{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T21:13:07Z","timestamp":1790802787341,"version":"4.1.0"},"reference-count":64,"publisher":"American Society for Microbiology","issue":"2","license":[{"start":{"date-parts":[[2019,3,13]],"date-time":"2019-03-13T00:00:00Z","timestamp":1552435200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2019,4,24]],"date-time":"2019-04-24T00:00:00Z","timestamp":1556064000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/100008269","name":"U-M | Michigan Institute for Clinical and Health Research","doi-asserted-by":"publisher","award":["UL1TR000433"],"award-info":[{"award-number":["UL1TR000433"]}],"id":[{"id":"10.13039\/100008269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000038","name":"HHS | U.S. Food and Drug Administration","doi-asserted-by":"publisher","award":["HHSF223201000082C"],"award-info":[{"award-number":["HHSF223201000082C"]}],"id":[{"id":"10.13039\/100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000060","name":"HHS | NIH | National Institute of Allergy and Infectious Diseases","doi-asserted-by":"publisher","award":["5U01AI124255-03"],"award-info":[{"award-number":["5U01AI124255-03"]}],"id":[{"id":"10.13039\/100000060","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["mSphere"],"published-print":{"date-parts":[[2019,4,24]]},"abstract":"<jats:p>The gut microbiota are linked to a variety of gastrointestinal diseases, including inflammatory bowel disease. Despite this importance, microbiota dynamics in the upper gastrointestinal tract are understudied. Our article seeks to understand what factors impact microbiota dynamics in the healthy human upper gut. We found that the upper gastrointestinal tract contains consistently prevalent bacterial OTUs that dominate the overall community. Microbiota variability is highest in the stomach and duodenum and correlates with pH.<\/jats:p>","DOI":"10.1128\/msphere.00126-19","type":"journal-article","created":{"date-parts":[[2019,3,12]],"date-time":"2019-03-12T06:29:56Z","timestamp":1552372196000},"update-policy":"https:\/\/doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":91,"title":["Spatial and Temporal Analysis of the Stomach and Small-Intestinal Microbiota in Fasted Healthy Humans"],"prefix":"10.1128","volume":"4","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2586-7498","authenticated-orcid":false,"given":"Anna M.","family":"Seekatz","sequence":"first","affiliation":[{"name":"Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0797-8357","authenticated-orcid":false,"given":"Matthew K.","family":"Schnizlein","sequence":"additional","affiliation":[{"name":"Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8287-784X","authenticated-orcid":false,"given":"Mark J.","family":"Koenigsknecht","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA"},{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason R.","family":"Baker","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6158-2871","authenticated-orcid":false,"given":"William L.","family":"Hasler","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Gastroenterology and Hepatology, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4299-0829","authenticated-orcid":false,"given":"Barry E.","family":"Bleske","sequence":"additional","affiliation":[{"name":"Department of Pharmacy Practice and Administrative Sciences, University of New Mexico, Albuquerque, New Mexico, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3687-2364","authenticated-orcid":false,"given":"Vincent B.","family":"Young","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Division of Infectious Disease, University of Michigan, Ann Arbor, Michigan, USA"},{"name":"Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Duxin","family":"Sun","sequence":"additional","affiliation":[{"name":"Department of Pharmaceutical Sciences, College of Pharmacy, University of Michigan, Ann Arbor, Michigan, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"235","reference":[{"key":"e_1_3_2_2_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.copbio.2014.09.005"},{"key":"e_1_3_2_3_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0016-5085(73)80008-3"},{"key":"e_1_3_2_4_2","doi-asserted-by":"publisher","DOI":"10.1097\/MOG.0000000000000057"},{"key":"e_1_3_2_5_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.biochi.2017.05.019"},{"key":"e_1_3_2_6_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2018.03.011"},{"key":"e_1_3_2_7_2","doi-asserted-by":"publisher","DOI":"10.1158\/1940-6207.CAPR-17-0370"},{"key":"e_1_3_2_8_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41564-018-0143-5"},{"key":"e_1_3_2_9_2","doi-asserted-by":"publisher","DOI":"10.1152\/physrev.00045.2009"},{"key":"e_1_3_2_10_2","doi-asserted-by":"publisher","DOI":"10.1038\/nrmicro3552"},{"key":"e_1_3_2_11_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2018.08.041"},{"key":"e_1_3_2_12_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.45935-0"},{"key":"e_1_3_2_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.femsec.2005.03.012"},{"key":"e_1_3_2_14_2","doi-asserted-by":"publisher","DOI":"10.1046\/j.1365-2672.2003.02005.x"},{"key":"e_1_3_2_15_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-230X-13-131"},{"key":"e_1_3_2_16_2","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.64"},{"key":"e_1_3_2_17_2","doi-asserted-by":"publisher","DOI":"10.1111\/nyas.13127"},{"key":"e_1_3_2_18_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00203-018-1505-3"},{"key":"e_1_3_2_19_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1462-2920.2010.02294.x"},{"key":"e_1_3_2_20_2","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6941.12127"},{"key":"e_1_3_2_21_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0137784"},{"key":"e_1_3_2_22_2","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2011.212"},{"key":"e_1_3_2_23_2","doi-asserted-by":"publisher","DOI":"10.3109\/00365521.2015.1018937"},{"key":"e_1_3_2_24_2","doi-asserted-by":"publisher","DOI":"10.1038\/nmicrobiol.2016.267"},{"key":"e_1_3_2_25_2","doi-asserted-by":"publisher","DOI":"10.1021\/acs.molpharmaceut.6b00641"},{"key":"e_1_3_2_26_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gendis.2017.06.001"},{"key":"e_1_3_2_27_2","doi-asserted-by":"publisher","DOI":"10.1126\/scitranslmed.3003605"},{"key":"e_1_3_2_28_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0116894"},{"key":"e_1_3_2_29_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0040758"},{"key":"e_1_3_2_30_2","doi-asserted-by":"publisher","DOI":"10.7717\/peerj.3437"},{"key":"e_1_3_2_31_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005706"},{"key":"e_1_3_2_32_2","doi-asserted-by":"publisher","DOI":"10.1186\/2049-2618-1-9"},{"key":"e_1_3_2_33_2","doi-asserted-by":"publisher","DOI":"10.1016\/S0016-5085(82)80140-6"},{"key":"e_1_3_2_34_2","doi-asserted-by":"publisher","DOI":"10.1099\/mic.0.000496"},{"key":"e_1_3_2_35_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.0904847106"},{"key":"e_1_3_2_36_2","doi-asserted-by":"publisher","DOI":"10.1186\/gb-2011-12-5-r50"},{"key":"e_1_3_2_37_2","doi-asserted-by":"publisher","DOI":"10.1073\/pnas.1000087107"},{"key":"e_1_3_2_38_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-23198-5"},{"key":"e_1_3_2_39_2","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-012-2165-9"},{"key":"e_1_3_2_40_2","doi-asserted-by":"publisher","DOI":"10.1093\/ecco-jcc\/jjw157"},{"key":"e_1_3_2_41_2","doi-asserted-by":"publisher","DOI":"10.1042\/CS20171110"},{"key":"e_1_3_2_42_2","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.12694"},{"key":"e_1_3_2_43_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.chom.2014.02.005"},{"key":"e_1_3_2_44_2","volume-title":"Streptococcus pyogenes: basic biology to clinical manifestations","author":"Pancholi V","year":"2016","unstructured":"Pancholi V, Caparon C. 2016. Streptococcus pyogenes metabolism. In Ferretti JJ, Stevens DL, Fischetti VA (ed), Streptococcus pyogenes: basic biology to clinical manifestations. University of Oklahoma Health Sciences Center, Oklahoma City, OK."},{"key":"e_1_3_2_45_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.phrs.2012.10.020"},{"key":"e_1_3_2_46_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.ejpb.2016.11.034"},{"key":"e_1_3_2_47_2","doi-asserted-by":"publisher","DOI":"10.1111\/1574-6976.12076"},{"key":"e_1_3_2_48_2","doi-asserted-by":"publisher","DOI":"10.1159\/000016487"},{"key":"e_1_3_2_49_2","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0000000000000382"},{"key":"e_1_3_2_50_2","doi-asserted-by":"publisher","DOI":"10.1002\/14651858.CD008870.pub2"},{"key":"e_1_3_2_51_2","doi-asserted-by":"publisher","DOI":"10.1159\/000480231"},{"key":"e_1_3_2_52_2","doi-asserted-by":"publisher","DOI":"10.1053\/j.gastro.2004.06.002"},{"key":"e_1_3_2_53_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gtc.2017.05.011"},{"key":"e_1_3_2_54_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.aan4834"},{"key":"e_1_3_2_55_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.gie.2011.03.1183"},{"key":"e_1_3_2_56_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00459-15"},{"key":"e_1_3_2_57_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01043-13"},{"key":"e_1_3_2_58_2","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.01541-09"},{"key":"e_1_3_2_59_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm864"},{"key":"e_1_3_2_60_2","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btr381"},{"key":"e_1_3_2_61_2","doi-asserted-by":"publisher","DOI":"10.1128\/mSphereDirect.00073-17"},{"key":"e_1_3_2_62_2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkn879"},{"key":"e_1_3_2_63_2","doi-asserted-by":"publisher","DOI":"10.1080\/STA-200066418"},{"key":"e_1_3_2_64_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v067.i01"},{"key":"e_1_3_2_65_2","doi-asserted-by":"publisher","DOI":"10.18637\/jss.v082.i13"}],"container-title":["mSphere"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSphere.00126-19","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/mSphere.00126-19","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,7]],"date-time":"2022-03-07T23:16:18Z","timestamp":1646694978000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/mSphere.00126-19"}},"subtitle":[],"editor":[{"given":"Katherine","family":"McMahon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,4,24]]},"references-count":64,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2019,4,24]]}},"alternative-id":["10.1128\/mSphere.00126-19"],"URL":"https:\/\/doi.org\/10.1128\/msphere.00126-19","relation":{"has-preprint":[{"id-type":"doi","id":"10.1101\/450221","asserted-by":"object"}]},"ISSN":["2379-5042"],"issn-type":[{"value":"2379-5042","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,24]]},"assertion":[{"value":"2019-02-22","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-02-23","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-03-13","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"e00126-19"}}