A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments

Tracking antibiotic resistance gene pollution from different sources using machine-learning classification

(2018) Li-Guan Li et al.   Microbiome

Seagrass ecosystems reduce exposure to bacterial pathogens of humans, fishes, and invertebrates

(2017) Joleah B. Lamb et al.   SCIENCE

Continental-scale pollution of estuaries with antibiotic resistance genes

(2017) Yong-Guan Zhu et al.   Nature Microbiology

Comparative metagenome of a stream impacted by the urbanization phenomenon

(2016) Julliane Dutra Medeiros et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Reefs of tomorrow: eutrophication reduces coral biodiversity in an urbanized seascape

(2016) Nicolas N. Duprey et al.   GLOBAL CHANGE BIOLOGY

Global occurrence and heterogeneity of the Roseobacter-clade species Ruegeria mobilis

(2016) Eva C Sonnenschein et al.   ISME Journal

Measurement of bacterial replication rates in microbial communities

(2016) Christopher T Brown et al.   NATURE BIOTECHNOLOGY

KEGG: new perspectives on genomes, pathways, diseases and drugs

(2016) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Probiotics modulated gut microbiota suppresses hepatocellular carcinoma growth in mice

(2016) Jun Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mitophagy confers resistance to siderophore-mediated killing byPseudomonas aeruginosa

(2015) Natalia V. Kirienko et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessment of planctomycetes cell viability after pollutants exposure

(2014) Carlos Flores et al.   ANTONIE VAN LEEUWENHOEK INTERNATIONAL JOURNAL OF GENERAL AND MOLECULAR MICROBIOLOGY

Improved annotation of antibiotic resistance determinants reveals microbial resistomes cluster by ecology

(2014) Molly K Gibson et al.   ISME Journal

Elevated nitrate enriches microbial functional genes for potential bioremediation of complexly contaminated sediments

(2014) Meiying Xu et al.   ISME Journal

Using the class 1 integron-integrase gene as a proxy for anthropogenic pollution

(2014) Michael R Gillings et al.   ISME Journal

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

The microbial nitrogen cycling potential is impacted by polyaromatic hydrocarbon pollution of marine sediments

(2014) Nicole M. Scott et al.   Frontiers in Microbiology

The Comprehensive Antibiotic Resistance Database

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

Transcriptional Response of the Archaeal Ammonia Oxidizer Nitrosopumilus maritimus to Low and Environmentally Relevant Ammonia Concentrations

(2013) Tatsunori Nakagawa et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Metagenomic Profiles of Antibiotic Resistance Genes (ARGs) between Human Impacted Estuary and Deep Ocean Sediments

(2013) Baowei Chen et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

PATRIC, the bacterial bioinformatics database and analysis resource

(2013) Alice R. Wattam 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

Architectural design influences the diversity and structure of the built environment microbiome

(2012) Steven W Kembel et al.   ISME Journal

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Genome Sequence of an Ammonia-Oxidizing Soil Archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1

(2011) B. K. Kim et al.   JOURNAL OF BACTERIOLOGY

Alzheimer's disease - a neurospirochetosis. Analysis of the evidence following Koch's and Hill's criteria

(2011) Judith Miklossy   Journal of Neuroinflammation

Beyond the bacterium: planctomycetes challenge our concepts of microbial structure and function

(2011) John A. Fuerst et al.   NATURE REVIEWS MICROBIOLOGY

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Functionally diverse reef-fish communities ameliorate coral disease

(2009) L. J. Raymundo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity, ecology, and genomics of the Roseobacter clade: a short overview

(2008) Thorsten Brinkhoff et al.   ARCHIVES OF MICROBIOLOGY

The ecology and biotechnology of sulphate-reducing bacteria

(2008) Gerard Muyzer et al.   NATURE REVIEWS MICROBIOLOGY

Shifting Baselines, Local Impacts, and Global Change on Coral Reefs

(2008) Nancy Knowlton et al.   PLOS BIOLOGY

Microbial diversity in polluted harbor sediments I: Bacterial community assessment based on four clone libraries of 16S rDNA

(2007) Wen Zhang et al.   ESTUARINE COASTAL AND SHELF SCIENCE

Microbial diversity in polluted harbor sediments II: Sulfate-reducing bacterial community assessment using terminal restriction fragment length polymorphism and clone library of dsrAB gene

(2007) Wen Zhang et al.   ESTUARINE COASTAL AND SHELF SCIENCE