{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,29]],"date-time":"2026-10-29T17:12:18Z","timestamp":1793293938669,"version":"4.5.0"},"reference-count":62,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T00:00:00Z","timestamp":1635811200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T00:00:00Z","timestamp":1635811200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"DOI":"10.13039\/100009576","name":"kenneth rainin foundation","doi-asserted-by":"publisher","award":["2018-1207"],"award-info":[{"award-number":["2018-1207"]}],"id":[{"id":"10.13039\/100009576","id-type":"DOI","asserted-by":"publisher"}]},{"name":"jacobs institute for molecular engineering for medicine","award":["n\/a"],"award-info":[{"award-number":["n\/a"]}]},{"DOI":"10.13039\/100000002","name":"national institutes of health","doi-asserted-by":"publisher","award":["T32GM112592"],"award-info":[{"award-number":["T32GM112592"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Microbiome"],"published-print":{"date-parts":[[2021,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p>Upper gastrointestinal (GI) disorders and abdominal pain afflict between 12 and 30% of the worldwide population and research suggests these conditions are linked to the gut microbiome. Although large-intestine microbiota have been linked to several GI diseases, the microbiota of the human small intestine and its relation to human disease has been understudied. The small intestine is the major site for immune surveillance in the gut, and compared with the large intestine, it has greater than 100 times the surface area and a thinner and more permeable mucus layer.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Using quantitative sequencing, we evaluated total and taxon-specific absolute microbial loads from 250 duodenal-aspirate samples and 21 paired duodenum-saliva samples from participants in the REIMAGINE study. Log-transformed total microbial loads spanned 5 logs and were normally distributed. Paired saliva-duodenum samples suggested potential transmission of oral microbes to the duodenum, including organisms from the HACEK group. Several taxa, including <jats:italic>Klebsiella, Escherichia<\/jats:italic>, <jats:italic>Enterococcus<\/jats:italic>, and <jats:italic>Clostridium<\/jats:italic>, seemed to displace strict anaerobes common in the duodenum, so we refer to these taxa as disruptors. Disruptor taxa were enriched in samples with high total microbial loads and in individuals with small intestinal bacterial overgrowth (SIBO). Absolute loads of disruptors were associated with more severe GI symptoms, highlighting the value of absolute taxon quantification when studying small-intestine health and function.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusion<\/jats:title>\n                <jats:p>This study provides the largest dataset of the absolute abundance of microbiota from the human duodenum to date. The results reveal a clear relationship between the oral microbiota and the duodenal microbiota and suggest an association between the absolute abundance of disruptor taxa, SIBO, and the prevalence of severe GI symptoms.<\/jats:p>\n                \n              <\/jats:sec>","DOI":"10.1186\/s40168-021-01162-2","type":"journal-article","created":{"date-parts":[[2021,11,2]],"date-time":"2021-11-02T04:29:44Z","timestamp":1635827384000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":84,"title":["Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome"],"prefix":"10.1186","volume":"9","author":[{"given":"Jacob T.","family":"Barlow","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gabriela","family":"Leite","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna E.","family":"Romano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rashin","family":"Sedighi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Chang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shreya","family":"Celly","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ali","family":"Rezaie","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruchi","family":"Mathur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mark","family":"Pimentel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3680-4399","authenticated-orcid":false,"given":"Rustem F.","family":"Ismagilov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2021,11,2]]},"reference":[{"issue":"1","key":"1162_CR1","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1038\/nrmicro3552","volume":"14","author":"GP Donaldson","year":"2016","unstructured":"Donaldson GP, Lee SM, Mazmanian SK. Gut biogeography of the bacterial microbiota. Nat Rev Microbiol. 2016;14(1):20\u201332. https:\/\/doi.org\/10.1038\/nrmicro3552.","journal-title":"Nat Rev Microbiol"},{"issue":"3","key":"1162_CR2","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.chom.2015.01.015","volume":"17","author":"K Yasuda","year":"2015","unstructured":"Yasuda K, Oh K, Ren B, Tickle TL, Franzosa EA, Wachtman LM, et al. Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque. Cell Host Microbe. 2015;17(3):385\u201391. https:\/\/doi.org\/10.1016\/j.chom.2015.01.015.","journal-title":"Cell Host Microbe"},{"issue":"9","key":"1162_CR3","doi-asserted-by":"publisher","first-page":"2595","DOI":"10.1007\/s10620-020-06173-x","volume":"65","author":"GGS Leite","year":"2020","unstructured":"Leite GGS, Weitsman S, Parodi G, Celly S, Sedighi R, Sanchez M, et al. Mapping the segmental microbiomes in the human small bowel in comparison with stool: a REIMAGINE study. Dig Dis Sci. 2020;65(9):2595\u2013604. https:\/\/doi.org\/10.1007\/s10620-020-06173-x.","journal-title":"Dig Dis Sci"},{"issue":"6","key":"1162_CR4","doi-asserted-by":"publisher","first-page":"352","DOI":"10.1038\/nrgastro.2013.35","volume":"10","author":"MEV Johansson","year":"2013","unstructured":"Johansson MEV, Sj\u00f6vall H, Hansson GC. The gastrointestinal mucus system in health and disease. Nat Rev Gastroenterol Hepatol. 2013;10(6):352\u201361. https:\/\/doi.org\/10.1038\/nrgastro.2013.35.","journal-title":"Nat Rev Gastroenterol Hepatol"},{"issue":"1","key":"1162_CR5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.4110\/in.2015.15.1.1","volume":"15","author":"H-J Ko","year":"2015","unstructured":"Ko H-J, Chang S-Y. Regulation of intestinal immune system by dendritic cells. Immune Netw. 2015;15(1):1\u20138. https:\/\/doi.org\/10.4110\/in.2015.15.1.1.","journal-title":"Immune Netw."},{"issue":"4","key":"1162_CR6","doi-asserted-by":"publisher","first-page":"907","DOI":"10.1038\/mi.2015.121","volume":"9","author":"D Rios","year":"2016","unstructured":"Rios D, Wood MB, Li J, Chassaing B, Gewirtz AT, Williams IR. Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria. Mucosal Immunol. 2016;9(4):907\u201316. https:\/\/doi.org\/10.1038\/mi.2015.121.","journal-title":"Mucosal Immunol."},{"key":"1162_CR7","first-page":"1","volume":"42","author":"KY Ebino","year":"1993","unstructured":"Ebino KY. Studies on coprophagy in experimental animals. Jikken Dobutsu. 1993;42:1\u20139.","journal-title":"Jikken Dobutsu"},{"issue":"1","key":"1162_CR8","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1186\/s40168-020-0785-4","volume":"8","author":"SR Bogatyrev","year":"2020","unstructured":"Bogatyrev SR, Rolando JC, Ismagilov RF. Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine. Microbiome. 2020;8(1):19. https:\/\/doi.org\/10.1186\/s40168-020-0785-4.","journal-title":"Microbiome"},{"issue":"1","key":"1162_CR9","doi-asserted-by":"publisher","first-page":"2590","DOI":"10.1038\/s41467-020-16224-6","volume":"11","author":"JT Barlow","year":"2020","unstructured":"Barlow JT, Bogatyrev SR, Ismagilov RF. A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities. Nat Commun. 2020;11(1):2590. https:\/\/doi.org\/10.1038\/s41467-020-16224-6.","journal-title":"Nat Commun"},{"key":"1162_CR10","doi-asserted-by":"crossref","unstructured":"Pimentel M, Saad RJ, Long MD, Rao SSC. ACG Clinical Guideline: Small Intestinal Bacterial Overgrowth. Official J Am Coll Gastroenterol | ACG. 2020;115:165\u201378.","DOI":"10.14309\/ajg.0000000000000501"},{"issue":"11-12","key":"1162_CR11","doi-asserted-by":"publisher","first-page":"1157","DOI":"10.1111\/j.1365-2036.2005.02690.x","volume":"22","author":"A Lupascu","year":"2005","unstructured":"Lupascu A, et al. Hydrogen glucose breath test to detect small intestinal bacterial overgrowth: a prevalence case\u2013control study in irritable bowel syndrome. Aliment Pharmacol Ther. 2005;22(11-12):1157\u201360. https:\/\/doi.org\/10.1111\/j.1365-2036.2005.02690.x.","journal-title":"Aliment Pharmacol Ther"},{"key":"1162_CR12","doi-asserted-by":"crossref","unstructured":"Shah A, et al. Small intestinal bacterial overgrowth in irritable bowel syndrome: a systematic review and meta-analysis of case-control studies. Official J Am College Gastroenterol | ACG. 2020;115:190\u2013201.","DOI":"10.14309\/ajg.0000000000000504"},{"key":"1162_CR13","doi-asserted-by":"crossref","unstructured":"Roland BC, et al. Small intestinal transit time is delayed in small intestinal bacterial overgrowth. J Clin Gastroenterol. 2015;49:571\u201376.","DOI":"10.1097\/MCG.0000000000000257"},{"issue":"3","key":"1162_CR14","doi-asserted-by":"publisher","first-page":"e13199","DOI":"10.1111\/nmo.13199","volume":"30","author":"BC Roland","year":"2018","unstructured":"Roland BC, Lee D, Miller LS, Vegesna A, Yolken R, Severance E, et al. Obesity increases the risk of small intestinal bacterial overgrowth (SIBO). Neurogastroenterol Motil. 2018;30(3):e13199. https:\/\/doi.org\/10.1111\/nmo.13199.","journal-title":"Neurogastroenterol Motil."},{"issue":"1","key":"1162_CR15","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1007\/s00535-017-1371-9","volume":"53","author":"T Su","year":"2018","unstructured":"Su T, Lai S, Lee A, He X, Chen S. Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth. J Gastroenterol. 2018;53(1):27\u201336. https:\/\/doi.org\/10.1007\/s00535-017-1371-9.","journal-title":"J Gastroenterol"},{"issue":"4","key":"1162_CR16","doi-asserted-by":"publisher","first-page":"1526","DOI":"10.1053\/j.gastro.2020.06.090","volume":"159","author":"EMM Quigley","year":"2020","unstructured":"Quigley EMM, Murray JA, Pimentel M. AGA clinical practice update on small intestinal bacterial overgrowth: expert review. Gastroenterology. 2020;159(4):1526\u201332. https:\/\/doi.org\/10.1053\/j.gastro.2020.06.090.","journal-title":"Gastroenterology"},{"issue":"6","key":"1162_CR17","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1007\/s10620-014-3157-8","volume":"59","author":"M Pimentel","year":"2014","unstructured":"Pimentel M, Chang C, Chua KS, Mirocha J, DiBaise J, Rao S, et al. Antibiotic treatment of constipation-predominant irritable bowel syndrome. Dig Dis Sci. 2014;59(6):1278\u201385. https:\/\/doi.org\/10.1007\/s10620-014-3157-8.","journal-title":"Dig Dis Sci"},{"issue":"7","key":"1162_CR18","doi-asserted-by":"publisher","first-page":"e0234906","DOI":"10.1371\/journal.pone.0234906","volume":"15","author":"G Leite","year":"2020","unstructured":"Leite G, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, et al. The duodenal microbiome is altered in small intestinal bacterial overgrowth. PLoS One. 2020;15(7):e0234906. https:\/\/doi.org\/10.1371\/journal.pone.0234906.","journal-title":"PLoS One"},{"issue":"1","key":"1162_CR19","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1111\/1574-6968.12103","volume":"342","author":"H Jonsson","year":"2013","unstructured":"Jonsson H. Segmented filamentous bacteria in human ileostomy samples after high-fiber intake. FEMS Microbiol Lett. 2013;342(1):24\u20139. https:\/\/doi.org\/10.1111\/1574-6968.12103.","journal-title":"FEMS Microbiol Lett."},{"issue":"7","key":"1162_CR20","doi-asserted-by":"publisher","first-page":"1415","DOI":"10.1038\/ismej.2011.212","volume":"6","author":"EG Zoetendal","year":"2012","unstructured":"Zoetendal EG, Raes J, van den Bogert B, Arumugam M, Booijink CCGM, Troost FJ, et al. The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates. ISME J. 2012;6(7):1415\u201326. https:\/\/doi.org\/10.1038\/ismej.2011.212.","journal-title":"ISME J"},{"issue":"40","key":"1162_CR21","doi-asserted-by":"publisher","first-page":"17187","DOI":"10.1073\/pnas.0904847106","volume":"106","author":"AL Hartman","year":"2009","unstructured":"Hartman AL, Lough DM, Barupal DK, Fiehn O, Fishbein T, Zasloff M, et al. Human gut microbiome adopts an alternative state following small bowel transplantation. Proc Natl Acad Sci U S A. 2009;106(40):17187\u201392. https:\/\/doi.org\/10.1073\/pnas.0904847106.","journal-title":"Proc Natl Acad Sci U S A."},{"issue":"1","key":"1162_CR22","doi-asserted-by":"publisher","first-page":"34055","DOI":"10.1038\/srep34055","volume":"6","author":"Y Chen","year":"2016","unstructured":"Chen Y, Ji F, Guo J, Shi D, Fang D, Li L. Dysbiosis of small intestinal microbiota in liver cirrhosis and its association with etiology. Sci Rep. 2016;6(1):34055. https:\/\/doi.org\/10.1038\/srep34055.","journal-title":"Sci Rep."},{"issue":"1","key":"1162_CR23","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, Yang Y, Lekatz HR, Hale VL, et al. Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders. Nat Commun. 2019;10(1):2012. https:\/\/doi.org\/10.1038\/s41467-019-09964-7.","journal-title":"Nat Commun"},{"key":"1162_CR24","doi-asserted-by":"publisher","first-page":"1388","DOI":"10.1016\/j.cell.2018.08.041","volume":"174","author":"N Zmora","year":"2018","unstructured":"Zmora N, et al. Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features. Cell. 2018;174:1388\u2013405.","journal-title":"Cell"},{"issue":"4","key":"1162_CR25","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1056\/NEJMoa1916004","volume":"383","author":"RY Chen","year":"2020","unstructured":"Chen RY, Kung VL, Das S, Hossain MS, Hibberd MC, Guruge J, et al. Duodenal microbiota in stunted undernourished children with enteropathy. NewEngl J Med. 2020;383(4):321\u201333. https:\/\/doi.org\/10.1056\/NEJMoa1916004.","journal-title":"NewEngl J Med."},{"issue":"7","key":"1162_CR26","doi-asserted-by":"publisher","first-page":"410","DOI":"10.1038\/s41579-018-0029-9","volume":"16","author":"R Knight","year":"2018","unstructured":"Knight R, Vrbanac A, Taylor BC, Aksenov A, Callewaert C, Debelius J, et al. Best practices for analysing microbiomes. Nat Rev Microbiol. 2018;16(7):410\u201322. https:\/\/doi.org\/10.1038\/s41579-018-0029-9.","journal-title":"Nat Rev Microbiol"},{"issue":"1","key":"1162_CR27","doi-asserted-by":"publisher","first-page":"2719","DOI":"10.1038\/s41467-019-10656-5","volume":"10","author":"JT Morton","year":"2019","unstructured":"Morton JT, Marotz C, Washburne A, Silverman J, Zaramela LS, Edlund A, et al. Establishing microbial composition measurement standards with reference frames. Nature Commun. 2019;10(1):2719. https:\/\/doi.org\/10.1038\/s41467-019-10656-5.","journal-title":"Nature Commun"},{"issue":"1","key":"1162_CR28","doi-asserted-by":"publisher","first-page":"239","DOI":"10.1186\/s12866-019-1617-1","volume":"19","author":"GGS Leite","year":"2019","unstructured":"Leite GGS, Morales W, Weitsman S, Celly S, Parodi G, Mathur R, et al. Optimizing microbiome sequencing for small intestinal aspirates: validation of novel techniques through the REIMAGINE study. BMC Microbiol. 2019;19(1):239. https:\/\/doi.org\/10.1186\/s12866-019-1617-1.","journal-title":"BMC Microbiol."},{"key":"1162_CR29","doi-asserted-by":"publisher","unstructured":"Bogatyrev SR, Ismagilov RF. Quantitative microbiome profiling in lumenal and tissue samples with broad coverage and dynamic range via a single-step 16S rRNA gene DNA copy quantification and amplicon barcoding. bioRxiv. 2020. https:\/\/doi.org\/10.1101\/2020.1101.1122.914705v914701.","DOI":"10.1101\/2020.1101.1122.914705v914701"},{"issue":"6361","key":"1162_CR30","doi-asserted-by":"publisher","first-page":"359","DOI":"10.1126\/science.aan4526","volume":"358","author":"K Atarashi","year":"2017","unstructured":"Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, et al. Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science. 2017;358(6361):359\u201365. https:\/\/doi.org\/10.1126\/science.aan4526.","journal-title":"Science"},{"key":"1162_CR31","doi-asserted-by":"publisher","first-page":"e42693","DOI":"10.7554\/eLife.42693","volume":"8","author":"TSB Schmidt","year":"2019","unstructured":"Schmidt TSB, Hayward MR, Coelho LP, Li SS, Costea PI, Voigt AY, et al. Extensive transmission of microbes along the gastrointestinal tract. eLife. 2019;8:e42693. https:\/\/doi.org\/10.7554\/eLife.42693.","journal-title":"eLife"},{"issue":"2","key":"1162_CR32","doi-asserted-by":"publisher","first-page":"486","DOI":"10.5812\/ijem.3505","volume":"10","author":"A Ghasemi","year":"2012","unstructured":"Ghasemi A, Zahediasl S. Normality tests for statistical analysis: a guide for non-statisticians. Int J Endocrinol Metab. 2012;10(2):486\u20139. https:\/\/doi.org\/10.5812\/ijem.3505.","journal-title":"Int J Endocrinol Metab"},{"issue":"5","key":"1162_CR33","doi-asserted-by":"publisher","first-page":"493","DOI":"10.1080\/19490976.2017.1320468","volume":"8","author":"I Lagkouvardos","year":"2017","unstructured":"Lagkouvardos I, Overmann J, Clavel T. Cultured microbes represent a substantial fraction of the human and mouse gut microbiota. Gut Microbes. 2017;8(5):493\u2013503. https:\/\/doi.org\/10.1080\/19490976.2017.1320468.","journal-title":"Gut Microbes"},{"issue":"4","key":"1162_CR34","doi-asserted-by":"publisher","first-page":"438","DOI":"10.1099\/jmm.0.000013","volume":"64","author":"R Ma","year":"2015","unstructured":"Ma R, Sapwell N, Chung HKL, Lee H, Mahendran V, Leong RW, et al. Investigation of the effects of pH and bile on the growth of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease and controls. J Med Microbiol. 2015;64(4):438\u201345. https:\/\/doi.org\/10.1099\/jmm.0.000013.","journal-title":"J Med Microbiol."},{"issue":"1","key":"1162_CR35","doi-asserted-by":"publisher","first-page":"71","DOI":"10.1128\/MMBR.62.1.71-109.1998","volume":"62","author":"H Marcotte","year":"1998","unstructured":"Marcotte H, Lavoie MC. Oral microbial ecology and the role of salivary immunoglobulin A. Microbiol Mol Biol Rev. 1998;62(1):71\u2013109. https:\/\/doi.org\/10.1128\/MMBR.62.1.71-109.1998.","journal-title":"Microbiol Mol Biol Rev"},{"issue":"11","key":"1162_CR36","doi-asserted-by":"publisher","first-page":"982","DOI":"10.1177\/0022034509346811","volume":"88","author":"K Hojo","year":"2009","unstructured":"Hojo K, Nagaoka S, Ohshima T, Maeda N. Bacterial Interactions in Dental Biofilm Development. J Dent Res. 2009;88(11):982\u201390. https:\/\/doi.org\/10.1177\/0022034509346811.","journal-title":"J Dent Res"},{"issue":"2","key":"1162_CR37","doi-asserted-by":"publisher","first-page":"e00062","DOI":"10.1128\/mBio.00062-19","volume":"10","author":"EGD Hopkins","year":"2019","unstructured":"Hopkins EGD, Roumeliotis TI, Mullineaux-Sanders C, Choudhary JS, Frankel G. Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection. mBio. 2019;10(2):e00062\u201319. https:\/\/doi.org\/10.1128\/mBio.00062-19.","journal-title":"mBio"},{"issue":"1","key":"1162_CR38","doi-asserted-by":"publisher","first-page":"7788","DOI":"10.1038\/s41598-018-26083-3","volume":"8","author":"H Arg\u00fcello","year":"2018","unstructured":"Arg\u00fcello H, Estell\u00e9 J, Zald\u00edvar-L\u00f3pez S, Jim\u00e9nez-Mar\u00edn \u00c1, Carvajal A, L\u00f3pez-Basc\u00f3n MA, et al. Early Salmonella Typhimurium infection in pigs disrupts Microbiome composition and functionality principally at the ileum mucosa. Sci Rep. 2018;8(1):7788. https:\/\/doi.org\/10.1038\/s41598-018-26083-3.","journal-title":"Sci Rep."},{"key":"1162_CR39","doi-asserted-by":"publisher","first-page":"e40553","DOI":"10.7554\/eLife.40553","volume":"8","author":"EJ Contijoch","year":"2019","unstructured":"Contijoch EJ, Britton GJ, Yang C, Mogno I, Li Z, Ng R, et al. Gut microbiota density influences host physiology and is shaped by host and microbial factors. eLife. 2019;8:e40553. https:\/\/doi.org\/10.7554\/eLife.40553.","journal-title":"eLife"},{"issue":"1","key":"1162_CR40","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1242\/dmm.017400","volume":"8","author":"TLA Nguyen","year":"2015","unstructured":"Nguyen TLA, Vieira-Silva S, Liston A, Raes J. How informative is the mouse for human gut microbiota research? Disease Models Mechanisms. 2015;8(1):1\u201316. https:\/\/doi.org\/10.1242\/dmm.017400.","journal-title":"Disease Models Mechanisms"},{"issue":"1","key":"1162_CR41","doi-asserted-by":"publisher","first-page":"e00163","DOI":"10.1128\/mSystems.00163-18","volume":"4","author":"V Caruso","year":"2019","unstructured":"Caruso V, Song X, Asquith M, Karstens L. Performance of Microbiome Sequence Inference Methods in Environments with Varying Biomass. mSystems. 2019;4(1):e00163\u201318. https:\/\/doi.org\/10.1128\/mSystems.00163-18.","journal-title":"mSystems"},{"issue":"1","key":"1162_CR42","doi-asserted-by":"publisher","first-page":"24","DOI":"10.1186\/s13099-016-0103-7","volume":"8","author":"A Glassing","year":"2016","unstructured":"Glassing A, Dowd SE, Galandiuk S, Davis B, Chiodini RJ. Inherent bacterial DNA contamination of extraction and sequencing reagents may affect interpretation of microbiota in low bacterial biomass samples. Gut Pathog. 2016;8(1):24. https:\/\/doi.org\/10.1186\/s13099-016-0103-7.","journal-title":"Gut Pathog."},{"issue":"3","key":"1162_CR43","doi-asserted-by":"publisher","first-page":"382","DOI":"10.1016\/j.chom.2014.02.005","volume":"15","author":"D Gevers","year":"2014","unstructured":"Gevers D, Kugathasan S, Denson LA, V\u00e1zquez-Baeza Y, van Treuren W, Ren B, et al. The treatment-naive microbiome in new-onset Crohn\u2019s disease. Cell Host Microbe. 2014;15(3):382\u201392. https:\/\/doi.org\/10.1016\/j.chom.2014.02.005.","journal-title":"Cell Host Microbe."},{"issue":"11","key":"1162_CR44","doi-asserted-by":"publisher","first-page":"1770","DOI":"10.1177\/00220345970760110801","volume":"76","author":"S Goldberg","year":"1997","unstructured":"Goldberg S, Cardash H, Browning H, Sahly H, Rosenberg M. Isolation of Enterobacteriaceae from the Mouth and Potential Association with Malodor. J Dent Res. 1997;76(11):1770\u20135. https:\/\/doi.org\/10.1177\/00220345970760110801.","journal-title":"J Dent Res"},{"key":"1162_CR45","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1016\/B978-0-12-384947-2.00260-9","volume-title":"Encyclopedia of Food and Health","author":"JL Smith","year":"2016","unstructured":"Smith JL, Fratamico PM. In: Caballero B, Finglas PM, Toldr\u00e1 F, editors. Encyclopedia of Food and Health. Oxford: Academic Press; 2016. p. 539\u201344."},{"issue":"5","key":"1162_CR46","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1111\/j.1472-765X.2007.02111.x","volume":"44","author":"MO Gon\u00e7alves","year":"2007","unstructured":"Gon\u00e7alves MO, Coutinho-Filho WP, Pimenta FP, Pereira GA, Pereira JAA, Mattos-Guaraldi AL, et al. Periodontal disease as reservoir for multi-resistant and hydrolytic enterobacterial species. Lett Appl Microbiol. 2007;44(5):488\u201394. https:\/\/doi.org\/10.1111\/j.1472-765X.2007.02111.x.","journal-title":"Lett Appl Microbiol"},{"issue":"6","key":"1162_CR47","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1080\/14787210.2016.1184085","volume":"14","author":"SL Sharara","year":"2016","unstructured":"Sharara SL, Tayyar R, Kanafani ZA, Kanj SS. HACEK endocarditis: a review. Expert Rev Anti Infect Ther. 2016;14(6):539\u201345. https:\/\/doi.org\/10.1080\/14787210.2016.1184085.","journal-title":"Expert Rev Anti Infect Ther"},{"key":"1162_CR48","doi-asserted-by":"publisher","first-page":"114","DOI":"10.1186\/s12866-015-0439-z","volume":"15","author":"M Karched","year":"2015","unstructured":"Karched M, Bhardwaj RG, Asikainen SE. Coaggregation and biofilm growth of Granulicatella spp. with Fusobacterium nucleatum and Aggregatibacter actinomycetemcomitans. BMC Microbiol. 2015;15:114.","journal-title":"BMC Microbiol"},{"issue":"7","key":"1162_CR49","doi-asserted-by":"publisher","first-page":"1256","DOI":"10.1038\/ismej.2013.80","volume":"7","author":"L Rigottier-Gois","year":"2013","unstructured":"Rigottier-Gois L. Dysbiosis in inflammatory bowel diseases: the oxygen hypothesis. ISME J. 2013;7(7):1256\u201361. https:\/\/doi.org\/10.1038\/ismej.2013.80.","journal-title":"ISME J"},{"key":"1162_CR50","doi-asserted-by":"publisher","first-page":"128","DOI":"10.1016\/j.chom.2018.12.003","volume":"25","author":"Y Litvak","year":"2019","unstructured":"Litvak Y, et al. Commensal Enterobacteriaceae Protect against Salmonella Colonization through Oxygen Competition. Cell Host Microbe. 2019;25:128\u201339.","journal-title":"Cell Host Microbe"},{"key":"1162_CR51","doi-asserted-by":"crossref","unstructured":"Khazaei T, et al. Metabolic multi-stability and hysteresis in a model aerobe-anaerobe microbiome community. Sci Adv. 2020;6(33):eaba0353.","DOI":"10.1126\/sciadv.aba0353"},{"issue":"6375","key":"1162_CR52","doi-asserted-by":"publisher","first-page":"592","DOI":"10.1126\/science.aah3648","volume":"359","author":"CM Dejea","year":"2018","unstructured":"Dejea CM, Fathi P, Craig JM, Boleij A, Taddese R, Geis AL, et al. Patients with familial adenomatous polyposis harbor colonic biofilms containing tumorigenic bacteria. Science. 2018;359(6375):592\u20137. https:\/\/doi.org\/10.1126\/science.aah3648.","journal-title":"Science"},{"issue":"5","key":"1162_CR53","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1038\/ajg.2017.46","volume":"112","author":"A Rezaie","year":"2017","unstructured":"Rezaie A, Buresi M, Lembo A, Lin H, McCallum R, Rao S, et al. Hydrogen and Methane-Based Breath Testing in Gastrointestinal Disorders: The North American Consensus. Am J Gastroenterol. 2017;112(5):775\u201384. https:\/\/doi.org\/10.1038\/ajg.2017.46.","journal-title":"Am J Gastroenterol"},{"issue":"12","key":"1162_CR54","doi-asserted-by":"publisher","first-page":"8966","DOI":"10.1128\/AEM.71.12.8966-8969.2005","volume":"71","author":"SG Acinas","year":"2005","unstructured":"Acinas SG, Sarma-Rupavtarm R, Klepac-Ceraj V, Polz MF. PCR-induced sequence artifacts and bias: insights from comparison of two 16S rRNA clone libraries constructed from the same sample. Appl Environ Microbiol. 2005;71(12):8966\u20139. https:\/\/doi.org\/10.1128\/AEM.71.12.8966-8969.2005.","journal-title":"Appl Environ Microbiol."},{"issue":"2","key":"1162_CR55","doi-asserted-by":"publisher","first-page":"625","DOI":"10.1128\/aem.62.2.625-630.1996","volume":"62","author":"MT Suzuki","year":"1996","unstructured":"Suzuki MT, Giovannoni SJ. Bias caused by template annealing in the amplification of mixtures of 16S rRNA genes by PCR. Appl Environ Microbiol. 1996;62(2):625\u201330. https:\/\/doi.org\/10.1128\/aem.62.2.625-630.1996.","journal-title":"Appl Environ Microbiol."},{"key":"1162_CR56","first-page":"e27295v27292","volume":"6","author":"E Bolyen","year":"2018","unstructured":"Bolyen E, et al. QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science. Peer J. 2018;6:e27295v27292.","journal-title":"Peer J"},{"issue":"7","key":"1162_CR57","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","volume":"13","author":"BJ Callahan","year":"2016","unstructured":"Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJA, Holmes SP. DADA2: High-resolution sample inference from Illumina amplicon data. Nat Methods. 2016;13(7):581\u20133. https:\/\/doi.org\/10.1038\/nmeth.3869.","journal-title":"Nat Methods"},{"issue":"1","key":"1162_CR58","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, Amir A, Bittinger K, Gonzalez A, et al. Normalization and microbial differential abundance strategies depend upon data characteristics. Microbiome. 2017;5(1):27. https:\/\/doi.org\/10.1186\/s40168-017-0237-y.","journal-title":"Microbiome"},{"issue":"1","key":"1162_CR59","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s40168-018-0470-z","volume":"6","author":"NA Bokulich","year":"2018","unstructured":"Bokulich NA, Kaehler BD, Rideout JR, Dillon M, Bolyen E, Knight R, et al. Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2's q2-feature-classifier plugin. Microbiome. 2018;6(1):90. https:\/\/doi.org\/10.1186\/s40168-018-0470-z.","journal-title":"Microbiome"},{"issue":"Database issue","key":"1162_CR60","doi-asserted-by":"publisher","first-page":"D590","DOI":"10.1093\/nar\/gks1219","volume":"41","author":"C Quast","year":"2013","unstructured":"Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2013;41(Database issue):D590\u20136. https:\/\/doi.org\/10.1093\/nar\/gks1219.","journal-title":"Nucleic Acids Res."},{"issue":"11","key":"1162_CR61","doi-asserted-by":"publisher","first-page":"e48558","DOI":"10.1371\/journal.pone.0048558","volume":"7","author":"RJ Clifford","year":"2012","unstructured":"Clifford RJ, Milillo M, Prestwood J, Quintero R, Zurawski DV, Kwak YI, et al. Detection of Bacterial 16S rRNA and Identification of Four Clinically Important Bacteria by Real-Time PCR. PLoS One. 2012;7(11):e48558. https:\/\/doi.org\/10.1371\/journal.pone.0048558.","journal-title":"PLoS One"},{"issue":"1","key":"1162_CR62","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1186\/1471-2105-13-134","volume":"13","author":"J Ye","year":"2012","unstructured":"Ye J, Coulouris G, Zaretskaya I, Cutcutache I, Rozen S, Madden TL. Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction. BMC Bioinformatics. 2012;13(1):134. https:\/\/doi.org\/10.1186\/1471-2105-13-134.","journal-title":"BMC Bioinformatics"}],"container-title":["Microbiome"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-021-01162-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s40168-021-01162-2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s40168-021-01162-2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,1]],"date-time":"2022-03-01T00:35:41Z","timestamp":1646094941000},"score":1,"resource":{"primary":{"URL":"https:\/\/microbiomejournal.biomedcentral.com\/articles\/10.1186\/s40168-021-01162-2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2021,11,2]]},"references-count":62,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2021,12]]}},"alternative-id":["1162"],"URL":"https:\/\/doi.org\/10.1186\/s40168-021-01162-2","relation":{},"ISSN":["2049-2618"],"issn-type":[{"value":"2049-2618","type":"electronic"}],"subject":[],"published":{"date-parts":[[2021,11,2]]},"assertion":[{"value":"15 June 2021","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 September 2021","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"2 November 2021","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Declarations"}},{"value":"The study was reviewed and approved by the Cedars-Sinai Medical Center IRB (Protocol #00035192). All participants provided written informed consent prior to participation.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The quantitative sequencing technology described in this publication is the subject of a patent application filed by Caltech. R.F.I. receives patent royalties from Bio-Rad related to droplet digital PCR.","order":4,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"214"}}