Metagenomic analysis of primary colorectal carcinomas and their metastases identifies potential microbial risk factors

Klebsiella pneumoniae producing bacterial toxin colibactin as a risk of colorectal cancer development - A systematic review

(2021) Nicol Strakova et al.   TOXICON

Phages and Their Role in Gastrointestinal Disease: Focus on Inflammatory Bowel Disease

(2020) Martin Maronek et al.   Cells

The population genetics of pathogenic Escherichia coli

(2020) Erick Denamur et al.   NATURE REVIEWS MICROBIOLOGY

Bacillus cereus: Epidemiology, Virulence Factors, and Host–Pathogen Interactions

(2020) Daniel Enosi Tuipulotu et al.   TRENDS IN MICROBIOLOGY

Parvimonas micra as a putative non-invasive faecal biomarker for colorectal cancer

(2020) Thyra Löwenmark et al.   Scientific Reports

Contribution of the gut microbiota to the regulation of host metabolism and energy balance: a focus on the gut–liver axis

(2019) N. M. Delzenne et al.   PROCEEDINGS OF THE NUTRITION SOCIETY

Going Viral: a Novel Role for Bacteriophage in Colorectal Cancer

(2019) Scott A. Handley et al.   mBio

First Case of Cutaneous Orbital Abscess Caused by Gemella: A Case Report and Review of the Literature

(2019) Michael McQuinn et al.   JOURNAL OF ORAL AND MAXILLOFACIAL SURGERY

Gut mucosal virome alterations in ulcerative colitis

(2019) Tao Zuo et al.   GUT

E6AP goes viral: the role of E6AP in viral- and non-viral-related cancers

(2019) Ivona Bandilovska et al.   CARCINOGENESIS

Meta-analysis of fecal metagenomes reveals global microbial signatures that are specific for colorectal cancer

(2019) Jakob Wirbel et al.   NATURE MEDICINE

Dynamic Modulation of the Gut Microbiota and Metabolome by Bacteriophages in a Mouse Model

(2019) Bryan B. Hsu et al.   Cell Host & Microbe

Circulating biomarkers for early detection and clinical management of colorectal cancer

(2019) María Marcuello et al.   MOLECULAR ASPECTS OF MEDICINE

Identification of Salivary Microbiota and Its Association With Host Inflammatory Mediators in Periodontitis

(2019) Anna Lundmark et al.   Frontiers in Cellular and Infection Microbiology

Virome and bacteriome: two sides of the same coin

(2019) Jonathan Stern et al.   Current Opinion in Virology

Influence of the Gut Microbiome, Diet, and Environment on Risk of Colorectal Cancer

(2019) Mingyang Song et al.   GASTROENTEROLOGY

Whole-Virome Analysis Sheds Light on Viral Dark Matter in Inflammatory Bowel Disease

(2019) Adam G. Clooney et al.   Cell Host & Microbe

Colorectal cancer liver metastases – a population-based study on incidence, management and survival

(2018) Jennie Engstrand et al.   BMC CANCER

Alterations in Enteric Virome Are Associated With Colorectal Cancer and Survival Outcomes

(2018) Geicho Nakatsu et al.   GASTROENTEROLOGY

Pathology and genetics of hereditary colorectal cancer

(2018) Huiying Ma et al.   PATHOLOGY

Epstein-Barr virus stably confers an invasive phenotype to epithelial cells through reprogramming of the WNT pathway

(2018) Christine E. Birdwell et al.   Oncotarget

Colibactin: More Than a New Bacterial Toxin

(2018) Tiphanie Faïs et al.   Toxins

Fusobacterium nucleatum and colorectal cancer: A review

(2018) Fu-Mei Shang et al.   World Journal of Gastrointestinal Oncology

Nonalcoholic Fatty Liver Disease in Humans Is Associated with Increased Plasma Endotoxin and Plasminogen Activator Inhibitor 1 Concentrations and with Fructose Intake

(2018) Sabine Thuy et al.   JOURNAL OF NUTRITION

More than just oncogenes: mechanisms of tumorigenesis by human viruses

(2018) Marta M Gaglia et al.   Current Opinion in Virology

Bacteriophages Contribute to Shaping Clostridioides (Clostridium) difficile Species

(2018) Louis-Charles Fortier   Frontiers in Microbiology

Biology and Taxonomy of crAss-like Bacteriophages, the Most Abundant Virus in the Human Gut

(2018) Emma Guerin et al.   Cell Host & Microbe

Prospective study of oral microbiome and colorectal cancer risk in low‐income and African American populations

(2018) Yaohua Yang et al.   INTERNATIONAL JOURNAL OF CANCER

The Epstein-Barr virus induces the expression of the LPAM-1 integrin in B-cells in vitro and in vivo

(2018) Susanne Delecluse et al.   JOURNAL OF VIROLOGY

Expressing cytotoxic compounds in Escherichia coli Nissle 1917 for tumor-targeting therapy

(2018) Ruijuan Li et al.   RESEARCH IN MICROBIOLOGY

Diagnostic Potential and Interactive Dynamics of the Colorectal Cancer Virome

(2018) Geoffrey D. Hannigan et al.   mBio

ΦCrAss001 represents the most abundant bacteriophage family in the human gut and infects Bacteroides intestinalis

(2018) Andrey N. Shkoporov et al.   Nature Communications

Whole genome sequencing puts forward hypotheses on metastasis evolution and therapy in colorectal cancer

(2018) Naveed Ishaque et al.   Nature Communications

Human Herpesvirus 6 and Malignancy: A Review

(2018) Eva Eliassen et al.   Frontiers in Oncology

Contamination in Low Microbial Biomass Microbiome Studies: Issues and Recommendations

(2018) Raphael Eisenhofer et al.   TRENDS IN MICROBIOLOGY

PhredEM: a phred-score-informed genotype-calling approach for next-generation sequencing studies

(2017) Peizhou Liao et al.   GENETIC EPIDEMIOLOGY

A bacteriophages journey through the human body

(2017) Jeremy J. Barr   IMMUNOLOGICAL REVIEWS

Human cytomegalovirus infection enhances cell proliferation, migration and upregulation of EMT markers in colorectal cancer-derived stem cell-like cells

(2017) Wan Huai Teo et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Deciphering Diversity Indices for a Better Understanding of Microbial Communities

(2017) Bo-Ra Kim et al.   JOURNAL OF MICROBIOLOGY AND BIOTECHNOLOGY

Layered defense: how mucus and tight junctions seal the intestinal barrier

(2017) Christopher T. Capaldo et al.   JOURNAL OF MOLECULAR MEDICINE-JMM

Microbiome and NAFLD: potential influence of aerobic fitness and lifestyle modification

(2017) Matthew R. Panasevich et al.   PHYSIOLOGICAL GENOMICS

Bacterial Biofilms in Colorectal Cancer Initiation and Progression

(2017) Shan Li et al.   TRENDS IN MOLECULAR MEDICINE

Oncogenic Role of Tumor Viruses in Humans

(2017) Nimrah Akram et al.   VIRAL IMMUNOLOGY

Epstein-Barr virus-positive ileal carcinomas associated with Crohn’s disease

(2017) Alessandro Vanoli et al.   VIRCHOWS ARCHIV

HHV-6A/B Integration and the Pathogenesis Associated with the Reactivation of Chromosomally Integrated HHV-6A/B

(2017) Vanessa Collin et al.   Viruses-Basel

The Human Gut Phage Community and Its Implications for Health and Disease

(2017) Pilar Manrique et al.   Viruses-Basel

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers

(2017) Sophie Nguyen et al.   mBio

Internalization of a polysialic acid-binding Escherichia coli bacteriophage into eukaryotic neuroblastoma cells

(2017) Timo A. Lehti et al.   Nature Communications

Bacteriophages in the gastrointestinal tract and their implications

(2017) Marzanna Łusiak-Szelachowska et al.   Gut Pathogens

Diversity index as a novel prognostic factor in breast cancer

(2017) Yul Ri Chung et al.   Oncotarget

Interactions of Intestinal Bacteria with Components of the Intestinal Mucus

(2017) Jean-Félix Sicard et al.   Frontiers in Cellular and Infection Microbiology

High-resolution bacterial 16S rRNA gene profile meta-analysis and biofilm status reveal common colorectal cancer consortia

(2017) Julia L. Drewes et al.   npj Biofilms and Microbiomes

Distinct gut microbiome patterns associate with consensus molecular subtypes of colorectal cancer

(2017) Rachel V. Purcell et al.   Scientific Reports

Gut Microbiota, Inflammation, and Colorectal Cancer

(2016) Caitlin A. Brennan et al.   Annual Review of Microbiology

Linking Virus Genomes with Host Taxonomy

(2016) Tomoko Mihara et al.   Viruses-Basel

Bacteriophage infections of microbiota can lead to leaky gut in an experimental rodent model

(2016) George Tetz et al.   Gut Pathogens

iNEXT: an R package for rarefaction and extrapolation of species diversity (Hill numbers)

(2016) T. C. Hsieh et al.   Methods in Ecology and Evolution

Human cytomegalovirus infection and colorectal cancer risk: a meta-analysis

(2016) Bingjun Bai et al.   Oncotarget

The gastrointestinal microbiota and colorectal cancer

(2015) Temitope O. Keku et al.   AMERICAN JOURNAL OF PHYSIOLOGY-GASTROINTESTINAL AND LIVER PHYSIOLOGY

National serosurvey of encephalomyocarditis virus in healthy people and pigs in China

(2015) Ruofei Feng et al.   ARCHIVES OF VIROLOGY

Sambamba: fast processing of NGS alignment formats

(2015) Artem Tarasov et al.   BIOINFORMATICS

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease

(2015) Jason M. Norman et al.   CELL

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

(2015) Jun Yu et al.   GUT

Metagenomic Analysis of Crohnʼs Disease Patients Identifies Changes in the Virome and Microbiome Related to Disease Status and Therapy, and Detects Potential Interactions and Biomarkers

(2015) Vicente Pérez-Brocal et al.   INFLAMMATORY BOWEL DISEASES

Association ofStreptococcus gallolyticussubspeciesgallolyticuswith colorectal cancer: Serological evidence

(2015) Julia Butt et al.   INTERNATIONAL JOURNAL OF CANCER

Update on Epstein-Barr virus and gastric cancer (Review)

(2015) AYA SHINOZAKI-USHIKU et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Cutaneous Human Polyomavirus Small T Antigens and 4E-BP1 Targeting

(2015) Julie H. Wu et al.   INTERVIROLOGY

Methods to determine intestinal permeability and bacterial translocation during liver disease

(2015) Lirui Wang et al.   JOURNAL OF IMMUNOLOGICAL METHODS

Detection and genotyping of torque teno virus (TTV) in healthy blood donors and patients infected with HBV or HCV in Qatar

(2015) Raed AbuOdeh et al.   JOURNAL OF MEDICAL VIROLOGY

Detection of Human Polyomavirus 7 in Human Thymic Epithelial Tumors

(2015) Dorit Rennspiess et al.   Journal of Thoracic Oncology

Torque Teno Midi Virus/Small Anellovirus in Sera of Healthy, HIV/HCV and HIV Infected Individuals in Lorestan Province, Iran

(2015) Maryam Fatholahi et al.   Jundishapur Journal of Microbiology

Human Endogenous Retrovirus (HERV-K) Reverse Transcriptase as a Breast Cancer Prognostic Marker

(2015) Maya Golan et al.   NEOPLASIA

Inference with viral quasispecies diversity indices: clonal and NGS approaches

(2014) Josep Gregori et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

The complex role of inflammasomes in the pathogenesis of Inflammatory Bowel Diseases – Lessons learned from experimental models

(2014) Mònica Aguilera et al.   CYTOKINE & GROWTH FACTOR REVIEWS

The prevalence of human papillomavirus in colorectal adenomas and adenocarcinomas: A systematic review and meta-analysis

(2014) Louise Baandrup et al.   EUROPEAN JOURNAL OF CANCER

α-Haemolysin ofEscherichia coliin IBD: a potentiator of inflammatory activity in the colon

(2014) Roland Bücker et al.   GUT

Bacterial genotoxin colibactin promotes colon tumour growth by inducing a senescence-associated secretory phenotype

(2014) Antony Cougnoux et al.   GUT

Viral infections and colorectal cancer: A systematic review of epidemiological studies

(2014) Hongda Chen et al.   INTERNATIONAL JOURNAL OF CANCER

Epstein-Barr Virus-Encoded Small RNAs (EBERs) Are Present in Fractions Related to Exosomes Released by EBV-Transformed Cells

(2014) Waqar Ahmed et al.   PLoS One

Epstein-Barr Virus Turns 50

(2014) P. M. Lieberman   SCIENCE

Inflammation and colorectal cancer, when microbiota-host mutualism breaks

(2014) Marco Candela   WORLD JOURNAL OF GASTROENTEROLOGY

A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes

(2014) Bas E. Dutilh et al.   Nature Communications

Adoptive Transfer of EBV Specific CD8+ T Cell Clones Can Transiently Control EBV Infection in Humanized Mice

(2014) Olga Antsiferova et al.   PLoS Pathogens

On the optimal trimming of high-throughput mRNA sequence data

(2014) Matthew D. MacManes   Frontiers in Genetics

Age-Specific Seroprevalences of Merkel Cell Polyomavirus, Human Polyomaviruses 6, 7, and 9, and Trichodysplasia Spinulosa-Associated Polyomavirus

(2013) Jérôme T. J. Nicol et al.   Clinical and Vaccine Immunology

Danger-Associated Molecular Patterns and Inflammatory Bowel Disease: Is There a Connection?

(2013) Christoph Mueller   DIGESTIVE DISEASES

Bacteriophages in Gut Samples From Pediatric Crohn’s Disease Patients

(2013) Josef Wagner et al.   INFLAMMATORY BOWEL DISEASES

Robust estimation of microbial diversity in theory and in practice

(2013) Bart Haegeman et al.   ISME Journal

A Consortium of Aggregatibacter actinomycetemcomitans, Streptococcus parasanguinis, and Filifactor alocis Is Present in Sites Prior to Bone Loss in a Longitudinal Study of Localized Aggressive Periodontitis

(2013) D. H. Fine et al.   JOURNAL OF CLINICAL MICROBIOLOGY

Pathological bacterial translocation in liver cirrhosis

(2013) Reiner Wiest et al.   JOURNAL OF HEPATOLOGY

Fusobacterium Is Associated with Colorectal Adenomas

(2013) Amber N. McCoy et al.   PLoS One

HHV-6 antigen and HHV-6 DNA expression in sporadic adenomatous polyps of the colon

(2013) Leena Halme et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Study of the Viral and Microbial Communities Associated With Crohn’s Disease: A Metagenomic Approach

(2013) Vicente Pérez-Brocal et al.   Clinical and Translational Gastroenterology

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

Higher rate of colorectal cancer among patients with pyogenic liver abscess withKlebsiella pneumoniaethan those without: an 11-year follow-up study

(2012) W.-K. Huang et al.   Colorectal Disease

Pattern recognition receptors—Molecular orchestrators of inflammation in inflammatory bowel disease

(2012) David Walsh et al.   CYTOKINE & GROWTH FACTOR REVIEWS

Recent Trends in the Prevalence of Crohn’s Disease and Ulcerative Colitis in a Commercially Insured US Population

(2012) Michael D. Kappelman et al.   DIGESTIVE DISEASES AND SCIENCES

Carcinogenic viruses and solid cancers without sufficient evidence of causal association

(2012) Paolo De Paoli et al.   INTERNATIONAL JOURNAL OF CANCER

Human cytomegalovirus preferentially infects the neoplastic epithelium of colorectal cancer: A quantitative and histological analysis

(2012) Hsin-Pai Chen et al.   JOURNAL OF CLINICAL VIROLOGY

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

A bacterial driver–passenger model for colorectal cancer: beyond the usual suspects

(2012) Harold Tjalsma et al.   NATURE REVIEWS MICROBIOLOGY

Epstein-Barr Virus Stimulates Torque Teno Virus Replication: A Possible Relationship to Multiple Sclerosis

(2012) Silvia S. Borkosky et al.   PLoS One

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

Enterococci as probiotics and their implications in food safety

(2011) Charles M.A.P. Franz et al.   INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY

Torque teno virus in fecal samples of patients with gastroenteritis: Prevalence, genogroups distribution, and viral load

(2011) Carlos Augusto Pinho-Nascimento et al.   JOURNAL OF MEDICAL VIROLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Human herpesvirus 6 and cytomegalovirus in ileocolonic mucosa in inflammatory bowel disease

(2011) Taina Sipponen et al.   SCANDINAVIAN JOURNAL OF GASTROENTEROLOGY

Human herpesvirus-6 in patients with Crohn’s disease

(2010) RADHAKRISHNA SURA et al.   APMIS

E3 ubiquitin protein ligase, E6-associated protein (E6-AP) regulates PI3K-Akt signaling and prostate cell growth

(2010) Sathish Srinivasan et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Merkel Cell Polyomavirus and Two Previously Unknown Polyomaviruses Are Chronically Shed from Human Skin

(2010) Rachel M. Schowalter et al.   Cell Host & Microbe

Estimates of worldwide burden of cancer in 2008: GLOBOCAN 2008

(2010) Jacques Ferlay et al.   INTERNATIONAL JOURNAL OF CANCER

Detection of SV40 in colon cancer: A molecular case-control study from Northeast Italy

(2010) Cesare Campello et al.   JOURNAL OF MEDICAL VIROLOGY

LMP1 antagonizes WNT/β-catenin signalling through inhibition of WTX and promotes nasopharyngeal dysplasia but not tumourigenesis in LMP1B95-8 transgenic mice

(2010) Zhang QingLing et al.   JOURNAL OF PATHOLOGY

Microbial and viral pathogens in colorectal cancer

(2010) Danielle Collins et al.   LANCET ONCOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Toll-like receptors as targets in chronic liver diseases

(2009) A Mencin et al.   GUT

A human colonic commensal promotes colon tumorigenesis via activation of T helper type 17 T cell responses

(2009) Shaoguang Wu et al.   NATURE MEDICINE

Prevalence of infectious pathogens in Crohn's disease

(2009) Thomas Knösel et al.   PATHOLOGY RESEARCH AND PRACTICE

Infectious Agents and Colorectal Cancer: A Review of Helicobacter pylori, Streptococcus bovis, JC Virus, and Human Papillomavirus

(2008) A. N. Burnett-Hartman et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Human endogenous retrovirus HERV-K113 is capable of producing intact viral particles

(2008) K. Boller et al.   JOURNAL OF GENERAL VIROLOGY

Characterisation of Escherichia coli strains involved in transcytosis across gut epithelial cells exposed to metabolic and inflammatory stress

(2008) Christian Macutkiewicz et al.   MICROBES AND INFECTION

Molecular cloning and functional characterization of the human endogenous retrovirus K113

(2008) Nadine Beimforde et al.   VIROLOGY

Hepatitis B virus prevalence and transmission risk factors in inflammatory bowel disease patients at Clementino Fraga Filho university hospital

(2008) Yolanda Faia Manhães Tolentino et al.   WORLD JOURNAL OF GASTROENTEROLOGY