Enrichment allows identification of diverse, rare elements in metagenomic resistome-virulome sequencing

Comparing and Evaluating Metagenome Assembly Tools from a Microbiologist’s Perspective - Not Only Size Matters!

(2017) John Vollmers et al.   PLoS One

An expansion of rare lineage intestinal microbes characterizes rheumatoid arthritis

(2016) Jun Chen et al.   Genome Medicine

Resistome diversity in cattle and the environment decreases during beef production

(2016) Noelle R Noyes et al.   eLife

Characterization of the resistome in manure, soil and wastewater from dairy and beef production systems

(2016) Noelle R. Noyes et al.   Scientific Reports

Antibiotic Selection Pressure Determination through Sequence-Based Metagenomics

(2015) Matthias Willmann et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Whole-Genome Sequencing in Outbreak Analysis

(2015) Carol A. Gilchrist et al.   CLINICAL MICROBIOLOGY REVIEWS

Enhanced virome sequencing using targeted sequence capture

(2015) Todd N. Wylie et al.   GENOME RESEARCH

Metagenomic and network analysis reveal wide distribution and co-occurrence of environmental antibiotic resistance genes

(2015) Bing Li et al.   ISME Journal

Ecology and exploration of the rare biosphere

(2015) Michael D. J. Lynch et al.   NATURE REVIEWS MICROBIOLOGY

Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis

(2015) Thomas Briese et al.   mBio

Limited dissemination of the wastewater treatment plant core resistome

(2015) Christian Munck et al.   Nature Communications

Fire in the Belly? Sulfur-Reducing Gut Microbes Fuel Arsenic Thiolation

(2014) Carol Potera   ENVIRONMENTAL HEALTH PERSPECTIVES

Coselection for resistance to multiple late-generation human therapeutic antibiotics encoded on tetracycline resistance plasmids captured from uncultivated stream and soil bacteria

(2014) J.B. Herrick et al.   JOURNAL OF APPLIED MICROBIOLOGY

Detecting ultralow-frequency mutations by Duplex Sequencing

(2014) Scott R Kennedy et al.   Nature Protocols

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

What is a resistance gene? Ranking risk in resistomes

(2014) José L. Martínez et al.   NATURE REVIEWS MICROBIOLOGY

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Enriching pathogen transcripts from infected samples: A capture-based approach to enhanced host–pathogen RNA sequencing

(2013) Zachary W. Bent et al.   ANALYTICAL BIOCHEMISTRY

The Comprehensive Antibiotic Resistance Database

(2013) Andrew G. McArthur et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes

(2013) Sushim Kumar Gupta et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Antimicrobial Resistance and Virulence: a Successful or Deleterious Association in the Bacterial World?

(2013) A. Beceiro et al.   CLINICAL MICROBIOLOGY REVIEWS

Differential abundance analysis for microbial marker-gene surveys

(2013) Joseph N Paulson et al.   NATURE METHODS

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

A Method for Selectively Enriching Microbial DNA from Contaminating Vertebrate Host DNA

(2013) George R. Feehery et al.   PLoS One

Distinguishable Epidemics of Multidrug-Resistant Salmonella Typhimurium DT104 in Different Hosts

(2013) A. E. Mather et al.   SCIENCE

Metagenomics for pathogen detection in public health

(2013) Ruth R Miller et al.   Genome Medicine

Identification of acquired antimicrobial resistance genes

(2012) E. Zankari et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Analyses of the Microbial Diversity across the Human Microbiome

(2012) Kelvin Li et al.   PLoS One

Gut inflammation can boost horizontal gene transfer between pathogenic and commensal Enterobacteriaceae

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

In-feed antibiotic effects on the swine intestinal microbiome

(2012) T. Looft et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Shared Antibiotic Resistome of Soil Bacteria and Human Pathogens

(2012) K. J. Forsberg et al.   SCIENCE

Comparative fecal metagenomics unveils unique functional capacity of the swine gut

(2011) Regina Lamendella et al.   BMC MICROBIOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

VFDB 2012 update: toward the genetic diversity and molecular evolution of bacterial virulence factors

(2011) L. Chen et al.   NUCLEIC ACIDS RESEARCH

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Updated Functional Classification of  -Lactamases

(2009) K. Bush et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

Evidence of Increasing Antibiotic Resistance Gene Abundances in Archived Soils since 1940

(2009) Charles W. Knapp et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing

(2009) Andreas Gnirke et al.   NATURE BIOTECHNOLOGY

Associations between Antimicrobial Resistance Genes in Fecal Generic Escherichia coli Isolates from Cow-Calf Herds in Western Canada

(2008) S. P. Gow et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The tragedy of the uncommon: understanding limitations in the analysis of microbial diversity

(2008) Stephen J Bent et al.   ISME Journal