Metagenomic analysis reveals antibiotic resistance genes in the bovine rumen

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

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Metagenomic analysis of bacterial communities and antibiotic resistance genes in the Eriocheir sinensis freshwater aquaculture environment

(2019) Hao Fang et al.   CHEMOSPHERE

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

(2019) Robert D. Stewart et al.   NATURE BIOTECHNOLOGY

Characterization of antibiotic resistance genes in the species of the rumen microbiota

(2019) Yasmin Neves Vieira Sabino et al.   Nature Communications

Deep sequence analysis reveals the ovine rumen as a reservoir of antibiotic resistance genes

(2018) Thomas C.A. Hitch et al.   ENVIRONMENTAL POLLUTION

Cultivation and sequencing of rumen microbiome members from the Hungate1000 Collection

(2018) Rekha Seshadri et al.   NATURE BIOTECHNOLOGY

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data

(2018) Gustavo Arango-Argoty et al.   Microbiome

Functional genera, potential pathogens and predicted antibiotic resistance genes in 16 full-scale wastewater treatment plants treating different types of wastewater

(2018) Xiao-Yan Fan et al.   BIORESOURCE TECHNOLOGY

MetaWRAP—a flexible pipeline for genome-resolved metagenomic data analysis

(2018) Gherman V. Uritskiy et al.   Microbiome

Horizontal gene transfer and shifts in linked bacterial community composition are associated with maintenance of antibiotic resistance genes during food waste composting

(2018) Hanpeng Liao et al.   SCIENCE OF THE TOTAL ENVIRONMENT

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

MEGARes: an antimicrobial resistance database for high throughput sequencing

(2016) Steven M. Lakin et al.   NUCLEIC ACIDS RESEARCH

Antimicrobial usage and resistance in beef production

(2016) Andrew Cameron et al.   Journal of Animal Science and Biotechnology

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

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MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) Dongwan D. Kang et al.   PeerJ

Antibiotic bacitracin induces hydrolytic degradation of nucleic acids

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Effect of Manure Application on Abundance of Antibiotic Resistance Genes and Their Attenuation Rates in Soil: Field-Scale Mass Balance Approach

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Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

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

Identification of acquired antimicrobial resistance genes

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

Insights into Physiological and Genetic Mupirocin Susceptibility in Bifidobacteria

(2011) Fausta Serafini et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Discovery of Biomass-Degrading Genes and Genomes from Cow Rumen

(2011) M. Hess et al.   SCIENCE

Fast and accurate long-read alignment with Burrows–Wheeler transform

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Updated Functional Classification of  -Lactamases

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Transfer of Antibiotic Resistance Marker Genes between Lactic Acid Bacteria in Model Rumen and Plant Environments

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ARDB--Antibiotic Resistance Genes Database

(2008) B. Liu et al.   NUCLEIC ACIDS RESEARCH