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

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

(2013) Corinne Ferrier Maurice et al.   CELL

Gut Immune Maturation Depends on Colonization with a Host-Specific Microbiota

(2012) Hachung Chung et al.   CELL

A systems biology approach to studying the role of microbes in human health

(2012) Ines Thiele et al.   CURRENT OPINION IN BIOTECHNOLOGY

Probiotic and postbiotic activity in health and disease: comparison on a novel polarised ex-vivo organ culture model

(2012) Katerina Tsilingiri et al.   GUT

Comparative analysis of the distribution of segmented filamentous bacteria in humans, mice and chickens

(2012) Yeshi Yin et al.   ISME Journal

A biomolecular isolation framework for eco-systems biology

(2012) Hugo Roume et al.   ISME Journal

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

(2012) Xiaolei Ze et al.   ISME Journal

Infant B Cell Memory Differentiation and Early Gut Bacterial Colonization

(2012) A.-C. Lundell et al.   JOURNAL OF IMMUNOLOGY

Human gut-on-a-chip inhabited by microbial flora that experiences intestinal peristalsis-like motions and flow

(2012) Hyun Jung Kim et al.   LAB ON A CHIP

Tissue factor and PAR1 promote microbiota-induced intestinal vascular remodelling

(2012) Christoph Reinhardt et al.   NATURE

Functional interactions between the gut microbiota and host metabolism

(2012) Valentina Tremaroli et al.   NATURE

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

The role of the gut microbiota in nutrition and health

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

Commensal Bacteria Modulate Innate Immune Responses of Vaginal Epithelial Cell Multilayer Cultures

(2012) William A. Rose et al.   PLoS One

Microbial Exposure During Early Life Has Persistent Effects on Natural Killer T Cell Function

(2012) T. Olszak et al.   SCIENCE

Human Microbiome in Health and Disease

(2011) Kathryn J. Pflughoeft et al.   Annual Review of Pathology-Mechanisms of Disease

Adherence and Cytokine Induction in Caco-2 Cells by Bacterial Populations from a Three-Stage Continuous-Culture Model of the Large Intestine

(2011) Bahram Bahrami et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

NLRP6 Inflammasome Regulates Colonic Microbial Ecology and Risk for Colitis

(2011) Eran Elinav et al.   CELL

Decreased colonization of fecal Clostridium coccoides/Eubacterium rectale species from ulcerative colitis patients in an in vitro dynamic gut model with mucin environment

(2011) Joan Vermeiren et al.   FEMS MICROBIOLOGY ECOLOGY

Bacterial biofilms associated with food particles in the human large bowel

(2011) Amy S. Van Wey et al.   MOLECULAR NUTRITION & FOOD RESEARCH

Peripheral education of the immune system by colonic commensal microbiota

(2011) Stephanie K. Lathrop et al.   NATURE

Bifidobacteria can protect from enteropathogenic infection through production of acetate

(2011) Shinji Fukuda et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Mucin dynamics and enteric pathogens

(2011) Michael A. McGuckin et al.   NATURE REVIEWS MICROBIOLOGY

Metatranscriptomic Approach to Analyze the Functional Human Gut Microbiota

(2011) María José Gosalbes et al.   PLoS One

Microdroplet-Enabled Highly Parallel Co-Cultivation of Microbial Communities

(2011) Jihyang Park et al.   PLoS One

Advances and perspectives in in vitro human gut fermentation modeling

(2011) Amanda N. Payne et al.   TRENDS IN BIOTECHNOLOGY

From 3D cell culture to organs-on-chips

(2011) Dongeun Huh et al.   TRENDS IN CELL BIOLOGY

Incorporating a mucosal environment in a dynamic gut model results in a more representative colonization by lactobacilli

(2011) Pieter Van den Abbeele et al.   Microbial Biotechnology

Competitive time- and density-dependent adhesion of staphylococci and osteoblasts on crosslinked poly(ethylene glycol)-based polymer coatings in co-culture flow chambers

(2010) Isabel C. Saldarriaga Fernández et al.   BIOMATERIALS

Reshaping the gut microbiome with bacterial transplantation and antibiotic intake

(2010) C. Manichanh et al.   GENOME RESEARCH

Dominant and diet-responsive groups of bacteria within the human colonic microbiota

(2010) Alan W Walker et al.   ISME Journal

COMPANION ANIMALS SYMPOSIUM: Humanized animal models of the microbiome1

(2010) D. B. Gootenberg et al.   JOURNAL OF ANIMAL SCIENCE

Induction of cytokine formation by human intestinal bacteria in gut epithelial cell lines

(2010) B. Bahrami et al.   JOURNAL OF APPLIED MICROBIOLOGY

Perspective: Microfluidic applications in microbiology

(2010) Saleema Saleh-Lakha et al.   JOURNAL OF MICROBIOLOGICAL METHODS

In vitro and in vivo model systems to study microbial biofilm formation

(2010) Tom Coenye et al.   JOURNAL OF MICROBIOLOGICAL METHODS

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Inducible Foxp3+ regulatory T-cell development by a commensal bacterium of the intestinal microbiota

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

Systemic gut microbial modulation of bile acid metabolism in host tissue compartments

(2010) J. R. Swann 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

Reversible Microbial Colonization of Germ-Free Mice Reveals the Dynamics of IgA Immune Responses

(2010) S. Hapfelmeier et al.   SCIENCE

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

Microbial biofilm growth vs. tissue integration: “The race for the surface” experimentally studied

(2009) Guruprakash Subbiahdoss et al.   Acta Biomaterialia

Micropatterned co-cultures of T-lymphocytes and epithelial cells as a model of mucosal immune system

(2009) Gulnaz Stybayeva et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Humanized Mice for Modeling Human Infectious Disease: Challenges, Progress, and Outlook

(2009) Nicolas Legrand et al.   Cell Host & Microbe

Towards the human intestinal microbiota phylogenetic core

(2009) Julien Tap et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity of human colonic butyrate-producing bacteria revealed by analysis of the butyryl-CoA:acetate CoA-transferase gene

(2009) Petra Louis et al.   ENVIRONMENTAL MICROBIOLOGY

Diversity, metabolism and microbial ecology of butyrate-producing bacteria from the human large intestine

(2009) Petra Louis et al.   FEMS MICROBIOLOGY LETTERS

The Key Role of Segmented Filamentous Bacteria in the Coordinated Maturation of Gut Helper T Cell Responses

(2009) Valérie Gaboriau-Routhiau et al.   IMMUNITY

The gut microbiota modulates host energy and lipid metabolism in mice

(2009) Vidya R. Velagapudi et al.   JOURNAL OF LIPID RESEARCH

Co-culture of epithelial cells and bacteria for investigating host–pathogen interactions

(2009) Jeongyun Kim et al.   LAB ON A CHIP

Use of human tissue explants to study human infectious agents

(2009) Jean-Charles Grivel et al.   Nature Protocols

The integrated microbial genomes system: an expanding comparative analysis resource

(2009) Victor M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

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

Bacterial Community Variation in Human Body Habitats Across Space and Time

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

The Effect of Diet on the Human Gut Microbiome: A Metagenomic Analysis in Humanized Gnotobiotic Mice

(2009) P. J. Turnbaugh et al.   Science Translational Medicine

Review: Tools for the tract: understanding the functionality of the gastrointestinal tract

(2009) Petia Kovatcheva-Datchary et al.   Therapeutic Advances in Gastroenterology

Diet-Induced Obesity Is Linked to Marked but Reversible Alterations in the Mouse Distal Gut Microbiome

(2008) Peter J. Turnbaugh et al.   Cell Host & Microbe

Immunology and zebrafish: Spawning new models of human disease

(2008) Nathan D. Meeker et al.   DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY

Shotgun metaproteomics of the human distal gut microbiota

(2008) Nathan C Verberkmoes et al.   ISME Journal

Co-culture of human gastric endoscopic biopsies with Helicobacter pylori: A simple method for studying early phases of bacteria–host interaction

(2008) Antonella Pellicanò et al.   JOURNAL OF MICROBIOLOGICAL METHODS

Development of a real-time PCR method forFirmicutesandBacteroidetesin faeces and its application to quantify intestinal population of obese and lean pigs

(2008) X. Guo et al.   LETTERS IN APPLIED MICROBIOLOGY