Metagenomics for pathogen detection in public health

Implications of the Human Microbiome Project for Epidemiology

(2013) Betsy Foxman et al.   AMERICAN JOURNAL OF EPIDEMIOLOGY

Widespread Colonization of the Lung byTropheryma whippleiin HIV Infection

(2013) Catherine Lozupone et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Comparative metagenomic and rRNA microbial diversity characterization using archaeal and bacterial synthetic communities

(2013) Migun Shakya et al.   ENVIRONMENTAL MICROBIOLOGY

The proof of concept that culturomics can be superior to metagenomics to study atypical stool samples

(2013) G. Dubourg et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Genome of the pathogen Porphyromonas gingivalis recovered from a biofilm in a hospital sink using a high-throughput single-cell genomics platform

(2013) J. S. McLean et al.   GENOME RESEARCH

Whole-genome sequences of Chlamydia trachomatis directly from clinical samples without culture

(2013) H. M. B. Seth-Smith et al.   GENOME RESEARCH

A Culture-Independent Sequence-Based Metagenomics Approach to the Investigation of an Outbreak of Shiga-Toxigenic Escherichia coli O104:H4

(2013) Nicholas J. Loman et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Metagenomics, Infectious Disease Diagnostics, and Outbreak Investigations

(2013) David A. Relman   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

A gut prediction

(2013) Willem M. de Vos et al.   NATURE

Gut metagenome in European women with normal, impaired and diabetic glucose control

(2013) Fredrik H. Karlsson et al.   NATURE

Metagenomic Analysis of Tuberculosis in a Mummy

(2013) Jacqueline Z.-M. Chan et al.   NEW ENGLAND JOURNAL OF MEDICINE

Human Infection with a Novel Avian-Origin Influenza A (H7N9) Virus

(2013) Rongbao Gao et al.   NEW ENGLAND JOURNAL OF MEDICINE

Identification of a Novel Human Papillomavirus by Metagenomic Analysis of Samples from Patients with Febrile Respiratory Illness

(2013) John L. Mokili et al.   PLoS One

The Genome Sequence of Lone Star Virus, a Highly Divergent Bunyavirus Found in the Amblyomma americanum Tick

(2013) Andrea Swei et al.   PLoS One

Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum

(2013) J. S. McLean et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hybrid DNA virus in Chinese patients with seronegative hepatitis discovered by deep sequencing

(2013) B. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metagenomic identification of viral pathogens

(2013) Kyle Bibby   TRENDS IN BIOTECHNOLOGY

The emerging world of the fungal microbiome

(2013) Gary B. Huffnagle et al.   TRENDS IN MICROBIOLOGY

Metagenomic sequencing of “HPV-negative” condylomas detects novel putative HPV types

(2013) Hanna Johansson et al.   VIROLOGY

Detection of African swine fever virus-like sequences in ponds in the Mississippi Delta through metagenomic sequencing

(2013) Xiu-Feng Wan et al.   VIRUS GENES

Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem

(2012) Sunil Kumar Sirohi et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Metagenomics: microbial diversity through a scratched lens

(2012) Ben Temperton et al.   CURRENT OPINION IN MICROBIOLOGY

A framework for human microbiome research

(2012)   NATURE

A metagenome-wide association study of gut microbiota in type 2 diabetes

(2012) Junjie Qin et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

(2012) Nicholas J. Loman et al.   NATURE REVIEWS MICROBIOLOGY

The keystone-pathogen hypothesis

(2012) George Hajishengallis et al.   NATURE REVIEWS MICROBIOLOGY

The changing face of pathogen discovery and surveillance

(2012) W. Ian Lipkin   NATURE REVIEWS MICROBIOLOGY

Isolation of a Novel Coronavirus from a Man with Pneumonia in Saudi Arabia

(2012) Ali M. Zaki et al.   NEW ENGLAND JOURNAL OF MEDICINE

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

Resolution and Characterization of Distinct cpn60-Based Subgroups of Gardnerella vaginalis in the Vaginal Microbiota

(2012) Teenus Paramel Jayaprakash et al.   PLoS One

The Chaperonin-60 Universal Target Is a Barcode for Bacteria That Enables De Novo Assembly of Metagenomic Sequence Data

(2012) Matthew G. Links et al.   PLoS One

Insights from Characterizing Extinct Human Gut Microbiomes

(2012) Raul Y. Tito et al.   PLoS One

Interactions Between Commensal Fungi and the C-Type Lectin Receptor Dectin-1 Influence Colitis

(2012) I. D. Iliev et al.   SCIENCE

Microbiota-Targeted Therapies: An Ecological Perspective

(2012) K. P. Lemon et al.   Science Translational Medicine

Metagenomics and future perspectives in virus discovery

(2012) John L Mokili et al.   Current Opinion in Virology

Bioinformatics for the Human Microbiome Project

(2012) Dirk Gevers et al.   PLoS Computational Biology

Microbial Co-occurrence Relationships in the Human Microbiome

(2012) Karoline Faust et al.   PLoS Computational Biology

Routine Use of Microbial Whole Genome Sequencing in Diagnostic and Public Health Microbiology

(2012) Claudio U. Köser et al.   PLoS Pathogens

A Novel Rhabdovirus Associated with Acute Hemorrhagic Fever in Central Africa

(2012) Gilda Grard et al.   PLoS Pathogens

Systematic Review of Intestinal Microbiota Transplantation (Fecal Bacteriotherapy) for Recurrent Clostridium difficile Infection

(2011) Ethan Gough et al.   CLINICAL INFECTIOUS DISEASES

Insights into antibiotic resistance through metagenomic approaches

(2011) Robert Schmieder et al.   Future Microbiology

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

Diagnostic Strategy Used To Establish Etiologies of Encephalitis in a Prospective Cohort of Patients in England

(2011) H. E. Ambrose et al.   JOURNAL OF CLINICAL MICROBIOLOGY

A draft genome of Yersinia pestis from victims of the Black Death

(2011) Kirsten I. Bos et al.   NATURE

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Stalking the Fourth Domain in Metagenomic Data: Searching for, Discovering, and Interpreting Novel, Deep Branches in Marker Gene Phylogenetic Trees

(2011) Dongying Wu et al.   PLoS One

The Sensitivity of Massively Parallel Sequencing for Detecting Candidate Infectious Agents Associated with Human Tissue

(2011) Richard A. Moore et al.   PLoS One

DNA Extraction Columns Contaminated with Murine Sequences

(2011) Otto Erlwein et al.   PLoS One

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Exploring the viral world through metagenomics

(2011) Karyna Rosario et al.   Current Opinion in Virology

Are diagnostic and public health bacteriology ready to become branches of genomic medicine?

(2011) Mark J Pallen et al.   Genome Medicine

The Fecal Viral Flora of Wild Rodents

(2011) Tung G. Phan et al.   PLoS Pathogens

Metagenomic Analysis of Fever, Thrombocytopenia and Leukopenia Syndrome (FTLS) in Henan Province, China: Discovery of a New Bunyavirus

(2011) Bianli Xu et al.   PLoS Pathogens

Role of hospital surfaces in the transmission of emerging health care-associated pathogens: Norovirus, Clostridium difficile, and Acinetobacter species

(2010) David J. Weber et al.   AMERICAN JOURNAL OF INFECTION CONTROL

A survey of sequence alignment algorithms for next-generation sequencing

(2010) H. Li et al.   BRIEFINGS IN BIOINFORMATICS

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

Metagenomic sequencing for virus identification in a public-health setting

(2010) S. Svraka et al.   JOURNAL OF GENERAL VIROLOGY

Assessment of protozoa in Yunnan Yellow Cattle rumen based on the 18S rRNA sequences

(2010) J. Leng et al.   MOLECULAR BIOLOGY REPORTS

Reference-Free Validation of Short Read Data

(2010) Jan Schröder et al.   PLoS One

A Metagenomic Analysis of Pandemic Influenza A (2009 H1N1) Infection in Patients from North America

(2010) Alexander L. Greninger et al.   PLoS One

Pyrosequencing of the Chaperonin-60 Universal Target as a Tool for Determining Microbial Community Composition

(2009) J. Schellenberg et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

Comparison of Automated Microarray Detection with Real-Time PCR Assays for Detection of Respiratory Viruses in Specimens Obtained from Children

(2009) F. Raymond et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Multiplex PCR tests sentinel the appearance of pandemic influenza viruses including H1N1 swine influenza

(2009) James B. Mahony et al.   JOURNAL OF CLINICAL VIROLOGY

Laboratory procedures to generate viral metagenomes

(2009) Rebecca V Thurber et al.   Nature Protocols

Discovery of a Novel Single-Stranded DNA Virus from a Sea Turtle Fibropapilloma by Using Viral Metagenomics

(2008) T. F. F. Ng et al.   JOURNAL OF VIROLOGY

Global trends in emerging infectious diseases

(2008) Kate E. Jones et al.   NATURE

Metagenomic Analysis of Human Diarrhea: Viral Detection and Discovery

(2008) Stacy R. Finkbeiner et al.   PLoS Pathogens