Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables

A Comparative Assessment of High-Throughput Quantitative Polymerase Chain Reaction versus Shotgun Metagenomic Sequencing in Sediment Resistome Profiling

(2023) Nazima Habibi et al.   Applied Sciences-Basel

Effects of residual monensin in livestock manure on nitrogen transformation and microbial community during “crop straw feeding-substrate fermentation-mushroom cultivation” recycling system

(2022) Fei Wang et al.   WASTE MANAGEMENT

The physical structure of compost and C and N utilization during composting and mushroom growth in Agaricus bisporus cultivation with rice, wheat, and reed straw-based composts

(2021) Qian Wang et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation

(2021) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

Key factors driving the fate of antibiotic resistance genes and controlling strategies during aerobic composting of animal manure: A review

(2021) Botao Liu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

ResFinder 4.0 for predictions of phenotypes from genotypes

(2020) Valeria Bortolaia et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Pathways for horizontal gene transfer in bacteria revealed by a global map of their plasmids

(2020) Santiago Redondo-Salvo et al.   Nature Communications

Analysis of compositions of microbiomes with bias correction

(2020) Huang Lin et al.   Nature Communications

Linking the resistome and plasmidome to the microbiome

(2019) Thibault Stalder et al.   ISME Journal

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

(2019) Dongwan D. Kang et al.   PeerJ

GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database

(2019) Pierre-Alain Chaumeil et al.   BIOINFORMATICS

MEGARes 2.0: a database for classification of antimicrobial drug, biocide and metal resistance determinants in metagenomic sequence data

(2019) Enrique Doster et al.   NUCLEIC ACIDS RESEARCH

Exploring the persistence and spreading of antibiotic resistance from manure to biocompost, soils and vegetables

(2019) Chengjun Pu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Scaling read aligners to hundreds of threads on general-purpose processors

(2018) Ben Langmead et al.   BIOINFORMATICS

Long-term agronomic practices alter the composition of asymbiotic diazotrophic bacterial community and their nitrogen fixation genes in an acidic red soil

(2018) Weibing Xun et al.   BIOLOGY AND FERTILITY OF SOILS

Housefly larvae (Musca domestica) significantly accelerates degradation of monensin by altering the structure and abundance of the associated bacterial community

(2018) Hao Li et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Does organically produced lettuce harbor higher abundance of antibiotic resistance genes than conventionally produced?

(2017) Bokai Zhu et al.   ENVIRONMENT INTERNATIONAL

Microbial phylogeny determines transcriptional response of resistome to dynamic composting processes

(2017) Cheng Wang et al.   Microbiome

Metagenomic characterization of the effect of feed additives on the gut microbiome and antibiotic resistome of feedlot cattle

(2017) Milton Thomas et al.   Scientific Reports

Fast and sensitive taxonomic classification for metagenomics with Kaiju

(2016) Peter Menzel et al.   Nature Communications

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

(2015) Yu-Wei Wu et al.   BIOINFORMATICS

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Antibiotic Resistome and Its Association with Bacterial Communities during Sewage Sludge Composting

(2015) Jian-Qiang Su et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

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

(2015) Donovan H. Parks 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

Evolutionary change and phylogenetic relationships in light of horizontal gene transfer

(2015) Luis Boto   JOURNAL OF BIOSCIENCES

Average genome size estimation improves comparative metagenomics and sheds light on the functional ecology of the human microbiome

(2015) Stephen Nayfach et al.   GENOME BIOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Biodegradation of Veterinary Ionophore Antibiotics in Broiler Litter and Soil Microcosms

(2014) Peizhe Sun et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Application and environmental risks of livestock manure

(2013) Ramasamy Rajesh Kumar et al.   Journal of the Korean Society for Applied Biological Chemistry

Diverse and abundant antibiotic resistance genes in Chinese swine farms

(2013) Yong-Guan Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure and Antimicrobial Properties of Monensin A and Its Derivatives: Summary of the Achievements

(2013) Daniel Łowicki et al.   Biomed Research International

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Reversible monensin adaptation in Enterococcus faecium, Enterococcus faecalis and Clostridium perfringens of cattle origin: potential impact on human food safety

(2012) S. Simjee et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

FastUniq: A Fast De Novo Duplicates Removal Tool for Paired Short Reads

(2012) Haibin Xu et al.   PLoS One

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

Decline in extractable antibiotics in manure-based composts during composting

(2011) K.-R. Kim et al.   WASTE MANAGEMENT

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Tetracycline in liquid manure selects for co-occurrence of the resistance genes tet(M) and tet(L) in Enterococcus faecalis

(2009) Karin Schwaiger et al.   VETERINARY MICROBIOLOGY

Piggery manure used for soil fertilization is a reservoir for transferable antibiotic resistance plasmids

(2008) Chu Thi Thanh Binh et al.   FEMS MICROBIOLOGY ECOLOGY