Comparative Genomic Analysis Reveals Novel Microcompartment-Associated Metabolic Pathways in the Human Gut Microbiome

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

Characterization of 1,2-Propanediol Dehydratases Reveals Distinct Mechanisms for B12-Dependent and Glycyl Radical Enzymes

(2018) Benjamin J. Levin et al.   BIOCHEMISTRY

Structure and Kinetics of the S-(+)-1-Amino-2-propanol Dehydrogenase from the RMM Microcompartment of Mycobacterium smegmatis

(2018) Evan Mallette et al.   BIOCHEMISTRY

Engineering nanoreactors using bacterial microcompartment architectures

(2018) Jefferson S Plegaria et al.   CURRENT OPINION IN BIOTECHNOLOGY

Modeling metabolism of the human gut microbiome

(2018) Stefanía Magnúsdóttir et al.   CURRENT OPINION IN BIOTECHNOLOGY

Discovery of enzymes for toluene synthesis from anoxic microbial communities

(2018) Harry R. Beller et al.   Nature Chemical Biology

The gut–liver axis and the intersection with the microbiome

(2018) Anupriya Tripathi et al.   Nature Reviews Gastroenterology & Hepatology

Bacterial microcompartments

(2018) Cheryl A. Kerfeld et al.   NATURE REVIEWS MICROBIOLOGY

The Microbiome Modeling Toolbox: from microbial interactions to personalized microbial communities

(2018) Federico Baldini et al.   BIOINFORMATICS

A prominent glycyl radical enzyme in human gut microbiomes metabolizestrans-4-hydroxy-l-proline

(2017) B. J. Levin et al.   SCIENCE

Assembly principles and structure of a 6.5-MDa bacterial microcompartment shell

(2017) Markus Sutter et al.   SCIENCE

Uncovering the trimethylamine-producing bacteria of the human gut microbiota

(2017) Silke Rath et al.   Microbiome

PaperBLAST: Text Mining Papers for Information about Homologs

(2017) Morgan N. Price et al.   mSystems

In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment

(2017) Jan Zarzycki et al.   Scientific Reports

Correction to Characterization of Choline Trimethylamine-Lyase Expands the Chemistry of Glycyl Radical Enzymes

(2016) Smaranda Craciun et al.   ACS Chemical Biology

A Complete Structural Inventory of the Mycobacterial Microcompartment Shell Proteins Constrains Models of Global Architecture and Transport

(2016) Evan Mallette et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

The Structural Basis of Coenzyme A Recycling in a Bacterial Organelle

(2016) Onur Erbilgin et al.   PLOS BIOLOGY

Dumpster Diving in the Gut: Bacterial Microcompartments as Part of a Host-Associated Lifestyle

(2016) Christopher M. Jakobson et al.   PLoS Pathogens

Genomic Analysis of the Human Gut Microbiome Suggests Novel Enzymes Involved in Quinone Biosynthesis

(2016) Dmitry A. Ravcheev et al.   Frontiers in Microbiology

Bioinformatic Characterization of Glycyl Radical Enzyme-Associated Bacterial Microcompartments

(2015) Jan Zarzycki et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Trimethylamine N-Oxide From Gut Microbiota in Chronic Kidney Disease Patients: Focus on Diet

(2015) Cristiane Moraes et al.   JOURNAL OF RENAL NUTRITION

Bacterial microcompartments and the modular construction of microbial metabolism

(2015) Cheryl A. Kerfeld et al.   TRENDS IN MICROBIOLOGY

Characterization and Detection of a Widely Distributed Gene Cluster That Predicts Anaerobic Choline Utilization by Human Gut Bacteria

(2015) Ana Martínez-del Campo et al.   mBio

Systematic genome assessment of B-vitamin biosynthesis suggests co-operation among gut microbes

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Characterization of a Planctomycetal Organelle: a Novel Bacterial Microcompartment for the Aerobic Degradation of Plant Saccharides

(2014) Onur Erbilgin et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Solution Structure of a Bacterial Microcompartment Targeting Peptide and Its Application in the Construction of an Ethanol Bioreactor

(2014) Andrew D. Lawrence et al.   ACS Synthetic Biology

A Taxonomy of Bacterial Microcompartment Loci Constructed by a Novel Scoring Method

(2014) Seth D. Axen et al.   PLoS Computational Biology

Systematic genomic analysis reveals the complementary aerobic and anaerobic respiration capacities of the human gut microbiota

(2014) Dmitry A. Ravcheev et al.   Frontiers in Microbiology

Evidence that a Metabolic Microcompartment Contains and Recycles Private Cofactor Pools

(2013) D. L. Huseby et al.   JOURNAL OF BACTERIOLOGY

The Shells of BMC-Type Microcompartment Organelles in Bacteria

(2013) Todd O. Yeates et al.   JOURNAL OF MOLECULAR MICROBIOLOGY AND BIOTECHNOLOGY

Functions, Compositions, and Evolution of the Two Types of Carboxysomes: Polyhedral Microcompartments That Facilitate CO2 Fixation in Cyanobacteria and Some Proteobacteria

(2013) B. D. Rae et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Involvement of a Bacterial Microcompartment in the Metabolism of Fucose and Rhamnose by Clostridium phytofermentans

(2013) Elsa Petit et al.   PLoS One

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

CDD: conserved domains and protein three-dimensional structure

(2012) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Structural Insight into the Clostridium difficile Ethanolamine Utilisation Microcompartment

(2012) Alison C. Pitts et al.   PLoS One

Interactions between the termini of lumen enzymes and shell proteins mediate enzyme encapsulation into bacterial microcompartments

(2012) C. Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Using comparative genomics to uncover new kinds of protein-based metabolic organelles in bacteria

(2012) Julien Jorda et al.   PROTEIN SCIENCE

Ethanolamine Controls Expression of Genes Encoding Components Involved in Interkingdom Signaling and Virulence in Enterohemorrhagic Escherichia coli O157:H7

(2012) M. M. Kendall et al.   mBio

The N-Terminal Region of the Medium Subunit (PduD) Packages Adenosylcobalamin-Dependent Diol Dehydratase (PduCDE) into the Pdu Microcompartment

(2011) C. Fan et al.   JOURNAL OF BACTERIOLOGY

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota

(2011) P. Thiennimitr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

Bacterial Microcompartments

(2010) Cheryl A. Kerfeld et al.   Annual Review of Microbiology

Ethanolamine Utilization Contributes to Proliferation ofSalmonella entericaSerovar Typhimurium in Food and in Nematodes

(2010) Shabarinath Srikumar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genetic analysis around aminoalcohol dehydrogenase gene of Rhodococcus erythropolis MAK154: a putative GntR transcription factor in transcriptional regulation

(2010) Nobuyuki Urano et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Accessing the SEED Genome Databases via Web Services API: Tools for Programmers

(2010) Terry Disz et al.   BMC BIOINFORMATICS

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

Synthesis of Empty Bacterial Microcompartments, Directed Organelle Protein Incorporation, and Evidence of Filament-Associated Organelle Movement

(2010) Joshua B. Parsons et al.   MOLECULAR CELL

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Cell Biology of Prokaryotic Organelles

(2010) D. Murat et al.   Cold Spring Harbor Perspectives in Biology

Structure of a trimeric bacterial microcompartment shell protein, EtuB, associated with ethanol utilization inClostridium kluyveri

(2009) Dana Heldt et al.   BIOCHEMICAL JOURNAL

Bacterial microcompartments: their properties and paradoxes

(2009) Shouqiang Cheng et al.   BIOESSAYS

Comparative Genomics of Ethanolamine Utilization

(2009) O. Tsoy et al.   JOURNAL OF BACTERIOLOGY

Exploiting genomic patterns to discover new supramolecular protein assemblies

(2009) Morgan Beeby et al.   PROTEIN SCIENCE

Insights from multiple structures of the shell proteins from the β-carboxysome

(2009) Shiho Tanaka et al.   PROTEIN SCIENCE

Cloning and expression of the l-1-amino-2-propanol dehydrogenase gene from Rhodococcus erythropolis, and its application to double chiral compound production

(2008) M. Kataoka et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Purine Utilization byKlebsiella oxytocaM5al: Genes for Ring-Oxidizing and -Opening Enzymes

(2008) Scott D. Pope et al.   JOURNAL OF BACTERIOLOGY

Lactobacillus reuteri DSM 20016 Produces Cobalamin-Dependent Diol Dehydratase in Metabolosomes and Metabolizes 1,2-Propanediol by Disproportionation

(2008) D. D. Sriramulu et al.   JOURNAL OF BACTERIOLOGY

The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features

(2008) H. Seedorf et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA