Streptozotocin-induced hyperglycemia alters the cecal metabolome and exacerbates antibiotic-induced dysbiosis

Role of dietary fiber in the recovery of the human gut microbiome and its metabolome

(2021) Ceylan Tanes et al.   Cell Host & Microbe

The Microbiome-Adipose Tissue Axis in Systemic Metabolism

(2020) Patrick Lundgren et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs

(2020) David Allaway et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Investigation of gut microbiome changes in type 1 diabetic mellitus rats based on high-throughput sequencing

(2020) Quantao Ma et al.   BIOMEDICINE & PHARMACOTHERAPY

The role of reactive oxygen species in the biological activity of antimicrobial agents: An updated mini review

(2020) P.-L. Lam et al.   CHEMICO-BIOLOGICAL INTERACTIONS

The Controversial Role of Human Gut Lachnospiraceae

(2020) Mirco Vacca et al.   Microorganisms

Salmonella finds a way: Metabolic versatility of Salmonella enterica serovar Typhimurium in diverse host environments

(2020) Savannah J. Taylor et al.   PLoS Pathogens

Consumption of a Western-Style Diet Modulates the Response of the Murine Gut Microbiome to Ciprofloxacin

(2020) Damien J. Cabral et al.   mSystems

Feature-based molecular networking in the GNPS analysis environment

(2020) Louis-Félix Nothias et al.   NATURE METHODS

Glucose transporters in the small intestine in health and disease

(2020) Hermann Koepsell   PFLUGERS ARCHIV-EUROPEAN JOURNAL OF PHYSIOLOGY

Deciphering functional redundancy in the human microbiome

(2020) Liang Tian et al.   Nature Communications

Growth strategy of microbes on mixed carbon sources

(2019) Xin Wang et al.   Nature Communications

Gut Microbiota Composition and Structure of the Ob/Ob and Db/Db Mice

(2019) Mingsheng Yang et al.   International Journal of Endocrinology

Inflammation associated ethanolamine facilitates infection by Crohn's disease-linked adherent-invasive Escherichia coli

(2019) Michael J. Ormsby et al.   EBioMedicine

Akkermansia muciniphila is a promising probiotic

(2019) Ting Zhang et al.   Microbial Biotechnology

Meta-Analysis Reveals Reproducible Gut Microbiome Alterations in Response to a High-Fat Diet

(2019) Jordan E. Bisanz et al.   Cell Host & Microbe

Bacterial Metabolism and Antibiotic Efficacy

(2019) Jonathan M. Stokes et al.   Cell Metabolism

Understanding Competition and Cooperation within the Mammalian Gut Microbiome

(2019) Katharine Z. Coyte et al.   CURRENT BIOLOGY

Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health

(2019) Kaitlyn Oliphant et al.   Microbiome

High-Fat Diet Alters the Intestinal Microbiota in Streptozotocin-Induced Type 2 Diabetic Mice

(2019) Sheng Liu et al.   Microorganisms

WITHDRAWN: Global and regional diabetes prevalence estimates for 2019 and projections for 2030 and 2045: results from the International Diabetes Federation Diabetes Atlas, 9th edition

(2019) Pouya Saeedi et al.   DIABETES RESEARCH AND CLINICAL PRACTICE

Consistent and correctable bias in metagenomic sequencing experiments

(2019) Michael R McLaren et al.   eLife

Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs

(2019) Katharine Michelle Ng et al.   Cell Host & Microbe

Microbial Metabolism Modulates Antibiotic Susceptibility within the Murine Gut Microbiome

(2019) Damien J. Cabral et al.   Cell Metabolism

Mutual Metabolic Interactions in Co-cultures of the Intestinal Anaerostipes rhamnosivorans With an Acetogen, Methanogen, or Pectin-Degrader Affecting Butyrate Production

(2019) Thi Phuong Nam Bui et al.   Frontiers in Microbiology

Vitamins for the Gut Microbiome

(2019) Robert E. Steinert et al.   TRENDS IN MOLECULAR MEDICINE

Investigation of insulin resistance in the popularly used four rat models of type-2 diabetes

(2018) Pin-Chun Chao et al.   BIOMEDICINE & PHARMACOTHERAPY

SAMSA2: a standalone metatranscriptome analysis pipeline

(2018) Samuel T. Westreich et al.   BMC BIOINFORMATICS

The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease

(2018) Kassem Makki et al.   Cell Host & Microbe

Ethanolamine is a valuable nutrient source that impacts Clostridium difficile pathogenesis

(2018) Kathryn L. Nawrocki et al.   ENVIRONMENTAL MICROBIOLOGY

The Ethanolamine Permease EutH Promotes Vacuole Adaptation of Salmonella enterica and Listeria monocytogenes during Macrophage Infection

(2018) Christopher J. Anderson et al.   INFECTION AND IMMUNITY

Mutual Interaction of Phenolic Compounds and Microbiota: Metabolism of Complex Phenolic Apigenin-C- and Kaempferol-O-Derivatives by Human Fecal Samples

(2018) Maren Vollmer et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Promises and pitfalls of untargeted metabolomics

(2018) Ilya Gertsman et al.   JOURNAL OF INHERITED METABOLIC DISEASE

Hyperglycemia drives intestinal barrier dysfunction and risk for enteric infection

(2018) Christoph A. Thaiss et al.   SCIENCE

Disruption of the Gut Ecosystem by Antibiotics

(2018) Mi Young Yoon et al.   YONSEI MEDICAL JOURNAL

Impact of the Gut Microbiota on Intestinal Immunity Mediated by Tryptophan Metabolism

(2018) Jing Gao et al.   Frontiers in Cellular and Infection Microbiology

Transglycosylated Starch Modulates the Gut Microbiome and Expression of Genes Related to Lipid Synthesis in Liver and Adipose Tissue of Pigs

(2018) Monica A. Newman et al.   Frontiers in Microbiology

Worlds Apart – Transcriptome Profiles of Key Oral Microbes in the Periodontal Pocket Compared to Single Laboratory Culture Reflect Synergistic Interactions

(2018) Zhi-Luo Deng et al.   Frontiers in Microbiology

The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders

(2018) Andrea Shin et al.   Clinical Gastroenterology and Hepatology

Metabolome analysis for investigating host-gut microbiota interactions

(2018) Michael X. Chen et al.   JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION

Dietary trehalose enhances virulence of epidemic Clostridium difficile

(2018) J. Collins et al.   NATURE

Thinking outside the cereal box: non-carbohydrate routes for dietary manipulation of the gut microbiota

(2018) Aspen T. Reese et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

(2018) Eric A. Franzosa et al.   NATURE METHODS

Ethanolamine Influences Human Commensal Escherichia coli Growth, Gene Expression, and Competition with Enterohemorrhagic E. coli O157:H7

(2018) Carol A. Rowley et al.   mBio

Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders

(2017) Hemi Luan et al.   MASS SPECTROMETRY REVIEWS

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania

(2017) Samuel A. Smits et al.   SCIENCE

Disentangling Interactions in the Microbiome: A Network Perspective

(2017) Mehdi Layeghifard et al.   TRENDS IN MICROBIOLOGY

Microbial Metabolic Networks at the Mucus Layer Lead to Diet-Independent Butyrate and Vitamin B 12 Production by Intestinal Symbionts

(2017) Clara Belzer et al.   mBio

High-fat feeding rather than obesity drives taxonomical and functional changes in the gut microbiota in mice

(2017) Liang Xiao et al.   Microbiome

A Highly Active Endo-Levanase BT1760 of a Dominant Mammalian Gut Commensal Bacteroides thetaiotaomicron Cleaves Not Only Various Bacterial Levans, but Also Levan of Timothy Grass

(2017) Karin Mardo et al.   PLoS One

The Leloir Pathway of Galactose Metabolism – A Novel Therapeutic Target for Hepatocellular Carcinoma

(2016) MANSHU TANG et al.   ANTICANCER RESEARCH

Dividing the Large Glycoside Hydrolase Family 43 into Subfamilies: a Motivation for Detailed Enzyme Characterization

(2016) Keith Mewis et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Analysis of the microbiome: Advantages of whole genome shotgun versus 16S amplicon sequencing

(2016) Ravi Ranjan et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

A Dietary Fiber-Deprived Gut Microbiota Degrades the Colonic Mucus Barrier and Enhances Pathogen Susceptibility

(2016) Mahesh S. Desai et al.   CELL

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

Challenges and issues with streptozotocin-induced diabetes – A clinically relevant animal model to understand the diabetes pathogenesis and evaluate therapeutics

(2016) Sameer N. Goyal et al.   CHEMICO-BIOLOGICAL INTERACTIONS

Roles of the Gut in Glucose Homeostasis

(2016) Jens Juul Holst et al.   DIABETES CARE

Role of Glyoxylate Shunt in Oxidative Stress Response

(2016) Sungeun Ahn et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Antibiotic effects on gut microbiota and metabolism are host dependent

(2016) Shiho Fujisaka et al.   JOURNAL OF CLINICAL INVESTIGATION

Untargeted Metabolomics Strategies—Challenges and Emerging Directions

(2016) Alexandra C. Schrimpe-Rutledge et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Mechanisms of inflammation-driven bacterial dysbiosis in the gut

(2016) M Y Zeng et al.   Mucosal Immunology

Interactions between the microbiota and pathogenic bacteria in the gut

(2016) Andreas J. Bäumler et al.   NATURE

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

(2016) Mingxun Wang et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Comparative genomics and physiology of the butyrate-producing bacteriumIntestinimonas butyriciproducens

(2016) Thi Phuong Nam Bui et al.   Environmental Microbiology Reports

Regulation of Intestinal Glucose Absorption by Ion Channels and Transporters

(2016) Lihong Chen et al.   Nutrients

Persister formation in Staphylococcus aureus is associated with ATP depletion

(2016) Brian P. Conlon et al.   Nature Microbiology

Antibiotic-Induced Alterations of the Gut Microbiota Alter Secondary Bile Acid Production and Allow for Clostridium difficile Spore Germination and Outgrowth in the Large Intestine

(2016) Casey M. Theriot et al.   mSphere

Metabolic Model-Based Integration of Microbiome Taxonomic and Metabolomic Profiles Elucidates Mechanistic Links between Ecological and Metabolic Variation

(2016) Cecilia Noecker et al.   mSystems

Comparing Apples and Oranges?: Next Generation Sequencing and Its Impact on Microbiome Analysis

(2016) Adam G. Clooney et al.   PLoS One

Interactions Between the Gastrointestinal Microbiome and Clostridium difficile

(2015) Casey M. Theriot et al.   Annual Review of Microbiology

Structural insight into the PTS sugar transporter EIIC

(2015) Jason G. McCoy et al.   BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS

TheSTM4195Gene Product (PanS) Transports Coenzyme A Precursors in Salmonella enterica

(2015) Dustin C. Ernst et al.   JOURNAL OF BACTERIOLOGY

Futile cycling increases sensitivity toward oxidative stress in Escherichia coli

(2015) Kristin J. Adolfsen et al.   METABOLIC ENGINEERING

Streptozotocin-induced type-1-diabetes disease onset in Sprague–Dawley rats is associated with an altered intestinal microbiota composition and decreased diversity

(2015) Elaine Patterson et al.   MICROBIOLOGY-SGM

Carnitine in bacterial physiology and metabolism

(2015) Jamie A. Meadows et al.   MICROBIOLOGY-SGM

Antibiotic efficacy is linked to bacterial cellular respiration

(2015) Michael A. Lobritz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pyruvate Dehydrogenase Activity and Quantity Decreases After Coronary Artery Bypass Grafting

(2015) Lars W. Andersen et al.   SHOCK

The Role of Microbial Amino Acid Metabolism in Host Metabolism

(2015) Evelien Neis et al.   Nutrients

Bactericidal Antibiotics Induce Toxic Metabolic Perturbations that Lead to Cellular Damage

(2015) Peter Belenky et al.   Cell Reports

Ethanolamine Signaling Promotes Salmonella Niche Recognition and Adaptation during Infection

(2015) Christopher J. Anderson et al.   PLoS Pathogens

Regulatory principles governing Salmonella and Yersinia virulence

(2015) Marc Erhardt et al.   Frontiers in Microbiology

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

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Diet and the Intestinal Microbiome: Associations, Functions, and Implications for Health and Disease

(2014) Lindsey G. Albenberg et al.   GASTROENTEROLOGY

Harnessing Microbiota to Kill a Pathogen: The sweet tooth of Clostridium difficile

(2014) Ruth E Ley   NATURE MEDICINE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The Biosynthetic Pathway of Indole-3-Carbaldehyde and Indole-3-Carboxylic Acid Derivatives in Arabidopsis

(2014) C. Bottcher et al.   PLANT PHYSIOLOGY

Strengths and Limitations of 16S rRNA Gene Amplicon Sequencing in Revealing Temporal Microbial Community Dynamics

(2014) Rachel Poretsky et al.   PLoS One

Antibiotics induce redox-related physiological alterations as part of their lethality

(2014) D. J. Dwyer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host–microbe interactions shaping the gastrointestinal environment

(2014) Gerard E. Kaiko et al.   TRENDS IN IMMUNOLOGY

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Salmonella Utilizes D-Glucosaminate via a Mannose Family Phosphotransferase System Permease and Associated Enzymes

(2013) K. A. Miller et al.   JOURNAL OF BACTERIOLOGY

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Commensal bacteria at the interface of host metabolism and the immune system

(2013) Jonathan R Brestoff et al.   NATURE IMMUNOLOGY

The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)

(2013) Ross Overbeek et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Prioritization of a plant polysaccharide over a mucus carbohydrate is enforced by a Bacteroides hybrid two-component system

(2012) Jonathan B. Lynch et al.   MOLECULAR MICROBIOLOGY

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Metabolomic analysis of rat serum in streptozotocin-induced diabetes and after treatment with oral triethylenetetramine (TETA)

(2012) Marta Ugarte et al.   Genome Medicine

High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry

(2011) Tobias Fuhrer et al.   ANALYTICAL CHEMISTRY

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

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

Profound Alterations of Intestinal Microbiota following a Single Dose of Clindamycin Results in Sustained Susceptibility to Clostridium difficile-Induced Colitis

(2011) Charlie G. Buffie et al.   INFECTION AND IMMUNITY

Mass Spectrometry Strategies in Metabolomics

(2011) Zhentian Lei et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Single dose streptozotocin-induced diabetes: considerations for study design in islet transplantation models

(2011) M C Deeds et al.   LABORATORY ANIMALS

Metabolite profiles and the risk of developing diabetes

(2011) Thomas J Wang et al.   NATURE MEDICINE

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

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

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

Pathway Activity Profiling (PAPi): from the metabolite profile to the metabolic pathway activity

(2010) Raphael B. M. Aggio et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

MZmine 2: Modular framework for processing, visualizing, and analyzing mass spectrometry-based molecular profile data

(2010) Tomáš Pluskal et al.   BMC BIOINFORMATICS

Dissecting thein VivoMetabolic Potential of Two Human Gut Acetogens

(2010) Federico E. Rey et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Pharmacokinetics of drugs in rats with diabetes mellitus induced by alloxan or streptozocin: comparison with those in patients with type I diabetes mellitus

(2010) Joo H. Lee et al.   JOURNAL OF PHARMACY AND PHARMACOLOGY

Gut inflammation provides a respiratory electron acceptor for Salmonella

(2010) Sebastian E. Winter et al.   NATURE

Ethanolamine utilization in bacterial pathogens: roles and regulation

(2010) Danielle A. Garsin   NATURE REVIEWS MICROBIOLOGY

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insulitis in Human Type 1 Diabetes

(2009) Toshiaki Hanafusa et al.   Annals of the New York Academy of Sciences

Streptozotocin, Type I Diabetes Severity and Bone

(2009) Katherine Motyl et al.   BIOLOGICAL PROCEDURES ONLINE

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

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

Prolonged Impact of Antibiotics on Intestinal Microbial Ecology and Susceptibility to Enteric Salmonella Infection

(2009) A. Croswell et al.   INFECTION AND IMMUNITY

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

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

Decreased Diversity of the Fecal Microbiome in RecurrentClostridium difficile–Associated Diarrhea

(2008) Ju Young Chang et al.   JOURNAL OF INFECTIOUS DISEASES

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH