{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T07:09:25Z","timestamp":1790838565326,"version":"4.1.0"},"reference-count":47,"publisher":"Elsevier BV","issue":"1","license":[{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,11,25]],"date-time":"2024-11-25T00:00:00Z","timestamp":1732492800000},"content-version":"am","delay-in-days":329,"URL":"http:\/\/www.elsevier.com\/open-access\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-017"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-012"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2024,1,1]],"date-time":"2024-01-01T00:00:00Z","timestamp":1704067200000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-004"}],"funder":[{"DOI":"10.13039\/100019486","name":"Biocodex Microbiota Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019486","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["clinicalkey.com","clinicalkey.com.au","clinicalkey.es","clinicalkey.fr","clinicalkey.jp","em-consulte.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Clinics and Research in Hepatology and Gastroenterology"],"published-print":{"date-parts":[[2024,1]]},"DOI":"10.1016\/j.clinre.2023.102247","type":"journal-article","created":{"date-parts":[[2023,11,18]],"date-time":"2023-11-18T00:17:39Z","timestamp":1700266659000},"page":"102247","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":8,"title":["Gastric microbiota in patients with gastric MALT lymphoma according to Helicobacter pylori infection"],"prefix":"10.1016","volume":"48","author":[{"given":"Antoine","family":"Martin","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marine","family":"Jauvain","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Emma","family":"Bergsten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vanessa","family":"Demontant","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philippe","family":"Lehours","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Caroline","family":"Barau","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael","family":"Levy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christophe","family":"Rodriguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Iradj","family":"Sobhani","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6676-1222","authenticated-orcid":false,"given":"Aurelien","family":"Amiot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.clinre.2023.102247_bib0001","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1111\/1574-6976.12027","article-title":"Survival in hostile territory: the microbiota of the stomach","volume":"37","author":"Yang","year":"2013","journal-title":"FEMS Microbiol Rev"},{"key":"10.1016\/j.clinre.2023.102247_bib0002","doi-asserted-by":"crossref","first-page":"170","DOI":"10.1038\/srep00170","article-title":"Bacterial biogeography of the human digestive tract","volume":"1","author":"Stearns","year":"2011","journal-title":"Sci Rep"},{"key":"10.1016\/j.clinre.2023.102247_bib0003","doi-asserted-by":"crossref","first-page":"1598","DOI":"10.1136\/gutjnl-2019-319696","article-title":"Effect of Helicobacter pylori on gastrointestinal microbiota: a population-based study in Linqu, a high-risk area of gastric cancer","volume":"69","author":"Guo","year":"2020","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0004","doi-asserted-by":"crossref","first-page":"1572","DOI":"10.1136\/gutjnl-2019-319826","article-title":"Gastric microbes associated with gastric inflammation, atrophy and intestinal metaplasia 1 year after Helicobacter pylori eradication","volume":"69","author":"Sung","year":"2020","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0005","doi-asserted-by":"crossref","first-page":"1188","DOI":"10.1002\/2211-5463.13390","article-title":"Helicobacter pylori infection affects the human gastric microbiome, as revealed by metagenomic sequencing","volume":"12","author":"Wang","year":"2022","journal-title":"FEBS Open Bio"},{"key":"10.1016\/j.clinre.2023.102247_bib0006","doi-asserted-by":"crossref","first-page":"e12899","DOI":"10.1111\/hel.12899","article-title":"Influences of Helicobacter pylori infection on diversity, heterogeneity, and composition of human gastric microbiomes across stages of gastric cancer development","volume":"27","author":"Xiao","year":"2022","journal-title":"Helicobacter"},{"key":"10.1016\/j.clinre.2023.102247_bib0007","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00955-19","article-title":"Modification of the gastric mucosal microbiota by a strain-specific Helicobacter pylori oncoprotein and carcinogenic histologic phenotype","volume":"10","author":"Noto","year":"2019","journal-title":"MBio"},{"key":"10.1016\/j.clinre.2023.102247_bib0008","doi-asserted-by":"crossref","first-page":"307","DOI":"10.1182\/asheducation-2005.1.307","article-title":"Clinical presentation and management of marginal zone lymphomas","author":"Thieblemont","year":"2005","journal-title":"Hematol Am Soc Hematol Educ Program"},{"key":"10.1016\/j.clinre.2023.102247_bib0009","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1111\/j.1365-2036.2011.04839.x","article-title":"Review article: common misconceptions in the management of Helicobacter pylori-associated gastric MALT-lymphoma","volume":"34","author":"Gisbert","year":"2011","journal-title":"Aliment Pharmacol Ther"},{"key":"10.1016\/j.clinre.2023.102247_bib0010","doi-asserted-by":"crossref","first-page":"1410","DOI":"10.1002\/1097-0142(19831015)52:8<1410::AID-CNCR2820520813>3.0.CO;2-3","article-title":"Malignant lymphoma of mucosa-associated lymphoid tissue. A distinctive type of B-cell lymphoma","volume":"52","author":"Isaacson","year":"1983","journal-title":"Cancer"},{"key":"10.1016\/j.clinre.2023.102247_bib0011","doi-asserted-by":"crossref","first-page":"5207","DOI":"10.1158\/1078-0432.CCR-14-0496","article-title":"Emerging role of infectious etiologies in the pathogenesis of marginal zone B-cell lymphomas","volume":"20","author":"Zucca","year":"2014","journal-title":"Clin Cancer Res"},{"key":"10.1016\/j.clinre.2023.102247_bib0012","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1136\/gut.2010.224949","article-title":"EGILS consensus report. Gastric extranodal marginal zone B-cell lymphoma of MALT","volume":"60","author":"Ruskone-Fourmestraux","year":"2011","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0013","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1002\/1098-2264(2000)9999:9999<::AID-GCC1036>3.0.CO;2-I","article-title":"Structure of the MLT gene and molecular characterization of the genomic breakpoint junctions in the t(11;18)(q21;q21) of marginal zone B-cell lymphomas of MALT type","volume":"29","author":"Baens","year":"2000","journal-title":"Genes Chromosomes Cancer"},{"key":"10.1016\/j.clinre.2023.102247_bib0014","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1007\/s12328-012-0355-9","article-title":"A case of Helicobacter heilmannii-associated primary gastric mucosa-associated lymphoid tissue lymphoma achieving complete remission after eradication","volume":"6","author":"Okamura","year":"2013","journal-title":"Clin J Gastroenterol"},{"key":"10.1016\/j.clinre.2023.102247_bib0015","doi-asserted-by":"crossref","first-page":"336","DOI":"10.1038\/nrgastro.2010.58","article-title":"Gastric MALT lymphoma: a model of chronic inflammation-induced tumor development","volume":"7","author":"Sagaert","year":"2010","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"10.1016\/j.clinre.2023.102247_bib0016","doi-asserted-by":"crossref","first-page":"e27287","DOI":"10.1097\/MD.0000000000027287","article-title":"Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma","volume":"100","author":"Tanaka","year":"2021","journal-title":"Medicine"},{"key":"10.1016\/j.clinre.2023.102247_bib0017","doi-asserted-by":"crossref","first-page":"5019","DOI":"10.1182\/blood-2011-01-293050","article-title":"The 2008 WHO classification of lymphoid neoplasms and beyond: evolving concepts and practical applications","volume":"117","author":"Campo","year":"2011","journal-title":"Blood"},{"key":"10.1016\/j.clinre.2023.102247_bib0018","doi-asserted-by":"crossref","first-page":"1656","DOI":"10.1136\/gut.52.11.1656","article-title":"Proposal for a new histological grading system for post-treatment evaluation of gastric MALT lymphoma","volume":"52","author":"Copie-Bergman","year":"2003","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0019","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1111\/apt.12635","article-title":"Rituximab, alkylating agents or combination therapy for gastric mucosa-associated lymphoid tissue lymphoma: a monocentric non-randomised observational study","volume":"39","author":"Amiot","year":"2014","journal-title":"Aliment Pharmacol Ther"},{"key":"10.1016\/j.clinre.2023.102247_bib0020","first-page":"T13","article-title":"The \u201cSidney System\u201d, a new classification of gastritis]","volume":"17","author":"Mainguet","year":"1993","journal-title":"Gastroenterol Clin Biol"},{"key":"10.1016\/j.clinre.2023.102247_bib0021","doi-asserted-by":"crossref","first-page":"1161","DOI":"10.1097\/00000478-199610000-00001","article-title":"Classification and grading of gastritis. The updated Sydney system. International workshop on the histopathology of Gastritis, Houston 1994","volume":"20","author":"Dixon","year":"1996","journal-title":"Am J Surg Pathol"},{"key":"10.1016\/j.clinre.2023.102247_bib0022","doi-asserted-by":"crossref","first-page":"e12855","DOI":"10.1111\/hel.12855","article-title":"Adaptation of an in-house PCR for the detection of Helicobacter pylori and the mutations associated with macrolide resistance into ready-to-use PCR microwell strips","volume":"26","author":"B\u00e9n\u00e9jat","year":"2021","journal-title":"Helicobacter"},{"key":"10.1016\/j.clinre.2023.102247_bib0023","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"Klindworth","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.clinre.2023.102247_bib0024","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.clinre.2023.102247_bib0025","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Mago\u010d","year":"2011","journal-title":"Bioinformatics"},{"key":"10.1016\/j.clinre.2023.102247_bib0026","doi-asserted-by":"crossref","first-page":"591","DOI":"10.1007\/978-1-4939-9074-0_19","article-title":"Introduction to the Analysis of Environmental Sequences: metagenomics with MEGAN","volume":"1910","author":"Ba\u011fc\u0131","year":"2019","journal-title":"Methods Mol Biol"},{"key":"10.1016\/j.clinre.2023.102247_bib0027","doi-asserted-by":"crossref","first-page":"D643","DOI":"10.1093\/nar\/gkt1209","article-title":"The SILVA and \u201call-species living tree project (LTP)\u201d taxonomic frameworks","volume":"42","author":"Yilmaz","year":"2014","journal-title":"Nucleic Acids Res"},{"key":"10.1016\/j.clinre.2023.102247_bib0028","doi-asserted-by":"crossref","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat Biotechnol"},{"key":"10.1016\/j.clinre.2023.102247_bib0029","doi-asserted-by":"crossref","DOI":"10.1128\/mSystems.00191-16","article-title":"Deblur rapidly resolves single-nucleotide community sequence patterns","volume":"2","author":"Amir","year":"2017","journal-title":"mSystems"},{"key":"10.1016\/j.clinre.2023.102247_bib0030","doi-asserted-by":"crossref","first-page":"e2584","DOI":"10.7717\/peerj.2584","article-title":"VSEARCH: a versatile open source tool for metagenomics","volume":"4","author":"Rognes","year":"2016","journal-title":"PeerJ"},{"key":"10.1016\/j.clinre.2023.102247_bib0031","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nmeth.2276","article-title":"Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing","volume":"10","author":"Bokulich","year":"2013","journal-title":"Nat Methods"},{"key":"10.1016\/j.clinre.2023.102247_bib0032","doi-asserted-by":"crossref","first-page":"1312","DOI":"10.1093\/bioinformatics\/btu033","article-title":"RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies","volume":"30","author":"Stamatakis","year":"2014","journal-title":"Bioinformatics"},{"key":"10.1016\/j.clinre.2023.102247_bib0033","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biol"},{"key":"10.1016\/j.clinre.2023.102247_bib0034","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.ejim.2017.10.005","article-title":"Gut microbiota and obesity: concepts relevant to clinical care","volume":"48","author":"Dao","year":"2018","journal-title":"Eur J Intern Med"},{"key":"10.1016\/j.clinre.2023.102247_bib0035","doi-asserted-by":"crossref","first-page":"e4693","DOI":"10.7717\/peerj.4693","article-title":"Effects of tobacco smoke and electronic cigarette vapor exposure on the oral and gut microbiota in humans: a pilot study","volume":"6","author":"Stewart","year":"2018","journal-title":"PeerJ"},{"key":"10.1016\/j.clinre.2023.102247_bib0036","doi-asserted-by":"crossref","first-page":"1630","DOI":"10.1200\/JCO.1989.7.11.1630","article-title":"Report of a committee convened to discuss the evaluation and staging of patients with Hodgkin's disease: cotswolds meeting","volume":"7","author":"Lister","year":"1989","journal-title":"J Clin Oncol"},{"key":"10.1016\/j.clinre.2023.102247_bib0037","doi-asserted-by":"crossref","first-page":"32","DOI":"10.1016\/j.beha.2017.01.001","article-title":"Bacteria associated with marginal zone lymphomas","volume":"30","author":"Ponzoni","year":"2017","journal-title":"Best Pract Res Clin Haematol"},{"key":"10.1016\/j.clinre.2023.102247_bib0038","doi-asserted-by":"crossref","first-page":"3599","DOI":"10.1038\/s41388-022-02377-9","article-title":"Meta-analysis of mucosal microbiota reveals universal microbial signatures and dysbiosis in gastric carcinogenesis","volume":"41","author":"Liu","year":"2022","journal-title":"Oncogene"},{"key":"10.1016\/j.clinre.2023.102247_bib0039","doi-asserted-by":"crossref","first-page":"e42693","DOI":"10.7554\/eLife.42693","article-title":"Extensive transmission of microbes along the gastrointestinal tract","volume":"8","author":"Schmidt","year":"2019","journal-title":"eLife"},{"key":"10.1016\/j.clinre.2023.102247_bib0040","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2022.864944","article-title":"Characterization of specific signatures of the oral cavity, sputum, and ileum microbiota in patients with Crohn's disease","volume":"12","author":"Xia","year":"2022","journal-title":"Front Cell Infect Microbiol"},{"key":"10.1016\/j.clinre.2023.102247_bib0041","doi-asserted-by":"crossref","first-page":"1359","DOI":"10.1136\/gutjnl-2021-324755","article-title":"A faecal microbiota signature with high specificity for pancreatic cancer","volume":"71","author":"Kartal","year":"2022","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0042","doi-asserted-by":"crossref","DOI":"10.3390\/cancers14041005","article-title":"Current status of the spectrum and therapeutics of Helicobacter pylori-negative mucosa-associated lymphoid tissue lymphoma","volume":"14","author":"Kuo","year":"2022","journal-title":"Cancers"},{"key":"10.1016\/j.clinre.2023.102247_bib0043","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1136\/gutjnl-2016-312288","article-title":"Management of Helicobacter pylori infection-the Maastricht V\/florence consensus report","volume":"66","author":"Malfertheiner","year":"2017","journal-title":"Gut"},{"key":"10.1016\/j.clinre.2023.102247_bib0044","doi-asserted-by":"crossref","first-page":"3600","DOI":"10.1128\/JCM.00744-09","article-title":"Evaluation of a new test, genotype HelicoDR, for molecular detection of antibiotic resistance in Helicobacter pylori","volume":"47","author":"Cambau","year":"2009","journal-title":"J Clin Microbiol"},{"key":"10.1016\/j.clinre.2023.102247_bib0045","doi-asserted-by":"crossref","first-page":"e12702","DOI":"10.1111\/hel.12702","article-title":"Evaluation of the Allplex\u2122 H pylori and ClariR PCR Assay for Helicobacter pylori detection on gastric biopsies","volume":"25","author":"Jehanne","year":"2020","journal-title":"Helicobacter"},{"key":"10.1016\/j.clinre.2023.102247_bib0046","doi-asserted-by":"crossref","DOI":"10.3390\/toxins9040132","article-title":"Helicobacter pylori strains and gastric MALT lymphoma","volume":"9","author":"Floch","year":"2017","journal-title":"Toxins"},{"key":"10.1016\/j.clinre.2023.102247_bib0047","doi-asserted-by":"crossref","first-page":"1473","DOI":"10.1016\/j.ajpath.2017.03.004","article-title":"A new animal model of gastric lymphomagenesis: APRIL transgenic mice infected by helicobacter species","volume":"187","author":"Floch","year":"2017","journal-title":"Am J Pathol"}],"container-title":["Clinics and Research in Hepatology and Gastroenterology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2210740123001729?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2210740123001729?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T07:34:36Z","timestamp":1761896076000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2210740123001729"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":47,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2024,1]]}},"alternative-id":["S2210740123001729"],"URL":"https:\/\/doi.org\/10.1016\/j.clinre.2023.102247","relation":{},"ISSN":["2210-7401"],"issn-type":[{"value":"2210-7401","type":"print"}],"subject":[],"published":{"date-parts":[[2024,1]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Gastric microbiota in patients with gastric MALT lymphoma according to Helicobacter pylori infection","name":"articletitle","label":"Article Title"},{"value":"Clinics and Research in Hepatology and Gastroenterology","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.clinre.2023.102247","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2023 Elsevier Masson SAS. All rights reserved.","name":"copyright","label":"Copyright"}],"article-number":"102247"}}