Microbiota profiling in esophageal diseases: Novel insights into molecular staining and clinical outcomes

[1]  D. Tang,et al.  Intratumoural microbiota: from theory to clinical application , 2023, Cell Communication and Signaling.

[2]  S. Danese,et al.  Endoscopic vacuum therapy versus self-expandable metal stent for treatment of anastomotic leaks < 30 mm following oncologic Ivor-Lewis esophagectomy: a matched case–control study , 2023, Surgical Endoscopy.

[3]  M. Kankainen,et al.  Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics. , 2023, Trends in genetics : TIG.

[4]  X. Xing,et al.  Achalasia: The Current Clinical Dilemma and Possible Pathogenesis , 2023, Journal of neurogastroenterology and motility.

[5]  S. Danese,et al.  Gastroparesis: The Complex Interplay with Microbiota and the Role of Exogenous Infections in the Pathogenesis of the Disease , 2023, Microorganisms.

[6]  Jia‐Feng Wu,et al.  Characteristics of the esophageal microbiome in patients with achalasia and its changes before and after peroral endoscopic myotomy: A pilot study , 2023, Journal of gastroenterology and hepatology.

[7]  E. Savarino,et al.  A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis , 2023, Journal of Translational Medicine.

[8]  W. Bemelman,et al.  Endoscopic Vacuum Therapy (EVT) versus Self-Expandable Metal Stent (SEMS) for Anastomotic Leaks after Upper Gastrointestinal Surgery: Systematic Review and Meta-Analysis , 2023, Life.

[9]  Nathaniel Krogel,et al.  Post-COVID-19 Achalasia? , 2022, Digestive Diseases and Sciences.

[10]  M. Icaza-Chávez,et al.  Is the Sars‐CoV‐2 virus a possible trigger agent for the development of achalasia? , 2022, medRxiv.

[11]  Y. Imamura,et al.  Fecal Microbes Associated with the Outcomes After Esophagectomy in Patients with Esophageal Cancer , 2022, Annals of Surgical Oncology.

[12]  M. Rehman,et al.  Multiomics technologies: role in disease biomarker discoveries and therapeutics. , 2022, Briefings in functional genomics.

[13]  Jean-Fred Fontaine,et al.  Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality , 2022, BMC Bioinformatics.

[14]  S. Keely,et al.  The microbiota in eosinophilic esophagitis: A systematic review , 2022, Journal of gastroenterology and hepatology.

[15]  E. Savarino,et al.  Salivary microbiota composition may discriminate between patients with eosinophilic oesophagitis (EoE) and non‐EoE subjects , 2022, Alimentary pharmacology & therapeutics.

[16]  J. Y. Lee,et al.  Esophageal Microbiota and Nutritional Intakes in Patients With Achalasia Before and After Peroral Endoscopic Myotomy , 2022, Journal of neurogastroenterology and motility.

[17]  S. Janga,et al.  Esophageal Microbiome in Healthy Children and Esophageal Eosinophilia , 2022, Journal of pediatric gastroenterology and nutrition.

[18]  F. Azzolini,et al.  The prophylactic use of endoscopic vacuum therapy for anastomotic dehiscence after rectal anterior resection: is it feasible for redo surgery? , 2022, Techniques in Coloproctology.

[19]  Y. Choksi,et al.  Microbiome in Eosinophilic Esophagitis—Metagenomic, Metatranscriptomic, and Metabolomic Changes: A Systematic Review , 2021, Frontiers in Physiology.

[20]  L. Peyrin-Biroulet,et al.  The Inflammatory Bowel Disease Transcriptome and Metatranscriptome Meta-Analysis (IBD TaMMA) framework , 2021, Nature Computational Science.

[21]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[22]  O. Zaborina,et al.  Enterococcus faecalis Is Associated with Anastomotic Leak in Patients Undergoing Colorectal Surgery. , 2021, Surgical infections.

[23]  D. Johnson,et al.  Role of microbial dysbiosis in the pathogenesis of esophageal mucosal disease: A paradigm shift from acid to bacteria? , 2021, World journal of gastroenterology.

[24]  M. Holzman,et al.  Association of Achalasia with Active Varicella Zoster Virus Infection of the Esophagus. , 2021, Gastroenterology.

[25]  Li Ning,et al.  Topic Evolution Analysis for Omics Data Integration in Cancers , 2021, Frontiers in Cell and Developmental Biology.

[26]  M. Claesson,et al.  Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies , 2021, Scientific Reports.

[27]  F. Azzolini,et al.  Double Layer Stent for the Treatment of Leaks and Fistula After Upper Gastrointestinal Oncologic Surgery: A Retrospective Study , 2021, Endoscopy.

[28]  A. Fiocchi,et al.  Eosinophilic Esophagitis and Microbiota: State of the Art , 2021, Frontiers in Immunology.

[29]  Arthur Flexer,et al.  DeepNOG: fast and accurate protein orthologous group assignment , 2020, Bioinform..

[30]  Moon Soo Kim,et al.  Delayed Gastric Emptying after Esophagectomy: Management and Prevention , 2020, The Korean journal of thoracic and cardiovascular surgery.

[31]  D. Harman,et al.  Distinct Microbiota Dysbiosis in Patients with Non-Erosive Reflux Disease and Esophageal Adenocarcinoma , 2020, Journal of clinical medicine.

[32]  J. Krischer,et al.  High Patient Disease Burden in a Cross-sectional, Multicenter Contact Registry Study of Eosinophilic Gastrointestinal Diseases , 2020, Journal of pediatric gastroenterology and nutrition.

[33]  C. Consolandi,et al.  Esophageal microbiome signature in patients with Barrett’s esophagus and esophageal adenocarcinoma , 2020, PloS one.

[34]  Sang Kil Lee,et al.  Exploring Esophageal Microbiomes in Esophageal Diseases: A Systematic Review , 2020, Journal of neurogastroenterology and motility.

[35]  R. Rosati,et al.  A large anastomotic leakage after esophageal surgery treated with endoluminal vacuum-assisted closure: a case report , 2020, Journal of surgical case reports.

[36]  S. Al-Abdi,et al.  A systematic comparison between infant formula compositions using the Bray-Curtis Similarity Index , 2020, International journal of pediatrics & adolescent medicine.

[37]  Jessica Galloway-Peña,et al.  Tools for Analysis of the Microbiome , 2020, Digestive Diseases and Sciences.

[38]  Prajwal Gurung,et al.  Recent Advances in Lipopolysaccharide Recognition Systems , 2020, International journal of molecular sciences.

[39]  H. Inoue,et al.  Identification of human herpes virus 1 encoded microRNAs in biopsy samples of lower esophageal sphincter muscle during peroral endoscopic myotomy for esophageal achalasia , 2020, Digestive endoscopy : official journal of the Japan Gastroenterological Endoscopy Society.

[40]  M. Gerstein,et al.  Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis , 2019, Nature Communications.

[41]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[42]  R. Fitzgerald,et al.  High-Fat Diet Accelerates Carcinogenesis in a Mouse Model of Barrett's Esophagus via Interleukin 8 and Alterations to the Gut Microbiome. , 2019, Gastroenterology.

[43]  S. Rajagopala,et al.  The Salivary Microbiome Is Altered in Children With Eosinophilic Esophagitis and Correlates With Disease Activity , 2019, Clinical and translational gastroenterology.

[44]  Heping Zhao,et al.  Alteration of the esophageal microbiota in Barrett's esophagus and esophageal adenocarcinoma , 2019, World journal of gastroenterology.

[45]  Martin Ayling,et al.  New approaches for metagenome assembly with short reads , 2019, Briefings Bioinform..

[46]  A. Nouvenne,et al.  Diagnosis of GERD in typical and atypical manifestations , 2018, Acta bio-medica : Atenei Parmensis.

[47]  R. van Hillegersberg,et al.  A Propensity Score Matched Analysis of Open Versus Minimally Invasive Transthoracic Esophagectomy in the Netherlands , 2018, Annals of surgery.

[48]  M. Khan,et al.  An insight into gut microbiota and its functionalities , 2018, Cellular and Molecular Life Sciences.

[49]  Sheng Pan,et al.  Metaproteomics Study of the Gut Microbiome. , 2018, Methods in molecular biology.

[50]  R. Fass,et al.  The Changing Epidemiology of Gastroesophageal Reflux Disease: Are Patients Getting Younger? , 2018, Journal of neurogastroenterology and motility.

[51]  Nora C. Toussaint,et al.  Increasing Dietary Fiber Intake Is Associated with a Distinct Esophageal Microbiome , 2018, Clinical and Translational Gastroenterology.

[52]  Eran Elinav,et al.  You are what you eat: diet, health and the gut microbiota , 2018, Nature Reviews Gastroenterology & Hepatology.

[53]  Andrew P. Copland,et al.  The Esophageal Microbiome in Health and Disease , 2018, Current Gastroenterology Reports.

[54]  N. Javid,et al.  Is There Any Evidence for a Viral Cause in Achalasia? , 2018, Middle East journal of digestive diseases.

[55]  M. Patti,et al.  Esophageal achalasia: current diagnosis and treatment , 2018, Expert review of gastroenterology & hepatology.

[56]  J. Marioni,et al.  Multi‐Omics Factor Analysis—a framework for unsupervised integration of multi‐omics data sets , 2018, Molecular systems biology.

[57]  M. Vaezi,et al.  Preliminary esophageal microbiome studies prompt important scientific questions , 2018, Clinical and Translational Gastroenterology.

[58]  M. Marco,et al.  Impact of DNA Sequencing and Analysis Methods on 16S rRNA Gene Bacterial Community Analysis of Dairy Products , 2018, mSphere.

[59]  M. Vicario,et al.  Toll-like receptors-mediated pathways activate inflammatory responses in the esophageal mucosa of adult eosinophilic esophagitis , 2018, Clinical and Translational Gastroenterology.

[60]  J. Boyce,et al.  Role of lipid mediators and control of lymphocyte responses in type 2 immunopathology , 2018, The Journal of allergy and clinical immunology.

[61]  D. Beer,et al.  Increased Variance in Oral and Gastric Microbiome Correlates With Esophagectomy Anastomotic Leak. , 2018, The Annals of thoracic surgery.

[62]  Nora C. Toussaint,et al.  Barrett’s esophagus is associated with a distinct oral microbiome , 2018, Clinical and Translational Gastroenterology.

[63]  Drew M. Pardoll,et al.  Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria , 2018, Science.

[64]  A. Hindmarsh,et al.  Endoluminal Vacuum Therapy (E-Vac): A Treatment Option in Oesophagogastric Surgery , 2018, World Journal of Surgery.

[65]  E. Quigley.  Microbiota-Brain-Gut Axis and Neurodegenerative Diseases , 2017, Current Neurology and Neuroscience Reports.

[66]  Lei Zhang,et al.  Risk factors for delayed gastric emptying in patients undergoing esophagectomy without pyloric drainage. , 2017, The Journal of surgical research.

[67]  R. van Hillegersberg,et al.  Hospital costs of complications after esophagectomy for cancer. , 2017, European journal of surgical oncology : the journal of the European Society of Surgical Oncology and the British Association of Surgical Oncology.

[68]  S. Kropf,et al.  Risk factors for delayed gastric emptying after esophagectomy , 2017, Langenbeck's Archives of Surgery.

[69]  R. van Hillegersberg,et al.  Early outcomes from the Dutch Upper Gastrointestinal Cancer Audit , 2016, The British journal of surgery.

[70]  P. Bechi,et al.  The esophageal microbiota in health and disease , 2016, Annals of the New York Academy of Sciences.

[71]  James N. Luo,et al.  Morphine Promotes Colonization of Anastomotic Tissues with Collagenase - Producing Enterococcus faecalis and Causes Leak , 2016, Journal of Gastrointestinal Surgery.

[72]  R. Odze,et al.  Association of Acute Gastroesophageal Reflux Disease With Esophageal Histologic Changes. , 2016, JAMA.

[73]  Caroline H. Johnson,et al.  Metabolomics: beyond biomarkers and towards mechanisms , 2016, Nature Reviews Molecular Cell Biology.

[74]  M. Vicario,et al.  Dietary treatment modulates mast cell phenotype, density, and activity in adult eosinophilic oesophagitis , 2016, Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology.

[75]  Eran Elinav,et al.  Use of Metatranscriptomics in Microbiome Research , 2016, Bioinformatics and biology insights.

[76]  R. Shulman,et al.  Esophageal Food Impaction and Eosinophilic Esophagitis: A Retrospective Study, Systematic Review, and Meta-Analysis , 2015, Digestive Diseases and Sciences.

[77]  S. Canizales-Quinteros,et al.  Combining metagenomics, metatranscriptomics and viromics to explore novel microbial interactions: towards a systems-level understanding of human microbiome , 2015, Computational and structural biotechnology journal.

[78]  F. Bushman,et al.  Inflammation-associated microbiota in pediatric eosinophilic esophagitis , 2015, Microbiome.

[79]  N. Pace,et al.  Esophageal Microbiome in Eosinophilic Esophagitis , 2015, PloS one.

[80]  James N. Luo,et al.  Collagen degradation and MMP9 activation by Enterococcus faecalis contribute to intestinal anastomotic leak , 2015, Science Translational Medicine.

[81]  A. Karthikesalingam,et al.  The impact of pyloric drainage on clinical outcome following esophagectomy: a systematic review. , 2015, Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus.

[82]  I. Sarosiek,et al.  Role of Saliva in Esophageal Defense: Implications in Patients With Nonerosive Reflux Disease , 2015, The American journal of the medical sciences.

[83]  Florence E. Turrentine,et al.  Morbidity, mortality, cost, and survival estimates of gastrointestinal anastomotic leaks. , 2015, Journal of the American College of Surgeons.

[84]  Marti J. Anderson,et al.  Measures of precision for dissimilarity-based multivariate analysis of ecological communities , 2014, Ecology letters.

[85]  Uri Gophna,et al.  Gastric microbiota is altered in oesophagitis and Barrett's oesophagus and further modified by proton pump inhibitors. , 2014, Environmental microbiology.

[86]  E. Fiebiger,et al.  Involvement of the iNKT Cell Pathway Is Associated With Early-Onset Eosinophilic Esophagitis and Response to Allergen Avoidance Therapy , 2014, The American Journal of Gastroenterology.

[87]  A. Kosinski,et al.  Predictors of anastomotic leak after esophagectomy: an analysis of the society of thoracic surgeons general thoracic database. , 2013, The Annals of thoracic surgery.

[88]  Christopher C Winchester,et al.  Update on the epidemiology of gastro-oesophageal reflux disease: a systematic review , 2013, Gut.

[89]  A. Barkun,et al.  Prolonged treatment duration is required for successful Helicobacter pylori eradication with proton pump inhibitor triple therapy in Canada. , 2013, Canadian journal of gastroenterology = Journal canadien de gastroenterologie.

[90]  G. D’Amico,et al.  JC Virus, Helicobacter pylori, and Oesophageal Achalasia: Preliminary Results from a Retrospective Case–Control Study , 2013, Digestive Diseases and Sciences.

[91]  N. Ishimura,et al.  Case-control study of association of eosinophilic gastrointestinal disorders with Helicobacter pylori infection in Japan , 2013, Journal of clinical biochemistry and nutrition.

[92]  Y. Yang,et al.  Upper gastrointestinal microbiota and digestive diseases. , 2013, World journal of gastroenterology.

[93]  P. Baldrian,et al.  The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses , 2013, PloS one.

[94]  A. Gasbarrini,et al.  The Gut Barrier: New Acquisitions and Therapeutic Approaches , 2012, Journal of clinical gastroenterology.

[95]  N. Pace,et al.  Novel Device to Sample the Esophageal Microbiome—The Esophageal String Test , 2012, PloS one.

[96]  A. Zaborin,et al.  Intestinal Tissues Induce an SNP Mutation in Pseudomonas aeruginosa That Enhances Its Virulence: Possible Role in Anastomotic Leak , 2012, PloS one.

[97]  Levi Waldron,et al.  Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples , 2012, Genome Biology.

[98]  J. Tack,et al.  Systematic review: the burden of disruptive gastro‐oesophageal reflux disease on health‐related quality of life , 2012, Alimentary pharmacology & therapeutics.

[99]  G. Siuzdak,et al.  Innovation: Metabolomics: the apogee of the omics trilogy , 2012, Nature Reviews Molecular Cell Biology.

[100]  Zhiheng Pei,et al.  Molecular Pathways: Pathogenesis and Clinical Implications of Microbiome Alteration in Esophagitis and Barrett Esophagus , 2012, Clinical Cancer Research.

[101]  D. Morgan,et al.  Inverse association of esophageal eosinophilia with Helicobacter pylori based on analysis of a US pathology database. , 2011, Gastroenterology.

[102]  A. Zullo,et al.  Helicobacter pylori and Nonmalignant Diseases , 2011, Helicobacter.

[103]  M. Rothenberg,et al.  Genetic dissection of eosinophilic esophagitis provides insight into disease pathogenesis and treatment strategies. , 2011, The Journal of allergy and clinical immunology.

[104]  K. Harnett,et al.  Viewpoints on Acid-Induced Inflammatory Mediators in Esophageal Mucosa , 2010, Journal of neurogastroenterology and motility.

[105]  Philip D Marsh,et al.  Microbiology of dental plaque biofilms and their role in oral health and caries. , 2010, Dental clinics of North America.

[106]  S. Spechler,et al.  Gastroesophageal reflux might cause esophagitis through a cytokine-mediated mechanism rather than caustic acid injury. , 2009, Gastroenterology.

[107]  P. Brun,et al.  T Cells in the Myenteric Plexus of Achalasia Patients Show a Skewed TCR Repertoire and React to HSV-1 Antigens , 2008, The American Journal of Gastroenterology.

[108]  G. Boeckxstaens.  Achalasia: Virus-Induced Euthanasia of Neurons? , 2008, The American Journal of Gastroenterology.

[109]  F. Shanahan,et al.  The gut flora as a forgotten organ , 2006, EMBO reports.

[110]  Adam Godzik,et al.  Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences , 2006, Bioinform..

[111]  Martin J Blaser,et al.  Bacterial biota in the human distal esophagus , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[112]  E. Ruchelli,et al.  Pollen and eosinophilic esophagitis. , 2003, The Journal of allergy and clinical immunology.

[113]  Christopher P. Wild,et al.  Reflux, Barrett's oesophagus and adenocarcinoma: burning questions , 2003, Nature Reviews Cancer.

[114]  J. Holst,et al.  Colonic fermentation influences lower esophageal sphincter function in gastroesophageal reflux disease. , 2003, Gastroenterology.

[115]  B. Zilberstein,et al.  Megaesophagus microbiota: A qualitative and quantitative analysis , 2002, Journal of Gastrointestinal Surgery.

[116]  J. Dent,et al.  Helicobacter pylori and symptomatic relapse of gastro-oesophageal reflux disease: a randomised controlled trial , 2001, The Lancet.

[117]  P. R. Corsi,et al.  Microbial flora of the normal esophagus. , 1998, Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus.

[118]  A. Mclarty,et al.  Esophageal resection for cancer of the esophagus: long-term function and quality of life. , 1997, The Annals of thoracic surgery.

[119]  A. Blum,et al.  Curing Helicobacter pylori infection in patients with duodenal ulcer may provoke reflux esophagitis. , 1997, Gastroenterology.

[120]  J. Holst,et al.  Colonic fermentation and proximal gastric tone in humans. , 1996, Gastroenterology.

[121]  D. Hume,et al.  Endotoxin signal transduction in macrophages , 1996, Journal of leukocyte biology.

[122]  K. Schulze-Delrieu.  Varicella virus in achalasia. , 1993, Gastroenterology.

[123]  B. A. Martin,et al.  Varicella-zoster virus DNA in the oesophageal myenteric plexus in achalasia. , 1993, Gut.

[124]  Steve M. D’Souza,et al.  Microbiome and Gastroesophageal Disease: Pathogenesis and Implications for Therapy , 2020 .

[125]  D. Ghosh,et al.  : Guidelines for the Diagnosis and Management of Gastroesophageal Reflux Disease , 2017 .

[126]  I. N. Rôças,et al.  The Oral Microbiota in Health and Disease: An Overview of Molecular Findings. , 2017, Methods in molecular biology.

[127]  K. Guyton,et al.  The gut microbiota and gastrointestinal surgery , 2017, Nature Reviews Gastroenterology &Hepatology.

[128]  M. Ruth,et al.  Bacterial flora of the human oral cavity, and the upper and lower esophagus. , 2013, Diseases of the esophagus : official journal of the International Society for Diseases of the Esophagus.

[129]  K. Goh,et al.  Non-Erosive Reflux Disease (NERD), Symptomatic and Asymptomatic Erosive Reflux Disease (ERD): From Hypersensitive to Hyposensitive Esophagus , 2010, Digestive Diseases and Sciences.

[130]  Anand Gupte,et al.  Eosinophilic esophagitis. , 2009, World journal of gastroenterology.

[131]  P. Mcdonald.  The microflora of the oesophagus. , 1984, Annals of the Royal College of Surgeons of England.

[132]  F. Azzolini,et al.  Endoscopic vacuum therapy in the treatment of postesophagectomy leaks: Is intracavitary the way? , 2022 .