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

Chemical communication in the gut: Effects of microbiota-generated metabolites on gastrointestinal bacterial pathogens

(2015) Stefanie L. Vogt et al.   ANAEROBE

Anoxic Conditions Promote Species-Specific Mutualism between Gut MicrobesIn Silico

(2015) Almut Heinken et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Update on Fecal Microbiota Transplantation 2015: Indications, Methodologies, Mechanisms, and Outlook

(2015) Colleen R. Kelly et al.   GASTROENTEROLOGY

Phenotypic differentiation of gastrointestinal microbes is reflected in their encoded metabolic repertoires

(2015) Eugen Bauer et al.   Microbiome

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

(2015) Stefanía Magnúsdóttir et al.   Frontiers in Genetics

Geographical variation of human gut microbial composition

(2014) T. A. Suzuki et al.   Biology Letters

Modeling the effects of commonly used drugs on human metabolism

(2014) Swagatika Sahoo et al.   FEBS Journal

The Futalosine Pathway Played an Important Role in Menaquinone Biosynthesis during Early Prokaryote Evolution

(2014) Xiao-Yang Zhi et al.   Genome Biology and Evolution

Functional Metabolic Map of Faecalibacterium prausnitzii, a Beneficial Human Gut Microbe

(2014) A. Heinken et al.   JOURNAL OF BACTERIOLOGY

Structural and Biochemical Characterization ofChlamydia trachomatisHypothetical Protein CT263 Supports That Menaquinone Synthesis Occurs through the Futalosine Pathway

(2014) Michael L. Barta et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Recent trends in the metabolism and cell biology of vitamin K with special reference to vitamin K cycling and MK-4 biosynthesis

(2014) Martin J. Shearer et al.   JOURNAL OF LIPID RESEARCH

Basis for substrate recognition and distinction by matrix metalloproteinases

(2014) Boris I. Ratnikov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogeny, culturing, and metagenomics of the human gut microbiota

(2014) Alan W. Walker et al.   TRENDS IN MICROBIOLOGY

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

Impact of spatial distribution on the development of mutualism in microbes

(2014) Ákos T. Kovács   Frontiers in Microbiology

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

(2013) Milkha M Leimena et al.   BMC GENOMICS

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Phylogenetic analysis and substrate specificity of GH2 β-mannosidases fromAspergillusspecies

(2013) Sumitha K. Reddy et al.   FEBS LETTERS

Identification of a Hotdog Fold Thioesterase Involved in the Biosynthesis of Menaquinone in Escherichia coli

(2013) M. Chen et al.   JOURNAL OF BACTERIOLOGY

Role of the gut microbiota in human nutrition and metabolism

(2013) Balakrishnan S Ramakrishna   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

A community-driven global reconstruction of human metabolism

(2013) Ines Thiele et al.   NATURE BIOTECHNOLOGY

IMG 4 version of the integrated microbial genomes comparative analysis system

(2013) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Community Flux Balance Analysis for Microbial Consortia at Balanced Growth

(2013) Ruchir A. Khandelwal et al.   PLoS One

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

Menaquinones, Bacteria, and the Food Supply: The Relevance of Dairy and Fermented Food Products to Vitamin K Requirements

(2013) Barbara Walther et al.   Advances in Nutrition

The Impact of the Gut Microbiota on Human Health: An Integrative View

(2012) Jose C. Clemente et al.   CELL

Metagenomics of human microbiome: beyond 16s rDNA

(2012) M.J. Gosalbes et al.   CLINICAL MICROBIOLOGY AND INFECTION

Towards metagenome-scale models for industrial applications—the case of Lactic Acid Bacteria

(2012) Filipe Branco dos Santos et al.   CURRENT OPINION IN BIOTECHNOLOGY

Bacteria as vitamin suppliers to their host: a gut microbiota perspective

(2012) Jean Guy LeBlanc et al.   CURRENT OPINION IN BIOTECHNOLOGY

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

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

A compendium of inborn errors of metabolism mapped onto the human metabolic network

(2012) Swagatika Sahoo et al.   Molecular BioSystems

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Human gut microbiome viewed across age and geography

(2012) Tanya Yatsunenko et al.   NATURE

The human microbiome: at the interface of health and disease

(2012) Ilseung Cho et al.   NATURE REVIEWS GENETICS

CDD: conserved domains and protein three-dimensional structure

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

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Microbiome and immunological interactions

(2012) Denise Kelly et al.   NUTRITION REVIEWS

Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage

(2012) Ines Thiele et al.   PLoS One

Vitamin K Nutrition, Metabolism, and Requirements: Current Concepts and Future Research

(2012) Martin J. Shearer et al.   Advances in Nutrition

OptCom: A Multi-Level Optimization Framework for the Metabolic Modeling and Analysis of Microbial Communities

(2012) Ali R. Zomorrodi et al.   PLoS Computational Biology

A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2

(2011) Ines Thiele et al.   BMC Systems Biology

Cross-feeding between bifidobacteria and butyrate-producing colon bacteria explains bifdobacterial competitiveness, butyrate production, and gas production

(2011) Luc De Vuyst et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011

(2011) J. D. Orth et al.   Molecular Systems Biology

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

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

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Competitive and cooperative metabolic interactions in bacterial communities

(2011) Shiri Freilich et al.   Nature Communications

UniProt Knowledgebase: a hub of integrated protein data

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

Gut microbiome-host interactions in health and disease

(2011) James M Kinross et al.   Genome Medicine

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

(2010) Pavel V Mazin et al.   Algorithms for Molecular Biology

Diversity of the Early Step of the Futalosine Pathway

(2010) Chisato Arakawa et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Metagenomic Analyses: Past and Future Trends

(2010) Carola Simon et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Occurrence, biosynthesis and function of isoprenoid quinones

(2010) Beatrycze Nowicka et al.   BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS

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

(2010) Terry Disz et al.   BMC BIOINFORMATICS

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

Combining Substrate Specificity Analysis with Support Vector Classifiers Reveals Feruloyl Esterase as a Phylogenetically Informative Protein Group

(2010) Roberto Olivares-Hernández et al.   PLoS One

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Roles for Vitamin K Beyond Coagulation

(2009) Sarah L. Booth   Annual Review of Nutrition

Electron transfer in syntrophic communities of anaerobic bacteria and archaea

(2009) Alfons J. M. Stams et al.   NATURE REVIEWS MICROBIOLOGY

MicrobesOnline: an integrated portal for comparative and functional genomics

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

A dedicated thioesterase of the Hotdog-fold family is required for the biosynthesis of the naphthoquinone ring of vitamin K1

(2009) J. R. Widhalm et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identification and Characterization of (1R,6R)-2-Succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate Synthase in the Menaquinone Biosynthesis of Escherichia coli†

(2008) Ming Jiang et al.   BIOCHEMISTRY

Vitamin K, an update for the paediatrician

(2008) Myriam Van Winckel et al.   EUROPEAN JOURNAL OF PEDIATRICS

Bacillus subtilis isolated from the human gastrointestinal tract

(2008) Huynh A. Hong et al.   RESEARCH IN MICROBIOLOGY

An Alternative Menaquinone Biosynthetic Pathway Operating in Microorganisms

(2008) T. Hiratsuka et al.   SCIENCE

Metabolism and cell biology of vitamin K

(2008) Paul Newman et al.   THROMBOSIS AND HAEMOSTASIS