Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

A Metabolic Pathway for Activation of Dietary Glucosinolates by a Human Gut Symbiont

(2020) Catherine S. Liou et al.   CELL

Effects of underfeeding and oral vancomycin on gut microbiome and nutrient absorption in humans

(2020) Alessio Basolo et al.   NATURE MEDICINE

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

(2019) Morgan N. Price et al.   mSystems

A rapid methods development workflow for high-throughput quantitative proteomic applications

(2019) Yan Chen et al.   PLoS One

SignalP 5.0 improves signal peptide predictions using deep neural networks

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

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

Vancomycin–Arginine Conjugate Inhibits Growth of Carbapenem-Resistant E. coli and Targets Cell-Wall Synthesis

(2019) Alexandra Antonoplis et al.   ACS Chemical Biology

Automated “Cells-To-Peptides” Sample Preparation Workflow for High-Throughput, Quantitative Proteomic Assays of Microbes

(2019) Yan Chen et al.   JOURNAL OF PROTEOME RESEARCH

A Ribose-Scavenging System Confers Colonization Fitness on the Human Gut Symbiont Bacteroides thetaiotaomicron in a Diet-Specific Manner

(2019) Robert W.P. Glowacki et al.   Cell Host & Microbe

Droplet Tn-Seq combines microfluidics with Tn-Seq for identifying complex single-cell phenotypes

(2019) Derek Thibault et al.   Nature Communications

Elucidation of the intra- and inter-molecular electron transfer pathways of glucoside 3-dehydrogenase

(2018) Ryota Miyazaki et al.   BIOELECTROCHEMISTRY

The Starch Utilization System Assembles around Stationary Starch-Binding Proteins

(2018) Hannah H. Tuson et al.   BIOPHYSICAL JOURNAL

Rapidly moving new bacteria to model-organism status

(2018) Hualan Liu et al.   CURRENT OPINION IN BIOTECHNOLOGY

SusE facilitates starch uptake independent of starch binding in B. thetaiotaomicron

(2018) Matthew H. Foley et al.   MOLECULAR MICROBIOLOGY

Human Gut Microbiome: Function Matters

(2018) Anna Heintz-Buschart et al.   TRENDS IN MICROBIOLOGY

A selective gut bacterial bile salt hydrolase alters host metabolism

(2018) Lina Yao et al.   eLife

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

(2018) Hualan Liu et al.   mSystems

The human gut microbe Bacteroides thetaiotaomicron encodes the founding member of a novel glycosaminoglycan-degrading polysaccharide lyase family PL29

(2018) Didier Ndeh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2019: improving coverage, classification and access to protein sequence annotations

(2018) Alex L Mitchell et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Alan Cartmell et al.   Nature Microbiology

Enabling genetic analysis of diverse bacteria with Mobile-CRISPRi

(2018) Jason M. Peters et al.   Nature Microbiology

Structural basis for nutrient acquisition by dominant members of the human gut microbiota

(2017) Amy J. Glenwright et al.   NATURE

Anticancer effects of the microbiome and its products

(2017) Laurence Zitvogel et al.   NATURE REVIEWS MICROBIOLOGY

PULDB: the expanded database of Polysaccharide Utilization Loci

(2017) Nicolas Terrapon et al.   NUCLEIC ACIDS RESEARCH

How members of the human gut microbiota overcome the sulfation problem posed by glycosaminoglycans

(2017) Alan Cartmell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Analysis of Caldithrix abyssi, the Thermophilic Anaerobic Bacterium of the Novel Bacterial Phylum Calditrichaeota

(2017) Ilya V. Kublanov et al.   Frontiers in 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

PaperBLAST: Text Mining Papers for Information about Homologs

(2017) Morgan N. Price et al.   mSystems

High-throughput bacterial functional genomics in the sequencing era

(2015) Andrew N Gray et al.   CURRENT OPINION IN MICROBIOLOGY

Species-Specific Dynamic Responses of Gut Bacteria to a Mammalian Glycan

(2015) Varsha Raghavan et al.   JOURNAL OF BACTERIOLOGY

Human gut Bacteroidetes can utilize yeast mannan through a selfish mechanism

(2015) Fiona Cuskin et al.   NATURE

Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides

(2015) M. Wu et al.   SCIENCE

Rapid Quantification of Mutant Fitness in Diverse Bacteria by Sequencing Randomly Bar-Coded Transposons

(2015) Kelly M. Wetmore et al.   mBio

Dose-Response Analysis Using R

(2015) Christian Ritz et al.   PLoS One

Cephalosporinases associated with outer membrane vesicles released by Bacteroides spp. protect gut pathogens and commensals against β-lactam antibiotics

(2014) Régis Stentz et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Tuning transcription of nutrient utilization genes to catabolic rate promotes growth in a gut bacterium

(2014) Varsha Raghavan et al.   MOLECULAR MICROBIOLOGY

Efficient utilization of complex N-linked glycans is a selective advantage for Bacteroides fragilis in extraintestinal infections

(2014) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Polysaccharides utilization in human gut bacterium Bacteroides thetaiotaomicron: comparative genomics reconstruction of metabolic and regulatory networks

(2013) Dmitry A Ravcheev et al.   BMC GENOMICS

The thuEFGKAB Operon of Rhizobia and Agrobacterium tumefaciens Codes for Transport of Trehalose, Maltitol, and Isomers of Sucrose and Their Assimilation through the Formation of Their 3-Keto Derivatives

(2013) O. Y. Ampomah et al.   JOURNAL OF BACTERIOLOGY

Dynamic responses ofBacteroides thetaiotaomicronduring growth on glycan mixtures

(2013) Theresa E. Rogers et al.   MOLECULAR MICROBIOLOGY

An anaerobic bacterium,Bacteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide

(2013) Surabhi Mishra et al.   MOLECULAR MICROBIOLOGY

Transposon insertion sequencing: a new tool for systems-level analysis of microorganisms

(2013) Tim van Opijnen et al.   NATURE REVIEWS MICROBIOLOGY

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Bile resistance mechanisms in Lactobacillus and Bifidobacterium

(2013) Lorena Ruiz et al.   Frontiers in Microbiology

Role of the gut microbiota in health and chronic gastrointestinal disease: understanding a hidden metabolic organ

(2013) Caitriona M. Guinane et al.   Therapeutic Advances in Gastroenterology

Multidomain Carbohydrate-binding Proteins Involved inBacteroides thetaiotaomicronStarch Metabolism

(2012) Elizabeth A. Cameron et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Smallest Active Carbamoyl Phosphate Synthetase Was Identified in the Human Gut ArchaeonMethanobrevibacter smithii

(2012) Elena Popa et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

Dual diaminopimelate biosynthesis pathways in Bacteroides fragilis and Clostridium thermocellum

(2011) André O. Hudson et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Faecal pharmacokinetics of orally administered vancomycin in patients with suspected Clostridium difficile infection

(2011) Milagros Gonzales et al.   BMC INFECTIOUS DISEASES

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

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

Sulfatases and a RadicalS-Adenosyl-l-methionine (AdoMet) Enzyme Are Key for Mucosal Foraging and Fitness of the Prominent Human Gut Symbiont,Bacteroides thetaiotaomicron

(2011) Alhosna Benjdia et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

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

Evidence-Based Annotation of Gene Function in Shewanella oneidensis MR-1 Using Genome-Wide Fitness Profiling across 121 Conditions

(2011) Adam Deutschbauer et al.   PLoS Genetics

Identification of a Dehydrogenase Required for Lactose Metabolism in Caulobacter crescentus

(2010) B. H. Arellano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

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

(2010) Erica D. Sonnenburg et al.   CELL

Phenotypic Landscape of a Bacterial Cell

(2010) Robert J. Nichols et al.   CELL

Amino acid metabolism in intestinal bacteria: links between gut ecology and host health

(2010) Zhao-Lai Dai   Frontiers in Bioscience-Landmark

SusG: A Unique Cell-Membrane-Associated α-Amylase from a Prominent Human Gut Symbiont Targets Complex Starch Molecules

(2010) Nicole M. Koropatkin et al.   STRUCTURE

Systematic analysis of genome-wide fitness data in yeast reveals novel gene function and drug action

(2010) Maureen E Hillenmeyer et al.   GENOME BIOLOGY

Identifying Genetic Determinants Needed to Establish a Human Gut Symbiont in Its Habitat

(2009) Andrew L. Goodman et al.   Cell Host & Microbe

The NIH Human Microbiome Project

(2009) 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

MicrobesOnline: an integrated portal for comparative and functional genomics

(2009) P. S. Dehal et al.   NUCLEIC ACIDS RESEARCH

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

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

Biochemical and Phylogenetic Characterization of a Novel Diaminopimelate Biosynthesis Pathway in Prokaryotes Identifies a Diverged Form of LL-Diaminopimelate Aminotransferase

(2008) A. O. Hudson et al.   JOURNAL OF BACTERIOLOGY

Structural and Functional Analysis of a Glycoside Hydrolase Family 97 Enzyme fromBacteroides thetaiotaomicron

(2008) Momoyo Kitamura et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2008) Nicole M. Koropatkin et al.   STRUCTURE