Metagenome-wide association analysis identifies microbial determinants of post-antibiotic ecological recovery in the gut

Investigating metabolic interactions in a microbial co-culture through integrated modelling and experiments

(2020) Aarthi Ravikrishnan et al.   Computational and Structural Biotechnology Journal

Cross-feeding modulates antibiotic tolerance in bacterial communities

(2018) Elizabeth M. Adamowicz et al.   ISME Journal

Global increase and geographic convergence in antibiotic consumption between 2000 and 2015

(2018) Eili Y. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Jotham Suez et al.   CELL

Environment dominates over host genetics in shaping human gut microbiota

(2018) Daphna Rothschild et al.   NATURE

Species-level functional profiling of metagenomes and metatranscriptomes

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

Recovery of gut microbiota of healthy adults following antibiotic exposure

(2018) Albert Palleja et al.   Nature Microbiology

Interspecies cross-feeding orchestrates carbon degradation in the rumen ecosystem

(2018) Lindsey M. Solden et al.   Nature Microbiology

Gut microbiome modulates response to anti–PD-1 immunotherapy in melanoma patients

(2017) V. Gopalakrishnan et al.   SCIENCE

Gut microbiome influences efficacy of PD-1–based immunotherapy against epithelial tumors

(2017) Bertrand Routy et al.   SCIENCE

Interactions of Intestinal Bacteria with Components of the Intestinal Mucus

(2017) Jean-Félix Sicard et al.   Frontiers in Cellular and Infection Microbiology

From Dietary Fiber to Host Physiology: Short-Chain Fatty Acids as Key Bacterial Metabolites

(2016) Ara Koh et al.   CELL

Composition of human faecal microbiota in resistance to Campylobacter infection

(2016) C. Kampmann et al.   CLINICAL MICROBIOLOGY AND INFECTION

Reduced Abundance of Butyrate-Producing Bacteria Species in the Fecal Microbial Community in Crohn's Disease

(2016) Kenichiro Takahashi et al.   DIGESTION

Bridging ecology and conservation: from ecological networks to ecosystem function

(2016) Eric Harvey et al.   JOURNAL OF APPLIED ECOLOGY

The Densely O-Glycosylated MUC2 Mucin Protects the Intestine and Provides Food for the Commensal Bacteria

(2016) Liisa Arike et al.   JOURNAL OF MOLECULAR BIOLOGY

Microbiome-wide association studies link dynamic microbial consortia to disease

(2016) Jack A. Gilbert et al.   NATURE

Interactions between the microbiota and pathogenic bacteria in the gut

(2016) Andreas J. Bäumler et al.   NATURE

Generation of genome-scale metabolic reconstructions for 773 members of the human gut microbiota

(2016) Stefanía Magnúsdóttir et al.   NATURE BIOTECHNOLOGY

Metagenome-wide association studies: fine-mining the microbiome

(2016) Jun Wang et al.   NATURE REVIEWS MICROBIOLOGY

Antibiotic use and its consequences for the normal microbiome

(2016) Martin J. Blaser   SCIENCE

Apple-Derived Pectin Modulates Gut Microbiota, Improves Gut Barrier Function, and Attenuates Metabolic Endotoxemia in Rats with Diet-Induced Obesity

(2016) Tingting Jiang et al.   Nutrients

The effects of antibiotics on the microbiome throughout development and alternative approaches for therapeutic modulation

(2016) Amy Langdon et al.   Genome Medicine

Bifidobacteria and Butyrate-Producing Colon Bacteria: Importance and Strategies for Their Stimulation in the Human Gut

(2016) Audrey Rivière et al.   Frontiers in Microbiology

Antibiotic-mediated gut microbiome perturbation accelerates development of type 1 diabetes in mice

(2016) Alexandra E. Livanos et al.   Nature Microbiology

The gut microbiota and host health: a new clinical frontier

(2015) Julian R Marchesi et al.   GUT

The initial state of the human gut microbiome determines its reshaping by antibiotics

(2015) Frédéric Raymond et al.   ISME Journal

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Same Exposure but Two Radically Different Responses to Antibiotics: Resilience of the Salivary Microbiome versus Long-Term Microbial Shifts in Feces

(2015) E. Zaura et al.   mBio

Probiotic bacteria, B. longum and L. acidophilus inhibit infection by rotavirus in vitro and decrease the duration of diarrhea in pediatric patients

(2015) Do Kyung Lee et al.   Clinics and Research in Hepatology and Gastroenterology

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

Mucin glycan foraging in the human gut microbiome

(2015) Louise E. Tailford et al.   Frontiers in Genetics

Exploring the influence of the gut microbiota and probiotics on health: a symposium report

(2014) Linda V. Thomas et al.   BRITISH JOURNAL OF NUTRITION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Antibiotics in early life and obesity

(2014) Laura M. Cox et al.   Nature Reviews Endocrinology

Metagenomic Data Utilization and Analysis (MEDUSA) and Construction of a Global Gut Microbial Gene Catalogue

(2014) Fredrik H. Karlsson et al.   PLoS Computational Biology

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Prebiotic stimulation of human colonic butyrate-producing bacteria and bifidobacteria,in vitro

(2013) Karen P. Scott et al.   FEMS MICROBIOLOGY ECOLOGY

Antibiotic treatment expands the resistance reservoir and ecological network of the phage metagenome

(2013) Sheetal R. Modi et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

The abundance and variety of carbohydrate-active enzymes in the human gut microbiota

(2013) Abdessamad El Kaoutari et al.   NATURE REVIEWS MICROBIOLOGY

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Insight into the prebiotic concept: lessons from an exploratory, double blind intervention study with inulin-type fructans in obese women

(2012) Evelyne M Dewulf et al.   GUT

Gut microbiota disturbance during antibiotic therapy: a multi-omic approach

(2012) Ana Elena Pérez-Cobas et al.   GUT

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Complex Carbohydrate Utilization by the Healthy Human Microbiome

(2012) Brandi L. Cantarel et al.   PLoS One

Bacteroides uniformis CECT 7771 Ameliorates Metabolic and Immunological Dysfunction in Mice with High-Fat-Diet Induced Obesity

(2012) Paola Gauffin Cano et al.   PLoS One

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Cumulative Antibiotic Exposures Over Time and the Risk of Clostridium difficile Infection

(2011) V. Stevens et al.   CLINICAL INFECTIOUS DISEASES

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Environmental and Gut Bacteroidetes: The Food Connection

(2011) François Thomas et al.   Frontiers in Microbiology

Microbial Community Development in a Dynamic Gut Model Is Reproducible, Colon Region Specific, and Selective for Bacteroidetes and Clostridium Cluster IX

(2010) P. Van den Abbeele et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2010) Heng Li et al.   BIOINFORMATICS

Short-Term Antibiotic Treatment Has Differing Long-Term Impacts on the Human Throat and Gut Microbiome

(2010) Hedvig E. Jakobsson et al.   PLoS One

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

What are the consequences of the disappearing human microbiota?

(2009) Martin J. Blaser et al.   NATURE REVIEWS MICROBIOLOGY

The assembly and disassembly of ecological networks

(2009) J. Bascompte et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY