{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,5]],"date-time":"2026-10-05T20:09:38Z","timestamp":1791230978563,"version":"4.1.0"},"reference-count":55,"publisher":"American Society for Microbiology","issue":"10","license":[{"start":{"date-parts":[[2017,10,1]],"date-time":"2017-10-01T00:00:00Z","timestamp":1506816000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100005009","name":"Assar Gabrielssons Foundation","doi-asserted-by":"crossref","award":["FB11-68"],"award-info":[{"award-number":["FB11-68"]}],"id":[{"id":"10.13039\/501100005009","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100005009","name":"Assar Gabrielssons Foundation","doi-asserted-by":"crossref","award":["FB12-84"],"award-info":[{"award-number":["FB12-84"]}],"id":[{"id":"10.13039\/501100005009","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100001729","name":"Swedish Foundation for Strategic Research","doi-asserted-by":"crossref","award":["SB12-0072"],"award-info":[{"award-number":["SB12-0072"]}],"id":[{"id":"10.13039\/501100001729","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Bioinformatics Infrastructure for Life Science"},{"DOI":"10.13039\/501100004063","name":"Knut och Alice Wallenbergs Stiftelse","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004063","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["K2012-56X-22029-01-3"],"award-info":[{"award-number":["K2012-56X-22029-01-3"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004359","name":"Vetenskapsr\u00e5det","doi-asserted-by":"publisher","award":["2012-3329"],"award-info":[{"award-number":["2012-3329"]}],"id":[{"id":"10.13039\/501100004359","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001858","name":"VINNOVA","doi-asserted-by":"publisher","award":["2011-03491"],"award-info":[{"award-number":["2011-03491"]}],"id":[{"id":"10.13039\/501100001858","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["Infect Immun"],"published-print":{"date-parts":[[2017,10]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>Emerging evidence shows that the human microbiota plays a larger role in disease progression and health than previously anticipated.<jats:named-content content-type=\"genus-species\">Helicobacter pylori<\/jats:named-content>, the causative agent of gastric cancer and duodenal and gastric ulcers, was early associated with gastric disease, but it has also been proposed that the accompanying microbiota in<jats:named-content content-type=\"genus-species\">Helicobacter pylori<\/jats:named-content>-infected individuals might affect disease progression and gastric cancer development. In this study, the composition of the transcriptionally active microbial community and<jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>gene expression were determined using metatranscriptomic RNA sequencing of stomach biopsy specimens from individuals with different<jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>infection statuses and premalignant tissue changes. The results show that<jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>completely dominates the microbiota not only in infected individuals but also in most individuals classified as<jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>uninfected using conventional methods. Furthermore,<jats:named-content content-type=\"genus-species\">H. pylori<\/jats:named-content>abundance is positively correlated with the presence of<jats:named-content content-type=\"genus-species\">Campylobacter<\/jats:named-content>,<jats:named-content content-type=\"genus-species\">Deinococcus<\/jats:named-content>, and<jats:named-content content-type=\"genus-species\">Sulfurospirillum<\/jats:named-content>. Finally, we quantified the expression of a large number of<jats:named-content content-type=\"genus-species\">Helicobacter pylori<\/jats:named-content>genes and found high expression of genes involved in pH regulation and nickel transport. Our study is the first to dissect the viable microbiota of the human stomach by metatranscriptomic analysis, and it shows that metatranscriptomic analysis of the gastric microbiota is feasible and can provide new insights into how bacteria respond<jats:italic>in vivo<\/jats:italic>to variations in the stomach microenvironment and at different stages of disease progression.<\/jats:p>","DOI":"10.1128\/iai.00031-17","type":"journal-article","created":{"date-parts":[[2017,7,11]],"date-time":"2017-07-11T00:20:11Z","timestamp":1499732411000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":72,"title":["<i>In Vivo<\/i>Analysis of the Viable Microbiota and Helicobacter pylori Transcriptome in Gastric Infection and Early Stages of Carcinogenesis"],"prefix":"10.1128","volume":"85","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4447-8968","authenticated-orcid":false,"given":"Kaisa","family":"Thorell","sequence":"first","affiliation":[{"name":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden"},{"name":"Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Johan","family":"Bengtsson-Palme","sequence":"additional","affiliation":[{"name":"Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"},{"name":"Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Oscar Hsin-Fu","family":"Liu","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Reyna Victoria","family":"Palacios Gonzales","sequence":"additional","affiliation":[{"name":"Laboratorio de Patolog\u00eda, Hospital Salud Integral, Managua, Nicaragua"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Intawat","family":"Nookaew","sequence":"additional","affiliation":[{"name":"Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"},{"name":"Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda","family":"Rabeneck","sequence":"additional","affiliation":[{"name":"Department of Medicine, University of Toronto, and Cancer Care Ontario, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lawrence","family":"Paszat","sequence":"additional","affiliation":[{"name":"Dalla Lana School of Public Health, University of Toronto, Toronto, Ontario, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David Y.","family":"Graham","sequence":"additional","affiliation":[{"name":"Department of Medicine, Michael E. DeBakey VA Medical Center and Baylor College of Medicine, Houston, Texas, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9955-6003","authenticated-orcid":false,"given":"Jens","family":"Nielsen","sequence":"additional","affiliation":[{"name":"Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samuel B.","family":"Lundin","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"},{"name":"Marshall Centre for Infectious Diseases Research and Training, University of Western Australia, Nedlands, Western Australia, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"\u00c5sa","family":"Sj\u00f6ling","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden"},{"name":"Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(84)91816-6"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1097\/00000658-198803000-00020"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-013-0192-5"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1590\/S1807-59322007000100008"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0506655103"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep04202"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2010.149"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep44935"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002836"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0007985"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gtc.2013.01.004"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1056\/NEJMoa001999"},{"key":"e_1_3_3_14_2","doi-asserted-by":"crossref","first-page":"192","DOI":"10.25100\/cm.v44i3.1263","article-title":"Gastric cancer: overview","volume":"44","author":"Piazuelo MB","year":"2013","unstructured":"Piazuelo MB Correa P . 2013. Gastric cancer: overview. Colomb Med (Cali)44:192\u2013201.","journal-title":"Colomb Med (Cali)"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2015.09.004"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1007\/978-3-319-41388-4_19"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.007302-0"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1111\/hel.12293"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1038\/srep18594"},{"key":"e_1_3_3_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1751-2980.2011.00550.x"},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1111\/1755-0998.12399"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.1111\/1751-2980.12116"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523-5378.2007.00526.x"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkr771"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10552-012-0117-5"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2010.04.008"},{"key":"e_1_3_3_27_2","doi-asserted-by":"publisher","DOI":"10.1186\/1755-8794-6-41"},{"key":"e_1_3_3_28_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1523-5378.2009.00692.x"},{"key":"e_1_3_3_29_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.1005312"},{"key":"e_1_3_3_30_2","doi-asserted-by":"publisher","DOI":"10.1038\/nature08756"},{"key":"e_1_3_3_31_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.10.5488-5495.2000"},{"key":"e_1_3_3_32_2","doi-asserted-by":"publisher","DOI":"10.1086\/368133"},{"key":"e_1_3_3_33_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.188.10.3449-3462.2006"},{"key":"e_1_3_3_34_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.01275-10"},{"key":"e_1_3_3_35_2","first-page":"1123","article-title":"Differential expression of laminin chains and their integrin receptors in human gastric mucosa","volume":"147","author":"Virtanen I","year":"1995","unstructured":"Virtanen I Tani T Back N Happola O Laitinen L Kiviluoto T Salo J Burgeson RE Lehto VP Kivilaakso E . 1995. Differential expression of laminin chains and their integrin receptors in human gastric mucosa. Am J Pathol147:1123\u20131132.","journal-title":"Am J Pathol"},{"key":"e_1_3_3_36_2","first-page":"781","article-title":"Alpha 6 beta 4 integrin and newly deposited laminin-1 and laminin-5 form the adhesion mechanism of gastric carcinoma. Continuous expression of laminins but not that of collagen VII is preserved in invasive parts of the carcinomas: implications for acquisition of the invading phenotype","volume":"149","author":"Tani T","year":"1996","unstructured":"Tani T Karttunen T Kiviluoto T Kivilaakso E Burgeson RE Sipponen P Virtanen I . 1996. Alpha 6 beta 4 integrin and newly deposited laminin-1 and laminin-5 form the adhesion mechanism of gastric carcinoma. Continuous expression of laminins but not that of collagen VII is preserved in invasive parts of the carcinomas: implications for acquisition of the invading phenotype. Am J Pathol149:781\u2013793.","journal-title":"Am J Pathol"},{"key":"e_1_3_3_37_2","doi-asserted-by":"publisher","DOI":"10.1126\/sciadv.1500183"},{"key":"e_1_3_3_38_2","doi-asserted-by":"publisher","DOI":"10.1128\/CDLI.5.3.288-293.1998"},{"key":"e_1_3_3_39_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0035827"},{"key":"e_1_3_3_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr026"},{"key":"e_1_3_3_41_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2006.13.1028"},{"key":"e_1_3_3_42_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gks1219"},{"key":"e_1_3_3_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ecoinf.2016.04.004"},{"key":"e_1_3_3_44_2","unstructured":"Oksanen J Blanchet FG Friendly M Kindt R Legendre P McGlinn D Minchin PR O'Hara RB Simpson GL Solymos PM Stevens HH Szoecs E Wagner H . 2017. vegan: community ecology package. https:\/\/cran.r-project.org\/web\/packages\/vegan\/."},{"key":"e_1_3_3_45_2","doi-asserted-by":"publisher","DOI":"10.14806\/ej.17.1.200"},{"key":"e_1_3_3_46_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.2584"},{"key":"e_1_3_3_47_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12862-016-0619-y"},{"key":"e_1_3_3_48_2","doi-asserted-by":"publisher","DOI":"10.1089\/cmb.2012.0021"},{"key":"e_1_3_3_49_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu153"},{"key":"e_1_3_3_50_2","doi-asserted-by":"publisher","DOI":"10.2390\/biecoll-jib-2013-233"},{"key":"e_1_3_3_51_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.7.4155-4168.2000"},{"key":"e_1_3_3_52_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00535-014-0938-y"},{"key":"e_1_3_3_53_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btq461"},{"key":"e_1_3_3_54_2","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3519"},{"key":"e_1_3_3_55_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkv007"},{"key":"e_1_3_3_56_2","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2386-y"}],"container-title":["Infection and Immunity"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00031-17","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/IAI.00031-17","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,6,21]],"date-time":"2025-06-21T20:55:20Z","timestamp":1750539320000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/IAI.00031-17"}},"subtitle":[],"editor":[{"given":"Vincent B.","family":"Young","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,10]]},"references-count":55,"journal-issue":{"issue":"10","published-print":{"date-parts":[[2017,10]]}},"alternative-id":["10.1128\/IAI.00031-17"],"URL":"https:\/\/doi.org\/10.1128\/iai.00031-17","relation":{},"ISSN":["0019-9567","1098-5522"],"issn-type":[{"value":"0019-9567","type":"print"},{"value":"1098-5522","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10]]},"assertion":[{"value":"2017-01-13","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-07-07","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2017-09-20","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00031-17"}}