Metagenomic analysis reveals the microbiome and resistome in migratory birds

Identification and reconstruction of novel antibiotic resistance genes from metagenomes

(2019) Fanny Berglund et al.   Microbiome

From “A”IV to “Z”IKV: Attacks from Emerging and Re-emerging Pathogens

(2018) George F. Gao   CELL

Structural and functional insights into MCR-2 mediated colistin resistance

(2018) Xudong Wang et al.   Science China-Life Sciences

CASCIRE surveillance network and work on avian influenza viruses

(2017) Yuhai Bi et al.   Science China-Life Sciences

Continental-scale pollution of estuaries with antibiotic resistance genes

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

Occurrence of the Plasmid-Bornemcr-1Colistin Resistance Gene in Extended-Spectrum-β-Lactamase-Producing Enterobacteriaceae in River Water and Imported Vegetable Samples in Switzerland

(2016) Katrin Zurfuh et al.   ANTIMICROBIAL AGENTS AND CHEMOTHERAPY

MOCAT2: a metagenomic assembly, annotation and profiling framework

(2016) Jens Roat Kultima et al.   BIOINFORMATICS

Phages rarely encode antibiotic resistance genes: a cautionary tale for virome analyses

(2016) François Enault et al.   ISME Journal

Detection of themcr-1gene inEscherichia coliprevalent in the migratory bird speciesLarus argentatus

(2016) Modestas Ruzauskas et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

The colistin resistancemcr-1gene is going wild: Table 1.

(2016) Apostolos Liakopoulos et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

Dissemination of the mcr-1 colistin resistance gene

(2016) Yongfei Hu et al.   LANCET INFECTIOUS DISEASES

Emergence of the mcr-1 colistin resistance gene in carbapenem-resistant Enterobacteriaceae

(2016) Hong Du et al.   LANCET INFECTIOUS DISEASES

Dissemination of the mcr-1 colistin resistance gene

(2016) Michael R Mulvey et al.   LANCET INFECTIOUS DISEASES

Emergence of plasmid-mediated colistin resistance mechanism MCR-1 in animals and human beings in China: a microbiological and molecular biological study

(2016) Yi-Yun Liu et al.   LANCET INFECTIOUS DISEASES

CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database

(2016) Baofeng Jia et al.   NUCLEIC ACIDS RESEARCH

CpxR Activates MexAB-OprM Efflux Pump Expression and Enhances Antibiotic Resistance in Both Laboratory and Clinical nalB-Type Isolates of Pseudomonas aeruginosa

(2016) Zhe-Xian Tian et al.   PLoS Pathogens

A reference gene catalogue of the pig gut microbiome

(2016) Liang Xiao et al.   Nature Microbiology

Profile and Fate of Bacterial Pathogens in Sewage Treatment Plants Revealed by High-Throughput Metagenomic Approach

(2015) Bing Li et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Comprehensive Evaluation of Antibiotics Emission and Fate in the River Basins of China: Source Analysis, Multimedia Modeling, and Linkage to Bacterial Resistance

(2015) Qian-Qian Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Diet is the primary determinant of bacterial community structure in the guts of higher termites

(2015) Aram Mikaelyan et al.   MOLECULAR ECOLOGY

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

(2015) Duy Tin Truong et al.   NATURE METHODS

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Something old, something new: revisiting natural products in antibiotic drug discovery

(2014) Gerard D. Wright   CANADIAN JOURNAL OF MICROBIOLOGY

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

(2014) Molly K Gibson et al.   ISME Journal

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Influenza and the Live Poultry Trade

(2014) G. F. Gao   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Comparative genomics reveals insights into avian genome evolution and adaptation

(2014) G. Zhang et al.   SCIENCE

Antibiotic resistance in wild birds

(2014) Jonas Bonnedahl et al.   UPSALA JOURNAL OF MEDICAL SCIENCES

The microbiome of New World vultures

(2014) Michael Roggenbuck et al.   Nature Communications

Characterizing the avian gut microbiota: membership, driving influences, and potential function

(2014) David W. Waite et al.   Frontiers in Microbiology

Antibiotic resistance: The last resort

(2013) Maryn McKenna   NATURE

Data, information, knowledge and principle: back to metabolism in KEGG

(2013) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Metagenome-wide analysis of antibiotic resistance genes in a large cohort of human gut microbiota

(2013) Yongfei Hu et al.   Nature Communications

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Multiplex PCR for detection of acquired carbapenemase genes

(2011) Laurent Poirel et al.   DIAGNOSTIC MICROBIOLOGY AND INFECTIOUS DISEASE

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

(2011) Chris S. Smillie et al.   NATURE

Diet Drives Convergence in Gut Microbiome Functions Across Mammalian Phylogeny and Within Humans

(2011) B. D. Muegge et al.   SCIENCE

Call of the wild: antibiotic resistance genes in natural environments

(2010) Heather K. Allen et al.   NATURE REVIEWS MICROBIOLOGY

Ab initio gene identification in metagenomic sequences

(2010) Wenhan Zhu et al.   NUCLEIC ACIDS RESEARCH

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors

(2010) A. K. Benson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

Importance of Glycans to the Host-Bacteroides Mutualism in the Mammalian Intestine

(2009) Laurie E. Comstock   Cell Host & Microbe

Towards the human intestinal microbiota phylogenetic core

(2009) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

CRP Regulator Modulates Multidrug Resistance of Escherichia coli by Repressing the mdtEF Multidrug Efflux Genes

(2009) Kunihiko Nishino et al.   JOURNAL OF ANTIBIOTICS

Bioactive substances produced by marine isolates of Pseudomonas

(2009) Alim Isnansetyo et al.   JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY

Antibiotic-Resistant Bugs in the 21st Century — A Clinical Super-Challenge

(2009) Cesar A. Arias et al.   NEW ENGLAND JOURNAL OF MEDICINE

Dissemination of Escherichia coli with CTX-M Type ESBL between Humans and Yellow-Legged Gulls in the South of France

(2009) Jonas Bonnedahl et al.   PLoS One

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

(2009) M. O. A. Sommer et al.   SCIENCE

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

(2008) Harry J. Flint et al.   NATURE REVIEWS MICROBIOLOGY

Evolution of Mammals and Their Gut Microbes

(2008) R. E. Ley et al.   SCIENCE