Establishment and characterization of stable, diverse, fecal-derived in vitro microbial communities that model the intestinal microbiota

Bacterial interspecies interactions modulate pH-mediated antibiotic tolerance

(2020) Andrés Aranda-Díaz et al.   eLife

Specific Eco-evolutionary Contexts in the Mouse Gut Reveal Escherichia coli Metabolic Versatility

(2020) João Barroso-Batista et al.   CURRENT BIOLOGY

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens

(2020) Carlos G. Gonzalez et al.   mSystems

Separating host and microbiome contributions to drug pharmacokinetics and toxicity

(2019) Michael Zimmermann et al.   SCIENCE

Massively parallel screening of synthetic microbial communities

(2019) Jared Kehe et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Deletions from Microbiome Consortia Reveal Key Metabolic Interactions between Gut Microbes

(2019) Natalia Gutiérrez et al.   mSystems

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

Transient Osmotic Perturbation Causes Long-Term Alteration to the Gut Microbiota

(2018) Carolina Tropini et al.   CELL

Cross-feeding modulates antibiotic tolerance in bacterial communities

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

Deciphering microbial interactions in synthetic human gut microbiome communities

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

Nutritional preferences of human gut bacteria reveal their metabolic idiosyncrasies

(2018) Melanie Tramontano et al.   Nature Microbiology

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Strain Library Imaging Protocol for high-throughput, automated single-cell microscopy of large bacterial collections arrayed on multiwell plates

(2017) Handuo Shi et al.   Nature Protocols

Interaction networks, ecological stability, and collective antibiotic tolerance in polymicrobial infections

(2017) Marjon G. J. de Vos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Spatial organization of a model 15-member human gut microbiota established in gnotobiotic mice

(2017) Jessica L. Mark Welch et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

Culturing of ‘unculturable’ human microbiota reveals novel taxa and extensive sporulation

(2016) Hilary P. Browne et al.   NATURE

Diet–microbiota interactions as moderators of human metabolism

(2016) Justin L. Sonnenburg et al.   NATURE

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Collective Resistance in Microbial Communities by Intracellular Antibiotic Deactivation

(2016) Robin A. Sorg et al.   PLOS BIOLOGY

Quantitative Imaging of Gut Microbiota Spatial Organization

(2015) Kristen A. Earle et al.   Cell Host & Microbe

Normalization of Host Intestinal Mucus Layers Requires Long-Term Microbial Colonization

(2015) Malin E.V. Johansson et al.   Cell Host & Microbe

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

Indirect resistance to several classes of antibiotics in cocultures with resistant bacteria expressing antibiotic-modifying or -degrading enzymes

(2015) Hervé Nicoloff et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Antibiotic-Induced Alterations of the Murine Gut Microbiota and Subsequent Effects on Colonization Resistance against Clostridium difficile

(2015) Alyxandria M. Schubert et al.   mBio

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

(2014) Laura M. Cox et al.   CELL

Emergence of fecal microbiota transplantation as an approach to repair disrupted microbial gut ecology

(2014) Alexander Khoruts et al.   IMMUNOLOGY LETTERS

Gut Microbes and the Brain: Paradigm Shift in Neuroscience

(2014) E. A. Mayer et al.   JOURNAL OF NEUROSCIENCE

Cultivation-based multiplex phenotyping of human gut microbiota allows targeted recovery of previously uncultured bacteria

(2014) Elizabeth A. Rettedal et al.   Nature Communications

Complex Interactions Among Diet, Gastrointestinal Transit, and Gut Microbiota in Humanized Mice

(2013) Purna C. Kashyap et al.   GASTROENTEROLOGY

Microbiota-liberated host sugars facilitate post-antibiotic expansion of enteric pathogens

(2013) Katharine M. Ng et al.   NATURE

Gnotobiotic mouse model of phage-bacterial host dynamics in the human gut

(2013) A. Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Antibiotics in early life alter the murine colonic microbiome and adiposity

(2012) Ilseung Cho et al.   NATURE

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

The role of beta-lactamase-producing-bacteria in mixed infections

(2009) Itzhak Brook   BMC INFECTIOUS DISEASES

Specific Microbiota Direct the Differentiation of IL-17-Producing T-Helper Cells in the Mucosa of the Small Intestine

(2008) Ivaylo I. Ivanov et al.   Cell Host & Microbe