Examining horizontal gene transfer in microbial communities

Complete, closed bacterial genomes from microbiomes using nanopore sequencing

(2020) Eli L. Moss et al.   NATURE BIOTECHNOLOGY

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale

(2020) Soumaya Zlitni et al.   Genome Medicine

Adsorption sequencing (AdsorpSeq) as a rapid method to link environmental bacteriophages to hosts

(2020) Patrick A. de Jonge et al.   iScience

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

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

Metagenomic engineering of the mammalian gut microbiome in situ

(2019) Carlotta Ronda et al.   NATURE METHODS

Mobile Compensatory Mutations Promote Plasmid Survival

(2019) Martin Zwanzig et al.   mSystems

Transmission of human-associated microbiota along family and social networks

(2019) Ilana L. Brito et al.   Nature Microbiology

Megaphages infect Prevotella and variants are widespread in gut microbiomes

(2019) Audra E. Devoto et al.   Nature Microbiology

MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches

(2019) Weizhi Song et al.   Microbiome

A human gut bacterial genome and culture collection for improved metagenomic analyses

(2019) Samuel C. Forster et al.   NATURE BIOTECHNOLOGY

Structural variation in the gut microbiome associates with host health

(2019) David Zeevi et al.   NATURE

Marine DNA Viral Macro- and Microdiversity from Pole to Pole

(2019) Ann C. Gregory et al.   CELL

Adaptive Evolution within Gut Microbiomes of Healthy People

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

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks

(2019) Ho Bin Jang et al.   NATURE BIOTECHNOLOGY

Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

(2019) Jun Li et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Long-read based de novo assembly of low-complexity metagenome samples results in finished genomes and reveals insights into strain diversity and an active phage system

(2019) Vincent Somerville et al.   BMC MICROBIOLOGY

CRISPR–Cas in mobile genetic elements: counter-defence and beyond

(2019) Guilhem Faure et al.   NATURE REVIEWS MICROBIOLOGY

Urinary tract colonization is enhanced by a plasmid that regulates uropathogenic Acinetobacter baumannii chromosomal genes

(2019) Gisela Di Venanzio et al.   Nature Communications

Where did you come from, where did you go: Refining metagenomic analysis tools for horizontal gene transfer characterisation

(2019) Enrico Seiler et al.   PLoS Computational Biology

A Reverse Ecology Approach Based on a Biological Definition of Microbial Populations

(2019) Philip Arevalo et al.   CELL

A library of human gut bacterial isolates paired with longitudinal multiomics data enables mechanistic microbiome research

(2019) M. Poyet et al.   NATURE MEDICINE

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut

(2019) Yoshihiko Suzuki et al.   Microbiome

Defining the human gut host–phage network through single-cell viral tagging

(2019) Mária Džunková et al.   Nature Microbiology

A simple, reproducible and cost-effective procedure to analyse gut phageome: from phage isolation to bioinformatic approach

(2019) Camille d’Humières et al.   Scientific Reports

A Bioinformatic Analysis of Integrative Mobile Genetic Elements Highlights Their Role in Bacterial Adaptation

(2019) Matthew G. Durrant et al.   Cell Host & Microbe

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools

(2019) Xiaofang Jiang et al.   PLoS One

Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation

(2019) Eitan Yaffe et al.   Nature Microbiology

Microbial genomic island discovery, visualization and analysis

(2018) Claire Bertelli et al.   BRIEFINGS IN BIOINFORMATICS

Anti-CRISPR Phages Cooperate to Overcome CRISPR-Cas Immunity

(2018) Mariann Landsberger et al.   CELL

PlasFlow: predicting plasmid sequences in metagenomic data using genome signatures

(2018) Pawel S Krawczyk et al.   NUCLEIC ACIDS RESEARCH

The global distribution and spread of the mobilized colistin resistance gene mcr-1

(2018) Ruobing Wang et al.   Nature Communications

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2018) Christian M. K. Sieber et al.   Nature Microbiology

Murine colitis reveals a disease-associated bacteriophage community

(2018) Breck A. Duerkop et al.   Nature Microbiology

Insights into the Human Virome Using CRISPR Spacers from Microbiomes

(2018) Claudio Hidalgo-Cantabrana et al.   Viruses-Basel

A Comparison of Methods for the Extraction of Plasmids Capable of Conferring Antibiotic Resistance in a Human Pathogen From Complex Broiler Cecal Samples

(2018) Sarah Delaney et al.   Frontiers in Microbiology

Minimum Information about an Uncultivated Virus Genome (MIUViG)

(2018) Simon Roux et al.   NATURE BIOTECHNOLOGY

Deciphering bacterial epigenomes using modern sequencing technologies

(2018) John Beaulaurier et al.   NATURE REVIEWS GENETICS

Phylogenetic barriers to horizontal transfer of antimicrobial peptide resistance genes in the human gut microbiota

(2018) Bálint Kintses et al.   Nature Microbiology

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Metagenomic binning and association of plasmids with bacterial host genomes using DNA methylation

(2017) John Beaulaurier et al.   NATURE BIOTECHNOLOGY

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Giant viruses with an expanded complement of translation system components

(2017) Frederik Schulz et al.   SCIENCE

Inflammation boosts bacteriophage transfer between Salmonella spp.

(2017) Médéric Diard et al.   SCIENCE

Assembly of a nucleus-like structure during viral replication in bacteria

(2017) Vorrapon Chaikeeratisak et al.   SCIENCE

Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles

(2017) Ramunas Stepanauskas et al.   Nature Communications

Extensive horizontal gene transfer in cheese-associated bacteria

(2017) Kevin S Bonham et al.   eLife

Scaffolding bacterial genomes and probing host-virus interactions in gut microbiome by proximity ligation (chromosome capture) assay

(2017) Martial Marbouty et al.   Science Advances

Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer

(2017) Frances Tran et al.   Scientific Reports

Detecting horizontal gene transfer by mapping sequencing reads across species boundaries

(2016) Kathrin Trappe et al.   BIOINFORMATICS

The diversity-generating benefits of a prokaryotic adaptive immune system

(2016) Stineke van Houte et al.   NATURE

Mobile genes in the human microbiome are structured from global to individual scales

(2016) I. L. Brito et al.   NATURE

Uncovering Earth’s virome

(2016) David Paez-Espino et al.   NATURE

A role for the bacterial GATC methylome in antibiotic stress survival

(2016) Nadia R Cohen et al.   NATURE GENETICS

Virtual microfluidics for digital quantification and single-cell sequencing

(2016) Liyi Xu et al.   NATURE METHODS

Indication of Horizontal DNA Gene Transfer by Extracellular Vesicles

(2016) Stefanie Fischer et al.   PLoS One

Vikodak - A Modular Framework for Inferring Functional Potential of Microbial Communities from 16S Metagenomic Datasets

(2016) Sunil Nagpal et al.   PLoS One

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Plasmid transfer in biofilms: a perspective on limitations and opportunities

(2016) Thibault Stalder et al.   npj Biofilms and Microbiomes

Evaluating the mobility potential of antibiotic resistance genes in environmental resistomes without metagenomics

(2016) Katariina Pärnänen et al.   Scientific Reports

MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

Massive horizontal gene transfer, strictly vertical inheritance and ancient duplications differentially shape the evolution of Bacillus cereus enterotoxin operons hbl, cytK and nhe

(2015) Maria-Elisabeth Böhm et al.   BMC EVOLUTIONARY BIOLOGY

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

Evaluation of methods to purify virus-like particles for metagenomic sequencing of intestinal viromes

(2015) Manuel Kleiner et al.   BMC GENOMICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

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

(2015) Sarah J Spencer et al.   ISME Journal

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Synthetic long-read sequencing reveals intraspecies diversity in the human microbiome

(2015) Volodymyr Kuleshov et al.   NATURE BIOTECHNOLOGY

Early life dynamics of the human gut virome and bacterial microbiome in infants

(2015) Efrem S Lim et al.   NATURE MEDICINE

Gut DNA viromes of Malawian twins discordant for severe acute malnutrition

(2015) Alejandro Reyes et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

VirSorter: mining viral signal from microbial genomic data

(2015) Simon Roux et al.   PeerJ

Optimizing protocols for extraction of bacteriophages prior to metagenomic analyses of phage communities in the human gut

(2015) Josué L. Castro-Mejía et al.   Microbiome

In SilicoDetection and Typing of Plasmids using PlasmidFinder and Plasmid Multilocus Sequence Typing

(2014) Alessandra Carattoli et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Gene Transfer Potential of Outer Membrane Vesicles of Acinetobacter baylyi and Effects of Stress on Vesiculation

(2014) Shweta Fulsundar et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2014) Uli Klümper et al.   ISME Journal

Viral tagging reveals discrete populations in Synechococcus viral genome sequence space

(2014) Li Deng et al.   NATURE

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Hundreds of Circular Novel Plasmids and DNA Elements Identified in a Rat Cecum Metamobilome

(2014) Tue Sparholt Jørgensen et al.   PLoS One

A Quantitative Comparison of Single-Cell Whole Genome Amplification Methods

(2014) Charles F. A. de Bourcy et al.   PLoS One

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

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

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

Metagenomic chromosome conformation capture (meta3C) unveils the diversity of chromosome organization in microorganisms

(2014) Martial Marbouty et al.   eLife

The methylome of the gut microbiome: disparate Dam methylation patterns in intestinal Bacteroides dorei

(2014) Michael T. Leonard et al.   Frontiers in Microbiology

Strain- and plasmid-level deconvolution of a synthetic metagenome by sequencing proximity ligation products

(2014) Christopher W. Beitel et al.   PeerJ

Microbes in the neonatal intensive care unit resemble those found in the gut of premature infants

(2014) Brandon Brooks et al.   Microbiome

Community-wide plasmid gene mobilization and selection

(2013) Vladimir Sentchilo et al.   ISME Journal

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Rapid evolution of the human gut virome

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

Exploring the costs of horizontal gene transfer

(2013) David A. Baltrus   TRENDS IN ECOLOGY & EVOLUTION

Prophage Excision Activates Listeria Competence Genes that Promote Phagosomal Escape and Virulence

(2012) Lev Rabinovich et al.   CELL

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

(2012) A. Stern et al.   GENOME RESEARCH

Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

(2012) I. Sharon et al.   GENOME RESEARCH

Determination of conjugation rates on solid surfaces

(2012) Irene del Campo et al.   PLASMID

Insights into the bovine rumen plasmidome

(2012) A. B. Kav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Contrasting Life Strategies of Viruses that Infect Photo- and Heterotrophic Bacteria, as Revealed by Viral Tagging

(2012) L. Deng et al.   mBio

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

(2012) Joyce E. Loper et al.   PLoS Genetics

Genetic bioaugmentation as an effective method for in situ bioremediation

(2012) Kaoru Ikuma et al.   Bioengineered

Large-Scale Analysis of Plasmid Relationships through Gene-Sharing Networks

(2011) M. Tamminen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ecology drives a global network of gene exchange connecting the human microbiome

(2011) Chris S. Smillie et al.   NATURE

Assembly complexity of prokaryotic genomes using short reads

(2010) Carl Kingsford et al.   BMC BIOINFORMATICS

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

Insertion Sequence Inversions Mediated by Ectopic Recombination between Terminal Inverted Repeats

(2010) Alison Ling et al.   PLoS One

High Frequency of Horizontal Gene Transfer in the Oceans

(2010) L. D. McDaniel et al.   SCIENCE

Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed

(2009) Trond Erik Vee Aune et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Genome assembly reborn: recent computational challenges

(2009) M. Pop   BRIEFINGS IN BIOINFORMATICS

Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family Enterobacteriaceae

(2009) J. Putze et al.   INFECTION AND IMMUNITY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

ACLAME: A CLAssification of Mobile genetic Elements, update 2010

(2009) Raphaël Leplae et al.   NUCLEIC ACIDS RESEARCH

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities

(2008) A. F. Andersson et al.   SCIENCE