{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,11,2]],"date-time":"2026-11-02T19:14:50Z","timestamp":1793646890131,"version":"4.5.1"},"reference-count":41,"publisher":"Springer Science and Business Media LLC","issue":"9","license":[{"start":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T00:00:00Z","timestamp":1583452800000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0"},{"start":{"date-parts":[[2020,3,6]],"date-time":"2020-03-06T00:00:00Z","timestamp":1583452800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Dig Dis Sci"],"published-print":{"date-parts":[[2020,9]]},"DOI":"10.1007\/s10620-020-06173-x","type":"journal-article","created":{"date-parts":[[2020,3,5]],"date-time":"2020-03-05T22:02:43Z","timestamp":1583445763000},"page":"2595-2604","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":133,"title":["Mapping the Segmental Microbiomes in the Human Small Bowel in Comparison with Stool: A REIMAGINE Study"],"prefix":"10.1007","volume":"65","author":[{"given":"Gabriela G. S.","family":"Leite","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Stacy","family":"Weitsman","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gonzalo","family":"Parodi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shreya","family":"Celly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashin","family":"Sedighi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maritza","family":"Sanchez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Walter","family":"Morales","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria Jesus","family":"Villanueva-Millan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gillian M.","family":"Barlow","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruchi","family":"Mathur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon K.","family":"Lo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laith H.","family":"Jamil","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shirley","family":"Paski","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Rezaie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Pimentel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,3,6]]},"reference":[{"key":"6173_CR1","doi-asserted-by":"publisher","first-page":"804","DOI":"10.1038\/nature06244","volume":"449","author":"PJ Turnbaugh","year":"2007","unstructured":"Turnbaugh PJ, Ley RE, Hamady M, Fraser-Liggett CM, Knight R, Gordon JI. The human microbiome project. Nature. 2007;449:804\u2013810.","journal-title":"Nature"},{"key":"6173_CR2","doi-asserted-by":"publisher","first-page":"1694","DOI":"10.1126\/science.1177486","volume":"326","author":"EK Costello","year":"2009","unstructured":"Costello EK, Lauber CL, Hamady M, Fierer N, Gordon JI, Knight R. Bacterial community variation in human body habitats across space and time. Science. 2009;326:1694\u20131697.","journal-title":"Science"},{"key":"6173_CR3","doi-asserted-by":"publisher","first-page":"300","DOI":"10.1264\/jsme2.ME17017","volume":"32","author":"ET Hillman","year":"2017","unstructured":"Hillman ET, Lu H, Yao T, Nakatsu CH. Microbial ecology along the gastrointestinal tract. Microbes Environ.. 2017;32:300\u2013313.","journal-title":"Microbes Environ."},{"key":"6173_CR4","doi-asserted-by":"publisher","first-page":"247","DOI":"10.1016\/j.anaerobe.2005.05.001","volume":"11","author":"CL Sears","year":"2005","unstructured":"Sears CL. A dynamic partnership: celebrating our gut flora. Anaerobe. 2005;11:247\u2013251.","journal-title":"Anaerobe"},{"key":"6173_CR5","doi-asserted-by":"publisher","first-page":"207","DOI":"10.1038\/nature11234","volume":"486","author":"HMP Consortium","year":"2012","unstructured":"Consortium HMP. Structure, function and diversity of the healthy human microbiome. Nature. 2012;486:207\u2013214.","journal-title":"Nature"},{"key":"6173_CR6","doi-asserted-by":"publisher","first-page":"1027","DOI":"10.1038\/nature05414","volume":"444","author":"PJ Turnbaugh","year":"2006","unstructured":"Turnbaugh PJ, Ley RE, Mahowald MA, Magrini V, Mardis ER, Gordon JI. An obesity-associated gut microbiome with increased capacity for energy harvest. Nature. 2006;444:1027\u20131031.","journal-title":"Nature"},{"key":"6173_CR7","doi-asserted-by":"publisher","first-page":"11070","DOI":"10.1073\/pnas.0504978102","volume":"102","author":"RE Ley","year":"2005","unstructured":"Ley RE, Backhed F, Turnbaugh P, Lozupone CA, Knight RD, Gordon JI. Obesity alters gut microbial ecology. Proc Natl Acad Sci USA. 2005;102:11070\u201311075.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6173_CR8","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1136\/gut.2005.073817","volume":"55","author":"C Manichanh","year":"2006","unstructured":"Manichanh C, Rigottier-Gois L, Bonnaud E, et al. Reduced diversity of faecal microbiota in Crohn\u2019s disease revealed by a metagenomic approach. Gut. 2006;55:205\u2013211.","journal-title":"Gut"},{"key":"6173_CR9","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1111\/j.1758-2229.2012.00327.x","volume":"4","author":"A Durban","year":"2012","unstructured":"Durban A, Abellan JJ, Jimenez-Hernandez N, et al. Structural alterations of faecal and mucosa-associated bacterial communities in irritable bowel syndrome. Environ Microbiol Rep. 2012;4:242\u2013247.","journal-title":"Environ Microbiol Rep"},{"key":"6173_CR10","doi-asserted-by":"publisher","first-page":"2194","DOI":"10.1111\/j.1462-2920.2009.01941.x","volume":"11","author":"TD Leser","year":"2009","unstructured":"Leser TD, Molbak L. Better living through microbial action: the benefits of the mammalian gastrointestinal microbiota on the host. Environ Microbiol. 2009;11:2194\u20132206.","journal-title":"Environ Microbiol"},{"key":"6173_CR11","doi-asserted-by":"publisher","first-page":"S-450","DOI":"10.1016\/S0016-5085(19)37978-8","volume":"156","author":"R Sedighi","year":"2019","unstructured":"Sedighi R, Mathur R, Celly S, et al. Sa1912\u2014revealing the entire intestinal microbiota and its associations to the genetic, immunologic, and neuroendocrine ecosystems: methodology for the REIMAGINE study. Gastroenterology. 2019;156:S-450.","journal-title":"Gastroenterology"},{"key":"6173_CR12","doi-asserted-by":"publisher","first-page":"e1002533","DOI":"10.1371\/journal.pbio.1002533","volume":"14","author":"R Sender","year":"2016","unstructured":"Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biol. 2016;14:e1002533.","journal-title":"PLoS Biol"},{"key":"6173_CR13","doi-asserted-by":"publisher","first-page":"481","DOI":"10.1111\/nmo.12516","volume":"27","author":"A Erdogan","year":"2015","unstructured":"Erdogan A, Rao SS, Gulley D, Jacobs C, Lee YY, Badger C. Small intestinal bacterial overgrowth: duodenal aspiration vs glucose breath test. Neurogastroenterol Motil. 2015;27:481\u2013489.","journal-title":"Neurogastroenterol Motil"},{"key":"6173_CR14","doi-asserted-by":"publisher","first-page":"1103","DOI":"10.1111\/apt.12304","volume":"37","author":"C Jacobs","year":"2013","unstructured":"Jacobs C, Coss Adame E, Attaluri A, Valestin J, Rao SS. Dysmotility and proton pump inhibitor use are independent risk factors for small intestinal bacterial and\/or fungal overgrowth. Aliment Pharmacol Ther. 2013;37:1103\u20131111.","journal-title":"Aliment Pharmacol Ther"},{"key":"6173_CR15","doi-asserted-by":"publisher","DOI":"10.1186\/s12866-12019-11617-12861","author":"G Leite","year":"2019","unstructured":"Leite G, Morales W, Weitsman S, et al. Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study. BMC Microbiol. 2019;. https:\/\/doi.org\/10.1186\/s12866-12019-11617-12861.","journal-title":"BMC Microbiol"},{"key":"6173_CR16","doi-asserted-by":"publisher","first-page":"e1","DOI":"10.1093\/nar\/gks808","volume":"41","author":"A Klindworth","year":"2013","unstructured":"Klindworth A, Pruesse E, Schweer T, et al. Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies. Nucleic Acids Res. 2013;41:e1.","journal-title":"Nucleic Acids Res"},{"key":"6173_CR17","doi-asserted-by":"publisher","first-page":"e1003531","DOI":"10.1371\/journal.pcbi.1003531","volume":"10","author":"PJ McMurdie","year":"2014","unstructured":"McMurdie PJ, Holmes S. Waste not, want not: why rarefying microbiome data is inadmissible. PLoS Comput Biol. 2014;10:e1003531.","journal-title":"PLoS Comput Biol"},{"key":"6173_CR18","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1186\/s40168-017-0237-y","volume":"5","author":"S Weiss","year":"2017","unstructured":"Weiss S, Xu ZZ, Peddada S, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5:27.","journal-title":"Microbiome"},{"key":"6173_CR19","doi-asserted-by":"publisher","first-page":"1136","DOI":"10.4014\/jmb.1412.12047","volume":"25","author":"G Li","year":"2015","unstructured":"Li G, Yang M, Zhou K, et al. Diversity of duodenal and rectal microbiota in biopsy tissues and luminal contents in healthy volunteers. J Microbiol Biotechnol. 2015;25:1136\u20131145.","journal-title":"J Microbiol Biotechnol"},{"key":"6173_CR20","doi-asserted-by":"publisher","first-page":"2012","DOI":"10.1038\/s41467-019-09964-7","volume":"10","author":"GB Saffouri","year":"2019","unstructured":"Saffouri GB, Shields-Cutler RR, Chen J, et al. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun. 2019;10:2012.","journal-title":"Nat Commun"},{"key":"6173_CR21","doi-asserted-by":"publisher","first-page":"e00126-19","DOI":"10.1128\/mSphere.00126-19","volume":"4","author":"AM Seekatz","year":"2019","unstructured":"Seekatz AM, Schnizlein MK, Koenigsknecht MJ, et al. Spatial and temporal analysis of the stomach and small-intestinal microbiota in fasted healthy humans. mSphere. 2019;4:e00126-19.","journal-title":"mSphere"},{"key":"6173_CR22","doi-asserted-by":"publisher","first-page":"236","DOI":"10.1099\/jmm.0.022848-0","volume":"60","author":"AP Kerckhoffs","year":"2011","unstructured":"Kerckhoffs AP, Ben-Amor K, Samsom M, et al. Molecular analysis of faecal and duodenal samples reveals significantly higher prevalence and numbers of Pseudomonas aeruginosa in irritable bowel syndrome. J Med Microbiol. 2011;60:236\u2013245.","journal-title":"J Med Microbiol"},{"key":"6173_CR23","doi-asserted-by":"publisher","first-page":"8508","DOI":"10.1038\/srep08508","volume":"5","author":"A Dlugosz","year":"2015","unstructured":"Dlugosz A, Winckler B, Lundin E, et al. No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls. Sci Rep. 2015;5:8508.","journal-title":"Sci Rep"},{"key":"6173_CR24","doi-asserted-by":"publisher","first-page":"410","DOI":"10.3109\/00365521.2015.1116107","volume":"51","author":"CS Chung","year":"2016","unstructured":"Chung CS, Chang PF, Liao CH, et al. Differences of microbiota in small bowel and faeces between irritable bowel syndrome patients and healthy subjects. Scand J Gastroenterol. 2016;51:410\u2013419.","journal-title":"Scand J Gastroenterol"},{"key":"6173_CR25","doi-asserted-by":"publisher","first-page":"1220","DOI":"10.1111\/jgh.14059","volume":"33","author":"G Li","year":"2018","unstructured":"Li G, Yang M, Jin Y, et al. Involvement of shared mucosal-associated microbiota in the duodenum and rectum in diarrhea-predominant irritable bowel syndrome. J Gastroenterol Hepatol. 2018;33:1220\u20131226.","journal-title":"J Gastroenterol Hepatol"},{"key":"6173_CR26","doi-asserted-by":"publisher","first-page":"332","DOI":"10.1097\/MOG.0000000000000057","volume":"30","author":"JM Ridlon","year":"2014","unstructured":"Ridlon JM, Kang DJ, Hylemon PB, Bajaj JS. Bile acids and the gut microbiome. Curr Opin Gastroenterol. 2014;30:332\u2013338.","journal-title":"Curr Opin Gastroenterol"},{"key":"6173_CR27","volume-title":"Lactic Acid Bacteria: Biodiversity and Taxonomy","author":"GE Felis","year":"2014","unstructured":"Felis GE, Pot B. The family Lactobacillaceae. In: Holzapfel WH, Wood BJB, eds. Lactic Acid Bacteria: Biodiversity and Taxonomy. New York: Wiley; 2014."},{"key":"6173_CR28","volume-title":"Lactic Acid Bacteria: Biodiversity and Taxonomy","author":"M du Toit","year":"2014","unstructured":"du Toit M, Huch M, Cho GS, Franz CMAP. The genus Streptococcus. In: Holzapfel WH, Wood BJB, eds. Lactic Acid Bacteria: Biodiversity and Taxonomy. New York: Wiley; 2014."},{"key":"6173_CR29","doi-asserted-by":"publisher","first-page":"86","DOI":"10.3389\/fcimb.2012.00086","volume":"2","author":"E Pessione","year":"2012","unstructured":"Pessione E. Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows. Front Cell Infect Microbiol. 2012;2:86.","journal-title":"Front Cell Infect Microbiol"},{"key":"6173_CR30","doi-asserted-by":"publisher","first-page":"S21","DOI":"10.1038\/sj.ejcn.1601658","volume":"56","author":"G Perdigon","year":"2002","unstructured":"Perdigon G, Maldonado Galdeano C, Valdez JC, Medici M. Interaction of lactic acid bacteria with the gut immune system. Eur J Clin Nutr. 2002;56:S21\u2013S26.","journal-title":"Eur J Clin Nutr"},{"key":"6173_CR31","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s00253-013-5346-3","volume":"98","author":"YT Tsai","year":"2014","unstructured":"Tsai YT, Cheng PC, Pan TM. Anti-obesity effects of gut microbiota are associated with lactic acid bacteria. Appl Microbiol Biotechnol. 2014;98:1\u201310.","journal-title":"Appl Microbiol Biotechnol"},{"key":"6173_CR32","doi-asserted-by":"publisher","first-page":"4041","DOI":"10.1128\/JCM.43.8.4041-4045.2005","volume":"43","author":"YA Warren","year":"2005","unstructured":"Warren YA, Citron DM, Merriam CV, Goldstein EJ. Biochemical differentiation and comparison of Desulfovibrio species and other phenotypically similar genera. J Clin Microbiol. 2005;43:4041\u20134045.","journal-title":"J Clin Microbiol"},{"key":"6173_CR33","doi-asserted-by":"publisher","first-page":"3171","DOI":"10.1073\/pnas.1815661116","volume":"116","author":"SC Peck","year":"2019","unstructured":"Peck SC, Denger K, Burrichter A, Irwin SM, Balskus EP, Schleheck D. A glycyl radical enzyme enables hydrogen sulfide production by the human intestinal bacterium Bilophila wadsworthia. Proc Natl Acad Sci USA. 2019;116:3171\u20133176.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6173_CR34","doi-asserted-by":"publisher","first-page":"9351507","DOI":"10.1155\/2017\/9351507","volume":"2017","author":"G Rizzatti","year":"2017","unstructured":"Rizzatti G, Lopetuso LR, Gibiino G, Binda C, Gasbarrini A. Proteobacteria: a common factor in human diseases. Biomed Res Int. 2017;2017:9351507.","journal-title":"Biomed Res Int"},{"key":"6173_CR35","doi-asserted-by":"publisher","first-page":"1016","DOI":"10.1177\/154405910808701104","volume":"87","author":"BJ Keijser","year":"2008","unstructured":"Keijser BJ, Zaura E, Huse SM, et al. Pyrosequencing analysis of the oral microflora of healthy adults. J Dent Res. 2008;87:1016\u20131020.","journal-title":"J Dent Res"},{"key":"6173_CR36","doi-asserted-by":"publisher","first-page":"244","DOI":"10.1073\/pnas.1419038112","volume":"112","author":"X He","year":"2015","unstructured":"He X, McLean JS, Edlund A, et al. Cultivation of a human-associated TM7 phylotype reveals a reduced genome and epibiotic parasitic lifestyle. Proc Natl Acad Sci USA. 2015;112:244\u2013249.","journal-title":"Proc Natl Acad Sci USA"},{"key":"6173_CR37","doi-asserted-by":"publisher","first-page":"3957","DOI":"10.1038\/srep03957","volume":"4","author":"B Ferrari","year":"2014","unstructured":"Ferrari B, Winsley T, Ji M, Neilan B. Insights into the distribution and abundance of the ubiquitous candidatus Saccharibacteria phylum following tag pyrosequencing. Sci Rep. 2014;4:3957.","journal-title":"Sci Rep"},{"key":"6173_CR38","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1038\/ajg.2016.95","volume":"111","author":"V D\u2019Argenio","year":"2016","unstructured":"D\u2019Argenio V, Casaburi G, Precone V, et al. Metagenomics reveals dysbiosis and a potentially pathogenic N. flavescens strain in duodenum of adult celiac patients. Am J Gastroenterol. 2016;111:879\u2013890.","journal-title":"Am J Gastroenterol"},{"key":"6173_CR39","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1016\/S1075-9964(03)00060-X","volume":"9","author":"A Sullivan","year":"2003","unstructured":"Sullivan A, Tornblom H, Lindberg G, et al. The micro-flora of the small bowel in health and disease. Anaerobe. 2003;9:11\u201314.","journal-title":"Anaerobe"},{"key":"6173_CR40","first-page":"1049","volume":"10","author":"IW Percy-Robb","year":"1969","unstructured":"Percy-Robb IW, Brunton WA, Jalan KN, McManus JP, Gould JC, Sircus W. The relationship between the bacterial content of ileal effluent and the metabolism of bile salts in patients with ileostomies. Gut. 1969;10:1049\u20131050.","journal-title":"Gut"},{"key":"6173_CR41","doi-asserted-by":"publisher","first-page":"3213","DOI":"10.1111\/j.1462-2920.2010.02294.x","volume":"12","author":"CC Booijink","year":"2010","unstructured":"Booijink CC, El-Aidy S, Rajilic-Stojanovic M, et al. High temporal and inter-individual variation detected in the human ileal microbiota. Environ Microbiol. 2010;12:3213\u20133227.","journal-title":"Environ Microbiol"}],"container-title":["Digestive Diseases and Sciences"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10620-020-06173-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1007\/s10620-020-06173-x\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/s10620-020-06173-x.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,3,5]],"date-time":"2021-03-05T19:11:21Z","timestamp":1614971481000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/s10620-020-06173-x"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,3,6]]},"references-count":41,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2020,9]]}},"alternative-id":["6173"],"URL":"https:\/\/doi.org\/10.1007\/s10620-020-06173-x","relation":{},"ISSN":["0163-2116","1573-2568"],"issn-type":[{"value":"0163-2116","type":"print"},{"value":"1573-2568","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,3,6]]},"assertion":[{"value":"19 December 2019","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"24 February 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"6 March 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Compliance with Ethical Standards"}},{"value":"The authors declare that they have no conflict of interest.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Conflict of interest"}}]}}