.   Microorganisms

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

SignalP 5.0 improves signal peptide predictions using deep neural networks

(2019) José Juan Almagro Armenteros et al.   NATURE BIOTECHNOLOGY

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Bacteroides thetaiotaomicron Starch Utilization Promotes Quercetin Degradation and Butyrate Production by Eubacterium ramulus

(2019) Gina Paola Rodriguez-Castaño et al.   Frontiers in Microbiology

Bacteroidetes use thousands of enzyme combinations to break down glycans

(2019) Pascal Lapébie et al.   Nature Communications

Complex N-glycan breakdown by gut Bacteroides involves an extensive enzymatic apparatus encoded by multiple co-regulated genetic loci

(2019) Justina Briliūtė et al.   Nature Microbiology

Streamlined Genetic Manipulation of Diverse Bacteroides and Parabacteroides Isolates from the Human Gut Microbiota

(2019) Leonor García-Bayona et al.   mBio

Adaptation of Syntenic Xyloglucan Utilization Loci of Human Gut Bacteroidetes to Polysaccharide Side Chain Diversity

(2019) Guillaume Déjean et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

(2019) Hannah Fehlner-Peach et al.   Cell Host & Microbe

Intestinal IgA Regulates Expression of a Fructan Polysaccharide Utilization Locus in Colonizing Gut Commensal Bacteroides thetaiotaomicron

(2019) Payal Joglekar et al.   mBio

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Molecular basis of an agarose metabolic pathway acquired by a human intestinal symbiont

(2018) Benjamin Pluvinage et al.   Nature Communications

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

A surface endogalactanase in Bacteroides thetaiotaomicron confers keystone status for arabinogalactan degradation

(2018) Alan Cartmell et al.   Nature Microbiology

Degradation of Marine Algae-Derived Carbohydrates by Bacteroidetes Isolated from Human Gut Microbiota

(2017) Miaomiao Li et al.   Marine Drugs

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

Reciprocal Prioritization to Dietary Glycans by Gut Bacteria in a Competitive Environment Promotes Stable Coexistence

(2017) Yunus E. Tuncil et al.   mBio

The Glycolytic Versatility of Bacteroides uniformis CECT 7771 and Its Genome Response to Oligo and Polysaccharides

(2017) Alfonso Benítez-Páez et al.   Frontiers in Cellular and Infection Microbiology

Dietary pectic glycans are degraded by coordinated enzyme pathways in human colonic Bacteroides

(2017) Ana S. Luis et al.   Nature Microbiology

An insider's perspective: Bacteroides as a window into the microbiome

(2017) Aaron G. Wexler et al.   Nature Microbiology

Xylan degradation by the human gut Bacteroides xylanisolvens XB1AT involves two distinct gene clusters that are linked at the transcriptional level

(2016) Jordane Despres et al.   BMC GENOMICS

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

Modulation of a Circulating Uremic Solute via Rational Genetic Manipulation of the Gut Microbiota

(2016) A. Sloan Devlin et al.   Cell Host & Microbe

A β-mannan utilization locus inBacteroides ovatusinvolves a GH36 α-galactosidase active on galactomannans

(2016) Sumitha K. Reddy et al.   FEBS LETTERS

Galactomannan Catabolism Conferred by a Polysaccharide Utilization Locus ofBacteroides ovatus

(2016) Viktoria Bågenholm et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The evolution of cooperation within the gut microbiota

(2016) Seth Rakoff-Nahoum et al.   NATURE

Molecular Dissection of Xyloglucan Recognition in a Prominent Human Gut Symbiont

(2016) Alexandra S. Tauzin et al.   mBio

Multiple Signals Govern Utilization of a Polysaccharide in the Gut Bacterium Bacteroides thetaiotaomicron

(2016) Nathan D. Schwalm et al.   mBio

The healthy human microbiome

(2016) Jason Lloyd-Price et al.   Genome Medicine

Structural dissection of a complexBacteroides ovatusgene locus conferring xyloglucan metabolism in the human gut

(2016) Glyn R. Hemsworth et al.   Open Biology

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

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

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

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

Glycan complexity dictates microbial resource allocation in the large intestine

(2015) Artur Rogowski et al.   Nature Communications

Population Diversification in a Yeast Metabolic Program Promotes Anticipation of Environmental Shifts

(2015) Ophelia S. Venturelli et al.   PLOS BIOLOGY

Programming a Human Commensal Bacterium, Bacteroides thetaiotaomicron, to Sense and Respond to Stimuli in the Murine Gut Microbiota

(2015) Mark Mimee et al.   Cell Systems

Development of a novel plasmid vector pTIO-1 adapted for electrotransformation of Porphyromonas gingivalis

(2014) Junpei Tagawa et al.   JOURNAL OF MICROBIOLOGICAL METHODS

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

(2014) Johan Larsbrink et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

CELLO2GO: A Web Server for Protein subCELlular LOcalization Prediction with Functional Gene Ontology Annotation

(2014) Chin-Sheng Yu et al.   PLoS One

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How glycan metabolism shapes the human gut microbiota

(2012) Nicole M. Koropatkin et al.   NATURE REVIEWS MICROBIOLOGY

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Eating For Two: How Metabolism Establishes Interspecies Interactions in the Gut

(2011) Michael A. Fischbach et al.   Cell Host & Microbe

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

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

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

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

PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes

(2010) Nancy Y. Yu et al.   BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

Dissecting thein VivoMetabolic Potential of Two Human Gut Acetogens

(2010) Federico E. Rey et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Coordinate Regulation of Glycan Degradation and Polysaccharide Capsule Biosynthesis by a Prominent Human Gut Symbiont

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

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

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

Characterizing a model human gut microbiota composed of members of its two dominant bacterial phyla

(2009) M. A. Mahowald et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices

(2008) Nicole M. Koropatkin et al.   STRUCTURE