The healthy human microbiome

Sialylated Milk Oligosaccharides Promote Microbiota-Dependent Growth in Models of Infant Undernutrition

(2016) Mark R. Charbonneau et al.   CELL

Diet-induced extinctions in the gut microbiota compound over generations

(2016) Erica D. Sonnenburg et al.   NATURE

Personalized Nutrition by Prediction of Glycemic Responses

(2015) David Zeevi et al.   CELL

Dynamics and Stabilization of the Human Gut Microbiome during the First Year of Life

(2015) Fredrik Bäckhed et al.   Cell Host & Microbe

Diet Dominates Host Genotype in Shaping the Murine Gut Microbiota

(2015) Rachel N. Carmody et al.   Cell Host & Microbe

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Using comparative genomics to drive new discoveries in microbiology

(2015) Daniel H Haft   CURRENT OPINION IN MICROBIOLOGY

Low prevalence of Blastocystis sp. in active ulcerative colitis patients

(2015) N. G. Rossen et al.   EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES

Cervicovaginal Bacteria Are a Major Modulator of Host Inflammatory Responses in the Female Genital Tract

(2015) Melis N. Anahtar et al.   IMMUNITY

The role of short chain fatty acids in appetite regulation and energy homeostasis

(2015) C S Byrne et al.   INTERNATIONAL JOURNAL OF OBESITY

A phylo-functional core of gut microbiota in healthy young Chinese cohorts across lifestyles, geography and ethnicities

(2015) Jiachao Zhang et al.   ISME Journal

Helminths and the microbiota: parts of the hygiene hypothesis

(2015) P. Loke et al.   PARASITE IMMUNOLOGY

Identifying personal microbiomes using metagenomic codes

(2015) Eric A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Temporal and spatial variation of the human microbiota during pregnancy

(2015) Daniel B. DiGiulio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Microbiomes in light of traits: A phylogenetic perspective

(2015) J. B. H. Martiny et al.   SCIENCE

Cancer and the microbiota

(2015) W. S. Garrett   SCIENCE

Cervical intraepithelial neoplasia disease progression is associated with increased vaginal microbiome diversity

(2015) A. Mitra et al.   Scientific Reports

Are Human Intestinal Eukaryotes Beneficial or Commensals?

(2015) Julius Lukeš et al.   PLoS Pathogens

Chemostat culture systems support diverse bacteriophage communities from human feces

(2015) Tasha M. Santiago-Rodriguez et al.   Microbiome

The microbiome of uncontacted Amerindians

(2015) J. C. Clemente et al.   Science Advances

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Conducting a Microbiome Study

(2014) Julia K. Goodrich et al.   CELL

The Virome in Mammalian Physiology and Disease

(2014) Herbert W. Virgin   CELL

The Integrative Human Microbiome Project: Dynamic Analysis of Microbiome-Host Omics Profiles during Periods of Human Health and Disease

(2014)   Cell Host & Microbe

Determining Microbial Products and Identifying Molecular Targets in the Human Microbiome

(2014) Regina Joice et al.   Cell Metabolism

Defining dysbiosis and its influence on host immunity and disease

(2014) Charisse Petersen et al.   CELLULAR MICROBIOLOGY

The microbial eukaryoteBlastocystisis a prevalent and diverse member of the healthy human gut microbiota

(2014) Pauline D. Scanlan et al.   FEMS MICROBIOLOGY ECOLOGY

Kingdom-Agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

(2014) Jason M. Norman et al.   GASTROENTEROLOGY

Inflammatory Bowel Disease as a Model for Translating the Microbiome

(2014) Curtis Huttenhower et al.   IMMUNITY

Which is more important for classifying microbial communities: who’s there or what they can do?

(2014) Zhenjiang Xu et al.   ISME Journal

Differences in vaginal microbiome in African American women versus women of European ancestry

(2014) Jennifer M. Fettweis et al.   MICROBIOLOGY-SGM

An integrated catalog of reference genes in the human gut microbiome

(2014) Junhua Li et al.   NATURE BIOTECHNOLOGY

Gut microbiota metabolism of dietary fiber influences allergic airway disease and hematopoiesis

(2014) Aurélien Trompette et al.   NATURE MEDICINE

The microbial metabolite butyrate regulates intestinal macrophage function via histone deacetylase inhibition

(2014) Pamela V. Chang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comment on "The placenta harbors a unique microbiome"

(2014) H. J. Kliman   Science Translational Medicine

Functional and phylogenetic assembly of microbial communities in the human microbiome

(2014) Afrah Shafquat et al.   TRENDS IN MICROBIOLOGY

Gut microbiome of the Hadza hunter-gatherers

(2014) Stephanie L. Schnorr et al.   Nature Communications

Distinct composition of the oral indigenous microbiota in South Korean and Japanese adults

(2014) Toru Takeshita et al.   Scientific Reports

Communities of microbial eukaryotes in the mammalian gut within the context of environmental eukaryotic diversity

(2014) Laura Wegener Parfrey et al.   Frontiers in Microbiology

Comparison of the Respiratory Microbiome in Healthy Nonsmokers and Smokers

(2013) Alison Morris et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Metagenome and metabolism: the tissue microbiota hypothesis

(2013) Rémy Burcelin et al.   DIABETES OBESITY & METABOLISM

Lactobacillus crispatus modulates epithelial cell defense against Candida albicans through Toll-like receptors 2 and 4, interleukin 8 and human β-defensins 2 and 3

(2013) Antonietta Rizzo et al.   IMMUNOLOGY LETTERS

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Diet rapidly and reproducibly alters the human gut microbiome

(2013) Lawrence A. David et al.   NATURE

Topographic diversity of fungal and bacterial communities in human skin

(2013) Keisha Findley et al.   NATURE

Treg induction by a rationally selected mixture of Clostridia strains from the human microbiota

(2013) Koji Atarashi et al.   NATURE

Rapid evolution of the human gut virome

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

The Microbial Metabolites, Short-Chain Fatty Acids, Regulate Colonic Treg Cell Homeostasis

(2013) P. M. Smith et al.   SCIENCE

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

The emerging world of the fungal microbiome

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

Human gut microbiota community structures in urban and rural populations in Russia

(2013) Alexander V. Tyakht et al.   Nature Communications

The microbiome extends to subepidermal compartments of normal skin

(2013) Teruaki Nakatsuji et al.   Nature Communications

Microbiomic Signatures of Psoriasis: Feasibility and Methodology Comparison

(2013) Alexander Statnikov et al.   Scientific Reports

Functional profiling of the gut microbiome in disease-associated inflammation

(2013) Daniela Börnigen et al.   Genome Medicine

The COMBREX Project: Design, Methodology, and Initial Results

(2013) Brian P. Anton et al.   PLOS BIOLOGY

Diagnostic Applications of High-Throughput DNA Sequencing

(2012) Scott D. Boyd   Annual Review of Pathology-Mechanisms of Disease

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

(2012) Fredrik Bäckhed et al.   Cell Host & Microbe

Taking a metagenomic view of human nutrition

(2012) Rachel J. Dutton et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

The Human Microbiome Project strategy for comprehensive sampling of the human microbiome and why it matters

(2012) Kjersti Aagaard et al.   FASEB JOURNAL

Temporal shifts in the skin microbiome associated with disease flares and treatment in children with atopic dermatitis

(2012) H. H. Kong et al.   GENOME RESEARCH

Regulation of intestinal inflammation by microbiota following allogeneic bone marrow transplantation

(2012) Robert R. Jenq et al.   JOURNAL OF EXPERIMENTAL MEDICINE

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

Diversity, stability and resilience of the human gut microbiota

(2012) Catherine A. Lozupone et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Genomic variation landscape of the human gut microbiome

(2012) Siegfried Schloissnig et al.   NATURE

The role of the gut microbiota in nutrition and health

(2012) Harry J. Flint et al.   Nature Reviews Gastroenterology & Hepatology

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

The oral microbiome in health and disease

(2012) William G. Wade   PHARMACOLOGICAL RESEARCH

A Dynamical-Systems View of Stem Cell Biology

(2012) C. Furusawa et al.   SCIENCE

The Application of Ecological Theory Toward an Understanding of the Human Microbiome

(2012) E. K. Costello et al.   SCIENCE

Microbiota-Targeted Therapies: An Ecological Perspective

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

Bovine Milk as a Source of Functional Oligosaccharides for Improving Human Health

(2012) Angela M. Zivkovic et al.   Advances in Nutrition

Metabolic Reconstruction for Metagenomic Data and Its Application to the Human Microbiome

(2012) Sahar Abubucker 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

Antimicrobial and Probiotic Properties of Yeasts: From Fundamental to Novel Applications

(2012) Rima Hatoum et al.   Frontiers in Microbiology

Topographical Continuity of Bacterial Populations in the Healthy Human Respiratory Tract

(2011) Emily S. Charlson et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

Intestinal Bacterial Colonization Induces Mutualistic Regulatory T Cell Responses

(2011) Markus B. Geuking et al.   IMMUNITY

Diversity and quantitative analysis of Archaea in aggressive periodontitis and periodontally healthy subjects

(2011) Flavia Matarazzo et al.   JOURNAL OF CLINICAL PERIODONTOLOGY

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Toll-Like Receptor 2 Pathway Establishes Colonization by a Commensal of the Human Microbiota

(2011) J. L. Round et al.   SCIENCE

Toward Understanding, Managing, and Protecting Microbial Ecosystems

(2011) Paul L. E. Bodelier   Frontiers in Microbiology

G-protein-coupled receptor for short-chain fatty acids suppresses colon cancer

(2010) Yong Tang et al.   INTERNATIONAL JOURNAL OF CANCER

A polysaccharide from the human commensal Bacteroides fragilis protects against CNS demyelinating disease

(2010) J Ochoa-Repáraz et al.   Mucosal Immunology

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

Disordered Microbial Communities in Asthmatic Airways

(2010) Markus Hilty et al.   PLoS One

Human milk glycobiome and its impact on the infant gastrointestinal microbiota

(2010) A. M. Zivkovic 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

Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation

(2010) L. Dethlefsen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa

(2010) C. De Filippo 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

The core gut microbiome, energy balance and obesity

(2009) Peter J. Turnbaugh et al.   JOURNAL OF PHYSIOLOGY-LONDON

What are the consequences of the disappearing human microbiota?

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

Infant Formula Oligosaccharides Opening the Gates (for Speculation): Commentary on the article by Barrat et al. on page 34

(2009) Milady R Ninonuevo et al.   PEDIATRIC RESEARCH

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

The Pangenome Structure of Escherichia coli: Comparative Genomic Analysis of E. coli Commensal and Pathogenic Isolates

(2008) D. A. Rasko et al.   JOURNAL OF BACTERIOLOGY

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Faecalibacterium prausnitzii is an anti-inflammatory commensal bacterium identified by gut microbiota analysis of Crohn disease patients

(2008) H. Sokol et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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