Microbiome-wide association studies link dynamic microbial consortia to disease

RecurrentClostridium difficileinfection associates with distinct bile acid and microbiome profiles

(2016) J. R. Allegretti et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Gut Microbial Metabolite TMAO Enhances Platelet Hyperreactivity and Thrombosis Risk

(2016) Weifei Zhu et al.   CELL

Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer

(2016) Maria G Dominguez-Bello et al.   NATURE MEDICINE

Tools for the Microbiome: Nano and Beyond

(2015) Julie S. Biteen et al.   ACS Nano

A genome-wide systems analysis reveals strong link between colorectal cancer and trimethylamine N-oxide (TMAO), a gut microbial metabolite of dietary meat and fat

(2015) Rong Xu et al.   BMC GENOMICS

Collecting Fecal Samples for Microbiome Analyses in Epidemiology Studies

(2015) R. Sinha et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

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

Prediction of Early Childhood Caries via Spatial-Temporal Variations of Oral Microbiota

(2015) Fei Teng 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

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Microbial, host and xenobiotic diversity in the cystic fibrosis sputum metabolome

(2015) Robert A Quinn et al.   ISME Journal

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

(2015) Kristoffer Forslund et al.   NATURE

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

(2015) Xuan Zhang et al.   NATURE MEDICINE

Feeding the brain and nurturing the mind: Linking nutrition and the gut microbiota to brain development

(2015) Manu S. Goyal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illuminating the dark matter in metabolomics: Fig. 1.

(2015) Ricardo R. da Silva et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The human oral metaproteome reveals potential biomarkers for caries disease

(2015) Pedro Belda-Ferre et al.   PROTEOMICS

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples

(2015) T. Korem et al.   SCIENCE

Small molecules from the human microbiota

(2015) M. S. Donia et al.   SCIENCE

Determinants of community structure in the global plankton interactome

(2015) G. Lima-Mendez et al.   SCIENCE

Vitamin B 12 modulates the transcriptome of the skin microbiota in acne pathogenesis

(2015) Dezhi Kang et al.   Science Translational Medicine

Predicting ecosystem emergent properties at multiple scales

(2015) Jack A. Gilbert et al.   Environmental Microbiology Reports

Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities

(2015) Zhanshan (Sam) Ma et al.   Scientific Reports

Proportionality: A Valid Alternative to Correlation for Relative Data

(2015) David Lovell et al.   PLoS Computational Biology

Dysbiosis of Gut Microbiota With Reduced Trimethylamine‐N‐Oxide Level in Patients With Large‐Artery Atherosclerotic Stroke or Transient Ischemic Attack

(2015) Jia Yin et al.   Journal of the American Heart Association

Dynamic changes in short- and long-term bacterial composition following fecal microbiota transplantation for recurrent Clostridium difficile infection

(2015) Alexa Weingarden et al.   Microbiome

Ecological Succession and Viability of Human-Associated Microbiota on Restroom Surfaces

(2014) Sean M. Gibbons et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Insights into Secondary Metabolism from a Global Analysis of Prokaryotic Biosynthetic Gene Clusters

(2014) Peter Cimermancic et al.   CELL

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

A Systematic Analysis of Biosynthetic Gene Clusters in the Human Microbiome Reveals a Common Family of Antibiotics

(2014) Mohamed S. Donia et al.   CELL

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

(2014)   Cell Host & Microbe

The Treatment-Naive Microbiome in New-Onset Crohn’s Disease

(2014) Dirk Gevers et al.   Cell Host & Microbe

Biological significance of short-chain fatty acid metabolism by the intestinal microbiome

(2014) Elena Puertollano et al.   CURRENT OPINION IN CLINICAL NUTRITION AND METABOLIC CARE

Bile acids and the gut microbiome

(2014) Jason M. Ridlon et al.   CURRENT OPINION IN GASTROENTEROLOGY

Prognostic value of choline and betaine depends on intestinal microbiota-generated metabolite trimethylamine-N-oxide

(2014) Z. Wang et al.   EUROPEAN HEART JOURNAL

Meta-analyses of human gut microbes associated with obesity and IBD

(2014) William A. Walters et al.   FEBS LETTERS

Dynamics and Establishment of Clostridium difficile Infection in the Murine Gastrointestinal Tract

(2014) Mark J. Koenigsknecht et al.   INFECTION AND IMMUNITY

Predictive modeling of gingivitis severity and susceptibility via oral microbiota

(2014) Shi Huang et al.   ISME Journal

Gut microbiota are related to Parkinson's disease and clinical phenotype

(2014) Filip Scheperjans et al.   MOVEMENT DISORDERS

Precision microbiome reconstitution restores bile acid mediated resistance to Clostridium difficile

(2014) Charlie G. Buffie et al.   NATURE

Dynamics and associations of microbial community types across the human body

(2014) Tao Ding et al.   NATURE

Correlation between the human fecal microbiota and depression

(2014) A. Naseribafrouei et al.   NEUROGASTROENTEROLOGY AND MOTILITY

Pharmacomicrobiomics: The Impact of Human Microbiome Variations on Systems Pharmacology and Personalized Therapeutics

(2014) Marwa ElRakaiby et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Longitudinal analysis of microbial interaction between humans and the indoor environment

(2014) S. Lax et al.   SCIENCE

Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity

(2014) A. Shade et al.   mBio

Understanding and Modulating Mammalian-Microbial Communication for Improved Human Health

(2013) Sridhar Mani et al.   Annual Review of Pharmacology and Toxicology

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

Xenobiotics Shape the Physiology and Gene Expression of the Active Human Gut Microbiome

(2013) Corinne Ferrier Maurice et al.   CELL

Genetic Control of Obesity and Gut Microbiota Composition in Response to High-Fat, High-Sucrose Diet in Mice

(2013) Brian W. Parks et al.   Cell Metabolism

Cometabolism of Microbes and Host: Implications for Drug Metabolism and Drug-Induced Toxicity

(2013) H Li et al.   CLINICAL PHARMACOLOGY & THERAPEUTICS

Exploring host-microbiota interactions in animal models and humans

(2013) A. D. Kostic et al.   GENES & DEVELOPMENT

Meta-analyses of studies of the human microbiota

(2013) C. A. Lozupone et al.   GENOME RESEARCH

Anal gas evacuation and colonic microbiota in patients with flatulence: effect of diet

(2013) Chaysavanh Manichanh et al.   GUT

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

(2013) Morgan G I Langille et al.   NATURE BIOTECHNOLOGY

Intestinal microbiota metabolism of l-carnitine, a nutrient in red meat, promotes atherosclerosis

(2013) Robert A Koeth et al.   NATURE MEDICINE

Intestinal Microbial Metabolism of Phosphatidylcholine and Cardiovascular Risk

(2013) W.H. Wilson Tang et al.   NEW ENGLAND JOURNAL OF MEDICINE

Reduced Incidence of Prevotella and Other Fermenters in Intestinal Microflora of Autistic Children

(2013) Dae-Wook Kang et al.   PLoS One

Bacteriophage adhering to mucus provide a non-host-derived immunity

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

Predicting and Manipulating Cardiac Drug Inactivation by the Human Gut Bacterium Eggerthella lenta

(2013) H. J. Haiser et al.   SCIENCE

Gut Microbiota from Twins Discordant for Obesity Modulate Metabolism in Mice

(2013) V. K. Ridaura et al.   SCIENCE

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

(2013) A. Murat Eren et al.   Methods in Ecology and Evolution

Expansion of intestinal Prevotella copri correlates with enhanced susceptibility to arthritis

(2013) Jose U Scher et al.   eLife

EMPeror: a tool for visualizing high-throughput microbial community data

(2013) Yoshiki Vázquez-Baeza et al.   GigaScience

Periodontal disease and the oral microbiota in new-onset rheumatoid arthritis

(2012) Jose U. Scher et al.   ARTHRITIS AND RHEUMATISM

Host Remodeling of the Gut Microbiome and Metabolic Changes during Pregnancy

(2012) Omry Koren et al.   CELL

Fecal Microbiota Composition Differs Between Children With  -Cell Autoimmunity and Those Without

(2012) M. C. de Goffau et al.   DIABETES

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Integrated Metagenomics/Metaproteomics Reveals Human Host-Microbiota Signatures of Crohn's Disease

(2012) Alison R. Erickson et al.   PLoS One

Modeling an autism risk factor in mice leads to permanent immune dysregulation

(2012) E. Y. Hsiao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

(2012) J. C. Arthur et al.   SCIENCE

Inferring Correlation Networks from Genomic Survey Data

(2012) Jonathan Friedman et al.   PLoS Computational Biology

Human-Associated Microbial Signatures: Examining Their Predictive Value

(2011) Dan Knights et al.   Cell Host & Microbe

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

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

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Bayesian community-wide culture-independent microbial source tracking

(2011) Dan Knights et al.   NATURE METHODS

Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project

(2011) Jack A. Gilbert et al.   Standards in Genomic Sciences

A Pyrosequencing Study in Twins Shows That Gastrointestinal Microbial Profiles Vary With Inflammatory Bowel Disease Phenotypes

(2010) Ben P. Willing et al.   GASTROENTEROLOGY

Toward defining the autoimmune microbiome for type 1 diabetes

(2010) Adriana Giongo et al.   ISME Journal

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Microbial community resemblance methods differ in their ability to detect biologically relevant patterns

(2010) Justin Kuczynski et al.   NATURE METHODS

Forensic identification using skin bacterial communities

(2010) N. Fierer 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

Succession of microbial consortia in the developing infant gut microbiome

(2010) J. E. Koenig 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

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

(2010) B. D. Wallace et al.   SCIENCE

Genetic Structure and Distribution of the Colibactin Genomic Island among Members of the Family Enterobacteriaceae

(2009) J. Putze et al.   INFECTION AND IMMUNITY

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

Metabolomics analysis reveals large effects of gut microflora on mammalian blood metabolites

(2009) W. R. Wikoff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Drugs, bugs, and personalized medicine: Pharmacometabonomics enters the ring

(2009) I. D. Wilson   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Accurate taxonomy assignments from 16S rRNA sequences produced by highly parallel pyrosequencers

(2008) Z. Liu et al.   NUCLEIC ACIDS RESEARCH

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