Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects

Infection trains the host for microbiota-enhanced resistance to pathogens

(2021) Apollo Stacy et al.   CELL

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

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

Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae

(2020) Christoph M. Ernst et al.   NATURE MEDICINE

Intestinal Dysbiosis in Carriers of Carbapenem-Resistant Enterobacteriaceae

(2020) Hila Korach-Rechtman et al.   mSphere

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

(2020) Kern Rei Chng et al.   Nature Ecology & Evolution

Butyrate mediates anti-inflammatory effects of Faecalibacterium prausnitzii in intestinal epithelial cells through Dact3

(2020) Marion Lenoir et al.   Gut Microbes

Salmonella versus the Microbiome

(2020) Andrew W. L. Rogers et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Bacteroides vulgatus and Bacteroides dorei Reduce Gut Microbial Lipopolysaccharide Production and Inhibit Atherosclerosis

(2019) Naofumi Yoshida et al.   CIRCULATION

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

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

Adaptive Evolution within Gut Microbiomes of Healthy People

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

Rethinking gut microbiome residency and the Enterobacteriaceae in healthy human adults

(2019) Jonathan N. V. Martinson et al.   ISME Journal

β-Lactamases and β-Lactamase Inhibitors in the 21st Century

(2019) Catherine L. Tooke et al.   JOURNAL OF MOLECULAR BIOLOGY

Establishing microbial composition measurement standards with reference frames

(2019) James T. Morton et al.   Nature Communications

Fecal microbiota transplantation beyond Clostridioides difficile infections

(2019) Koen Wortelboer et al.   EBioMedicine

Viral quasispecies

(2019) Esteban Domingo et al.   PLoS Genetics

Inhibition of histone deacetylase 1 (HDAC1) and HDAC2 enhances CRISPR/Cas9 genome editing

(2019) Bin Liu et al.   NUCLEIC ACIDS RESEARCH

Different adaptive strategies in E. coli populations evolving under macronutrient limitation and metal ion limitation

(2018) Omar M. Warsi et al.   BMC EVOLUTIONARY BIOLOGY

Multiscale Evolutionary Dynamics of Host-Associated Microbiomes

(2018) Aura Ferreiro et al.   CELL

Microbiota-Derived Metabolic Factors Reduce Campylobacteriosis in Mice

(2018) Xiaolun Sun et al.   GASTROENTEROLOGY

Species-level functional profiling of metagenomes and metatranscriptomes

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

Oxygen as a driver of gut dysbiosis

(2017) Fabian Rivera-Chávez et al.   FREE RADICAL BIOLOGY AND MEDICINE

Increased expression of Qnr is sufficient to confer clinical resistance to ciprofloxacin in Escherichia coli

(2017) Linnéa Garoff et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution

(2017) Hemanshu Mundhada et al.   METABOLIC ENGINEERING

The fire ant social chromosome supergene variant Sb shows low diversity but high divergence from SB

(2017) Rodrigo Pracana et al.   MOLECULAR ECOLOGY

The trajectory of microbial single-cell sequencing

(2017) Tanja Woyke et al.   NATURE METHODS

Time-Resolved Tracking of Mutations Reveals Diverse Allele Dynamics during Escherichia coli Antimicrobial Adaptive Evolution to Single Drugs and Drug Pairs

(2017) Rachel A. Hickman et al.   Frontiers in Microbiology

Profiling Living Bacteria Informs Preparation of Fecal Microbiota Transplantations

(2017) Nathaniel D. Chu et al.   PLoS One

Mechanisms of inflammation-driven bacterial dysbiosis in the gut

(2016) M Y Zeng et al.   Mucosal Immunology

Dissemination of Antimicrobial Resistance in Microbial Ecosystems through Horizontal Gene Transfer

(2016) Christian J. H. von Wintersdorff et al.   Frontiers in Microbiology

Duration of Colonization WithKlebsiella pneumoniaeCarbapenemase-Producing Bacteria at Long-Term Acute Care Hospitals in Chicago, Illinois

(2016) Manon R. Haverkate et al.   Open Forum Infectious Diseases

Fecal microbiota transplantation: in perspective

(2015) Shaan Gupta et al.   Therapeutic Advances in Gastroenterology

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Molecular mechanisms of antibiotic resistance

(2014) Jessica M. A. Blair et al.   NATURE REVIEWS MICROBIOLOGY

SRST2: Rapid genomic surveillance for public health and hospital microbiology labs

(2014) Michael Inouye et al.   Genome Medicine

Bacterial colonization factors control specificity and stability of the gut microbiota

(2013) S. Melanie Lee et al.   NATURE

The human microbiome as a reservoir of antimicrobial resistance

(2013) John Penders et al.   Frontiers in Microbiology

Asymptomatic rectal carriage of blaKPC producing carbapenem-resistant Enterobacteriaceae: who is prone to become clinically infected?

(2012) V. Schechner et al.   CLINICAL MICROBIOLOGY AND INFECTION

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

(2012) Pablo Cingolani et al.   FLY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

LPS remodeling is an evolved survival strategy for bacteria

(2012) Y. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

LacZβ-galactosidase: Structure and function of an enzyme of historical and molecular biological importance

(2012) Douglas H. Juers et al.   PROTEIN SCIENCE

Adaptive Evolution of the Lactose Utilization Network in Experimentally Evolved Populations of Escherichia coli

(2012) Selwyn Quan et al.   PLoS Genetics

Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

(2011) Tami D Lieberman et al.   NATURE GENETICS

Stress-induced evolution of Escherichia coli points to original concepts in respiratory cofactor selectivity

(2011) C. Auriol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiota regulates immune defense against respiratory tract influenza A virus infection

(2011) T. Ichinohe 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

Directed Evolution of the DnaK Chaperone: Mutations in the Lid Domain Result in Enhanced Chaperone Activity

(2010) Raphael A. Aponte et al.   JOURNAL OF MOLECULAR BIOLOGY

The population genetics of commensal Escherichia coli

(2010) Olivier Tenaillon et al.   NATURE REVIEWS MICROBIOLOGY

RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media

(2010) T. M. Conrad et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SrmB, a DEAD-box helicase involved in Escherichia coli ribosome assembly, is specifically targeted to 23S rRNA in vivo

(2009) Dmitrii Trubetskoy et al.   NUCLEIC ACIDS RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH