Diet leaves a genetic signature in a keystone member of the gut microbiota

Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice

(2021) Bahtiyar Yilmaz et al.   Cell Host & Microbe

Functional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments

(2021) Hualan Liu et al.   Cell Reports

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

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

The Landscape of Adaptive Evolution of a Gut Commensal Bacteria in Aging Mice

(2020) Hugo C. Barreto et al.   CURRENT BIOLOGY

Thinking about the microbiome as a causal factor in human health and disease: philosophical and experimental considerations

(2020) David A Relman   CURRENT OPINION IN MICROBIOLOGY

Low mutational load and high mutation rate variation in gut commensal bacteria

(2020) Ricardo S. Ramiro et al.   PLOS BIOLOGY

How Food Affects Colonization Resistance Against Enteropathogenic Bacteria

(2020) Markus Kreuzer et al.   Annual Review of Microbiology

Dysbiosis individualizes the fitness effect of antibiotic resistance in the mammalian gut

(2020) Luís Leónidas Cardoso et al.   Nature Ecology & Evolution

Gut microbial metabolites as multi-kingdom intermediates

(2020) Kimberly A. Krautkramer et al.   NATURE REVIEWS MICROBIOLOGY

Health and disease markers correlate with gut microbiome composition across thousands of people

(2020) Ohad Manor et al.   Nature Communications

The Protective Role of Hydrogen Sulfide Against Obesity-Associated Cellular Stress in Blood Glucose Regulation

(2020) Ania Mezouari et al.   Antioxidants

DIABLO: an integrative approach for identifying key molecular drivers from multi-omic assays

(2019) Amrit Singh et al.   BIOINFORMATICS

Role of the microbiome in human development

(2019) Maria Gloria Dominguez-Bello et al.   GUT

Evolutionary dynamics of bacteria in the gut microbiome within and across hosts

(2019) Nandita R. Garud et al.   PLOS BIOLOGY

Adaptive Strategies of the Candidate Probiotic E. coli Nissle in the Mammalian Gut

(2019) Nathan Crook et al.   Cell Host & Microbe

Distinct Genetic and Functional Traits of Human Intestinal Prevotella copri Strains Are Associated with Different Habitual Diets

(2019) Francesca De Filippis et al.   Cell Host & Microbe

Adaptive Evolution within Gut Microbiomes of Healthy People

(2019) Shijie Zhao et al.   Cell Host & Microbe

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Long‐term evolution of the natural isolate of Escherichia coli 536 in the mouse gut colonized after maternal transmission reveals convergence in the constitutive expression of the lactose operon

(2019) Mohamed Ghalayini et al.   MOLECULAR ECOLOGY

Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle

(2019) Alfonso Santos-Lopez et al.   eLife

A field guide for the compositional analysis of any-omics data

(2019) Thomas P Quinn et al.   GigaScience

Distinct Polysaccharide Utilization Profiles of Human Intestinal Prevotella copri Isolates

(2019) Hannah Fehlner-Peach et al.   Cell Host & Microbe

Escherichia coli limits Salmonella Typhimurium infections after diet shifts and fat-mediated microbiota perturbation in mice

(2019) Sandra Y. Wotzka et al.   Nature Microbiology

Current understanding of the human microbiome

(2018) Jack A Gilbert et al.   NATURE MEDICINE

Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model

(2018) Andrew J. Hryckowian et al.   Nature Microbiology

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

A shifting mutational landscape in 6 nutritional states: Stress-induced mutagenesis as a series of distinct stress input–mutation output relationships

(2017) Ram P. Maharjan et al.   PLOS BIOLOGY

mixOmics: An R package for ‘omics feature selection and multiple data integration

(2017) Florian Rohart et al.   PLoS Computational Biology

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

(2016) Mahesh S. Desai et al.   CELL

Using long-term experimental evolution to uncover the patterns and determinants of molecular evolution of an Escherichia coli natural isolate in the streptomycin-treated mouse gut

(2016) Mathilde Lescat et al.   MOLECULAR ECOLOGY

Interactions between the microbiota and pathogenic bacteria in the gut

(2016) Andreas J. Bäumler 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

A Mutational Hotspot and Strong Selection Contribute to the Order of Mutations Selected for during Escherichia coli Adaptation to the Gut

(2016) Marta Lourenço et al.   PLoS Genetics

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

Antimicrobial peptide resistance mediates resilience of prominent gut commensals during inflammation

(2015) T. W. Cullen et al.   SCIENCE

Symbiotic Human Gut Bacteria with Variable Metabolic Priorities for Host Mucosal Glycans

(2015) N. A. Pudlo et al.   mBio

Adaptive immunity increases the pace and predictability of evolutionary change in commensal gut bacteria

(2015) João Barroso-Batista et al.   Nature Communications

Manipulation of the Quorum Sensing Signal AI-2 Affects the Antibiotic-Treated Gut Microbiota

(2015) Jessica Ann Thompson et al.   Cell Reports

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

Inexpensive Multiplexed Library Preparation for Megabase-Sized Genomes

(2015) Michael Baym et al.   PLoS One

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Starving our Microbial Self: The Deleterious Consequences of a Diet Deficient in Microbiota-Accessible Carbohydrates

(2014) Erica D. Sonnenburg et al.   Cell Metabolism

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

(2014) Lindsey G. Albenberg et al.   GASTROENTEROLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps

(2014) João Barroso-Batista et al.   PLoS Genetics

Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis

(2014) Andrew D Fernandes et al.   Microbiome

An Ecological Network of Polysaccharide Utilization among Human Intestinal Symbionts

(2013) Seth Rakoff-Nahoum et al.   CURRENT BIOLOGY

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

The gastrointestinal mucus system in health and disease

(2013) Malin E. V. Johansson et al.   Nature Reviews Gastroenterology & Hepatology

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

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

Metabolic niche of a prominent sulfate-reducing human gut bacterium

(2013) F. E. Rey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetically dictated change in host mucus carbohydrate landscape exerts a diet-dependent effect on the gut microbiota

(2013) P. C. Kashyap et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Effects of Diet on Resource Utilization by a Model Human Gut Microbiota Containing Bacteroides cellulosilyticus WH2, a Symbiont with an Extensive Glycobiome

(2013) Nathan P. McNulty et al.   PLOS BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Structural resilience of the gut microbiota in adult mice under high-fat dietary perturbations

(2012) Chenhong Zhang et al.   ISME Journal

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

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

Bacteroides in the Infant Gut Consume Milk Oligosaccharides via Mucus-Utilization Pathways

(2011) Angela Marcobal et al.   Cell Host & Microbe

Genotype and Phenotypes of an Intestine-Adapted Escherichia coli K-12 Mutant Selected by Animal Passage for Superior Colonization

(2011) Andrew J. Fabich et al.   INFECTION AND IMMUNITY

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

(2011) J. J. Faith et al.   SCIENCE

Recognition and Degradation of Plant Cell Wall Polysaccharides by Two Human Gut Symbionts

(2011) Eric C. Martens et al.   PLOS BIOLOGY

Trade-Off between Bile Resistance and Nutritional Competence Drives Escherichia coli Diversification in the Mouse Gut

(2011) Marianne De Paepe et al.   PLoS Genetics

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Specificity of Polysaccharide Use in Intestinal Bacteroides Species Determines Diet-Induced Microbiota Alterations

(2010) Erica D. Sonnenburg et al.   CELL

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome evolution and adaptation in a long-term experiment with Escherichia coli

(2009) Jeffrey E. Barrick et al.   NATURE

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

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

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Dissecting the Genetic Components of Adaptation of Escherichia coli to the Mouse Gut

(2008) Antoine Giraud et al.   PLoS Genetics