{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,11]],"date-time":"2026-10-11T14:14:15Z","timestamp":1791728055332,"version":"4.3.4"},"reference-count":68,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2018,12,12]],"date-time":"2018-12-12T00:00:00Z","timestamp":1544572800000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Cell. Infect. Microbiol."],"DOI":"10.3389\/fcimb.2018.00433","type":"journal-article","created":{"date-parts":[[2018,12,12]],"date-time":"2018-12-12T09:15:45Z","timestamp":1544606145000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":125,"title":["The Gastric Microbiome Is Perturbed in Advanced Gastric Adenocarcinoma Identified Through Shotgun Metagenomics"],"prefix":"10.3389","volume":"8","author":[{"given":"Yuan-Liang","family":"Hu","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Pang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yun","family":"Huang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chao-Jun","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2018,12,12]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"681","DOI":"10.1080\/00365520510015430","article-title":"Tooth loss is associated with increased risk of gastric non-cardia adenocarcinoma in a cohort of Finnish smokers","volume":"40","author":"Abnet","year":"2005","journal-title":"Scand. J. Gastroenterol"},{"key":"B2","doi-asserted-by":"publisher","first-page":"847","DOI":"10.1023\/A:1012290009545","article-title":"Prospective study of tooth loss and incident esophageal and gastric cancers in China","volume":"12","author":"Abnet","year":"2001","journal-title":"Cancer Causes Control"},{"key":"B3","doi-asserted-by":"publisher","first-page":"e1002358","DOI":"10.1371\/journal.pcbi.1002358","article-title":"Metabolic reconstruction for metagenomic data and its application to the human microbiome","volume":"8","author":"Abubucker","year":"2012","journal-title":"PLoS Comput. Biol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1007\/s10552-011-9892-7","article-title":"Oral microbiome and oral and gastrointestinal cancer risk","volume":"23","author":"Ahn","year":"2012","journal-title":"Cancer Causes Control"},{"key":"B5","doi-asserted-by":"publisher","first-page":"26985","DOI":"10.1038\/srep26985","article-title":"Microbiological profiles of sputum and gastric juice aspirates in Cystic Fibrosis patients","volume":"6","author":"Al-Momani","year":"2016","journal-title":"Sci. Rep."},{"key":"B6","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1053\/j.gastro.2015.09.004","article-title":"Pathobiology of helicobacter pylori-induced gastric cancer","volume":"150","author":"Amieva","year":"2016","journal-title":"Gastroenterology"},{"key":"B7","doi-asserted-by":"publisher","first-page":"4202","DOI":"10.1038\/srep04202","article-title":"Stomach microbiota composition varies between patients with non-atrophic gastritis and patients with intestinal type of gastric cancer","volume":"4","author":"Aviles-Jimenez","year":"2014","journal-title":"Sci. Rep."},{"key":"B8","doi-asserted-by":"publisher","first-page":"732","DOI":"10.1073\/pnas.0506655103","article-title":"Molecular analysis of the bacterial microbiota in the human stomach","volume":"103","author":"Bik","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B9","doi-asserted-by":"publisher","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":"B10","doi-asserted-by":"publisher","first-page":"1169","DOI":"10.1038\/mi.2016.131","article-title":"Helicobacter pylori infection is associated with an altered gastric microbiota in children","volume":"10","author":"Brawner","year":"2017","journal-title":"Mucosal Immunol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"2","author":"Buchfink","year":"2014","journal-title":"Nat. Methods"},{"key":"B12","doi-asserted-by":"publisher","first-page":"D633","DOI":"10.1093\/nar\/gkx935","article-title":"The MetaCyc database of metabolic pathways and enzymes","volume":"46","author":"Caspi","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"B13","doi-asserted-by":"publisher","first-page":"15957","DOI":"10.1038\/s41598-017-16289-2","article-title":"Dysbiosis of the microbiome in gastric carcinogenesis","volume":"7","author":"Casta\u00f1o-Rodr\u00edguez","year":"2017","journal-title":"Sci. Rep."},{"key":"B14","doi-asserted-by":"publisher","first-page":"28061","DOI":"10.1038\/srep28061","article-title":"Characterization of the microbiome of nipple aspirate fluid of breast cancer survivors","volume":"6","author":"Chan","year":"2016","journal-title":"Sci. Rep."},{"key":"B15","doi-asserted-by":"publisher","first-page":"957","DOI":"10.1164\/rccm.201104-0655OC","article-title":"Topographical continuity of bacterial populations in the healthy human respiratory tract","volume":"184","author":"Charlson","year":"2011","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"B16","doi-asserted-by":"publisher","first-page":"875","DOI":"10.1038\/s41467-017-00901-0","article-title":"The microbiota continuum along the female reproductive tract and its relation to uterine-related diseases","volume":"8","author":"Chen","year":"2017","journal-title":"Nat. Commun."},{"key":"B17","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/j.smim.2017.08.001","article-title":"Microbiota dysbiosis in select human cancers: evidence of association and causality","volume":"32","author":"Chen","year":"2017","journal-title":"Semin. Immunol."},{"key":"B18","doi-asserted-by":"publisher","first-page":"1024","DOI":"10.1136\/gutjnl-2017-314281","article-title":"Mucosal microbiome dysbiosis in gastric carcinogenesis","volume":"67","author":"Coker","year":"2017","journal-title":"Gut"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1128\/mSystems.00127-16","article-title":"Microbiome helper: a custom and streamlined workflow for microbiome research","author":"Comeau","year":"2017","journal-title":"mSystems"},{"key":"B20","doi-asserted-by":"publisher","first-page":"e280","DOI":"10.1371\/journal.pbio.0060280","article-title":"The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing","volume":"6","author":"Dethlefsen","year":"2008","journal-title":"PLoS Biol."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1000087107","article-title":"Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation","author":"Dethlefsen","year":"2011","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B22","doi-asserted-by":"publisher","first-page":"542168","DOI":"10.1155\/2013\/542168","article-title":"Hydroquinone: environmental pollution, toxicity, and microbial answers","volume":"3","author":"Enguita","year":"2013","journal-title":"Biomed Res. Int."},{"key":"B23","doi-asserted-by":"publisher","first-page":"120","DOI":"10.1136\/gutjnl-2016-312580","article-title":"Human oral microbiome and prospective risk for pancreatic cancer: a population-based nested case-control study","volume":"67","author":"Fan","year":"2018","journal-title":"Gut"},{"key":"B24","doi-asserted-by":"publisher","first-page":"226","DOI":"10.1136\/gutjnl-2017-314205","article-title":"Gastric microbial community profiling reveals a dysbiotic cancer-associated microbiota","volume":"67","author":"Ferreira","year":"2017","journal-title":"Gut"},{"key":"B25","doi-asserted-by":"publisher","first-page":"776","DOI":"10.1016\/j.cell.2014.03.006","article-title":"The fire within: microbes inflame tumors","volume":"157","author":"Gagliani","year":"2014","journal-title":"Cell"},{"key":"B26","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1007\/s13238-018-0548-1","article-title":"Oral microbiomes: more and more importance in oral cavity and whole body","volume":"9","author":"Gao","year":"2018","journal-title":"Protein Cell"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1369","DOI":"10.3389\/fmicb.2016.01369","article-title":"Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): a review","volume":"7","author":"Ghosal","year":"2016","journal-title":"Front. Microbiol."},{"key":"B28","doi-asserted-by":"publisher","first-page":"167","DOI":"10.1016\/j.ebiom.2014.11.004","article-title":"Diversity and composition of the adult fecal microbiome associated with history of cesarean birth or appendectomy: Analysis of the American Gut Project","volume":"1","author":"Goedert","year":"2014","journal-title":"EBioMed."},{"key":"B29","doi-asserted-by":"publisher","first-page":"158","DOI":"10.1038\/s41598-017-18596-0","article-title":"Increased abundance of clostridium and fusobacterium in gastric microbiota of patients with gastric cancer in Taiwan","volume":"8","author":"Hsieh","year":"2018","journal-title":"Sci. Rep."},{"key":"B30","doi-asserted-by":"publisher","first-page":"768","DOI":"10.1038\/nprot.2015.046","article-title":"Optimized DNA extraction and metagenomic sequencing of airborne microbial communities","volume":"10","author":"Jiang","year":"2015","journal-title":"Nat. Protoc."},{"key":"B31","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1146\/annurev-genom-083115-022438","article-title":"The microbiome and human biology","volume":"18","author":"Knight","year":"2017","journal-title":"Annu. Rev. Genomics Hum. Genet."},{"key":"B32","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/s41579-018-0029-9","article-title":"Best practices for analysing microbiomes","volume":"16","author":"Knight","year":"2018","journal-title":"Nat. Rev. Microbiol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"Langmead","year":"2012","journal-title":"Nat. Methods"},{"key":"B34","doi-asserted-by":"publisher","first-page":"1113","DOI":"10.1053\/j.gastro.2016.01.028","article-title":"Association between Helicobacter pylori eradication and gastric cancer incidence: a systematic review and meta-analysis","volume":"150","author":"Lee","year":"2016","journal-title":"Gastroenterology"},{"key":"B35","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1136\/gutjnl-2013-305178","article-title":"Gastric colonisation with a restricted commensal microbiota replicates the promotion of neoplastic lesions by diverse intestinal microbiota in the Helicobacter pylori INS-GAS mouse model of gastric carcinogenesis","volume":"63","author":"Lertpiriyapong","year":"2014","journal-title":"Gut"},{"key":"B36","doi-asserted-by":"publisher","first-page":"44935","DOI":"10.1038\/srep44935","article-title":"Alterations in gastric microbiota after, H. Pylori eradication and in different histological stages of gastric carcinogenesis","volume":"7","author":"Li","year":"2017","journal-title":"Sci. Rep"},{"key":"B37","doi-asserted-by":"publisher","first-page":"e39522","DOI":"10.1371\/journal.pone.0039522","article-title":"Carotenoids play a positive role in the degradation of heterocycles by Sphingobium yanoikuyae","volume":"7","author":"Liu","year":"2012","journal-title":"PLoS ONE"},{"key":"B38","doi-asserted-by":"publisher","first-page":"210","DOI":"10.1053\/j.gastro.2010.09.048","article-title":"Lack of commensal flora in Helicobacter pylori-infected INS-GAS mice reduces gastritis and delays intraepithelial neoplasia","volume":"140","author":"Lofgren","year":"2011","journal-title":"Gastroenterology"},{"key":"B39","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nrmicro3344","article-title":"The gut microbiota, bacterial metabolites and colorectal cancer","volume":"12","author":"Louis","year":"2014","journal-title":"Nat. Rev. Microbiol."},{"key":"B40","doi-asserted-by":"publisher","first-page":"220","DOI":"10.1038\/nature11550","article-title":"Diversity, stability and resilience of the human gut microbiota","volume":"489","author":"Lozupone","year":"2012","journal-title":"Nature"},{"key":"B41","doi-asserted-by":"publisher","first-page":"2369","DOI":"10.1056\/NEJMra1600266","article-title":"The human intestinal microbiome in health and disease","volume":"375","author":"Lynch","year":"2016","journal-title":"N. Engl. J. Med."},{"key":"B42","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1093\/jnci\/djs003","article-title":"Fifteen-year effects of Helicobacter pylori, garlic, and vitamin treatments on gastric cancer incidence and mortality","volume":"104","author":"Ma","year":"2012","journal-title":"J. Natl. Cancer Inst."},{"key":"B43","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/s40168-018-0426-3","article-title":"Improving saliva shotgun metagenomics by chemical host DNA depletion","volume":"6","author":"Marotz","year":"2018","journal-title":"Microbiome"},{"key":"B44","doi-asserted-by":"publisher","first-page":"255","DOI":"10.1177\/2050640614566846","article-title":"The human gastric microbiota: Is it time to rethink the pathogenesis of stomach diseases","volume":"3","author":"Nardone","year":"2015","journal-title":"United Eur. Gastroenterol. J"},{"key":"B45","doi-asserted-by":"publisher","first-page":"6777","DOI":"10.1158\/0008-5472.CAN-17-1296","article-title":"Oral microbiome composition reflects prospective risk for esophageal cancers","volume":"77","author":"Peters","year":"2017","journal-title":"Cancer Res."},{"key":"B46","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1038\/nrc2857","article-title":"Helicobacter pylori: gastric cancer and beyond","volume":"10","author":"Polk","year":"2010","journal-title":"Nat. Rev. Cancer"},{"key":"B47","doi-asserted-by":"publisher","first-page":"1211","DOI":"10.1038\/nbt1217-1211b","article-title":"Corrigendum: Shotgun metagenomics, from sampling to analysis","volume":"5","author":"Quince","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B48","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1038\/nrc2541","article-title":"Toll-like receptors and cancer","volume":"9","author":"Rakoff-Nahoum","year":"2009","journal-title":"Nat. Rev. Cancer"},{"key":"B49","doi-asserted-by":"publisher","first-page":"260","DOI":"10.1097\/MPA.0000000000000726","article-title":"Disturbances of the perioperative microbiome across multiple body sites in patients undergoing pancreaticoduodenectomy","volume":"46","author":"Rogers","year":"2017","journal-title":"Pancreas"},{"key":"B50","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1038\/nrc.2017.13","article-title":"Microbiota: a key orchestrator of cancer therapy","volume":"17","author":"Roy","year":"2017","journal-title":"Nat. Rev. Cancer"},{"key":"B51","doi-asserted-by":"publisher","first-page":"399","DOI":"10.1093\/carcin\/bgr284","article-title":"Association between oral health and gastric precancerous lesions","volume":"33","author":"Salazar","year":"2012","journal-title":"Carcinogenesis"},{"key":"B52","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/j.chom.2014.02.007","article-title":"Microbes, microbiota, and colon cancer","volume":"15","author":"Sears","year":"2014","journal-title":"Cell Host Microbe"},{"key":"B53","doi-asserted-by":"publisher","first-page":"R42","DOI":"10.1186\/gb-2012-13-6-r42","article-title":"Composition of the adult digestive tract bacterial microbiome based on seven mouth surfaces, tonsils, throat and stool samples","volume":"13","author":"Segata","year":"","journal-title":"Genome Biol."},{"key":"B54","doi-asserted-by":"publisher","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":"B55","doi-asserted-by":"publisher","first-page":"811","DOI":"10.1038\/nmeth.2066","article-title":"Metagenomic microbial community profiling using unique clade-specific marker genes","volume":"9","author":"Segata","year":"","journal-title":"Nat. Methods"},{"key":"B56","doi-asserted-by":"publisher","first-page":"692","DOI":"10.1038\/nrgastro.2017.140","article-title":"Gastric cancer: the gastric microbiota - bacterial diversity and implications","volume":"14","author":"Shah","year":"2017","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"B57","doi-asserted-by":"publisher","first-page":"1077","DOI":"10.1038\/nbt.3981","article-title":"Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium","volume":"35","author":"Sinha","year":"2017","journal-title":"Nat. Biotechnol."},{"key":"B58","doi-asserted-by":"publisher","first-page":"270","DOI":"10.3389\/fmicb.2018.00270","article-title":"Comparison of Meconium DNA Extraction Methods for Use in Microbiome Studies","volume":"9","author":"Stinson","year":"2018","journal-title":"Front. Microbiol."},{"key":"B59","doi-asserted-by":"publisher","first-page":"2217","DOI":"10.3892\/or.2018.6286","article-title":"A screening method for gastric cancer by oral microbiome detection","volume":"39","author":"Sun","year":"2018","journal-title":"Oncol. Rep."},{"key":"B60","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1093\/bioinformatics\/btu739","article-title":"UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches","volume":"31","author":"Suzek","year":"2015","journal-title":"Bioinformatics"},{"key":"B61","doi-asserted-by":"publisher","first-page":"87","DOI":"10.3322\/caac.21262","article-title":"Global cancer statistics, 2012","volume":"65","author":"Torre","year":"2015","journal-title":"CA Cancer J. Clin."},{"key":"B62","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1038\/ismej.2013.33","article-title":"Immune status, antibiotic medication and pH are associated with changes in the stomach fluid microbiota","volume":"7","author":"von Rosenvinge","year":"2013","journal-title":"ISME J."},{"key":"B63","doi-asserted-by":"publisher","first-page":"e83744","DOI":"10.1371\/journal.pone.0083744","article-title":"Microbial dysbiosis is associated with human breast cancer","volume":"9","author":"Xuan","year":"2014","journal-title":"PLoS ONE"},{"key":"B64","doi-asserted-by":"publisher","first-page":"18594","DOI":"10.1038\/srep18594","article-title":"Different gastric microbiota compositions in two human populations with high and low gastric cancer risk in Colombia","volume":"6","author":"Yang","year":"2016","journal-title":"Sci. Rep."},{"key":"B65","doi-asserted-by":"publisher","first-page":"474","DOI":"10.1007\/s13238-018-0543-6","article-title":"The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get","volume":"9","author":"Yang","year":"2018","journal-title":"Protein Cell"},{"key":"B66","doi-asserted-by":"publisher","first-page":"e1000465","DOI":"10.1371\/journal.pcbi.1000465","article-title":"A parsimony approach to biological pathway reconstruction\/inference for genomes and metagenomes","volume":"5","author":"Ye","year":"2009","journal-title":"PLoS Comput. Biol."},{"key":"B67","doi-asserted-by":"publisher","first-page":"302","DOI":"10.3389\/fcimb.2017.00302","article-title":"Molecular characterization of the human stomach microbiota in gastric cancer patients","volume":"7","author":"Yu","year":"2017","journal-title":"Front. Cell. Infect. Microbiol."},{"key":"B68","doi-asserted-by":"publisher","first-page":"11773","DOI":"10.1038\/s41598-017-11779-9","article-title":"Variations in oral microbiota associated with oral cancer","volume":"7","author":"Zhao","year":"2017","journal-title":"Sci. Rep."}],"container-title":["Frontiers in Cellular and Infection Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2018.00433\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,12,12]],"date-time":"2018-12-12T09:15:49Z","timestamp":1544606149000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fcimb.2018.00433\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,12,12]]},"references-count":68,"alternative-id":["10.3389\/fcimb.2018.00433"],"URL":"https:\/\/doi.org\/10.3389\/fcimb.2018.00433","relation":{},"ISSN":["2235-2988"],"issn-type":[{"value":"2235-2988","type":"electronic"}],"subject":[],"published":{"date-parts":[[2018,12,12]]},"article-number":"433"}}