The Impact of Mercury Selection and Conjugative Genetic Elements on Community Structure and Resistance Gene Transfer

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The Ecology and Evolution of Pangenomes

(2019) Michael A. Brockhurst et al.   CURRENT BIOLOGY

Extremely fast amelioration of plasmid fitness costs by multiple functionally diverse pathways

(2019) James P. J. Hall et al.   MICROBIOLOGY-SGM

The Transposon Registry

(2019) Supathep Tansirichaiya et al.   Mobile DNA

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria

(2018) Kelly L .Wyres et al.   CURRENT OPINION IN MICROBIOLOGY

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Gene mobility promotes the spread of resistance in bacterial populations

(2017) Cagla Stevenson et al.   ISME Journal

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

(2017) Sang-Hoon Lee et al.   ISME Journal

The Divided Bacterial Genome: Structure, Function, and Evolution

(2017) George C. diCenzo et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Integrative and conjugative elements and their hosts: composition, distribution and organization

(2017) Jean Cury et al.   NUCLEIC ACIDS RESEARCH

Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria

(2017) James P. J. Hall et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Tolerance of the forest soil microbiome to increasing mercury concentrations

(2017) Aline Frossard et al.   SOIL BIOLOGY & BIOCHEMISTRY

The CRISPR Spacer Space Is Dominated by Sequences from Species-Specific Mobilomes

(2017) Sergey A. Shmakov et al.   mBio

Plasmid-Mediated Bioaugmentation for the Bioremediation of Contaminated Soils

(2017) Carlos Garbisu et al.   Frontiers in Microbiology

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

(2017) James P. J. Hall et al.   Nature Ecology & Evolution

Evolution and Ecology of CRISPR

(2016) Edze R. Westra et al.   Annual Review of Ecology Evolution and Systematics

Metal stressors consistently modulate bacterial conjugal plasmid uptake potential in a phylogenetically conserved manner

(2016) Uli Klümper et al.   ISME Journal

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Regulation of genetic flux between bacteria by restriction–modification systems

(2016) Pedro H. Oliveira et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Local adaptation of a bacterium is as important as its presence in structuring a natural microbial community

(2016) Pedro Gómez et al.   Nature Communications

Combined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations

(2016) Alan McNally et al.   PLoS Genetics

Antibiotics as a selective driver for conjugation dynamics

(2016) Allison J. Lopatkin et al.   Nature Microbiology

Co-occurrence of resistance genes to antibiotics, biocides and metals reveals novel insights into their co-selection potential

(2015) Chandan Pal et al.   BMC GENOMICS

Parallel Compensatory Evolution Stabilizes Plasmids across the Parasitism-Mutualism Continuum

(2015) Ellie Harrison et al.   CURRENT BIOLOGY

The sociality of bioremediation: Hijacking the social lives of microbial populations to clean up heavy metal contamination

(2015) S. O'Brien et al.   EMBO REPORTS

Environmentally co-occurring mercury resistance plasmids are genetically and phenotypically diverse and confer variable context-dependent fitness effects

(2015) James P.J. Hall et al.   ENVIRONMENTAL MICROBIOLOGY

Massively parallel sequencing of single cells by epicPCR links functional genes with phylogenetic markers

(2015) Sarah J Spencer et al.   ISME Journal

Migration and horizontal gene transfer divide microbial genomes into multiple niches

(2015) Rene Niehus et al.   Nature Communications

Broad host range plasmids can invade an unexpectedly diverse fraction of a soil bacterial community

(2014) Uli Klümper et al.   ISME Journal

Natural microbial communities supporting the transfer of the IncP-1β plasmid pB10 exhibit a higher initial content of plasmids from the same incompatibility group

(2014) Xavier Bellanger et al.   Frontiers in Microbiology

Broad host range plasmids

(2013) Aayushi Jain et al.   FEMS MICROBIOLOGY LETTERS

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

(2013) Sheetal R. Modi et al.   NATURE

Dealing with the Evolutionary Downside of CRISPR Immunity: Bacteria and Beneficial Plasmids

(2013) Wenyan Jiang et al.   PLoS Genetics

Structural characteristics of genomic islands associated with GMP synthases as integration hotspot among sequenced microbial genomes

(2012) Lei Song et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

The Mercury Resistance Operon: From an Origin in a Geothermal Environment to an Efficient Detoxification Machine

(2012) Eric S. Boyd et al.   Frontiers in Microbiology

Broad-Host-Range Plasmids from Agricultural Soils Have IncP-1 Backbones with Diverse Accessory Genes

(2011) Diya Sen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A cooperative virulence plasmid imposes a high fitness cost under conditions that induce pathogenesis

(2011) T. G. Platt et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS