High‐efficiency delivery of CRISPR‐Cas9 by engineered probiotics enables precise microbiome editing

Targeted-antibacterial-plasmids (TAPs) combining conjugation and CRISPR/Cas systems achieve strain-specific antibacterial activity

(2021) Audrey Reuter et al.   NUCLEIC ACIDS RESEARCH

On-target activity predictions enable improved CRISPR–dCas9 screens in bacteria

(2020) Alicia Calvo-Villamañán et al.   NUCLEIC ACIDS RESEARCH

In situ reprogramming of gut bacteria by oral delivery

(2020) Bryan B. Hsu et al.   Nature Communications

Highly efficient gene transfer in the mouse gut microbiota is enabled by the Incl2 conjugative plasmid TP114

(2020) Kevin Neil et al.   Communications Biology

Engineered toxin–intein antimicrobials can selectively target and kill antibiotic-resistant bacteria in mixed populations

(2019) Rocío López-Igual et al.   NATURE BIOTECHNOLOGY

Origins and evolution of CRISPR-Cas systems

(2019) Eugene V. Koonin et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Assembly of large mobilizable genetic cargo by double recombinase operated insertion of DNA (DROID)

(2019) Kevin Neil et al.   PLASMID

GenPipes: an open-source framework for distributed and scalable genomic analyses

(2019) Mathieu Bourgey et al.   GigaScience

Midbiotics: conjugative plasmids for genetic engineering of natural gut flora

(2019) Pilvi Ruotsalainen et al.   Gut Microbes

Conjugative delivery of CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci

(2019) Marinelle Rodrigues et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Efficient inter-species conjugative transfer of a CRISPR nuclease for targeted bacterial killing

(2019) Thomas A. Hamilton et al.   Nature Communications

OUP accepted manuscript

(2018)   NUCLEIC ACIDS RESEARCH

Exploiting a conjugative CRISPR/Cas9 system to eliminate plasmid harboring mcr-1 gene from Escherichia coli

(2018) Haisi Dong et al.   INTERNATIONAL JOURNAL OF ANTIMICROBIAL AGENTS

Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysis

(2018) Alessandro Cassini et al.   LANCET INFECTIOUS DISEASES

Adherent-invasiveEscherichia coliin inflammatory bowel disease

(2017) Carolina Palmela et al.   GUT

Comparative Evaluation of Four Bacteria-Specific Primer Pairs for 16S rRNA Gene Surveys

(2017) Sofie Thijs et al.   Frontiers in Microbiology

Plasmid interference for curing antibiotic resistance plasmids in vivo

(2017) Muhammad Kamruzzaman et al.   PLoS One

Citrobacter rodentium mouse model of bacterial infection

(2016) Valerie F Crepin et al.   Nature Protocols

Consequences of Cas9 cleavage in the chromosome ofEscherichia coli

(2016) Lun Cui et al.   NUCLEIC ACIDS RESEARCH

Genetically manipulated phages with improved pH resistance for oral administration in veterinary medicine

(2016) Franklin L. Nobrega et al.   Scientific Reports

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

(2016) Amy Langdon et al.   Genome Medicine

Bacteria vs. Bacteriophages: Parallel Evolution of Immune Arsenals

(2016) Muhammad A. B. Shabbir et al.   Frontiers in Microbiology

A diaminopimelic acid auxotrophic Escherichia coli donor provides improved counterselection following intergeneric conjugation with actinomycetes

(2015) Nancy Allard et al.   CANADIAN JOURNAL OF MICROBIOLOGY

Escherichia coli EDL933 Requires Gluconeogenic Nutrients To Successfully Colonize the Intestines of Streptomycin-Treated Mice Precolonized with E. coli Nissle 1917

(2015) Silvia A. C. Schinner et al.   INFECTION AND IMMUNITY

The human gut resistome

(2015) W. van Schaik   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Temperate and lytic bacteriophages programmed to sensitize and kill antibiotic-resistant bacteria

(2015) Ido Yosef et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of potent in vivo mutagenesis plasmids with broad mutational spectra

(2015) Ahmed H. Badran et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Sequence-specific antimicrobials using efficiently delivered RNA-guided nucleases

(2014) Robert J Citorik et al.   NATURE BIOTECHNOLOGY

Exploiting CRISPR-Cas nucleases to produce sequence-specific antimicrobials

(2014) David Bikard et al.   NATURE BIOTECHNOLOGY

Programmable Removal of Bacterial Strains by Use of Genome-Targeting CRISPR-Cas Systems

(2014) A. A. Gomaa et al.   mBio

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

F conjugation: Back to the beginning

(2013) Denis Arutyunov et al.   PLASMID

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

(2012) Pablo Cingolani et al.   FLY

Escherichia coli Nissle 1917 (Mutaflor): New Insights into an Old Probiotic Bacterium

(2011) Christoph A. Jacobi et al.   DIGESTIVE DISEASES

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Regulation of Aerobic-to-Anaerobic Transitions by the FNR Cycle in Escherichia coli

(2010) Dean A. Tolla et al.   JOURNAL OF MOLECULAR BIOLOGY

Conjugative plasmids: vessels of the communal gene pool

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