Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Standard Colonic Lavage Alters the Natural State of Mucosal-Associated Microbiota in the Human Colon

(2012) Laura Harrell et al.   PLoS One

Inflammatory Bowel Diseases Phenotype, C. difficile and NOD2 Genotype Are Associated with Shifts in Human Ileum Associated Microbial Composition

(2012) Ellen Li et al.   PLoS One

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

(2012) Eliseo Papa et al.   PLoS One

Interactions Between the Microbiota and the Immune System

(2012) L. V. Hooper et al.   SCIENCE

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

(2012) Sahar Abubucker et al.   PLoS Computational Biology

Cultured Representatives of Two Major Phylogroups of Human Colonic Faecalibacterium prausnitzii Can Utilize Pectin, Uronic Acids, and Host-Derived Substrates for Growth

(2011) Mireia Lopez-Siles et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Characterization of Phascolarctobacterium succinatutens sp. nov., an Asaccharolytic, Succinate-Utilizing Bacterium Isolated from Human Feces

(2011) Yohei Watanabe et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

The Genome of Th17 Cell-Inducing Segmented Filamentous Bacteria Reveals Extensive Auxotrophy and Adaptations to the Intestinal Environment

(2011) Andrew Sczesnak et al.   Cell Host & Microbe

The Lifestyle of the Segmented Filamentous Bacterium: A Non-Culturable Gut-Associated Immunostimulating Microbe Inferred by Whole-Genome Sequencing

(2011) T. Kuwahara et al.   DNA RESEARCH

Distal gut microbiota of adolescent children is different from that of adults

(2011) Richard Agans et al.   FEMS MICROBIOLOGY ECOLOGY

Epidemiology and Natural History of Inflammatory Bowel Diseases

(2011) Jacques Cosnes et al.   GASTROENTEROLOGY

Twin Study Indicates Loss of Interaction Between Microbiota and Mucosa of Patients With Ulcerative Colitis

(2011) Patricia Lepage et al.   GASTROENTEROLOGY

Fusobacterium nucleatum infection is prevalent in human colorectal carcinoma

(2011) M. Castellarin et al.   GENOME RESEARCH

Genomic analysis identifies association of Fusobacterium with colorectal carcinoma

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

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Dysbiosis of the faecal microbiota in patients with Crohn's disease and their unaffected relatives

(2011) M. Joossens et al.   GUT

Genetics and pathogenesis of inflammatory bowel disease

(2011) Bernard Khor et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Pyrosequencing-Based Analysis of the Mucosal Microbiota in Healthy Individuals Reveals Ubiquitous Bacterial Groups and Micro-Heterogeneity

(2011) Pei-Ying Hong et al.   PLoS One

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

Intestinal inflammation allows Salmonella to use ethanolamine to compete with the microbiota

(2011) P. Thiennimitr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive personal human gut microbiota culture collections characterized and manipulated in gnotobiotic mice

(2011) A. L. Goodman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

(2011) Markus Göker et al.   Standards in Genomic Sciences

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Enterobacteriaceae Act in Concert with the Gut Microbiota to Induce Spontaneous and Maternally Transmitted Colitis

(2010) Wendy S. Garrett et al.   Cell Host & Microbe

The intestinal microbiota in inflammatory bowel diseases: time to connect with the host

(2010) Harry Sokol et al.   CURRENT OPINION IN GASTROENTEROLOGY

Enterohaemorrhagic Escherichia coli gains a competitive advantage by using ethanolamine as a nitrogen source in the bovine intestinal content

(2010) Yolande Bertin et al.   ENVIRONMENTAL MICROBIOLOGY

Dysbiosis of fecal microbiota in Crohnʼs disease patients as revealed by a custom phylogenetic microarray

(2010) Seungha Kang et al.   INFLAMMATORY BOWEL DISEASES

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

Genome-wide association identifies multiple ulcerative colitis susceptibility loci

(2010) Dermot P B McGovern et al.   NATURE GENETICS

Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

(2010) Andre Franke et al.   NATURE GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Induction of Colonic Regulatory T Cells by Indigenous Clostridium Species

(2010) K. Atarashi et al.   SCIENCE

The Firmicutes/Bacteroidetes ratio of the human microbiota changes with age

(2009) D Mariat et al.   BMC MICROBIOLOGY

Induction of Intestinal Th17 Cells by Segmented Filamentous Bacteria

(2009) Ivaylo I. Ivanov et al.   CELL

Commensal bacteria, traditional and opportunistic pathogens, dysbiosis and bacterial killing in inflammatory bowel diseases

(2009) Christopher D Packey et al.   CURRENT OPINION IN INFECTIOUS DISEASES

Crohn's disease: Th1, Th17 or both? The change of a paradigm: new immunological and genetic insights implicate Th17 cells in the pathogenesis of Crohn's disease

(2009) S. Brand   GUT

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

(2009) Valérie Gaboriau-Routhiau et al.   IMMUNITY

Low counts of Faecalibacterium prausnitzii in colitis microbiota

(2009) H. Sokol et al.   INFLAMMATORY BOWEL DISEASES

KEGG for representation and analysis of molecular networks involving diseases and drugs

(2009) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

A Parsimony Approach to Biological Pathway Reconstruction/Inference for Genomes and Metagenomes

(2009) Yuzhen Ye et al.   PLoS Computational Biology

A statistical toolbox for metagenomics: assessing functional diversity in microbial communities

(2008) Patrick D Schloss et al.   BMC BIOINFORMATICS

Insights into networks of functional microbes catalysing methanization of cellulose under mesophilic conditions

(2008) Tianlun Li et al.   ENVIRONMENTAL MICROBIOLOGY

Isolation of lactate-utilizing butyrate-producing bacteria from human feces and in vivo administration of Anaerostipes caccae strain L2 and galacto-oligosaccharides in a rat model

(2008) Tadashi Sato et al.   FEMS MICROBIOLOGY ECOLOGY

Analysis of bacterial bowel communities of IBD patients: What has it revealed?

(2008) Harry Sokol et al.   INFLAMMATORY BOWEL DISEASES

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease

(2008) Jeffrey C Barrett et al.   NATURE GENETICS

Polysaccharide utilization by gut bacteria: potential for new insights from genomic analysis

(2008) Harry J. Flint et al.   NATURE REVIEWS MICROBIOLOGY

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH

Paneth cells directly sense gut commensals and maintain homeostasis at the intestinal host-microbial interface

(2008) S. Vaishnava et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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