Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing

Litter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens

(2022) Adelumola Oladeinde et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Ecological dynamics of plasmid transfer and persistence in microbial communities

(2022) Michael J Bottery   CURRENT OPINION IN MICROBIOLOGY

Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant

(2022) David Calderón-Franco et al.   WATER RESEARCH

Detection and various environmental factors of antibiotic resistance gene horizontal transfer

(2022) Weiying Li et al.   ENVIRONMENTAL RESEARCH

Endocytosis-like DNA uptake by cell wall-deficient bacteria

(2022) Renée Kapteijn et al.   Nature Communications

Quantitative analysis of horizontal gene transfer in complex systems

(2021) Jenifer Moralez et al.   CURRENT OPINION IN MICROBIOLOGY

AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence

(2021) Michael Feldgarden et al.   Scientific Reports

Temperature and Nutrient Limitations Decrease Transfer of Conjugative IncP-1 Plasmid pKJK5 to Wild Escherichia coli Strains

(2021) Rebeca Pallares-Vega et al.   Frontiers in Microbiology

Antimicrobial resistance acquisition via natural transformation: context is everything

(2021) Macaulay Winter et al.   CURRENT OPINION IN MICROBIOLOGY

Antibiotic resistance in the environment

(2021) D. G. Joakim Larsson et al.   NATURE REVIEWS MICROBIOLOGY

Proton Motive Force Disruptors Block Bacterial Competence and Horizontal Gene Transfer

(2020) Arnau Domenech et al.   Cell Host & Microbe

MiDAS 3: An ecosystem-specific reference database, taxonomy and knowledge platform for activated sludge and anaerobic digesters reveals species-level microbiome composition of activated sludge

(2020) Marta Nierychlo et al.   WATER RESEARCH

Slightly beneficial genes are retained by bacteria evolving DNA uptake despite selfish elements

(2020) Bram van Dijk et al.   eLife

Cell-Free DNA: An Underestimated Source of Antibiotic Resistance Gene Dissemination at the Interface Between Human Activities and Downstream Environments in the Context of Wastewater Reuse

(2020) Markus Woegerbauer et al.   Frontiers in Microbiology

Resistance of Gram-Positive Bacteria to Current Antibacterial Agents and Overcoming Approaches

(2020) Buthaina Jubeh et al.   MOLECULES

Widespread transfer of mobile antibiotic resistance genes within individual gut microbiomes revealed through bacterial Hi-C

(2020) Alyssa G. Kent et al.   Nature Communications

Free-floating extracellular DNA: Systematic profiling of mobile genetic elements and antibiotic resistance from wastewater

(2020) David Calderón-Franco et al.   WATER RESEARCH

Antibiotic resistance in European wastewater treatment plants mirrors the pattern of clinical antibiotic resistance prevalence

(2019) Katariina M. M. Pärnänen et al.   Science Advances

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Exploring the antibiotic resistome in activated sludge and anaerobic digestion sludge in an urban wastewater treatment plant via metagenomic analysis

(2019) Keunje Yoo et al.   JOURNAL OF MICROBIOLOGY

OUP accepted manuscript

(2018)   BIOINFORMATICS

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

(2018) Robert D. Stewart et al.   Nature Communications

metaSPAdes: a new versatile metagenomic assembler

(2017) Sergey Nurk et al.   GENOME RESEARCH

Inter-species population dynamics enhance microbial horizontal gene transfer and spread of antibiotic resistance

(2017) Robert M Cooper et al.   eLife

Natural competence for transformation

(2016) Melanie Blokesch   CURRENT BIOLOGY

Antibiotics as a selective driver for conjugation dynamics

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

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

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

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

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

(2015) Sarah J Spencer et al.   ISME Journal

SAMBLASTER: fast duplicate marking and structural variant read extraction

(2014) G. G. Faust et al.   BIOINFORMATICS

Inhibition of the ANT(2″)-Ia resistance enzyme and rescue of aminoglycoside antibiotic activity by synthetic α-hydroxytropolones

(2014) Danielle R. Hirsch et al.   BIOORGANIC & MEDICINAL CHEMISTRY LETTERS

Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

(2014) Jelle Slager et al.   CELL

Natural Competence and the Evolution of DNA Uptake Specificity

(2014) J. C. Mell et al.   JOURNAL OF BACTERIOLOGY

Characterization of a Novel Plasmid-Borne Thiopeptide Gene Cluster in Staphylococcus epidermidis Strain 115

(2014) P. R. Bennallack et al.   JOURNAL OF BACTERIOLOGY

Species-Level Deconvolution of Metagenome Assemblies with Hi-C–Based Contact Probability Maps

(2014) Joshua N. Burton et al.   G3-Genes Genomes Genetics

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Bacterial natural transformation by highly fragmented and damaged DNA

(2013) S. Overballe-Petersen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The roles of extracellular DNA in the structural integrity of extracellular polymeric substance and bacterial biofilm development

(2013) Theerthankar Das et al.   Environmental Microbiology Reports

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

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Bacterial Selection during the Formation of Early-Stage Aerobic Granules in Wastewater Treatment Systems Operated Under Wash-Out Dynamics

(2012) David G. Weissbrodt et al.   Frontiers in Microbiology

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Competence in Streptococcus pneumoniae Is Regulated by the Rate of Ribosomal Decoding Errors

(2011) K. E. Stevens et al.   mBio

Horizontal Gene Exchange in Environmental Microbiota

(2011) Rustam I. Aminov   Frontiers in Microbiology

Rational Design of a Plasmid Origin That Replicates Efficiently in Both Gram-Positive and Gram-Negative Bacteria

(2010) Anton V. Bryksin et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Escherichia coli genes affecting recipient ability in plasmid conjugation: Are there any?

(2009) Daniel Pérez-Mendoza et al.   BMC GENOMICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Natural Transformation of Helicobacter pylori Involves the Integration of Short DNA Fragments Interrupted by Gaps of Variable Size

(2009) Edward A. Lin et al.   PLoS Pathogens

Extracellular DNA in soil and sediment: fate and ecological relevance

(2008) G. Pietramellara et al.   BIOLOGY AND FERTILITY OF SOILS