Engineering Bacteroides thetaiotaomicron to produce non-native butyrate based on a genome-scale metabolic model-guided design

Production and Sensing of Butyrate in a Probiotic E. coli Strain

(2020) Yanfen Bai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Engineered butyrate-producing bacteria prevents high fat diet-induced obesity in mice

(2020) Liang Bai et al.   Microbial Cell Factories

Functional cooperation of the glycine synthase-reductase and Wood–Ljungdahl pathways for autotrophic growth of Clostridium drakei

(2020) Yoseb Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sodium butyrate reduces bovine mammary epithelial cell inflammatory responses induced by exogenous lipopolysaccharide, by inactivating NF-κB signaling

(2020) Xudong Sun et al.   JOURNAL OF DAIRY SCIENCE

Microbial therapeutics for acute colitis based on genetically modified Lactococcus lactis hypersecreting IL-1Ra in mice

(2020) Fu Namai et al.   EXPERIMENTAL AND MOLECULAR MEDICINE

Metabolic Feedback Inhibition Influences Metabolite Secretion by the Human Gut Symbiont Bacteroides thetaiotaomicron

(2020) Jennie L. Catlett et al.   mSystems

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

(2019) Xiaofang Jiang et al.   SCIENCE

An engineered E. coli Nissle improves hyperammonemia and survival in mice and shows dose-dependent exposure in healthy humans

(2019) Caroline B. Kurtz et al.   Science Translational Medicine

Adaptive laboratory evolution of a genome-reduced Escherichia coli

(2019) Donghui Choe et al.   Nature Communications

Metabolic engineering of Escherichia coli for the production of butyric acid at high titer and productivity

(2019) Liang Wang et al.   Biotechnology for Biofuels

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis

(2019) Eric M. Brown et al.   Cell Host & Microbe

Microbial therapeutics: New opportunities for drug delivery

(2019) Miguel Jimenez et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

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

High-resolution 13C metabolic flux analysis

(2019) Christopher P. Long et al.   Nature Protocols

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

(2019) Leonor García-Bayona et al.   mBio

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis

(2018) Promi Das et al.   PLoS One

Bacteroides thetaiotaomicron Ameliorates Colon Inflammation in Preclinical Models of Crohn’s Disease

(2018) Margaret Delday et al.   INFLAMMATORY BOWEL DISEASES

Development of a synthetic live bacterial therapeutic for the human metabolic disease phenylketonuria

(2018) Vincent M Isabella et al.   NATURE BIOTECHNOLOGY

Bacteroides thetaiotaomicron

(2018) Nathan T. Porter et al.   TRENDS IN MICROBIOLOGY

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

UniProt: a worldwide hub of protein knowledge

(2018)   NUCLEIC ACIDS RESEARCH

An Insight Into the Intestinal Web of Mucosal Immunity, Microbiota, and Diet in Inflammation

(2018) Yu Anne Yap et al.   Frontiers in Immunology

Butyrate production under aerobic growth conditions by engineered Escherichia coli

(2017) Naoya Kataoka et al.   JOURNAL OF BIOSCIENCE AND BIOENGINEERING

Complex pectin metabolism by gut bacteria reveals novel catalytic functions

(2017) Didier Ndeh et al.   NATURE

iML1515, a knowledgebase that computes Escherichia coli traits

(2017) Jonathan M Monk et al.   NATURE BIOTECHNOLOGY

Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion

(2017) Mariana X. Byndloss et al.   SCIENCE

The Microbial Metabolite Butyrate Induces Expression of Th1-Associated Factors in CD4+ T Cells

(2017) Meike Kespohl et al.   Frontiers in Immunology

Butyrate modifies intestinal barrier function in IPEC-J2 cells through a selective upregulation of tight junction proteins and activation of the Akt signaling pathway

(2017) Hui Yan et al.   PLoS One

Depletion of Butyrate-Producing Clostridia from the Gut Microbiota Drives an Aerobic Luminal Expansion of Salmonella

(2016) Fabian Rivera-Chávez et al.   Cell Host & Microbe

Comparative In silico Analysis of Butyrate Production Pathways in Gut Commensals and Pathogens

(2016) Swadha Anand et al.   Frontiers in Microbiology

Colitogenic Bacteroides thetaiotaomicron Antigens Access Host Immune Cells in a Sulfatase-Dependent Manner via Outer Membrane Vesicles

(2015) Christina A. Hickey et al.   Cell Host & Microbe

Physiological, biomass elemental composition and proteomic analyses of Escherichia coli ammonium-limited chemostat growth, and comparison with iron- and glucose-limited chemostat growth

(2015) James Patrick Folsom et al.   MICROBIOLOGY-SGM

Biocontainment of genetically modified organisms by synthetic protein design

(2015) Daniel J. Mandell et al.   NATURE

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

Structural genomics analysis of uncharacterized protein families overrepresented in human gut bacteria identifies a novel glycoside hydrolase

(2014) Anna Sheydina et al.   BMC BIOINFORMATICS

Metabolic Engineering of Escherichia coli for Production of Butyric Acid

(2014) Mukesh Saini et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands

(2014) Sung Ho Yoon et al.   NUCLEIC ACIDS RESEARCH

Converting Carbon Dioxide to Butyrate with an Engineered Strain of Clostridium ljungdahlii

(2014) T. Ueki et al.   mBio

Butyrate production in engineeredEscherichia coliwith synthetic scaffolds

(2013) Jang-Mi Baek et al.   BIOTECHNOLOGY AND BIOENGINEERING

Bacteroides thetaiotaomicron and Faecalibacterium prausnitzii influence the production of mucus glycans and the development of goblet cells in the colonic epithelium of a gnotobiotic model rodent

(2013) Laura Wrzosek et al.   BMC BIOLOGY

Live-attenuatedListeria-based immunotherapy

(2013) John Rothman et al.   Expert Review of Vaccines

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

Understanding the interactions between bacteria in the human gut through metabolic modeling

(2013) Saeed Shoaie et al.   Scientific Reports

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows

(2012) Enrica Pessione   Frontiers in Cellular and Infection Microbiology

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

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

The Microbiome and Butyrate Regulate Energy Metabolism and Autophagy in the Mammalian Colon

(2011) Dallas R. Donohoe et al.   Cell Metabolism

Metabolic engineering of Escherichia coli for direct production of 1,4-butanediol

(2011) Harry Yim et al.   Nature Chemical Biology

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

(2011) Jan Schellenberger et al.   Nature Protocols

The biomass objective function

(2010) Adam M Feist et al.   CURRENT OPINION IN MICROBIOLOGY

High-throughput generation, optimization and analysis of genome-scale metabolic models

(2010) Christopher S Henry et al.   NATURE BIOTECHNOLOGY

What is flux balance analysis?

(2010) Jeffrey D Orth et al.   NATURE BIOTECHNOLOGY

A protocol for generating a high-quality genome-scale metabolic reconstruction

(2010) Ines Thiele et al.   Nature Protocols

A fluorescent, genetically engineered microorganism that degrades organophosphates and commits suicide when required

(2009) Qin Li et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Predicting metabolic engineering knockout strategies for chemical production: accounting for competing pathways

(2009) N. Tepper et al.   BIOINFORMATICS

Flux balance analysis of biological systems: applications and challenges

(2009) K. Raman et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Clinical use of E. coli Nissle 1917 in inflammatory bowel disease

(2008) Michael Schultz   INFLAMMATORY BOWEL DISEASES

Metabolic Network Model of a Human Oral Pathogen

(2008) V. Mazumdar et al.   JOURNAL OF BACTERIOLOGY

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Context-Specific Metabolic Networks Are Consistent with Experiments

(2008) Scott A. Becker et al.   PLoS Computational Biology