The Human Microbiome: Our Second Genome

Functional analysis of metagenomes and metatranscriptomes using SEED and KEGG

(2011) Suparna Mitra et al.   BMC BIOINFORMATICS

The Human Microbiome Project in 2011 and Beyond

(2011) Lita M. Proctor   Cell Host & Microbe

Low-Abundance Biofilm Species Orchestrates Inflammatory Periodontal Disease through the Commensal Microbiota and Complement

(2011) George Hajishengallis et al.   Cell Host & Microbe

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

The human gut virome: Inter-individual variation and dynamic response to diet

(2011) S. Minot et al.   GENOME RESEARCH

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

(2011) A. D. Kostic et al.   GENOME RESEARCH

Evidence of a robust resident bacteriophage population revealed through analysis of the human salivary virome

(2011) David T Pride et al.   ISME Journal

The oral metagenome in health and disease

(2011) Pedro Belda-Ferre et al.   ISME Journal

Gut flora metabolism of phosphatidylcholine promotes cardiovascular disease

(2011) Zeneng Wang et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Experimental and analytical tools for studying the human microbiome

(2011) Justin Kuczynski et al.   NATURE REVIEWS GENETICS

Open-Source Genomic Analysis of Shiga-Toxin–ProducingE. coliO104:H4

(2011) Holger Rohde et al.   NEW ENGLAND JOURNAL OF MEDICINE

The Inflammatory Microenvironment in Colorectal Neoplasia

(2011) Mairi H. McLean 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

Predicting a Human Gut Microbiota's Response to Diet in Gnotobiotic Mice

(2011) J. J. Faith et al.   SCIENCE

Drosophila Microbiome Modulates Host Developmental and Metabolic Homeostasis via Insulin Signaling

(2011) S. C. Shin et al.   SCIENCE

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Use of Ichip for High-Throughput In Situ Cultivation of "Uncultivable" Microbial Species

(2010) D. Nichols et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molecular analysis of the diversity of vaginal microbiota associated with bacterial vaginosis

(2010) Xin Z Ling et al.   BMC GENOMICS

Demodex mites: Facts and controversies

(2010) Dirk M. Elston   CLINICS IN DERMATOLOGY

Demodex and skin infection: fact or fiction

(2010) Roderick Hay   CURRENT OPINION IN INFECTIOUS DISEASES

Analysis of streptococcal CRISPRs from human saliva reveals substantial sequence diversity within and between subjects over time

(2010) D. T. Pride et al.   GENOME RESEARCH

AMD biofilms: using model communities to study microbial evolution and ecological complexity in nature

(2010) Vincent J Denef et al.   ISME Journal

Bacterial diversity in the oral cavity of 10 healthy individuals

(2010) Elisabeth M Bik et al.   ISME Journal

Vancomycin-resistant Enterococcus domination of intestinal microbiota is enabled by antibiotic treatment in mice and precedes bloodstream invasion in humans

(2010) Carles Ubeda et al.   JOURNAL OF CLINICAL INVESTIGATION

Quantitation of Major Human Cutaneous Bacterial and Fungal Populations

(2010) Z. Gao et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Viruses in the faecal microbiota of monozygotic twins and their mothers

(2010) Alejandro Reyes et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

TOPSAN: a dynamic web database for structural genomics

(2010) K. Ellrott et al.   NUCLEIC ACIDS RESEARCH

Correlation between Ocular Demodex Infestation and Serum Immunoreactivity to Bacillus Proteins in Patients with Facial Rosacea

(2010) Jianjing Li et al.   OPHTHALMOLOGY

The Effects of Circumcision on the Penis Microbiome

(2010) Lance B. Price et al.   PLoS One

Temporal Variability of Human Vaginal Bacteria and Relationship with Bacterial Vaginosis

(2010) Sujatha Srinivasan et al.   PLoS One

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

Characteristic Male Urine Microbiomes Associate with Asymptomatic Sexually Transmitted Infection

(2010) David E. Nelson et al.   PLoS One

Metagenomic detection of phage-encoded platelet-binding factors in the human oral cavity

(2010) D. Willner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Human oral, gut, and plaque microbiota in patients with atherosclerosis

(2010) O. Koren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Vaginal microbiome of reproductive-age women

(2010) J. Ravel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns

(2010) M. G. Dominguez-Bello et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Syndrome and Altered Gut Microbiota in Mice Lacking Toll-Like Receptor 5

(2010) M. Vijay-Kumar et al.   SCIENCE

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

SNP detection for massively parallel whole-genome resequencing

(2009) R. Li et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

(2009) Shaoguang Wu et al.   NATURE MEDICINE

What are the consequences of the disappearing human microbiota?

(2009) Martin J. Blaser et al.   NATURE REVIEWS MICROBIOLOGY

Whole Genome Amplification and De novo Assembly of Single Bacterial Cells

(2009) Sébastien Rodrigue et al.   PLoS One

Pharmacometabonomic identification of a significant host-microbiome metabolic interaction affecting human drug metabolism

(2009) T. A. Clayton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Bacterial Community Variation in Human Body Habitats Across Space and Time

(2009) E. K. Costello et al.   SCIENCE

Functional Characterization of the Antibiotic Resistance Reservoir in the Human Microflora

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

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology

Diversity of Human Vaginal Bacterial Communities and Associations with Clinically Defined Bacterial Vaginosis

(2008) B. B. Oakley et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Analysis of Malassezia microbiota in healthy superficial human skin and in psoriatic lesions by multiplex real-time PCR

(2008) Luciana C. Paulino et al.   FEMS YEAST RESEARCH

A diversity profile of the human skin microbiota

(2008) E. A. Grice et al.   GENOME RESEARCH

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Innate immunity and intestinal microbiota in the development of Type 1 diabetes

(2008) Li Wen et al.   NATURE

The influence of sex, handedness, and washing on the diversity of hand surface bacteria

(2008) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial Protection of Beetle-Fungus Mutualism

(2008) J. J. Scott et al.   SCIENCE

Bacteria Subsisting on Antibiotics

(2008) G. Dantas et al.   SCIENCE

Innate Immune Homeostasis by the Homeobox Gene Caudal and Commensal-Gut Mutualism in Drosophila

(2008) J.-H. Ryu et al.   SCIENCE

The Pervasive Effects of an Antibiotic on the Human Gut Microbiota, as Revealed by Deep 16S rRNA Sequencing

(2008) Les Dethlefsen et al.   PLOS BIOLOGY