The human gut microbiome and its dysfunctions through the meta-omics prism

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

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

Gut microbiota richness promotes its stability upon increased dietary fibre intake in healthy adults

(2015) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

Food, Immunity, and the Microbiome

(2015) Herbert Tilg et al.   GASTROENTEROLOGY

A decade of metaproteomics: Where we stand and what the future holds

(2015) Paul Wilmes et al.   PROTEOMICS

Colonic metaproteomic signatures of active bacteria and the host in obesity

(2015) Carolin A. Kolmeder et al.   PROTEOMICS

Metaproteomics reveals functional shifts in microbial and human proteins during a preterm infant gut colonization case

(2015) Jacque C. Young et al.   PROTEOMICS

Anticancer immunotherapy by CTLA-4 blockade relies on the gut microbiota

(2015) M. Vetizou et al.   SCIENCE

Human Genetics Shape the Gut Microbiome

(2014) Julia K. Goodrich et al.   CELL

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

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

Bacterial protein signals are associated with Crohn’s disease

(2014) Catherine Juste et al.   GUT

Metabonomics of human fecal extracts characterize ulcerative colitis, Crohn’s disease and healthy individuals

(2014) Jacob Tveiten Bjerrum et al.   Metabolomics

A Robust and Adaptable High Throughput Screening Method to Study Host-Microbiota Interactions in the Human Intestine

(2014) Tomas de Wouters et al.   PLoS One

Relating the metatranscriptome and metagenome of the human gut

(2014) E. A. Franzosa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets

(2013) Milkha M Leimena et al.   BMC GENOMICS

High-fat diet alters gut microbiota physiology in mice

(2013) Hannelore Daniel et al.   ISME Journal

Microbiological Survey of the Human Gastric Ecosystem Using Culturing and Pyrosequencing Methods

(2013) Susana Delgado et al.   MICROBIAL ECOLOGY

Computational meta'omics for microbial community studies

(2013) N. Segata et al.   Molecular Systems Biology

Richness of human gut microbiome correlates with metabolic markers

(2013) Emmanuelle Le Chatelier et al.   NATURE

Dietary intervention impact on gut microbial gene richness

(2013) Aurélie Cotillard et al.   NATURE

Functional Metagenomics Reveals Novel Pathways of Prebiotic Breakdown by Human Gut Bacteria

(2013) Davide A. Cecchini et al.   PLoS One

From meta-omics to causality: experimental models for human microbiome research

(2013) Joëlle V Fritz et al.   Microbiome

A metagenomic insight into our gut's microbiome

(2012) Patricia Lepage et al.   GUT

Early-life gut microbiota under physiological and pathological conditions: The central role of combined meta-omics-based approaches

(2012) Federica Del Chierico et al.   Journal of Proteomics

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

(2012) Junjie Qin et al.   NATURE

Categorization of the gut microbiota: enterotypes or gradients?

(2012) Ian B. Jeffery et al.   NATURE REVIEWS MICROBIOLOGY

Microbial interactions: from networks to models

(2012) Karoline Faust et al.   NATURE REVIEWS MICROBIOLOGY

Comparative Metaproteomics and Diversity Analysis of Human Intestinal Microbiota Testifies for Its Temporal Stability and Expression of Core Functions

(2012) Carolin A. Kolmeder et al.   PLoS One

Host-Gut Microbiota Metabolic Interactions

(2012) J. K. Nicholson et al.   SCIENCE

Energy-balance studies reveal associations between gut microbes, caloric load, and nutrient absorption in humans

(2011) Reiner Jumpertz et al.   AMERICAN JOURNAL OF CLINICAL NUTRITION

Landscape of Next-Generation Sequencing Technologies

(2011) Thomas P. Niedringhaus et al.   ANALYTICAL CHEMISTRY

Role of the microbiota in inflammatory bowel diseases

(2011) Nabeetha A. Nagalingam et al.   INFLAMMATORY BOWEL DISEASES

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic systems biology of the human gut microbiome reveals topological shifts associated with obesity and inflammatory bowel disease

(2011) S. Greenblum et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

Functional Metagenomic Investigations of the Human Intestinal Microbiota

(2011) Aimee M. Moore et al.   Frontiers in Microbiology

The Human Gut Microbiome: Ecology and Recent Evolutionary Changes

(2010) Jens Walter et al.   Annual Review of Microbiology

Metatranscriptome Analysis of the Human Fecal Microbiota Reveals Subject-Specific Expression Profiles, with Genes Encoding Proteins Involved in Carbohydrate Metabolism Being Dominantly Expressed

(2010) C. C. G. M. Booijink et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The human intestinal microbiota

(2010) J. Doré et al.   GASTROENTEROLOGIE CLINIQUE ET BIOLOGIQUE

Functional metagenomics to mine the human gut microbiome for dietary fiber catabolic enzymes

(2010) L. Tasse et al.   GENOME RESEARCH

Gut microbiome-derived metabolites characterize a peculiar obese urinary metabotype

(2010) R Calvani et al.   INTERNATIONAL JOURNAL OF OBESITY

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Abundant Oligonucleotides Common to Most Bacteria

(2010) Colin F. Davenport et al.   PLoS One

Correction: Functional Metagenomics: A High Throughput Screening Method to Decipher Microbiota-Driven NF-κB Modulation in the Human Gut

(2010) Omar Lakhdari et al.   PLoS One

A metagenomic  -glucuronidase uncovers a core adaptive function of the human intestinal microbiome

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

Towards the human intestinal microbiota phylogenetic core

(2009) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

Gut microbiota: Changes throughout the lifespan from infancy to elderly

(2009) Paul W. O'Toole et al.   INTERNATIONAL DAIRY JOURNAL

Molecular characterization of the stomach microbiota in patients with gastric cancer and in controls

(2009) J. Dicksved et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Microbiota and SCFA in Lean and Overweight Healthy Subjects

(2009) Andreas Schwiertz et al.   Obesity

Metabolomics Reveals Metabolic Biomarkers of Crohn's Disease

(2009) Janet Jansson et al.   PLoS One

Human gut microbiota in obesity and after gastric bypass

(2009) H. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High-throughput diversity and functionality analysis of the gastrointestinal tract microbiota

(2008) E G Zoetendal et al.   GUT

Human colonic microbiota associated with diet, obesity and weight loss

(2008) S H Duncan et al.   INTERNATIONAL JOURNAL OF OBESITY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Human metabolic phenotype diversity and its association with diet and blood pressure

(2008) Elaine Holmes et al.   NATURE

Microbial community gene expression in ocean surface waters

(2008) J. Frias-Lopez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA