Co‐occurrence of antibiotic, biocide, and heavy metal resistance genes in bacteria from metal and radionuclide contaminated soils at the Savannah River Site

Understanding antimicrobial discovery and resistance from a metagenomic and metatranscriptomic perspective: Advances and applications

(2019) Jonathan Asante et al.   Environmental Microbiology Reports

Identification of Resistance Genes and Response to Arsenic in Rhodococcus aetherivorans BCP1

(2019) Andrea Firrincieli et al.   Frontiers in Microbiology

Multiple Lines of Evidences Reveal Mechanisms Underpinning Mercury Resistance and Volatilization by Stenotrophomonas sp. MA5 Isolated from the Savannah River Site (SRS), USA

(2019) Meenakshi Agarwal et al.   Cells

A global survey of arsenic-related genes in soil microbiomes

(2019) Taylor K. Dunivin et al.   BMC BIOLOGY

Metagenomic insights into the abundance and composition of resistance genes in aquatic environments: Influence of stratification and geography

(2019) Yuyi Yang et al.   ENVIRONMENT INTERNATIONAL

Phosphate amendments for chemical immobilization of uranium in contaminated soil

(2019) Matthew R. Baker et al.   ENVIRONMENT INTERNATIONAL

Bacterial Heavy-Metal and Antibiotic Resistance Genes in a Copper Tailing Dam Area in Northern China

(2019) Jianwen Chen et al.   Frontiers in Microbiology

Adapterama II: universal amplicon sequencing on Illumina platforms (TaggiMatrix)

(2019) Travis C. Glenn et al.   PeerJ

Adapterama I: universal stubs and primers for 384 unique dual-indexed or 147,456 combinatorially-indexed Illumina libraries (iTru & iNext)

(2019) Travis C. Glenn et al.   PeerJ

ARGs-OAP v2.0 with an expanded SARG database and Hidden Markov Models for enhancement characterization and quantification of antibiotic resistance genes in environmental metagenomes

(2018) Xiaole Yin et al.   BIOINFORMATICS

Global increase and geographic convergence in antibiotic consumption between 2000 and 2015

(2018) Eili Y. Klein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Feed additives shift gut microbiota and enrich antibiotic resistance in swine gut

(2018) Yi Zhao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Aerobic composting reduces antibiotic resistance genes in cattle manure and the resistome dissemination in agricultural soils

(2018) Min Gou et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Distribution of Arsenic Resistance Genes in Prokaryotes

(2018) Ibtissem Ben Fekih et al.   Frontiers in Microbiology

The effects of low-level ionizing radiation and copper exposure on the incidence of antibiotic resistance in lentic biofilm bacteria

(2017) J. Vaun McArthur et al.   ENVIRONMENTAL POLLUTION

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution

(2017) Yucheng Wu et al.   Scientific Reports

Coal mining practices reduce the microbial biomass, richness and diversity of soil

(2016) Patricia Dorr de Quadros et al.   APPLIED SOIL ECOLOGY

Validating mammalian resistance to stressor-mediated reproductive impact using rodent sperm analysis

(2016) Lawrence V. Tannenbaum et al.   ECOTOXICOLOGY

Long-Term Nickel Contamination Increases the Occurrence of Antibiotic Resistance Genes in Agricultural Soils

(2016) Hang-Wei Hu et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Relationship between antibiotic resistance genes and metals in residential soil samples from Western Australia

(2016) Charles W Knapp et al.   ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH

Co-occurrence of antibiotic and metal resistance genes revealed in complete genome collection

(2016) Li-Guan Li et al.   ISME Journal

Co-selection of antibiotic and heavy metal resistance in freshwater bacteria

(2016) Andrea Di Cesare et al.   JOURNAL OF LIMNOLOGY

Co-selection of antibiotic and metal(loid) resistance in gram-negative epiphytic bacteria from contaminated salt marshes

(2016) Isabel Henriques et al.   MARINE POLLUTION BULLETIN

Application of multivariate statistical techniques in microbial ecology

(2016) O. Paliy et al.   MOLECULAR ECOLOGY

Antibiotic resistance genes and human bacterial pathogens: Co-occurrence, removal, and enrichment in municipal sewage sludge digesters

(2016) Feng Ju et al.   WATER RESEARCH

Co-spread of metal and antibiotic resistance within ST3-IncHI2 plasmids from E. coli isolates of food-producing animals

(2016) Liangxing Fang et al.   Scientific Reports

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Driving forces of soil bacterial community structure, diversity, and function in temperate grasslands and forests

(2016) Kristin Kaiser et al.   Scientific Reports

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

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

(2015) Bing Li et al.   ISME Journal

Initial community and environment determine the response of bacterial communities to dispersant and oil contamination

(2015) Alice C. Ortmann et al.   MARINE POLLUTION BULLETIN

The Bacterial and Fungal Diversity of an Aged PAH- and Heavy Metal-Contaminated Soil is Affected by Plant Cover and Edaphic Parameters

(2015) Amélia Bourceret et al.   MICROBIAL ECOLOGY

Patterns of Multi-Antibiotic-Resistant Escherichia Coli from Streams with No History of Antimicrobial Inputs

(2015) J. V. McArthur et al.   MICROBIAL ECOLOGY

Highly Heterogeneous Soil Bacterial Communities around Terra Nova Bay of Northern Victoria Land, Antarctica

(2015) Mincheol Kim et al.   PLoS One

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

Metagenomic profiles and antibiotic resistance genes in gut microbiota of mice exposed to arsenic and iron

(2014) Xuechao Guo et al.   CHEMOSPHERE

Large-Scale Metagenomic-Based Study of Antibiotic Resistance in the Environment

(2014) Joseph Nesme et al.   CURRENT BIOLOGY

The soil resistome: a critical review on antibiotic resistance origins, ecology and dissemination potential in telluric bacteria

(2014) Joseph Nesme et al.   ENVIRONMENTAL MICROBIOLOGY

Bacterial phylogeny structures soil resistomes across habitats

(2014) Kevin J. Forsberg et al.   NATURE

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Evaluation of a Hybrid Approach Using UBLAST and BLASTX for Metagenomic Sequences Annotation of Specific Functional Genes

(2014) Ying Yang et al.   PLoS One

Rhizosphere Effect on Nutrient Availability in Soil and Its Uptake by Plants: A Review

(2014) M. L. Dotaniya et al.   Proceedings of the National Academy of Sciences, India. Section B

The Comprehensive Antibiotic Resistance Database

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

Soil bacterial communities shaped by geochemical factors and land use in a less-explored area, Tibetan Plateau

(2013) Xiangyu Guan et al.   BMC GENOMICS

Management Options for Reducing the Release of Antibiotics and Antibiotic Resistance Genes to the Environment

(2013) Amy Pruden et al.   ENVIRONMENTAL HEALTH PERSPECTIVES

Taxonomic relatedness shapes bacterial assembly in activated sludge of globally distributed wastewater treatment plants

(2013) Feng Ju et al.   ENVIRONMENTAL MICROBIOLOGY

Heavy metal pollution decreases microbial abundance, diversity and activity within particle-size fractions of a paddy soil

(2013) Junhui Chen et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

BacMet: antibacterial biocide and metal resistance genes database

(2013) Chandan Pal et al.   NUCLEIC ACIDS RESEARCH

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Identification of acquired antimicrobial resistance genes

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

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

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

Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies

(2012) Anna Klindworth et al.   NUCLEIC ACIDS RESEARCH

Heavy metal driven co-selection of antibiotic resistance in soil and water bodies impacted by agriculture and aquaculture

(2012) Claudia Seiler et al.   Frontiers in Microbiology

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

DNA Double-Strand Breakage as an Endpoint to Examine Metal and Radionuclide Exposure Effects to Water Snakes on a Nuclear Industrial Site

(2011) Stephanie M. Murray et al.   HUMAN AND ECOLOGICAL RISK ASSESSMENT

Antibiotic resistance is ancient

(2011) Vanessa M. D’Costa et al.   NATURE

Antibiotic Resistance Gene Abundances Correlate with Metal and Geochemical Conditions in Archived Scottish Soils

(2011) Charles W. Knapp et al.   PLoS One

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Antibiotic resistance and its cost: is it possible to reverse resistance?

(2010) Dan I. Andersson et al.   NATURE REVIEWS MICROBIOLOGY

Characterization of the RND family of multidrug efflux pumps: in silico to in vivo confirmation of four functionally distinct subgroups

(2010) Patricia Godoy et al.   Microbial Biotechnology

Pyrosequencing-Based Assessment of Soil pH as a Predictor of Soil Bacterial Community Structure at the Continental Scale

(2009) C. L. Lauber et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

A review of heavy metal contaminations in urban soils, urban road dusts and agricultural soils from China

(2009) Binggan Wei et al.   MICROCHEMICAL JOURNAL