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Rational Engineering of Facultative Anaerobiosis Enables Commensal Survival in the Oxygenated Gut

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The radical impact of oxygen on prokaryotic evolution—enzyme inhibition first, uninhibited essential biosyntheses second, aerobic respiration third
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Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines
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A rapid colorimetric assay for carbamyl phosphate synthetase I
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Flavodoxin: A compromise between efficiency and versatility in the electron transfer from Photosystem I to Ferredoxin-NADP+ reductase
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Communicable Ulcerative Colitis Induced by T-bet Deficiency in the Innate Immune System
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A Quantitative Tissue-Specific Landscape of Protein Redox Regulation during Aging
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An anaerobic pathogen rewires host metabolism to fuel oxidative growth in the inflamed gut
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Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont
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The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape
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Microbiota and Host Nutrition across Plant and Animal Kingdoms
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The Stringent Response Determines the Ability of a Commensal Bacterium to Survive Starvation and to Persist in the Gut
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An early-life microbiota metabolite protects against obesity by regulating intestinal lipid metabolism
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Epithelial hypoxia maintains colonization resistance against Candida albicans
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Salmonella re-engineers the intestinal environment to break colonization resistance in the presence of a compositionally intact microbiota
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Biogeography-associated emergence of enhanced oxygen tolerance in the abundant human gut commensal Segatella copri
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The Redox architecture of physiological function
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Oxygen as a driver of gut dysbiosis
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Avoiding high-valent iron intermediates: Superoxide reductase and rubrerythrin
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Dysbiotic Proteobacteria expansion: a microbial signature of epithelial dysfunction
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Vitamins, the gut microbiome and gastrointestinal health in humans
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A conserved motif liganding the [4Fe–4S] cluster in [4Fe–4S] fumarases prevents irreversible inactivation of the enzyme during hydrogen peroxide stress
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Starch Catabolism by a Prominent Human Gut Symbiont Is Directed by the Recognition of Amylose Helices
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Identification of amino acids responsible for the oxygen sensitivity of ferredoxins from Anabaena variabilis using site-directed mutagenesis
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Regulation of pyruvate dehydrogenase kinase and phosphatase by acetyl-CoA/CoA and NADH/NAD ratios
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A two-step mechanism for the photosynthetic reduction of oxygen by ferredoxin
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Adenosylmethionine-dependent synthesis of the glycyl radical in pyruvate formate-lyase by abstraction of the glycine C-2 pro-S hydrogen atom. Studies of [2H]glycine-substituted enzyme and peptides homologous to the glycine 734 site.
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The Generation of Superoxide Radical during the Autoxidation of Ferredoxins
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Pasteur, oxygen and the anaerobes revisited
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Isotopically-Labeled Iodoacetamide-Alkyne Probes for Quantitative Cysteine-Reactivity Profiling
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Identification of Protein Targets of S-Nitroso-Coenzyme A-Mediated S-Nitrosation Using Chemoproteomics
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Photoaffinity Ligand of Cystic Fibrosis Corrector VX-445 Identifies SCCPDH as an Off-Target
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Inactivation of Pyruvate Formate-Lyase by Dioxygen: Defining the Mechanistic Interplay of Glycine 734 and Cysteine 419 by Rapid Freeze-Quench EPR
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Isolation and characterization of rubrerythrin, a non-heme iron protein from Desulfovibrio vulgaris that contains rubredoxin centers and a hemerythrin-like binuclear iron cluster
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Mechanisms of Redox-Coupled Proton Transfer in Proteins: Role of the Proximal Proline in Reactions of the [3Fe-4S] Cluster in Azotobacter vinelandii Ferredoxin I,
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Structure of Carbamoyl Phosphate Synthetase: A Journey of 96 Å from Substrate to Product,
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Diverse Functional Roles of Reactive Cysteines
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Electrochemical Definitions of O2Sensitivity and Oxidative Inactivation in Hydrogenases
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Principles of Sustained Enzymatic Hydrogen Oxidation in the Presence of Oxygen – The Crucial Influence of High Potential Fe–S Clusters in the Electron Relay of [NiFe]-Hydrogenases
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[FeFe]-Hydrogenase Oxygen Inactivation Is Initiated at the H Cluster 2Fe Subcluster
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Theoretical Study of the Antioxidant Properties of Pyridoxine
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Crystal structures of the key anaerobic enzyme pyruvate:ferredoxin oxidoreductase, free and in complex with pyruvate.
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Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis
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The strict anaerobe Bacteroides fragilis grows in and benefits from nanomolar concentrations of oxygen
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Gut inflammation provides a respiratory electron acceptor for Salmonella
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Quantitative reactivity profiling predicts functional cysteines in proteomes
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Bacterial colonization factors control specificity and stability of the gut microbiota
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The rise of oxygen in Earth’s early ocean and atmosphere
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Precision editing of the gut microbiota ameliorates colitis
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Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota
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Simultaneous generation of many RNA-seq libraries in a single reaction
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ModelFinder: fast model selection for accurate phylogenetic estimates
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Semi-supervised learning for peptide identification from shotgun proteomics datasets
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An insider's perspective: Bacteroides as a window into the microbiome
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Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics
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ROS as signalling molecules: mechanisms that generate specificity in ROS homeostasis
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Molecular principles of redox-coupled sodium pumping of the ancient Rnf machinery
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Covariation MS uncovers a protein that controls cysteine catabolism
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Monitoring Fe–S cluster occupancy across the E. coli proteome using chemoproteomics
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Global profiling of phosphorylation-dependent changes in cysteine reactivity
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Exploring and retrieving sequence and metadata for species across the tree of life with NCBI Datasets
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Reactive oxygen species limit intestinal mucosa-bacteria homeostasis in vitro
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Citrulline synthesis in rat tissues and liver content of carbamoyl phosphate and ornithine
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Pyruvate formate-lyase mechanism involving the protein-based glycyl radical
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Mechanism of thermal decomposition of carbamoyl phosphate and its stabilization by aspartate and ornithine transcarbamoylases
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Iron conservation by reduction of metalloenzyme inventories in the marine diazotroph Crocosphaera watsonii
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Inactivation of a single gene enables microaerobic growth of the obligate anaerobe Bacteroides fragilis
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How oxygen reacts with oxygen-tolerant respiratory [NiFe]-hydrogenases
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Endogenous superoxide is a key effector of the oxygen sensitivity of a model obligate anaerobe
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Nanaerobic growth enables direct visualization of dynamic cellular processes in human gut symbionts
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The free radical in pyruvate formate-lyase is located on glycine-734.
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Noninvasive measurement of anatomic structure and intraluminal oxygenation in the gastrointestinal tract of living mice with spatial and spectral EPR imaging
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The Identification of Primary Sites of Superoxide and Hydrogen Peroxide Formation in the Aerobic Respiratory Chain and Sulfite Reductase Complex of Escherichia coli
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How Escherichia coli Is Equipped to Oxidize Hydrogen under Different Redox Conditions
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Mononuclear Iron Enzymes Are Primary Targets of Hydrogen Peroxide Stress
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Micromolar Intracellular Hydrogen Peroxide Disrupts Metabolism by Damaging Iron-Sulfur Enzymes
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H2metabolism is widespread and diverse among human colonic microbes
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Hydrogen cross-feeders of the human gastrointestinal tract
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Disruption of intestinal oxygen balance in acute colitis alters the gut microbiome
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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
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Prokka: rapid prokaryotic genome annotation
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Distribution of metronidazole susceptibility factors in obligate anaerobes
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IQ-TREE 3: phylogenomic inference software using complex evolutionary models
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MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
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STRIDE: Species Tree Root Inference from Gene Duplication Events
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UFBoot2: Improving the Ultrafast Bootstrap Approximation
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HMDB 3.0—The Human Metabolome Database in 2013
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ENDOTHELIAL-DEPENDENT VASCULAR REACTIVITY AFTER CARDIOPULMONARY BYPASS IS ASSOCIATED WITH UNIQUE METABOLOMIC SIGNATURES
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A widespread hydrogenase drives fermentative growth of gut bacteria in healthy people
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STAG: Species Tree Inference from All Genes
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Functional Replacement of Ferredoxin by a Cyanobacterial Flavodoxin in Tobacco Confers Broad-Range Stress Tolerance
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Iron‐sulphur clusters and the problem with oxygen
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Two sources of endogenous hydrogen peroxide in Escherichia coli
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Biosynthetic pathways, gene replacement and the antiquity of life
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An anaerobic bacterium, B acteroides thetaiotaomicron, uses a consortium of enzymes to scavenge hydrogen peroxide
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Do reactive oxygen species or does oxygen itself confer obligate anaerobiosis? The case of Bacteroides thetaiotaomicron
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The Barrier Properties of Biological Membranes Dictate How Cells Experience Oxidative Stress
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The timetable of evolution
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A New Enzyme of General Occurrence in Organisms
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Network Context and Selection in the Evolution to Enzyme Specificity
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Interactions Between the Microbiota and the Immune System
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Microbiota-activated PPAR-γ signaling inhibits dysbiotic Enterobacteriaceae expansion
inferredcites →https://doi.org/10.1126/science.aat9076openalex-snapshot
Colonocyte metabolism shapes the gut microbiota
inferredcites →https://doi.org/10.1126/scisignal.aaw3159openalex-snapshot
Host mitochondria influence gut microbiome diversity: A role for ROS
inferredcites →https://doi.org/10.1126/scisignal.aay7315openalex-snapshot
Spatial and temporal alterations in protein structure by EGF regulate cryptic cysteine oxidation
inferredcites →https://doi.org/10.1128/ecosalplus.3.5.3openalex-snapshot
Fermentative Pyruvate and Acetyl-Coenzyme A Metabolism
inferredcites →https://doi.org/10.1128/ecosalplus.esp-0011-2016openalex-snapshot
Anaerobic Formate and Hydrogen Metabolism
inferredcites →https://doi.org/10.1128/jb.00425-06openalex-snapshot
Rubredoxin:Oxygen Oxidoreductase Enhances Survival of Desulfovibrio vulgaris Hildenborough under Microaerophilic Conditions
inferredcites →https://doi.org/10.1128/jb.00554-06openalex-snapshot
Detection and Quantification of Superoxide Formed within the Periplasm of Escherichia coli
inferredcites →https://doi.org/10.1128/mbio.01873-16openalex-snapshot
The Fumarate Reductase of Bacteroides thetaiotaomicron , unlike That of Escherichia coli , Is Configured so that It Does Not Generate Reactive Oxygen Species
inferredcites →https://doi.org/10.1128/spectrum.04733-22openalex-snapshot
Iron Deficiency Modulates Metabolic Landscape of Bacteroidetes Promoting Its Resilience during Inflammation
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Physiologic hypoxia and oxygen homeostasis in the healthy intestine. A Review in the Theme: Cellular Responses to Hypoxia
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Reconstruction of genome-scale metabolic models for 126 human tissues using mCADRE
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Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy
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OrthoFinder: phylogenetic orthology inference for comparative genomics
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Homologous production, one-step purification, and proof of Na+ transport by the Rnf complex from Acetobacterium woodii, a model for acetogenic conversion of C1 substrates to biofuels
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H2 generated by fermentation in the human gut microbiome influences metabolism and competitive fitness of gut butyrate producers
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CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures
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StanDep: Capturing transcriptomic variability improves context-specific metabolic models
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Alterations in Cerebrospinal Fluid Urea Occur in Late Manifest Huntington’s Disease
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Commensal Obligate Anaerobic Bacteria and Health: Production, Storage, and Delivery Strategies
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Investigation of the Ferredoxin’s Influence on the Anaerobic and Aerobic, Enzymatic H2 Production
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Metabolism of parathyroid organoids
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How Microbes Defend Themselves From Incoming Hydrogen Peroxide
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Systems-level characterization of a host-microbe metabolic symbiosis in the mammalian gut
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The tangled past of eukaryotic enzymes involved in anaerobic metabolism
inferredcites →https://doi.org/10.7554/elife.37138openalex-snapshot
Human gut Bacteroides capture vitamin B12 via cell surface-exposed lipoproteins
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Pyruvate:ferredoxin oxidoreductase and low abundant ferredoxins support aerobic photomixotrophic growth in cyanobacteria
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