Fecal microbiota and bile acids in IBD patients undergoing screening for colorectal cancer

Colorectal cancer screening in IBD - can characterization of GI microbiome signatures enhance neoplasia detection?

(2022) Molly Pratt et al.   GASTROENTEROLOGY

Microbiome differential abundance methods produce different results across 38 datasets

(2022) Jacob T. Nearing et al.   Nature Communications

Gut microbiota-derived metabolites as key actors in inflammatory bowel disease

(2020) Aonghus Lavelle et al.   Nature Reviews Gastroenterology & Hepatology

Fecal microbiota transplantation to maintain remission in Crohn’s disease: a pilot randomized controlled study

(2020) Harry Sokol et al.   Microbiome

Effect of Fecal Microbiota Transplantation on 8-Week Remission in Patients With Ulcerative Colitis

(2019) Samuel P. Costello et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases

(2019) Jason Lloyd-Price et al.   NATURE

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease

(2019) Almut Heinken et al.   Microbiome

Editing of the gut microbiota reduces carcinogenesis in mouse models of colitis-associated colorectal cancer

(2019) Wenhan Zhu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The ‘in vivo lifestyle’ of bile acid 7α-dehydroxylating bacteria: comparative genomics, metatranscriptomic, and bile acid metabolomics analysis of a defined microbial community in gnotobiotic mice

(2019) Jason M. Ridlon et al.   Gut Microbes

Differences in Gut Microbiota in Patients With vs Without Inflammatory Bowel Diseases: A Systematic Review

(2019) Rapat Pittayanon et al.   GASTROENTEROLOGY

MetaboAnalystR: an R package for flexible and reproducible analysis of metabolomics data

(2018) Jasmine Chong et al.   BIOINFORMATICS

No Association Between Pseudopolyps and Colorectal Neoplasia in Patients With Inflammatory Bowel Diseases

(2018) Remi Mahmoud et al.   GASTROENTEROLOGY

Multidonor intensive faecal microbiota transplantation for active ulcerative colitis: a randomised placebo-controlled trial

(2017) Sudarshan Paramsothy et al.   LANCET

Analysis ofFusobacteriumpersistence and antibiotic response in colorectal cancer

(2017) Susan Bullman et al.   SCIENCE

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients

(2017) Andrew Brantley Hall et al.   Genome Medicine

Lipocalin 2 Protects from Inflammation and Tumorigenesis Associated with Gut Microbiota Alterations

(2016) Alexander R. Moschen et al.   Cell Host & Microbe

Fungal microbiota dysbiosis in IBD

(2016) Harry Sokol et al.   GUT

Objections to the proposed reclassification of Eubacterium rectale as Agathobacter rectalis

(2016) Paul O. Sheridan et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Neonatal gut microbiota associates with childhood multisensitized atopy and T cell differentiation

(2016) Kei E Fujimura et al.   NATURE MEDICINE

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Fecal Microbiota in Pediatric Inflammatory Bowel Disease and Its Relation to Inflammation

(2015) Kaija-Leena Kolho et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

zCompositions — R package for multivariate imputation of left-censored data under a compositional approach

(2015) Javier Palarea-Albaladejo et al.   CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS

Fecal Microbiota Transplantation Induces Remission in Patients With Active Ulcerative Colitis in a Randomized Controlled Trial

(2015) Paul Moayyedi et al.   GASTROENTEROLOGY

Findings From a Randomized Controlled Trial of Fecal Transplantation for Patients With Ulcerative Colitis

(2015) Noortje G. Rossen et al.   GASTROENTEROLOGY

Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer

(2015) Jun Yu et al.   GUT

Cancers Complicating Inflammatory Bowel Disease

(2015) Laurent Beaugerie et al.   NEW ENGLAND JOURNAL OF MEDICINE

Gut microbiome development along the colorectal adenoma–carcinoma sequence

(2015) Qiang Feng et al.   Nature Communications

Microbial genomic analysis reveals the essential role of inflammation in bacteria-induced colorectal cancer

(2014) Janelle C. Arthur et al.   Nature Communications

Fusobacterium nucleatum Potentiates Intestinal Tumorigenesis and Modulates the Tumor-Immune Microenvironment

(2013) Aleksandar D. Kostic et al.   Cell Host & Microbe

Phylogenetic Analysis of Dysbiosis in Ulcerative Colitis During Remission

(2013) Mirjana Rajilić-Stojanović et al.   INFLAMMATORY BOWEL DISEASES

Altered Gut Microbiota Promotes Colitis-Associated Cancer in IL-1 Receptor–Associated Kinase M–Deficient Mice

(2013) Klara Klimesova et al.   INFLAMMATORY BOWEL DISEASES

Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells

(2013) Yukihiro Furusawa et al.   NATURE

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

ANOVA-Like Differential Expression (ALDEx) Analysis for Mixed Population RNA-Seq

(2013) Andrew D. Fernandes et al.   PLoS One

Connecting dysbiosis, bile-acid dysmetabolism and gut inflammation in inflammatory bowel diseases

(2012) Henri Duboc et al.   GUT

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Dirichlet Multinomial Mixtures: Generative Models for Microbial Metagenomics

(2012) Ian Holmes et al.   PLoS One

Intestinal Inflammation Targets Cancer-Inducing Activity of the Microbiota

(2012) J. C. Arthur et al.   SCIENCE

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Mucolytic Bacteria With Increased Prevalence in IBD Mucosa Augment In Vitro Utilization of Mucin by Other Bacteria

(2010) Chin Wen Png et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

Modulation of the Intestinal Microbiota Alters Colitis-Associated Colorectal Cancer Susceptibility

(2009) Joshua M. Uronis et al.   PLoS One

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