The antibiotic resistome of swine manure is significantly altered by association with the Musca domestica larvae gut microbiome

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

(2015) Dinghua Li et al.   BIOINFORMATICS

Pattern of multiresistant to antimicrobials and heavy metal tolerance in bacteria isolated from sewage sludge samples from a composting process at a recycling plant in southern Brazil

(2015) Karina Heck et al.   ENVIRONMENTAL MONITORING AND ASSESSMENT

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

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Functional metagenomic characterization of antibiotic resistance genes in agricultural soils from China

(2014) Jian Qiang Su et al.   ENVIRONMENT INTERNATIONAL

High Throughput Profiling of Antibiotic Resistance Genes in Urban Park Soils with Reclaimed Water Irrigation

(2014) Feng-Hua Wang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Exploring the immediate and long-term impact on bacterial communities in soil amended with animal and urban organic waste fertilizers using pyrosequencing and screening for horizontal transfer of antibiotic resistance

(2014) Leise Riber et al.   FEMS MICROBIOLOGY ECOLOGY

Taxonomical and functional microbial community selection in soybean rhizosphere

(2014) Lucas W Mendes et al.   ISME Journal

Attenuation of veterinary antibiotics in full-scale vermicomposting of swine manure via the housefly larvae (Musca domestica)

(2014) ZhiJian Zhang et al.   Scientific Reports

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

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

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

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

A full-scale house fly (Diptera: Muscidae) larvae bioconversion system for value-added swine manure reduction

(2013) Hang Wang et al.   WASTE MANAGEMENT & RESEARCH

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Swine manure vermicomposting via housefly larvae (Musca domestica): The dynamics of biochemical and microbial features

(2012) ZhiJian Zhang et al.   BIORESOURCE TECHNOLOGY

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

China Takes Aim at Rampant Antibiotic Resistance

(2012) M. Hvistendahl   SCIENCE

Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates

(2011) Li C Xia et al.   BMC Systems Biology

Endogeic earthworms shape bacterial functional communities and affect organic matter mineralization in a tropical soil

(2011) Laetitia Bernard et al.   ISME Journal

Impacts of anthropogenic activity on the ecology of class 1 integrons and integron-associated genes in the environment

(2011) William H Gaze et al.   ISME Journal

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

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

(2011) Chris S. Smillie et al.   NATURE

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Horizontal Gene Exchange in Environmental Microbiota

(2011) Rustam I. Aminov   Frontiers in Microbiology

Comparison of Bacterial Diversity in Wheat Bran and in the Gut of Larvae and Newly Emerged Adult of Musca domestica (Diptera: Muscidae) by Use of Ethidium Monoazide Reveals Bacterial Colonization

(2010) Zhijian Su et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

FragGeneScan: predicting genes in short and error-prone reads

(2010) Mina Rho et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Diverse aadA gene cassettes on class 1 integrons introduced into soil via spread manure

(2009) Chu T.T. Binh et al.   RESEARCH IN MICROBIOLOGY

The RAST Server: Rapid Annotations using Subsystems Technology

(2008) Ramy K Aziz et al.   BMC GENOMICS

Black Soldier Fly (Diptera: Stratiomyidae) Larvae Reduce Escherichia coli in Dairy Manure

(2008) Qiaolin Liu et al.   ENVIRONMENTAL ENTOMOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

ARDB--Antibiotic Resistance Genes Database

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