Towards a mechanistic understanding of reciprocal drug–microbiome interactions

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents

(2020) Jens Walter et al.   CELL

Organ-level protein networks as a reference for the host effects of the microbiome

(2020) Robert H. Mills et al.   GENOME RESEARCH

Thermal proteome profiling for interrogating protein interactions

(2020) André Mateus et al.   Molecular Systems Biology

New insights into intestinal phages

(2020) R. Sausset et al.   Mucosal Immunology

Mutational signature in colorectal cancer caused by genotoxic pks+ E. coli

(2020) Cayetano Pleguezuelos-Manzano et al.   NATURE

Engineered probiotics for local tumor delivery of checkpoint blockade nanobodies

(2020) Candice R. Gurbatri et al.   Science Translational Medicine

Impact of commonly used drugs on the composition and metabolic function of the gut microbiota

(2020) Arnau Vich Vila et al.   Nature Communications

Molecular mechanisms of collateral sensitivity to the antibiotic nitrofurantoin

(2020) Roderich Roemhild et al.   PLOS BIOLOGY

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance

(2020) Andrés Aranda-Díaz et al.   eLife

From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism

(2020) Ara Koh et al.   MOLECULAR CELL

Statin therapy is associated with lower prevalence of gut microbiota dysbiosis

(2020) Sara Vieira-Silva et al.   NATURE

Targeted inhibition of gut bacterial β-glucuronidase activity enhances anticancer drug efficacy

(2020) Aadra P. Bhatt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rosuvastatin alters the genetic composition of the human gut microbiome

(2020) Martin Kummen et al.   Scientific Reports

Manipulation of the Gut Microbiome Alters Acetaminophen Biodisposition in Mice

(2020) Michael A. Malfatti et al.   Scientific Reports

RapidAIM: a culture- and metaproteomics-based Rapid Assay of Individual Microbiome responses to drugs

(2020) Leyuan Li et al.   Microbiome

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome

(2020) Bahar Javdan et al.   CELL

Directed remodeling of the mouse gut microbiome inhibits the development of atherosclerosis

(2020) Poshen B. Chen et al.   NATURE BIOTECHNOLOGY

Gut microbiota modulation: a novel strategy for prevention and treatment of colorectal cancer

(2020) Winnie Fong et al.   ONCOGENE

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy

(2020) Lukas F. Mager et al.   SCIENCE

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

(2019) Edoardo Pasolli et al.   CELL

Proteomic analysis of small intestinal epithelial cells in antibiotic-treated mice: changes in drug transporters and metabolizing enzymes

(2019) Takuya Kuno et al.   Drug Metabolism and Pharmacokinetics

BioTransformer: a comprehensive computational tool for small molecule metabolism prediction and metabolite identification

(2019) Yannick Djoumbou-Feunang et al.   Journal of Cheminformatics

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses

(2019) Yuanqiang Zou et al.   NATURE BIOTECHNOLOGY

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Novel insights from uncultivated genomes of the global human gut microbiome

(2019) Stephen Nayfach et al.   NATURE

A new genomic blueprint of the human gut microbiota

(2019) Alexandre Almeida et al.   NATURE

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity

(2019) Takeshi Tanoue et al.   NATURE

A Forward Chemical Genetic Screen Reveals Gut Microbiota Metabolites That Modulate Host Physiology

(2019) Haiwei Chen et al.   CELL

The Integrative Human Microbiome Project

(2019)   NATURE

The pros, cons, and many unknowns of probiotics

(2019) Jotham Suez et al.   NATURE MEDICINE

A complex human gut microbiome cultured in an anaerobic intestine-on-a-chip

(2019) Sasan Jalili-Firoozinezhad et al.   Nature Biomedical Engineering

Mapping human microbiome drug metabolism by gut bacteria and their genes

(2019) Michael Zimmermann et al.   NATURE

Discovery and inhibition of an interspecies gut bacterial pathway for Levodopa metabolism

(2019) Vayu Maini Rekdal et al.   SCIENCE

The human gut chemical landscape predicts microbe-mediated biotransformation of foods and drugs

(2019) Leah Guthrie et al.   eLife

GLORY: Generator of the Structures of Likely Cytochrome P450 Metabolites Based on Predicted Sites of Metabolism

(2019) Christina de Bruyn Kops et al.   Frontiers in Chemistry

Phage-guided modulation of the gut microbiota of mouse models of colorectal cancer augments their responses to chemotherapy

(2019) Di-Wei Zheng et al.   Nature Biomedical Engineering

The Role of the Microbiome in Drug Response

(2019) Rosina Pryor et al.   Annual Review of Pharmacology and Toxicology

Antibiotics-Driven Gut Microbiome Perturbation Alters Immunity to Vaccines in Humans

(2019) Thomas Hagan et al.   CELL

Host-Microbe-Drug-Nutrient Screen Identifies Bacterial Effectors of Metformin Therapy

(2019) Rosina Pryor et al.   CELL

Mapping Interactions of Microbial Metabolites with Human G-Protein-Coupled Receptors

(2019) Dominic A. Colosimo et al.   Cell Host & Microbe

Reconstructing functional networks in the human intestinal tract using synthetic microbiomes

(2019) Sudarshan A Shetty et al.   CURRENT OPINION IN BIOTECHNOLOGY

International consensus conference on stool banking for faecal microbiota transplantation in clinical practice

(2019) Giovanni Cammarota et al.   GUT

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond

(2019) Wegh et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The functional repertoire contained within the native microbiota of the model nematode Caenorhabditis elegans

(2019) Johannes Zimmermann et al.   ISME Journal

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

Simple animal models for microbiome research

(2019) Angela E. Douglas   NATURE REVIEWS MICROBIOLOGY

The future of faecal transplants

(2019) Edward M. Giles et al.   NATURE REVIEWS MICROBIOLOGY

Vancomycin relieves mycophenolate mofetil–induced gastrointestinal toxicity by eliminating gut bacterial β-glucuronidase activity

(2019) Michael R. Taylor et al.   Science Advances

Insights from pharmacokinetic models of host-microbiome drug metabolism

(2019) Maria Zimmermann-Kogadeeva et al.   Gut Microbes

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

Drug-Resistant E. coli Bacteremia Transmitted by Fecal Microbiota Transplant

(2019) Zachariah DeFilipp et al.   NEW ENGLAND JOURNAL OF MEDICINE

Microbiota-derived peptide mimics drive lethal inflammatory cardiomyopathy

(2019) Cristina Gil-Cruz et al.   SCIENCE

Functional Multigenomic Screening of Human-Associated Bacteria for NF-κB-Inducing Bioactive Effectors

(2019) Andreia B. Estrela et al.   mBio

An in vitro model maintaining taxon-specific functional activities of the gut microbiome

(2019) Leyuan Li et al.   Nature Communications

Discovering the Microbial Enzymes Driving Drug Toxicity with Activity-Based Protein Profiling

(2019) Parth B. Jariwala et al.   ACS Chemical Biology

Chemical-genetic profiling reveals limited cross-resistance between antimicrobial peptides with different modes of action

(2019) Bálint Kintses et al.   Nature Communications

Marked differences in tight junction composition and macromolecular permeability among different intestinal cell types

(2018) Sarah C. Pearce et al.   BMC BIOLOGY

Early-Life Antibiotic-Driven Dysbiosis Leads to Dysregulated Vaccine Immune Responses in Mice

(2018) Miriam Anne Lynn et al.   Cell Host & Microbe

Metformin Alters Upper Small Intestinal Microbiota that Impact a Glucose-SGLT1-Sensing Glucoregulatory Pathway

(2018) Paige V. Bauer et al.   Cell Metabolism

Deciphering microbial interactions in synthetic human gut microbiome communities

(2018) Ophelia S Venturelli et al.   Molecular Systems Biology

The microbiome in cancer immunotherapy: Diagnostic tools and therapeutic strategies

(2018) Laurence Zitvogel et al.   SCIENCE

High-throughput metabolomic analysis predicts mode of action of uncharacterized antimicrobial compounds

(2018) Mattia Zampieri et al.   Science Translational Medicine

Gut microbiota associations with common diseases and prescription medications in a population-based cohort

(2018) Matthew A. Jackson et al.   Nature Communications

Modifying and reacting to the environmental pH can drive bacterial interactions

(2018) Christoph Ratzke et al.   PLOS BIOLOGY

Discovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins

(2018) Nitzan Koppel et al.   eLife

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Stability of the human faecal microbiome in a cohort of adult men

(2018) Raaj S. Mehta et al.   Nature Microbiology

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

(2018) Jotham Suez et al.   CELL

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

(2018) Niv Zmora et al.   CELL

Advances in Engineered Human Liver Platforms for Drug Metabolism Studies

(2018) Gregory H Underhill et al.   DRUG METABOLISM AND DISPOSITION

An ex vivo fermentation screening platform to study drug metabolism by human gut microbiota

(2018) Evita van de Steeg et al.   DRUG METABOLISM AND DISPOSITION

Antibodies Set Boundaries Limiting Microbial Metabolite Penetration and the Resultant Mammalian Host Response

(2018) Yasuhiro Uchimura et al.   IMMUNITY

Using bioreactors to study the effects of drugs on the human microbiota

(2018) Mabel Guzman-Rodriguez et al.   METHODS

Extensive impact of non-antibiotic drugs on human gut bacteria

(2018) Lisa Maier et al.   NATURE

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Reconstitution of the gut microbiota of antibiotic-treated patients by autologous fecal microbiota transplant

(2018) Ying Taur et al.   Science Translational Medicine

Gut microbiota and intestinal FXR mediate the clinical benefits of metformin

(2018) Lulu Sun et al.   NATURE MEDICINE

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Commensal bacteria make GPCR ligands that mimic human signalling molecules

(2017) Louis J. Cohen et al.   NATURE

Metformin alters the gut microbiome of individuals with treatment-naive type 2 diabetes, contributing to the therapeutic effects of the drug

(2017) Hao Wu et al.   NATURE MEDICINE

Measuring protein structural changes on a proteome-wide scale using limited proteolysis-coupled mass spectrometry

(2017) Simone Schopper et al.   Nature Protocols

The resilience of the intestinal microbiota influences health and disease

(2017) Felix Sommer et al.   NATURE REVIEWS MICROBIOLOGY

An Atlas of β-Glucuronidases in the Human Intestinal Microbiome

(2017) Rebecca M. Pollet et al.   STRUCTURE

Gut microbiome interactions with drug metabolism, efficacy, and toxicity

(2017) Ian D. Wilson et al.   Translational Research

Lipopolysaccharide from Crypt-Specific Core Microbiota Modulates the Colonic Epithelial Proliferation-to-Differentiation Balance

(2017) Tomoaki Naito et al.   mBio

A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity

(2017) Victoria E. Ruiz et al.   Nature Communications

Harmonised high throughput microsomal stability assay

(2017) Beth Williamson et al.   JOURNAL OF PHARMACOLOGICAL AND TOXICOLOGICAL METHODS

Drosophila melanogaster as a High-Throughput Model for Host–Microbiota Interactions

(2017) Mark Trinder et al.   Frontiers in Microbiology

Colonization and Succession within the Human Gut Microbiome by Archaea, Bacteria, and Microeukaryotes during the First Year of Life

(2017) Linda Wampach et al.   Frontiers in Microbiology

Next-generation probiotics: the spectrum from probiotics to live biotherapeutics

(2017) Paul W. O’Toole et al.   Nature Microbiology

Gut microbiota composition is associated with polypharmacy in elderly hospitalized patients

(2017) Andrea Ticinesi et al.   Scientific Reports

Screening applications in drug discovery based on microfluidic technology

(2016) P. Eribol et al.   Biomicrofluidics

Cognitive impairment by antibiotic-induced gut dysbiosis: Analysis of gut microbiota-brain communication

(2016) Esther E. Fröhlich et al.   BRAIN BEHAVIOR AND IMMUNITY

The Host Shapes the Gut Microbiota via Fecal MicroRNA

(2016) Shirong Liu et al.   Cell Host & Microbe

The translational relevance ofDrosophilain drug discovery

(2016) Ismael Fernández‐Hernández et al.   EMBO REPORTS

Bio‐banking gut microbiome samples

(2016) Shankar Bolan et al.   EMBO REPORTS

Effect of Intestinal Flora on Protein Expression of Drug-Metabolizing Enzymes and Transporters in the Liver and Kidney of Germ-Free and Antibiotics-Treated Mice

(2016) Takuya Kuno et al.   MOLECULAR PHARMACEUTICS

Promotion of Intestinal Epithelial Cell Turnover by Commensal Bacteria: Role of Short-Chain Fatty Acids

(2016) Jung-ha Park et al.   PLoS One

Population-level analysis of gut microbiome variation

(2016) Gwen Falony et al.   SCIENCE

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Determining the Long-term Effect of Antibiotic Administration on the Human Normal Intestinal Microbiota Using Culture and Pyrosequencing Methods

(2015) Mamun-Ur Rashid et al.   CLINICAL INFECTIOUS DISEASES

How informative is the mouse for human gut microbiota research?

(2015) T. L. A. Nguyen et al.   Disease Models & Mechanisms

Alteration of gut microbiota by vancomycin and bacitracin improves insulin resistance via glucagon-like peptide 1 in diet-induced obesity

(2015) Injae Hwang et al.   FASEB JOURNAL

Proton pump inhibitors affect the gut microbiome

(2015) Floris Imhann et al.   GUT

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

Predicting drug metabolism: experiment and/or computation?

(2015) Johannes Kirchmair et al.   NATURE REVIEWS DRUG DISCOVERY

The SIDER database of drugs and side effects

(2015) Michael Kuhn et al.   NUCLEIC ACIDS RESEARCH

Identifying personal microbiomes using metagenomic codes

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

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

Multidrug evolutionary strategies to reverse antibiotic resistance

(2015) M. Baym et al.   SCIENCE

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

Collateral sensitivity of antibiotic-resistant microbes

(2015) Csaba Pál et al.   TRENDS IN MICROBIOLOGY

Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment

(2015) Yael R. Nobel et al.   Nature Communications

Altering the Intestinal Microbiota during a Critical Developmental Window Has Lasting Metabolic Consequences

(2014) Laura M. Cox et al.   CELL

The Cytosolic Bacterial Peptidoglycan Sensor Nod2 Affords Stem Cell Protection and Links Microbes to Gut Epithelial Regeneration

(2014) Giulia Nigro et al.   Cell Host & Microbe

Collective antibiotic resistance: mechanisms and implications

(2014) Nicole M Vega et al.   CURRENT OPINION IN MICROBIOLOGY

On the Colonic Bacterial Metabolism of Azo-Bonded Prodrugsof 5-Aminosalicylic Acid

(2014) Tiago Sousa et al.   JOURNAL OF PHARMACEUTICAL SCIENCES

Novel Gut-Based Pharmacology of Metformin in Patients with Type 2 Diabetes Mellitus

(2014) Antonella Napolitano et al.   PLoS One

Computational tools for modeling xenometabolism of the human gut microbiota

(2014) Martina Klünemann et al.   TRENDS IN BIOTECHNOLOGY

Evidence of Extensive DNA Transfer between Bacteroidales Species within the Human Gut

(2014) M. J. Coyne et al.   mBio

Differential Modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of Host Peripheral Lipid Metabolism and Histone Acetylation in Mouse Gut Organoids

(2014) S. Lukovac et al.   mBio

C. elegans in high-throughput drug discovery

(2013) Linda P. O'Reilly et al.   ADVANCED DRUG DELIVERY REVIEWS

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

(2013) Corinne Ferrier Maurice et al.   CELL

Metformin Retards Aging in C. elegans by Altering Microbial Folate and Methionine Metabolism

(2013) Filipe Cabreiro et al.   CELL

An increase in theAkkermansiaspp. population induced by metformin treatment improves glucose homeostasis in diet-induced obese mice

(2013) Na-Ri Shin et al.   GUT

Niche-independent high-purity cultures of Lgr5+ intestinal stem cells and their progeny

(2013) Xiaolei Yin et al.   NATURE METHODS

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

The Intestinal Microbiota Modulates the Anticancer Immune Effects of Cyclophosphamide

(2013) S. Viaud et al.   SCIENCE

Change in Pharmacokinetics of Mycophenolic Acid as a Function of Age in Rats and Effect of Coadministered Amoxicillin/Clavulanate

(2012) Junko Ishizaki et al.   BIOLOGICAL & PHARMACEUTICAL BULLETIN

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Trends in the exploitation of novel drug targets

(2011) Mathias Rask-Andersen et al.   NATURE REVIEWS DRUG DISCOVERY

Shifting the balance: antibiotic effects on host–microbiota mutualism

(2011) Benjamin P. Willing et al.   NATURE REVIEWS MICROBIOLOGY

Human Disease Models in Drosophila melanogaster and the Role of the Fly in Therapeutic Drug Discovery

(2011) U. B. Pandey et al.   PHARMACOLOGICAL REVIEWS

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

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

(2010) B. D. Wallace et al.   SCIENCE

Single Lgr5 stem cells build crypt-villus structures in vitro without a mesenchymal niche

(2009) Toshiro Sato et al.   NATURE

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

(2009) T. A. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA