Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn’s disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets

Inactivation of the Pyrimidine Biosynthesis pyrD Gene Negatively Affects Biofilm Formation and Virulence Determinants in the Crohn’s Disease-Associated Adherent Invasive Escherichia coli LF82 Strain

(2022) Elio Rossi et al.   Microorganisms

Proteomic profiling of the rat hippocampus from the kindling and pilocarpine models of epilepsy: potential targets in calcium regulatory network

(2021) Leila Sadeghi et al.   Scientific Reports

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

(2021) Francesco Beghini et al.   eLife

High throughput sequencing provides exact genomic locations of inducible prophages and accurate phage-to-host ratios in gut microbial strains

(2021) Mirjam Zünd et al.   Microbiome

The Role of Enterobacteriaceae in Gut Microbiota Dysbiosis in Inflammatory Bowel Diseases

(2021) Valerio Baldelli et al.   Microorganisms

Some Gammaproteobacteria are enriched within CD14+ macrophages from intestinal lamina propria of Crohn’s disease patients versus mucus

(2020) Yuki Sekido et al.   Scientific Reports

Enterobacterial Common Antigen: Synthesis and Function of an Enigmatic Molecule

(2020) Ashutosh K. Rai et al.   mBio

Gut microbial co-abundance networks show specificity in inflammatory bowel disease and obesity

(2020) Lianmin Chen et al.   Nature Communications

The Relationship Between Gut Microbiota and Inflammatory Diseases: The Role of Macrophages

(2020) Ji Wang et al.   Frontiers in Microbiology

Prevalence of the pathobiont adherent‐invasive Escherichia coli and inflammatory bowel disease: a systematic review and meta‐analysis

(2020) Banafsheh Nadalian et al.   JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY

Exploring the Human Microbiome: The Potential Future Role of Next-Generation Sequencing in Disease Diagnosis and Treatment

(2019) Muneer Ahmad Malla et al.   Frontiers in Immunology

Escherichia coli Pathobionts Associated with Inflammatory Bowel Disease

(2019) Hengameh Chloé Mirsepasi-Lauridsen et al.   CLINICAL MICROBIOLOGY REVIEWS

Environmental Risk Factors for Inflammatory Bowel Diseases: an Umbrella Review of Meta-analyses

(2019) Daniele Piovani et al.   GASTROENTEROLOGY

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

(2019) Jason Lloyd-Price et al.   NATURE

Microbial genes and pathways in inflammatory bowel disease

(2019) Melanie Schirmer et al.   NATURE REVIEWS MICROBIOLOGY

Increased abundance of proteobacteria in aggressive Crohn’s disease seven years after diagnosis

(2019) M. K. Vester-Andersen et al.   Scientific Reports

Escherichia coli isolates from patients with inflammatory bowel disease: ExPEC virulence- and colicin-determinants are more frequent compared to healthy controls

(2018) Lenka Micenková et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome

(2018) Melanie Schirmer et al.   Nature Microbiology

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course

(2018) Melanie Schirmer et al.   Cell Host & Microbe

Gut microbiome structure and metabolic activity in inflammatory bowel disease

(2018) Eric A. Franzosa et al.   Nature Microbiology

Adherent-invasiveEscherichia coliin inflammatory bowel disease

(2017) Carolina Palmela et al.   GUT

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation

(2017) Koji Atarashi et al.   SCIENCE

Cancer Odor Database (COD): a critical databank for cancer diagnosis research

(2017) Sajjad Janfaza et al.   Database-The Journal of Biological Databases and Curation

Acute dextran sulfate sodium (DSS)-induced colitis promotes gut microbial dysbiosis in mice

(2016) Peris Mumbi Munyaka et al.   JOURNAL OF BASIC MICROBIOLOGY

Secretion of Alpha-Hemolysin by Escherichia coli Disrupts Tight Junctions in Ulcerative Colitis Patients

(2016) Hengameh Chloé Mirsepasi-Lauridsen et al.   Clinical and Translational Gastroenterology

Inflammation, Antibiotics, and Diet as Environmental Stressors of the Gut Microbiome in Pediatric Crohn’s Disease

(2015) James D. Lewis et al.   Cell Host & Microbe

Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers

(2015) A Lavelle et al.   GUT

Metagenomic Analysis of Microbiome in Colon Tissue from Subjects with Inflammatory Bowel Diseases Reveals Interplay of Viruses and Bacteria

(2015) Weiwei Wang et al.   INFLAMMATORY BOWEL DISEASES

Distinct inflammatory and cytopathic characteristics of Escherichia coli isolates from inflammatory bowel disease patients

(2015) Stina Rikke Jensen et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

STAMP: statistical analysis of taxonomic and functional profiles

(2014) Donovan H. Parks et al.   BIOINFORMATICS

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

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

Inflammation-associated Adherent-invasive Escherichia coli Are Enriched in Pathways for Use of Propanediol and Iron and M-cell Translocation

(2014) Belgin Dogan et al.   INFLAMMATORY BOWEL DISEASES

Endotoxicity of Lipopolysaccharide as a Determinant of T-Cell−Mediated Colitis Induction in Mice

(2013) Kerstin Gronbach et al.   GASTROENTEROLOGY

Persistent infection with Crohn’s disease-associated adherent-invasive Escherichia coli leads to chronic inflammation and intestinal fibrosis

(2013) Cherrie-Lee N. Small et al.   Nature Communications

Menaquinones, Bacteria, and the Food Supply: The Relevance of Dairy and Fermented Food Products to Vitamin K Requirements

(2013) Barbara Walther et al.   Advances in Nutrition

In vivo bioluminescence imaging of Escherichia coli O104:H4 and role of aerobactin during colonization of a mouse model of infection

(2012) Alfredo G Torres et al.   BMC MICROBIOLOGY

Hospitalisations and surgery in Crohn's disease

(2012) Charles N Bernstein et al.   GUT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

IBD—what role do Proteobacteria play?

(2012) Indrani Mukhopadhya et al.   Nature Reviews Gastroenterology & Hepatology

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

(2012) Xochitl C Morgan et al.   GENOME BIOLOGY

Klebsiella pneumoniaeincreases the risk of inflammation and colitis in a murine model of intestinal bowel disease

(2011) In-Ah Lee et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

Genome sequence of adherent-invasive Escherichia coli and comparative genomic analysis with other E. coli pathotypes

(2010) John HE Nash et al.   BMC GENOMICS

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

Crohn's disease adherent-invasiveEscherichia colicolonize and induce strong gut inflammation in transgenic mice expressing human CEACAM

(2009) Frédéric A. Carvalho et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohnʼs disease

(2008) Ben Willing et al.   INFLAMMATORY BOWEL DISEASES

Identification and Characterisation of Pseudomonas 16S Ribosomal DNA from Ileal Biopsies of Children with Crohn's Disease

(2008) Josef Wagner et al.   PLoS One