Data mining the human gut microbiota for therapeutic targets

Review article: faecal transplantation therapy for gastrointestinal disease

(2011) J. Landy et al.   ALIMENTARY PHARMACOLOGY & THERAPEUTICS

Association Between the Use of Antibiotics and New Diagnoses of Crohn's Disease and Ulcerative Colitis

(2011) Souradet Y Shaw et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Probiotic (symbiotic) bacterial languages

(2011) B.A. Shenderov   ANAEROBE

The genital econiche: focus on microbiota and bacterial vaginosis

(2011) Dan Danielsson et al.   Annals of the New York Academy of Sciences

In vitro maintenance of a human proximal colon microbiota using the continuous fermentation system P-ECSIM

(2011) David Feria-Gervasio et al.   APPLIED MICROBIOLOGY AND BIOTECHNOLOGY

Probiotics function mechanistically as delivery vehicles for neuroactive compounds: Microbial endocrinology in the design and use of probiotics

(2011) Mark Lyte   BIOESSAYS

HHfrag: HMM-based fragment detection using HHpred

(2011) Ivan Kalev et al.   BIOINFORMATICS

Customizable views on semantically integrated networks for systems biology

(2011) Jochen Weile et al.   BIOINFORMATICS

Interactive metagenomic visualization in a Web browser

(2011) Brian D Ondov et al.   BMC BIOINFORMATICS

Immunostimulation in the era of the metagenome

(2011) Amy D Proal et al.   Cellular & Molecular Immunology

Advancing Respiratory Research

(2011) James P. Kiley   CHEST

Gut microbiota and the role of probiotics in therapy

(2011) Eamonn MM Quigley   CURRENT OPINION IN PHARMACOLOGY

Metagenomics and the protein universe

(2011) Adam Godzik   CURRENT OPINION IN STRUCTURAL BIOLOGY

Computational biology approaches for selecting host–pathogen drug targets

(2011) James R. Brown et al.   DRUG DISCOVERY TODAY

From DNA binding to metabolic control: integration of -omics data reveals drug targets for prostate cancer

(2011) Hui Gao et al.   EMBO JOURNAL

Colonic mucosal DNA methylation, immune response, and microbiome patterns in Toll-like receptor 2-knockout mice

(2011) Richard Kellermayer et al.   FASEB JOURNAL

Interactions Between the Host Innate Immune System and Microbes in Inflammatory Bowel Disease

(2011) Clara Abraham et al.   GASTROENTEROLOGY

Gastrointestinal Microbiome Signatures of Pediatric Patients With Irritable Bowel Syndrome

(2011) Delphine M. Saulnier et al.   GASTROENTEROLOGY

Influence of gastrointestinal commensal bacteria on the immune responses that mediate allergy and asthma

(2011) Rachel M. McLoughlin et al.   JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY

Stop the killing of beneficial bacteria

(2011) Martin Blaser   NATURE

Human nutrition, the gut microbiome and the immune system

(2011) Andrew L. Kau et al.   NATURE

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

The skin microbiome

(2011) Elizabeth A. Grice et al.   NATURE REVIEWS MICROBIOLOGY

Unravelling the effects of the environment and host genotype on the gut microbiome

(2011) Aymé Spor et al.   NATURE REVIEWS MICROBIOLOGY

CoMet—a web server for comparative functional profiling of metagenomes

(2011) Thomas Lingner et al.   NUCLEIC ACIDS RESEARCH

The gut microbiome as therapeutic target

(2011) Patrice D. Cani et al.   PHARMACOLOGY & THERAPEUTICS

Towards the Human Colorectal Cancer Microbiome

(2011) Julian R. Marchesi et al.   PLoS One

The Phylogenetic Diversity of Metagenomes

(2011) Steven W. Kembel et al.   PLoS One

Identification and Characterisation of an Iron-Responsive Candidate Probiotic

(2011) Jennifer R. Bailey et al.   PLoS One

Enteric Microbiome Metabolites Correlate with Response to Simvastatin Treatment

(2011) Rima Kaddurah-Daouk et al.   PLoS One

Linking Long-Term Dietary Patterns with Gut Microbial Enterotypes

(2011) G. D. Wu et al.   SCIENCE

PhylOTU: A High-Throughput Procedure Quantifies Microbial Community Diversity and Resolves Novel Taxa from Metagenomic Data

(2011) Thomas J. Sharpton et al.   PLoS Computational Biology

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

Moving pictures of the human microbiome

(2011) J Gregory Caporaso et al.   GENOME BIOLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

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

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

Integrating ‘-omics’ and natural product discovery platforms to investigate metabolic exchange in microbiomes

(2010) Jane Y Yang et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Probiotics in Perspective

(2010) Fergus Shanahan   GASTROENTEROLOGY

Antibiotic use and inflammatory bowel diseases in childhood

(2010) A. Hviid et al.   GUT

Disease phenotype and genotype are associated with shifts in intestinal-associated microbiota in inflammatory bowel diseases

(2010) Daniel N. Frank et al.   INFLAMMATORY BOWEL DISEASES

Postprandial remodeling of the gut microbiota in Burmese pythons

(2010) Elizabeth K Costello et al.   ISME Journal

Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota

(2010) Jan-Hendrik Hehemann et al.   NATURE

A human gut microbial gene catalogue established by metagenomic sequencing

(2010) Junjie Qin et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Pharmacometabonomics as an effector for personalized medicine

(2010) Jeremy K Nicholson et al.   PHARMACOGENOMICS

Gut Microbiota in Health and Disease

(2010) Inna Sekirov et al.   PHYSIOLOGICAL REVIEWS

Vancomycin Treatment of Infective Endocarditis Is Linked with Recently Acquired Obesity

(2010) Franck Thuny et al.   PLoS One

Through Ageing, and Beyond: Gut Microbiota and Inflammatory Status in Seniors and Centenarians

(2010) Elena Biagi et al.   PLoS One

Epithelial crosstalk at the microbiota-mucosal interface

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

Forensic identification using skin bacterial communities

(2010) N. Fierer 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

Alleviating Cancer Drug Toxicity by Inhibiting a Bacterial Enzyme

(2010) B. D. Wallace et al.   SCIENCE

A Catalog of Reference Genomes from the Human Microbiome

(2010) et al.   SCIENCE

Expansion of the Protein Repertoire in Newly Explored Environments: Human Gut Microbiome Specific Protein Families

(2010) Kyle Ellrott et al.   PLoS Computational Biology

Comparative genomics of lactic acid bacteria reveals a niche-specific gene set

(2009) Orla O'Sullivan et al.   BMC MICROBIOLOGY

Targeting the Human Microbiome With Antibiotics, Probiotics, and Prebiotics: Gastroenterology Enters the Metagenomics Era

(2009) Geoffrey A. Preidis et al.   GASTROENTEROLOGY

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

(2009) M. Hamady et al.   GENOME RESEARCH

The NIH Human Microbiome Project

(2009) et al.   GENOME RESEARCH

Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery

(2009) Michael R. Barnes et al.   NATURE REVIEWS DRUG DISCOVERY

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

Human gut microbiome adopts an alternative state following small bowel transplantation

(2009) A. L. Hartman 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

Regulation of myocardial ketone body metabolism by the gut microbiota during nutrient deprivation

(2009) P. A. Crawford et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate automatic structure prediction with HHpred

(2009) Andrea Hildebrand et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

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

The metagenomics RAST server – a public resource for the automatic phylogenetic and functional analysis of metagenomes

(2008) F Meyer et al.   BMC BIOINFORMATICS

Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth

(2008) Ju-Hoon Lee et al.   BMC GENOMICS

Host-bacteria interaction in inflammatory bowel disease

(2008) P. Knight et al.   BRITISH MEDICAL BULLETIN

Metabolic Phenotyping in Health and Disease

(2008) Elaine Holmes et al.   CELL

Mucosal Glycan Foraging Enhances Fitness and Transmission of a Saccharolytic Human Gut Bacterial Symbiont

(2008) Eric C. Martens et al.   Cell Host & Microbe

Host-bacterial coevolution and the search for new drug targets

(2008) Jesse Zaneveld et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Helminths and the IBD hygiene hypothesis

(2008) Joel V. Weinstock et al.   INFLAMMATORY BOWEL DISEASES

The gastrointestinal microbiota as a site for the biotransformation of drugs

(2008) Tiago Sousa et al.   INTERNATIONAL JOURNAL OF PHARMACEUTICS

Meta-basic estimates the size of druggable human genome

(2008) Dariusz Plewczynski et al.   JOURNAL OF MOLECULAR MODELING

A core gut microbiome in obese and lean twins

(2008) Peter J. Turnbaugh et al.   NATURE

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