{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T00:25:51Z","timestamp":1792110351712,"version":"4.4.0"},"reference-count":337,"publisher":"Oxford University Press (OUP)","issue":"3","license":[{"start":{"date-parts":[[2023,5,17]],"date-time":"2023-05-17T00:00:00Z","timestamp":1684281600000},"content-version":"vor","delay-in-days":16,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004385","name":"Ghent University","doi-asserted-by":"publisher","award":["BOFGOA2022000803"],"award-info":[{"award-number":["BOFGOA2022000803"]}],"id":[{"id":"10.13039\/501100004385","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,5,19]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Growing evidence suggests the importance of the small intestinal bacteria in the diet\u2013host\u2013microbiota dialogue in various facets of health and disease. Yet, this body site is still poorly explored and its ecology and mechanisms of interaction with the host are just starting to be unraveled. In this review, we describe the current knowledge on the small intestinal ecology, its composition and diversity, and how the intestinal bacteria in homeostatic conditions participate in nutrient digestion and absorption. We illustrate the importance of a controlled bacterial density and of the preservation of absorptive surface for the host\u2019s nutritional status. In particular, we discuss these aspects of the small intestinal environment in the framework of two disease conditions, namely small intestinal bacterial overgrowth (SIBO) and short bowel syndrome (SBS). We also detail in vivo, ex vivo, and in vitro models developed to simulate the small intestinal environment, some applied for (diet\u2013)host\u2013bacteria interaction studies. Lastly, we highlight recent technological, medical, and scientific advances applicable to investigate this complex and yet understudied body environment to broaden our knowledge in support of further progress in the medical practice, and to proceed towards the integration of the (small)intestinal bacteria in personalized therapeutic approaches.<\/jats:p>","DOI":"10.1093\/femsre\/fuad022","type":"journal-article","created":{"date-parts":[[2023,5,16]],"date-time":"2023-05-16T22:37:42Z","timestamp":1684276662000},"source":"Crossref","is-referenced-by-count":70,"title":["The small intestine: dining table of host\u2013microbiota meetings"],"prefix":"10.1093","volume":"47","author":[{"given":"Karen","family":"Delbaere","sequence":"first","affiliation":[{"name":"Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University , Coupure Links 653 , Building A, 9000 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Inez","family":"Roegiers","sequence":"additional","affiliation":[{"name":"Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University , Coupure Links 653 , Building A, 9000 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Auriane","family":"Bron","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Clermont Auvergne, UMR 454 MEDIS UCA-INRAE , Place Henri Dunant 28, F-63000 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude","family":"Durif","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Clermont Auvergne, UMR 454 MEDIS UCA-INRAE , Place Henri Dunant 28, F-63000 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tom","family":"Van de\u00a0Wiele","sequence":"additional","affiliation":[{"name":"Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University , Coupure Links 653 , Building A, 9000 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"St\u00e9phanie","family":"Blanquet-Diot","sequence":"additional","affiliation":[{"name":"Universit\u00e9 Clermont Auvergne, UMR 454 MEDIS UCA-INRAE , Place Henri Dunant 28, F-63000 Clermont-Ferrand, France"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2995-5105","authenticated-orcid":false,"given":"Ludovica","family":"Marinelli","sequence":"additional","affiliation":[{"name":"Center for Microbial Ecology and Technology (CMET), Department of Biotechnology, Ghent University , Coupure Links 653 , Building A, 9000 Ghent, Belgium"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2023,5,16]]},"reference":[{"key":"2023060914235560500_bib1","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1007\/s42242-020-00120-5","article-title":"Engineering biomimetic intestinal topological features in 3D tissue models\u202f: retrospects and prospects","volume":"4","author":"Agarwal","year":"2021","journal-title":"Bio Design Manuf"},{"key":"2023060914235560500_bib2","first-page":"48","article-title":"Physiology of the pancreas","volume":"38","author":"Agrawal","year":"2014","journal-title":"Pract Gastroenterol"},{"key":"2023060914235560500_bib4","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.copbio.2014.09.005","article-title":"The small intestine microbiota, nutritional modulation and relevance for health","volume":"32","author":"Aidy","year":"2015","journal-title":"Curr Opin Biotechnol"},{"key":"2023060914235560500_bib7","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/S0168-1605(98)00182-2","article-title":"The effect of probiotic strains on the microbiota of the Simulator of the Human Intestinal Microbial Ecosystem (SHIME)","volume":"46","author":"Alander","year":"1999","journal-title":"Int J Food Microbiol"},{"key":"2023060914235560500_bib5","doi-asserted-by":"crossref","first-page":"2517","DOI":"10.2527\/jas.2006-237","article-title":"Changes in small intestinal nutrient transport and barrier function after lipopolysaccharide exposure in two pig breeds","volume":"85","author":"Albin","year":"2007","journal-title":"J Anim Sci"},{"key":"2023060914235560500_bib6","doi-asserted-by":"crossref","first-page":"159","DOI":"10.2527\/asasmw.2017.327","article-title":"A humanized gnotobiotic piglet model to study host\u2013microbiota interactions","volume":"95","author":"Aluthge","year":"2017","journal-title":"J Anim Sci"},{"key":"2023060914235560500_bib8","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s42003-020-01477-0","article-title":"Differential longitudinal establishment of human fecal bacterial communities in germ-free porcine and murine models","volume":"3","author":"Aluthge","year":"2020","journal-title":"Commun Biol"},{"key":"2023060914235560500_bib9","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1186\/s40168-015-0120-7","article-title":"Variable responses of human and non-human primate gut microbiomes to a Western diet","volume":"3","author":"Amato","year":"2015","journal-title":"Microbiome"},{"key":"2023060914235560500_bib10","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1016\/j.clnu.2012.08.007","article-title":"Determinants of home parenteral nutrition dependence and survival of 268 patients with non-malignant short bowel syndrome","volume":"32","author":"Amiot","year":"2013","journal-title":"Clin Nutr"},{"key":"2023060914235560500_bib11","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/j.bbcan.2006.01.002","article-title":"Regulation of mucin expression: mechanistic aspects and implications for cancer and inflammatory diseases","volume":"1765","author":"Andrianifahanana","year":"2006","journal-title":"Biochim Biophys Acta Rev Cancer"},{"key":"2023060914235560500_bib12","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.nmni.2018.10.009","article-title":"Treponema species enrich the gut microbiota of traditional rural populations but are absent from urban individuals","volume":"27","author":"Angelakis","year":"2019","journal-title":"New Microbes New Infect"},{"key":"2023060914235560500_bib13","doi-asserted-by":"crossref","first-page":"1187","DOI":"10.1016\/j.biomaterials.2005.10.009","article-title":"Modelling approach in cell\/material interactions studies","volume":"27","author":"Anselme","year":"2006","journal-title":"Biomaterials"},{"key":"2023060914235560500_bib14","doi-asserted-by":"crossref","first-page":"421","DOI":"10.3920\/BM2015.0169","article-title":"Lactobacillus rhamnosus GG increases Toll-like receptor 3 gene expression in murine small intestine ex vivo and in vivo","volume":"7","author":"Aoki-Yoshida","year":"2016","journal-title":"Benef Microbes"},{"key":"2023060914235560500_bib15","doi-asserted-by":"crossref","first-page":"1479","DOI":"10.1177\/41.10.8245407","article-title":"Expression of human mucin genes in respiratory, digestive, and reproductive tracts ascertained by in situ hybridization","volume":"41","author":"Audie","year":"1993","journal-title":"J Histochem Cytochem"},{"key":"2023060914235560500_bib16","doi-asserted-by":"crossref","first-page":"2101","DOI":"10.1053\/j.gastro.2020.08.029","article-title":"Specification of tuft cells to suppress ileal inflammation","volume":"159","author":"Banerjee","year":"2021","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib18","doi-asserted-by":"crossref","first-page":"1003","DOI":"10.1038\/nature06196","article-title":"Identification of stem cells in small intestine and colon by marker gene Lgr5","volume":"449","author":"Barker","year":"2007","journal-title":"Nature"},{"key":"2023060914235560500_bib17","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/nrm3721","article-title":"Adult intestinal stem cells: critical drivers of epithelial homeostasis and regeneration","volume":"15","author":"Barker","year":"2014","journal-title":"Nat Rev Mol Cell Biol"},{"key":"2023060914235560500_bib19","first-page":"111","article-title":"Preferential usage of rifaximin for the treatment of hydrogen-positive small intestinal bacterial overgrowth","volume":"39","author":"Barkin","year":"2019","journal-title":"Rev Gastroenterol Peru"},{"key":"2023060914235560500_bib20","doi-asserted-by":"crossref","DOI":"10.1186\/s40168-021-01162-2","article-title":"Quantitative sequencing clarifies the role of disruptor taxa, oral microbiota, and strict anaerobes in the human small-intestine microbiome","volume":"9","author":"Barlow","year":"2021","journal-title":"Microbiome"},{"key":"2023060914235560500_bib21","doi-asserted-by":"crossref","first-page":"210","DOI":"10.1177\/0148607104028004210","article-title":"Supplementation of total parenteral nutrition with butyrate acutely increases structural aspects of intestinal adaptation after an 80% jejunoileal resection in neonatal piglets","volume":"28","author":"Bartholome","year":"2004","journal-title":"J Parenteral Enteral Nutr"},{"key":"2023060914235560500_bib22","first-page":"1649","volume-title":"Anatomy, Histology, Embryology, and Developmental Anomalies of the Small and Large Intestine. Sleisenger and Fordtran\u2019s Gastrointestinal and Liver Disease: Pathophysiology, Diagnosis, Management","author":"Bass","year":"2015"},{"key":"2023060914235560500_bib23","doi-asserted-by":"crossref","first-page":"1158","DOI":"10.1007\/s10620-018-5420-x","article-title":"Villus growth, increased intestinal epithelial sodium selectivity, and hyperaldosteronism are mechanisms of adaptation in a murine model of short bowel syndrome","volume":"64","author":"Berlin","year":"2019","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib24","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0036262","article-title":"Microbiota\/host crosstalk biomarkers: regulatory response of human intestinal dendritic cells exposed to Lactobacillus extracellular encrypted peptide","volume":"7","author":"Bernardo","year":"2012","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib25","doi-asserted-by":"crossref","first-page":"5406","DOI":"10.1002\/anie.200805179","article-title":"Engineering substrate topography at the micro- and nanoscale to control cell function","volume":"48","author":"Bettinger","year":"2009","journal-title":"Angew Chem Int Ed"},{"key":"2023060914235560500_bib26","doi-asserted-by":"crossref","first-page":"102208","DOI":"10.1016\/j.coph.2022.102208","article-title":"Low FODMAP diet beyond IBS: evidence for use in other conditions","volume":"64","author":"Biesiekierski","year":"2022","journal-title":"Curr Opin Pharmacol"},{"key":"2023060914235560500_bib27","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1080\/17474124.2019.1569514","article-title":"Emerging treatments for short bowel syndrome in adult patients","volume":"13","author":"Billiauws","year":"2019","journal-title":"Expert Rev Gastroenterol Hepatol"},{"key":"2023060914235560500_bib28","first-page":"731","article-title":"Intestinal adaptation in short bowel syndrome. What is new?","volume":"35","author":"Billiauws","year":"2018","journal-title":"Nutr Hosp"},{"key":"2023060914235560500_bib29","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41467-021-25056-x","article-title":"An extended reconstruction of human gut microbiota metabolism of dietary compounds","volume":"12","author":"Blasco","year":"2021","journal-title":"Nat Commun"},{"key":"2023060914235560500_bib30","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-020-0785-4","article-title":"Self-reinoculation with fecal flora changes microbiota density and composition leading to an altered bile-acid profile in the mouse small intestine","volume":"8","author":"Bogatyrev","year":"2020","journal-title":"Microbiome"},{"key":"2023060914235560500_bib32","doi-asserted-by":"crossref","first-page":"G1770","DOI":"10.1152\/ajpgi.00249.2006","article-title":"Enteroendocrine cells express functional Toll-like receptors","volume":"292","author":"Bogunovic","year":"2007","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib33","doi-asserted-by":"crossref","first-page":"106","DOI":"10.1097\/MCG.0b013e3182688e73","article-title":"Mucin function in inflammatory bowel disease: an update","volume":"47","author":"Boltin","year":"2013","journal-title":"J Clin Gastroenterol"},{"key":"2023060914235560500_bib34","doi-asserted-by":"crossref","first-page":"3213","DOI":"10.1111\/j.1462-2920.2010.02294.x","article-title":"High temporal and inter-individual variation detected in the human ileal microbiota","volume":"12","author":"Booijink","year":"2010","journal-title":"Environ Microbiol"},{"key":"2023060914235560500_bib35","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1124\/dmd.111.042465","article-title":"Gene expression profiling of systems involved in the metabolism and the disposition of xenobiotics: comparison between human intestinal biopsy samples and colon cell lines","volume":"40","author":"Bourgine","year":"2012","journal-title":"Drug Metab Dispos"},{"key":"2023060914235560500_bib36","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1016\/j.vetmic.2011.10.017","article-title":"Porcine IPEC-J2 intestinal epithelial cells in microbiological investigations","volume":"156","author":"Brosnahan","year":"2012","journal-title":"Vet Microbiol"},{"key":"2023060914235560500_bib37","doi-asserted-by":"crossref","first-page":"11312","DOI":"10.1074\/jbc.M211609200","article-title":"The orphan G protein-coupled receptors GPR41 and GPR43 are activated by propionate and other short chain carboxylic acids","volume":"278","author":"Brown","year":"2003","journal-title":"J Biol Chem"},{"key":"2023060914235560500_bib38","doi-asserted-by":"crossref","DOI":"10.5772\/21602","article-title":"The ECSIM concept (environmental control system for intestinal microbiota) and its derivative versions to help better understand human gut biology","volume-title":"Applied Biomedical Engineering","author":"Bruge\u0300re","year":"2011"},{"key":"2023060914235560500_bib40","doi-asserted-by":"crossref","first-page":"1111","DOI":"10.1016\/S0016-5085(03)70064-X","article-title":"AGA technical review on short bowel syndrome and intestinal transplantation","volume":"124","author":"Buchman","year":"2003","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib41","doi-asserted-by":"crossref","first-page":"544","DOI":"10.1136\/gut.49.4.544","article-title":"Mucin gene expression in intestinal epithelial cells in Crohn\u2019s disease","volume":"49","author":"Buisine","year":"2001","journal-title":"Gut"},{"key":"2023060914235560500_bib42","doi-asserted-by":"crossref","first-page":"3985","DOI":"10.1096\/fj.201801414R","article-title":"Development of a host-microbiome model of the small intestine","volume":"33","author":"Calatayud","year":"2019","journal-title":"FASEB J"},{"key":"2023060914235560500_bib43","doi-asserted-by":"crossref","first-page":"609","DOI":"10.1007\/BF01297027","article-title":"Towards a less costly but accurate test of gastric emptying and small bowel transit","volume":"36","author":"Camilleri","year":"1991","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib44","doi-asserted-by":"crossref","first-page":"D233","DOI":"10.1093\/nar\/gkn663","article-title":"The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics","volume":"37","author":"Cantarel","year":"2009","journal-title":"Nucleic Acids Res"},{"key":"2023060914235560500_bib45","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1177\/002215549704501111","article-title":"Mucins (MUC1 and MUC3) of gastrointestinal and breast epithelia reveal different and heterogeneous tumor-associated aberrations in glycosylation","volume":"45","author":"Cao","year":"1997","journal-title":"J Histochem Cytochem"},{"key":"2023060914235560500_bib46","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1016\/j.ijfoodmicro.2012.02.013","article-title":"Impact of intestinal microbiota and gastrointestinal conditions on the in vitro survival and growth of Bacillus cereus","volume":"155","author":"Ceuppens","year":"2012","journal-title":"Int J Food Microbiol"},{"key":"2023060914235560500_bib47","doi-asserted-by":"crossref","first-page":"3525","DOI":"10.1007\/s10620-017-4726-4","article-title":"A prospective evaluation of ileocecal valve dysfunction and intestinal motility derangements in small intestinal bacterial overgrowth","volume":"62","author":"Chander\u00a0Roland","year":"2017","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib48","doi-asserted-by":"crossref","first-page":"G1287","DOI":"10.1152\/ajpgi.00196.2010","article-title":"Lactobacillus plantarum ameliorates colonic epithelial barrier dysfunction by modulating the apical junctional complex and PepT1 in IL-10 knockout mice","volume":"299","author":"Chen","year":"2010","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib49","doi-asserted-by":"crossref","first-page":"321","DOI":"10.1056\/NEJMoa1916004","article-title":"Duodenal microbiota in stunted undernourished children with enteropathy","volume":"383","author":"Chen","year":"2020","journal-title":"N Engl J Med"},{"key":"2023060914235560500_bib50","doi-asserted-by":"crossref","first-page":"1059","DOI":"10.1111\/j.1365-2036.2011.04625.x","article-title":"Clinical predictors of small intestinal bacterial overgrowth by duodenal aspirate culture","volume":"33","author":"Choung","year":"2011","journal-title":"Aliment Pharmacol Ther"},{"key":"2023060914235560500_bib51","doi-asserted-by":"crossref","first-page":"1578","DOI":"10.1016\/j.cell.2012.04.037","article-title":"Gut immune maturation depends on colonization with a host-specific microbiota","volume":"149","author":"Chung","year":"2012","journal-title":"Cell"},{"key":"2023060914235560500_bib52","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/femsle\/fny231","article-title":"The Smallest Intestine (TSI) - a low volume in vitro model of the small intestine with increased throughput","volume":"365","author":"Cieplak","year":"2018","journal-title":"FEMS Microbiol Lett"},{"key":"2023060914235560500_bib53","doi-asserted-by":"crossref","first-page":"1177","DOI":"10.1002\/jps.21502","article-title":"Postprandial evolution in composition and characteristics of human duodenal fluids in different nutritional states","volume":"98","author":"Clarysse","year":"2008","journal-title":"J Pharm Sci"},{"key":"2023060914235560500_bib54","doi-asserted-by":"crossref","first-page":"10376","DOI":"10.1073\/pnas.1521835113","article-title":"Captivity humanizes the primate microbiome","volume":"113","author":"Clayton","year":"2016","journal-title":"Proc Natl Acad Sci"},{"key":"2023060914235560500_bib55","volume-title":"Abdominal Gas","author":"Cormier","year":"1990","edition":"3rd edn"},{"key":"2023060914235560500_bib56","doi-asserted-by":"crossref","first-page":"12727","DOI":"10.1038\/s41598-018-30932-6","article-title":"Characterization of bacterial microbiota compositions along the intestinal tract in pigs and their interactions and functions","volume":"8","author":"Crespo-Piazuelo","year":"2018","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib57","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1097\/00004630-199405000-00002","article-title":"The Caco-2 cell monolayer system as an in vitro model for studying bacterial-enterocyte interactions and bacterial translocation","volume":"15","author":"Cruz","year":"1994","journal-title":"J Burn Care Rehabil"},{"key":"2023060914235560500_bib58","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1089\/tmj.2007.0118","article-title":"The study of a remote-controlled gastrointestinal drug delivery and sampling system","volume":"14","author":"Cui","year":"2008","journal-title":"Telemed e-Health"},{"key":"2023060914235560500_bib59","doi-asserted-by":"crossref","first-page":"1221","DOI":"10.1136\/gut.28.10.1221","article-title":"Short chain fatty acids in human large intestine, portal, hepatic and venous blood","volume":"28","author":"Cummings","year":"1987","journal-title":"Gut"},{"key":"2023060914235560500_bib60","doi-asserted-by":"crossref","first-page":"G670","DOI":"10.1152\/ajpgi.00293.2002","article-title":"Role of luminal nutrients and endogenous GLP-2 in intestinal adaptation to mid-small bowel resection","volume":"284","author":"Dahly","year":"2003","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib61","doi-asserted-by":"crossref","first-page":"1201","DOI":"10.1007\/s00726-010-0556-9","article-title":"Utilization of amino acids by bacteria from the pig small intestine","volume":"39","author":"Dai","year":"2010","journal-title":"Amino Acids"},{"key":"2023060914235560500_bib62","doi-asserted-by":"crossref","first-page":"2016","DOI":"10.1124\/dmd.114.058404","article-title":"Meta-analysis of the turnover of intestinal epithelia in preclinical animal species and humans","volume":"42","author":"Darwich","year":"2014","journal-title":"Drug Metab Dispos"},{"key":"2023060914235560500_bib63","doi-asserted-by":"crossref","first-page":"637","DOI":"10.1016\/j.sbi.2005.10.008","article-title":"Recent structural insights into the expanding world of carbohydrate-active enzymes","volume":"15","author":"Davies","year":"2005","journal-title":"Curr Opin Struct Biol"},{"key":"2023060914235560500_bib64","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1194\/jlr.R900012-JLR200","article-title":"Thematic review series: bile acids. Bile acid transporters","volume":"50","author":"Dawson","year":"2009","journal-title":"J Lipid Res"},{"key":"2023060914235560500_bib3","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.cmet.2013.03.013","article-title":"Pleiotropic roles of bile acids in metabolism","volume":"17","author":"De\u00a0Aguiar\u00a0Vallim","year":"2013","journal-title":"Cell Metab"},{"key":"2023060914235560500_bib39","first-page":"773","article-title":"Extracellular matrix components induce endocrine differentiation in vitro in NCI-H716 cells","volume":"142","author":"De\u00a0Bruine","year":"1993","journal-title":"Am J Pathol"},{"key":"2023060914235560500_bib65","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1136\/gut.39.2.299","article-title":"Variability of gastrointestinal transit in healthy women and men","volume":"39","author":"Degen","year":"1996","journal-title":"Gut"},{"key":"2023060914235560500_bib66","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1016\/j.chom.2013.12.007","article-title":"Human gut microbes use multiple transporters to distinguish vitamin B 12 analogs and compete in the gut","volume":"15","author":"Degnan","year":"2014","journal-title":"Cell Host Microbe"},{"key":"2023060914235560500_bib67","doi-asserted-by":"crossref","first-page":"10233","DOI":"10.1007\/s00253-020-10959-4","article-title":"Comparative methods for fecal sample storage to preserve gut microbial structure and function in an in vitro model of the human colon","volume":"104","author":"Deschamps","year":"2020","journal-title":"Appl Microbiol Biotechnol"},{"key":"2023060914235560500_bib99","doi-asserted-by":"crossref","first-page":"1780","DOI":"10.3390\/ijms22041780","article-title":"Physiology and physical chemistry of bile acids","volume":"22","author":"di\u00a0Gregorio","year":"2021","journal-title":"Int J Mol Sci"},{"key":"2023060914235560500_bib68","first-page":"1","article-title":"No difference in small bowel microbiota between patients with irritable bowel syndrome and healthy controls","volume":"5","author":"Dlugosz","year":"2014","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib69","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1126\/scisignal.abl5848","article-title":"Clearance of small intestinal crypts involves goblet cell mucus secretion by intracellular granule rupture and enterocyte ion transport","volume":"15","author":"Dolan","year":"2022","journal-title":"Sci Signal"},{"key":"2023060914235560500_bib70","first-page":"112","article-title":"Small intestinal bacterial overgrowth: a comprehensive review","volume":"3","author":"Dukowicz","year":"2007","journal-title":"Gastroenterol Hepatol"},{"key":"2023060914235560500_bib71","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1016\/j.devcel.2020.11.010","article-title":"Single-cell sequencing of developing human gut reveals transcriptional links to childhood Crohn\u2019s disease","volume":"55","author":"Elmentaite","year":"2020","journal-title":"Dev Cell"},{"key":"2023060914235560500_bib72","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0261191","article-title":"Characterization of increased mucus production of HT29-MTX-E12 cells grown under semi-wet interface with mechanical stimulation","volume":"16","author":"Elzinga","year":"2021","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib73","first-page":"221","article-title":"Human-derived Bifidobacterium dentium modulates the mammalian serotonergic system and gut\u2013brain axis","volume":"11","author":"Engevik","year":"2021","journal-title":"CMGH"},{"key":"2023060914235560500_bib74","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11894-015-0436-2","article-title":"Small intestinal fungal overgrowth","volume":"17","author":"Erdogan","year":"2015","journal-title":"Curr Gastroenterol Rep"},{"key":"2023060914235560500_bib75","first-page":"1","article-title":"Chronic consumption of sweeteners in mice; effect on immune system and microbiota of small intestine","volume":"41","author":"Escoto","year":"2021","journal-title":"Biomedica"},{"key":"2023060914235560500_bib76","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1016\/j.freeradbiomed.2012.10.554","article-title":"Role of oxygen gradients in shaping redox relationships between the human intestine and its microbiota","volume":"55","author":"Espey","year":"2013","journal-title":"Free Radical Biol Med"},{"key":"2023060914235560500_bib77","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1177\/0148607105029005315","article-title":"Dietary supplementation with orotate and uracil increases asaptive growth of jejunal mucosa after massive small bowel resection in rats","volume":"29","author":"Evans","year":"2005","journal-title":"J Parenteral Enteral Nutr"},{"key":"2023060914235560500_bib78","doi-asserted-by":"crossref","first-page":"104104","DOI":"10.1016\/j.micpath.2020.104104","article-title":"Mild changes in the mucosal microbiome during terminal ileum inflammation","volume":"142","author":"Fan","year":"2020","journal-title":"Microb Pathog"},{"key":"2023060914235560500_bib79","doi-asserted-by":"crossref","first-page":"1241","DOI":"10.1002\/mds.25522","article-title":"The role of small intestinal bacterial overgrowth in Parkinson\u2019s disease","volume":"28","author":"Fasano","year":"2013","journal-title":"Mov Disord"},{"key":"2023060914235560500_bib80","doi-asserted-by":"crossref","first-page":"975","DOI":"10.18632\/aging.203854","article-title":"The prevalence of small intestinal bacterial overgrowth in diabetes mellitus: a systematic review and meta-analysis","volume":"14","author":"Feng","year":"2022","journal-title":"Aging"},{"key":"2023060914235560500_bib81","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.nut.2020.111118","article-title":"Dose-dependent beneficial effects of citrulline supplementation in short bowel syndrome in rats","volume":"85","author":"Filippi","year":"2021","journal-title":"Nutrition"},{"key":"2023060914235560500_bib82","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1002\/ajp.23023","article-title":"Metagenomic assessment of the Cebus apella gut microbiota","volume":"81","author":"Firrman","year":"2019","journal-title":"Am J Primatol"},{"key":"2023060914235560500_bib83","doi-asserted-by":"crossref","DOI":"10.1128\/CVI.00172-17","article-title":"Protein malnutrition alters tryptophan and angiotensin-converting enzyme 2 homeostasis and adaptive immune responses in human rotavirus-infected gnotobiotic pigs with human infant fecal microbiota transplant","volume":"24","author":"Fischer","year":"2017","journal-title":"Clin Vaccine Immunol"},{"key":"2023060914235560500_bib84","doi-asserted-by":"crossref","DOI":"10.1186\/s12876-019-0960-x","article-title":"The role of Small Intestinal Bacterial Overgrowth (SIBO) in Non-alcoholic Fatty Liver Disease (NAFLD) patients evaluated using Controlled Attenuation Parameter (CAP) Transient Elastography (TE): a tertiary referral center experience","volume":"19","author":"Fitriakusumah","year":"2019","journal-title":"BMC Gastroenterology"},{"key":"2023060914235560500_bib85","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1093\/jn\/84.2.155","article-title":"Effects of coprophagy prevention on intestinal microflora in rats","volume":"84","author":"Fitzgerald","year":"1964","journal-title":"J Nutr"},{"key":"2023060914235560500_bib86","doi-asserted-by":"crossref","first-page":"428","DOI":"10.1080\/19490976.2017.1334033","article-title":"Fecal microbiota variation across the lifespan of the healthy laboratory rat","volume":"8","author":"Flemer","year":"2017","journal-title":"Gut Microbes"},{"key":"2023060914235560500_bib88","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1152\/jappl.1967.23.3.387","article-title":"Dose response and minimal daily requirement for vitamin K in man","volume":"23","author":"Frick","year":"1967","journal-title":"J Appl Physiol"},{"key":"2023060914235560500_bib89","doi-asserted-by":"crossref","first-page":"1621","DOI":"10.1038\/ismej.2014.13","article-title":"Reset of a critically disturbed microbial ecosystem: faecal transplant in recurrent Clostridium difficile infection","volume":"8","author":"Fuentes","year":"2014","journal-title":"ISME J"},{"key":"2023060914235560500_bib90","doi-asserted-by":"crossref","first-page":"E2960","DOI":"10.1073\/pnas.1720696115","article-title":"Chronic stress promotes colitis by disturbing the gut microbiota and triggering immune system response","volume":"115","author":"Gao","year":"2018","journal-title":"Proc Natl Acad Sci"},{"key":"2023060914235560500_bib91","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1111\/apt.13928","article-title":"Systematic review with meta-analysis: rifaximin is effective and safe for the treatment of small intestine bacterial overgrowth","volume":"45","author":"Gatta","year":"2017","journal-title":"Aliment Pharmacol Ther"},{"key":"2023060914235560500_bib92","doi-asserted-by":"crossref","first-page":"54","DOI":"10.1177\/0192623313518113","article-title":"Comparative anatomy, physiology, and mechanisms of disease production of the esophagus, stomach, and small intestine","volume":"42","author":"Gelberg","year":"2014","journal-title":"Toxicol Pathol"},{"key":"2023060914235560500_bib93","doi-asserted-by":"crossref","first-page":"2907","DOI":"10.1007\/s00018-012-0984-7","article-title":"The intestinal epithelium tuft cells: specification and function","volume":"69","author":"Gerbe","year":"2012","journal-title":"Cell Mol Life Sci"},{"key":"2023060914235560500_bib94","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1016\/j.jceh.2018.08.006","article-title":"Small intestinal bacterial overgrowth in patients with cirrhosis","volume":"9","author":"Ghosh","year":"2019","journal-title":"J Clin Exp Hepatol"},{"key":"2023060914235560500_bib95","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1007\/s12664-021-01211-6","article-title":"Small intestinal bacterial overgrowth in patients with inflammatory bowel disease: a case-control stuy","volume":"41","author":"Ghoshal","year":"2022","journal-title":"Ind J Gastroenterol"},{"key":"2023060914235560500_bib96","doi-asserted-by":"crossref","first-page":"C846","DOI":"10.1152\/ajpcell.00112.2005","article-title":"Expression and membrane localization of MCT isoforms along the length of the human intestine","volume":"289","author":"Gill","year":"2005","journal-title":"Am J Physiol Cell Physiol"},{"key":"2023060914235560500_bib97","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1152\/advan.00094.2009","article-title":"Insights into digestion and absorption of major nutrients in humans","volume":"34","author":"Goodman","year":"2010","journal-title":"Adv Physiol Educ"},{"key":"2023060914235560500_bib98","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1046\/j.1365-2281.2001.00308.x","article-title":"Gastrointestinal mean transit times in young and middle-aged healthy subjects","volume":"21","author":"Graff","year":"2001","journal-title":"Clin Physiol"},{"key":"2023060914235560500_bib100","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.chom.2020.06.013","article-title":"Co-evolution and co-speciation of host-gut bacteria systems","volume":"28","author":"Groussin","year":"2020","journal-title":"Cell Host Microbe"},{"key":"2023060914235560500_bib101","doi-asserted-by":"crossref","first-page":"e74957","DOI":"10.1371\/journal.pone.0074957","article-title":"Bacterial community mapping of the mouse gastrointestinal tract","volume":"8","author":"Gu","year":"2013","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib102","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1006\/bbrc.2002.6475","article-title":"MUC17, a novel membrane-tethered mucin","volume":"291","author":"Gum","year":"2002","journal-title":"Biochem Biophys Res Commun"},{"key":"2023060914235560500_bib103","doi-asserted-by":"crossref","first-page":"4773","DOI":"10.1111\/febs.16067","article-title":"The specification and function of enteroendocrine cells in Drosophila and mammals: a comparative review","volume":"289","author":"Guo","year":"2022","journal-title":"FEBS J"},{"key":"2023060914235560500_bib104","doi-asserted-by":"crossref","first-page":"17187","DOI":"10.1073\/pnas.0904847106","article-title":"Human gut microbiome adopts an alternative state following small bowel transplantation","volume":"106","author":"Hartman","year":"2009","journal-title":"Proc Natl Acad Sci"},{"key":"2023060914235560500_bib105","doi-asserted-by":"crossref","first-page":"1093","DOI":"10.1099\/jmm.0.45935-0","article-title":"Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism","volume":"54","author":"Hayashi","year":"2005","journal-title":"J Med Microbiol"},{"key":"2023060914235560500_bib106","doi-asserted-by":"crossref","first-page":"14184","DOI":"10.1038\/s41598-018-32366-6","article-title":"Commensal microbiota induces colonic barrier structure and functions that contribute to homeostasis","volume":"8","author":"Hayes","year":"2018","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib108","doi-asserted-by":"crossref","first-page":"681","DOI":"10.3109\/00365521.2014.898326","article-title":"Surface area of the digestive tract-revisited","volume":"49","author":"Helander","year":"2014","journal-title":"Scand J Gastroenterol"},{"key":"2023060914235560500_bib109","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1016\/j.ejps.2014.07.008","article-title":"Gastrointestinal transfer: in vivo evaluation and implementation in in vitro and in silico predictive tools","volume":"63","author":"Hens","year":"2014","journal-title":"Eur J Pharm Sci"},{"key":"2023060914235560500_bib110","doi-asserted-by":"crossref","first-page":"736","DOI":"10.1016\/S0016-5085(89)80072-1","article-title":"Characterization of the human colon carcinoma cell line (Caco-2) as a model system for intestinal epithelial permeability","volume":"96","author":"Hidalgo","year":"1989","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib111","first-page":"902","article-title":"Caco-2 cell monolayers as a model for drug transport across the intestinal mucosa","volume":"7","author":"Hilgers","year":"1990","journal-title":"Pharm Res An Off J Am Assoc Pharm Sci"},{"key":"2023060914235560500_bib112","doi-asserted-by":"crossref","first-page":"S43","DOI":"10.1097\/00008469-199703001-00009","article-title":"Intestinal flora vitamin biosynthesis","volume":"6","author":"Hill","year":"1997","journal-title":"Eur J Cancer Prev"},{"key":"2023060914235560500_bib113","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1016\/0022-2836(68)90430-0","article-title":"Products in the initial stages of digestion of polydeoxynucleotides by pancreatic deoxyribonuclease (DNase I)","volume":"31","author":"Hoard","year":"1968","journal-title":"J Mol Biol"},{"key":"2023060914235560500_bib114","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1017\/S0007114520001385","article-title":"Ileal and hindgut fermentation in the growing pig fed a human-type diet","volume":"124","author":"Hoogeveen","year":"2020","journal-title":"Br J Nutr"},{"key":"2023060914235560500_bib115","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/112_2015_24","article-title":"The secretion and action of brush border enzymes in the mammalian small intestine","volume-title":"Reviews of Physiology, Biochemistry and Pharmacology","author":"Hooton","year":"2015"},{"key":"2023060914235560500_bib116","doi-asserted-by":"crossref","first-page":"4785","DOI":"10.1242\/jcs.02608","article-title":"Interaction between secretogranin III and carboxypeptidase E facilities prohormone sorting within secretory granules","volume":"118","author":"Hosaka","year":"2005","journal-title":"J Cell Sci"},{"key":"2023060914235560500_bib117","doi-asserted-by":"crossref","first-page":"585","DOI":"10.1053\/j.gastro.2017.10.007","article-title":"DNA methylation and transcription patterns in intestinal epithelial cells from pediatric patients with inflammatory bowel diseases differentiate disease subtypes and associate with outcome","volume":"154","author":"Howell","year":"2018","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib118","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12879-021-06270-w","article-title":"Therapeutic potential of an intestinotrophic hormone, glucagon-like peptide 2, for treatment of type 2 short bowel syndrome rats with intestinal bacterial and fungal dysbiosis","volume":"21","author":"Hu","year":"2021","journal-title":"BMC Infect Dis"},{"key":"2023060914235560500_bib119","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1007\/s10620-019-05802-4","article-title":"Severe intestinal dysbiosis in rat models of short bowel syndrome with ileocecal resection","volume":"65","author":"Huang","year":"2020","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib120","doi-asserted-by":"crossref","first-page":"1949","DOI":"10.1111\/jgh.13806","article-title":"Fecal microbiota signatures of adult patients with different types of short bowel syndrome","volume":"32","author":"Huang","year":"2017","journal-title":"J Gastroenterol Hepatol"},{"key":"2023060914235560500_bib121","doi-asserted-by":"crossref","first-page":"162","DOI":"10.1067\/mpr.2001.113778","article-title":"A review of saliva: normal composition, flow, and function","volume":"85","author":"Humphrey","year":"2001","journal-title":"J Prosthet Dent"},{"key":"2023060914235560500_bib122","doi-asserted-by":"crossref","first-page":"1828","DOI":"10.1007\/s11095-008-9580-9","article-title":"Interplay between intestinal pH, transit time and feed status on the in vivo performance of pH responsive ileo-colonic release systems","volume":"25","author":"Ibekwe","year":"2008","journal-title":"Pharm Res"},{"key":"2023060914235560500_bib123","doi-asserted-by":"crossref","first-page":"277","DOI":"10.3109\/00365521.2015.1086020","article-title":"Macronutrient intakes in obese subjects with or without small intestinal bacterial overgrowth: an alimentary survey","volume":"51","author":"Ierardi","year":"2016","journal-title":"Scand J Gastroenterol"},{"key":"2023060914235560500_bib124","doi-asserted-by":"crossref","first-page":"132","DOI":"10.1006\/jsre.1999.5813","article-title":"Aggregation substance promotes colonic mucosal invasion of Enterococcus faecalis in an ex vivo model","volume":"89","author":"Isenmann","year":"2000","journal-title":"J Surg Res"},{"key":"2023060914235560500_bib125","doi-asserted-by":"crossref","first-page":"243","DOI":"10.2220\/biomedres.27.243","article-title":"Cellular expression of monocarboxylate transporters (MCT) in the digestive tract of the mouse, rat, and humans, with special reference to slc5a8","volume":"27","author":"Iwanaga","year":"2006","journal-title":"Biomed Res"},{"key":"2023060914235560500_bib126","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1016\/j.anaerobe.2015.12.007","article-title":"Clostridium difficile-mediated effects on human intestinal epithelia: modelling host-pathogen interactions in a vertical diffusion chamber","volume":"37","author":"Jafari","year":"2016","journal-title":"Anaerobe"},{"key":"2023060914235560500_bib127","doi-asserted-by":"crossref","first-page":"190","DOI":"10.3390\/v14020190","volume":"14","author":"Jakobsen","year":"2022","journal-title":"Viruses"},{"key":"2023060914235560500_bib129","doi-asserted-by":"crossref","first-page":"370","DOI":"10.1136\/gut.47.3.370","article-title":"Elevated plasma glucagon-like peptide 1 and 2 concentrations in ileum resected short bowel patients with a preserved colon","volume":"47","author":"Jeppesen","year":"2000","journal-title":"Gut"},{"key":"2023060914235560500_bib128","doi-asserted-by":"crossref","first-page":"8S","DOI":"10.1177\/0148607114520994","article-title":"Spectrum of short bowel syndrome in adults: intestinal insufficiency to intestinal failure","volume":"38","author":"Jeppesen","year":"2014","journal-title":"J Parenteral Enteral Nutr"},{"key":"2023060914235560500_bib130","doi-asserted-by":"crossref","first-page":"S","DOI":"10.1016\/S0016-5085(19)37309-3","article-title":"Intestine Microbiome Aspiration (IMBA) capsule: a new autonomous and minimally-invasive device for whole gut microbiome sampling and mapping","volume":"156","author":"Jin","year":"2019","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib131","doi-asserted-by":"crossref","first-page":"2491","DOI":"10.1038\/s41396-022-01287-8","article-title":"Amino acid utilization allows intestinal dominance of Lactobacillus amylovorus","volume":"16","author":"Jing","year":"2022","journal-title":"ISME J"},{"key":"2023060914235560500_bib132","doi-asserted-by":"crossref","first-page":"753","DOI":"10.1016\/j.biochi.2010.02.015","article-title":"Drastic changes in fecal and mucosa-associated microbiota in adult patients with short bowel syndrome","volume":"92","author":"Joly","year":"2010","journal-title":"Biochimie"},{"key":"2023060914235560500_bib133","doi-asserted-by":"crossref","first-page":"2856","DOI":"10.1016\/j.clnu.2019.12.019","article-title":"Six-month outcomes of teduglutide treatment in adult patients with short bowel syndrome with chronic intestinal failure: a real-world French observational cohort study","volume":"39","author":"Joly","year":"2020","journal-title":"Clin Nutr"},{"key":"2023060914235560500_bib134","doi-asserted-by":"crossref","first-page":"13580","DOI":"10.1073\/pnas.0804437105","article-title":"Functional and comparative metagenomic analysis of bile salt hydrolase activity in the human gut microbiome","volume":"105","author":"Jones","year":"2008","journal-title":"Proc Natl Acad Sci"},{"key":"2023060914235560500_bib135","doi-asserted-by":"crossref","first-page":"24","DOI":"10.1111\/1574-6968.12103","article-title":"Segmented filamentous bacteria in human ileostomy samples after high-fiber intake","volume":"342","author":"Jonsson","year":"2013","journal-title":"FEMS Microbiol Lett"},{"key":"2023060914235560500_bib136","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fbioe.2022.879024","article-title":"Reversing epithelial polarity in pluripotent stem cell-derived intestinal organoids","volume":"10","author":"Kakni","year":"2022","journal-title":"Front Bioeng Biotechnol"},{"key":"2023060914235560500_bib137","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/j.ejpb.2016.03.020","article-title":"Prediction of the precipitation profiles of weak base drugs in the small intestine using a simplified transfer (\u201cdumping\u201d) model coupled with in silico modeling and simulation approach","volume":"103","author":"Kambayashi","year":"2016","journal-title":"Eur J Pharm Biopharm"},{"key":"2023060914235560500_bib138","doi-asserted-by":"crossref","first-page":"752","DOI":"10.1016\/j.tibs.2018.05.003","article-title":"Amino acid transporters revisited: new views in health and disease","volume":"43","author":"Kandasamy","year":"2018","journal-title":"Trends Biochem Sci"},{"key":"2023060914235560500_bib139","doi-asserted-by":"crossref","first-page":"497","DOI":"10.1038\/nrmicro3050","article-title":"The abundance and variety of carbohydrate-active enzymes in the human gut microbiota","volume":"11","author":"Kaoutari","year":"2013","journal-title":"Nat Rev Microbiol"},{"key":"2023060914235560500_bib140","doi-asserted-by":"crossref","first-page":"e0188282","DOI":"10.1371\/journal.pone.0188282","article-title":"Dietary protein sources differentially affect microbiota, mTOR activity and transcription of mTOR signaling pathways in the small intestine","volume":"12","author":"Kar","year":"2017","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib141","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-018-21201-7","article-title":"Development of a primary human Small Intestine-on-a-Chip using biopsy-derived organoids","volume":"8","author":"Kasendra","year":"2018","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib142","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1159\/000496102","article-title":"Mucosa-associated microbiota in the gastrointestinal tract of healthy Japanese subjects","volume":"101","author":"Kashiwagi","year":"2020","journal-title":"Digestion"},{"key":"2023060914235560500_bib143","doi-asserted-by":"crossref","first-page":"e67224","DOI":"10.1371\/journal.pone.0067224","article-title":"Exposure of Bifidobacterium longum subsp. infantis to milk oligosaccharides increases adhesion to epithelial cells and induces a substantial transcriptional response","volume":"8","author":"Kavanaugh","year":"2013","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib144","doi-asserted-by":"crossref","first-page":"1534","DOI":"10.3389\/fphys.2018.01534","article-title":"Mouse microbiota models: comparing germ-free mice and antibiotics treatment as tools for modifying gut bacteria","volume":"9","author":"Kennedy","year":"2018","journal-title":"Front Physiol"},{"key":"2023060914235560500_bib145","doi-asserted-by":"crossref","first-page":"1443","DOI":"10.1007\/s10620-007-0065-1","article-title":"A systematic review of diagnostic tests for small intestinal bacterial overgrowth","volume":"53","author":"Khoshini","year":"2008","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib146","doi-asserted-by":"crossref","first-page":"258","DOI":"10.3168\/jds.S0022-0302(04)73164-1","article-title":"Purification and characterization of three different types of bile salt hydrolases from Bifidobacterium strains","volume":"87","author":"Kim","year":"2004","journal-title":"J Dairy Sci"},{"key":"2023060914235560500_bib147","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1039\/c3ib40126j","article-title":"Gut-on-a-Chip microenvironment induces human intestinal cells to undergo villus differentiation","volume":"5","author":"Kim","year":"2013","journal-title":"Integr Biol"},{"key":"2023060914235560500_bib148","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1080\/19490976.2021.1892441","article-title":"Mucin degrader Akkermansia muciniphila accelerates intestinal stem cell-mediated epithelial development","volume":"13","author":"Kim","year":"2021","journal-title":"Gut Microbes"},{"key":"2023060914235560500_bib149","doi-asserted-by":"crossref","first-page":"817","DOI":"10.1097\/MEG.0000000000001959","article-title":"Decreased number of colonic tuft cells in quiescent ulcerative colitis patients","volume":"33","author":"Kj\u00e6rgaard","year":"2021","journal-title":"Eur J Gastroenterol Hepatol"},{"key":"2023060914235560500_bib150","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1016\/j.clnu.2016.04.009","article-title":"Management of acute intestinal failure: a position paper from the European Society for Clinical Nutrition and Metabolism (ESPEN) special interest group","volume":"35","author":"Klek","year":"2016","journal-title":"Clin Nutr"},{"key":"2023060914235560500_bib152","doi-asserted-by":"crossref","first-page":"1207","DOI":"10.1007\/s00424-020-02439-5","article-title":"Glucose transporters in the small intestine in health and disease","volume":"472","author":"Koepsell","year":"2020","journal-title":"Pfl\u00fcgers Archiv Eur J Physiol"},{"key":"2023060914235560500_bib153","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1007\/s00702-021-02440-x","article-title":"Small intestinal bacterial overgrowth in Alzheimer\u2019s disease","volume":"129","author":"Kowalski","year":"2022","journal-title":"J Neural Transm"},{"key":"2023060914235560500_bib154","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2015\/476215","article-title":"D-lactic acidosis: an underrecognized complication of short bowel syndrome","volume":"2015","author":"Kowlgi","year":"2015","journal-title":"Gastroenterol Res Pract"},{"key":"2023060914235560500_bib155","doi-asserted-by":"crossref","first-page":"2855","DOI":"10.1002\/jps.24274","article-title":"Investigation of pH and temperature profiles in the GI tract of fasted human subjects using the Intellicap\u00ae system","volume":"104","author":"Koziolek","year":"2015","journal-title":"J Pharm Sci"},{"key":"2023060914235560500_bib156","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.jconrel.2015.10.022","article-title":"Intragastric pH and pressure profiles after intake of the high-caloric, high-fat meal as used for food effect studies","volume":"220","author":"Koziolek","year":"2015","journal-title":"J Control Rel"},{"key":"2023060914235560500_bib157","doi-asserted-by":"crossref","first-page":"49","DOI":"10.1136\/gutjnl-2017-314817","article-title":"DNA methylation defines regional identity of human intestinal epithelial organoids and undergoes dynamic changes during development","volume":"68","author":"Kraiczy","year":"2019","journal-title":"Gut"},{"key":"2023060914235560500_bib158","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1371\/journal.pone.0260479","article-title":"Association of small intestinal bacterial overgrowth with nonalcoholic fatty liver disease in children: a meta-analysis","volume":"16","author":"Kuang","year":"2021","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib159","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1530\/JME-15-0293","article-title":"Peptide production and secretion in GLUTag, NCI-H716 and STC-1 cells: a comparison to native L-cells","volume":"56","author":"Kuhre","year":"2016","journal-title":"J Mol Endocrinol"},{"key":"2023060914235560500_bib160","first-page":"612","article-title":"An investigation of the effect of gastrointestinal microbial activity on oral arsenic bioavailability","volume":"48","author":"Laird","year":"2013","journal-title":"J Environ Sci Health Part A Toxic\/Hazard Subst Environ Eng"},{"key":"2023060914235560500_bib161","doi-asserted-by":"crossref","first-page":"1142","DOI":"10.1007\/s10620-009-0826-0","article-title":"Frequency and factors associated with small intestinal bacterial overgrowth in patients with cirrhosis of the liver and extra hepatic portal venous obstruction","volume":"55","author":"Lakshmi","year":"2010","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib162","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1002\/jpen.1011","article-title":"Single-center experience with the use of teduglutide in adult patients with short bowel syndrome","volume":"42","author":"Lam","year":"2018","journal-title":"J Parenteral Enteral Nutr"},{"key":"2023060914235560500_bib163","doi-asserted-by":"crossref","first-page":"814","DOI":"10.1038\/nbt.2676","article-title":"Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences","volume":"31","author":"Langille","year":"2013","journal-title":"Nat Biotechnol"},{"key":"2023060914235560500_bib164","doi-asserted-by":"crossref","first-page":"264","DOI":"10.5858\/134.2.264","article-title":"Small intestinal bacterial overgrowth histopathologic features and clinical correlates in an underrecognized entity","volume":"134","author":"Lappinga","year":"2010","journal-title":"Arch Pathol Lab Med"},{"key":"2023060914235560500_bib165","doi-asserted-by":"crossref","first-page":"e12648","DOI":"10.1111\/cmi.12648","article-title":"TLR ligands and butyrate increase Pyy expression through two distinct but inter-regulated pathways","volume":"19","author":"Larraufie","year":"2017","journal-title":"Cell Microbiol"},{"key":"2023060914235560500_bib166","doi-asserted-by":"crossref","DOI":"10.1038\/s41598-017-18259-0","article-title":"SCFAs strongly stimulate PYY production in human enteroendocrine cells","volume":"8","author":"Larraufie","year":"2018","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib167","doi-asserted-by":"crossref","first-page":"2031","DOI":"10.1111\/j.1572-0241.2008.02030.x","article-title":"Small intestinal bacterial overgrowth recurrence after antibiotic therapy","volume":"103","author":"Lauritano","year":"2008","journal-title":"Am J Gastroenterol"},{"key":"2023060914235560500_bib168","doi-asserted-by":"crossref","first-page":"e0234906","DOI":"10.1371\/journal.pone.0234906","article-title":"The duodenal microbiome is altered in small intestinal bacterial overgrowth","volume":"15","author":"Leite","year":"2020","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib169","doi-asserted-by":"crossref","first-page":"109765","DOI":"10.1016\/j.celrep.2021.109765","article-title":"Age and the aging process significantly alter the small bowel microbiome","volume":"36","author":"Leite","year":"2021","journal-title":"Cell Rep"},{"key":"2023060914235560500_bib170","doi-asserted-by":"crossref","first-page":"2595","DOI":"10.1007\/s10620-020-06173-x","article-title":"Mapping the segmental microbiomes in the human small bowel in comparison with stool: a REIMAGINE study","volume":"65","author":"Leite","year":"2020","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib171","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1016\/j.biochi.2020.09.007","article-title":"Jejunum: the understudied meeting place of dietary lipids and the microbiota","volume":"178","author":"Lema","year":"2020","journal-title":"Biochimie"},{"key":"2023060914235560500_bib172","first-page":"6334","article-title":"Growth adaptation to methotrexate of HT-29 human colon carcinoma cells is associated with their ability to differentiate into columnar absorptive and mucus-secreting cells","volume":"50","author":"Lesuffleur","year":"1990","journal-title":"Cancer Res"},{"key":"2023060914235560500_bib173","article-title":"Microbial biogeography and core microbiota of the rat digestive tract","volume":"7","author":"Li","year":"2017","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib174","doi-asserted-by":"crossref","first-page":"1136","DOI":"10.4014\/jmb.1412.12047","article-title":"Diversity of duodenal and rectal microbiota in biopsy tissues and luminal contents in healthy volunteers","volume":"25","author":"Li","year":"2015","journal-title":"J Microbiol Biotechnol"},{"key":"2023060914235560500_bib175","first-page":"2179","article-title":"Mucosa-associated microbial profile is altered in small intestinal bacterial overgrowth","volume":"12","author":"Li","year":"2021","journal-title":"Front Microbiol"},{"key":"2023060914235560500_bib176","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-020-00917-7","article-title":"Spatial heterogeneity of bacterial colonization across different gut segments following inter-species microbiota transplantation","volume":"8","author":"Li","year":"2020","journal-title":"Microbiome"},{"key":"2023060914235560500_bib177","doi-asserted-by":"crossref","DOI":"10.1128\/JVI.01006-20","article-title":"Next-generation porcine intestinal organoids: an apical-out organoid model for swine enteric virus infection and immune response investigations","volume":"94","author":"Li","year":"2020","journal-title":"J Virol"},{"key":"2023060914235560500_bib178","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1128\/CMR.19.2.315-337.2006","article-title":"The front line of enteric host defense against unwelcome intrusion of harmful microorganisms: mucins, antimicrobial peptides, and microbiota","volume":"19","author":"Li\u00e9vin-Le\u00a0Moal","year":"2006","journal-title":"Clin Microbiol Rev"},{"key":"2023060914235560500_bib179","doi-asserted-by":"crossref","first-page":"2062","DOI":"10.3390\/cells10082062","article-title":"Physiological shear stress enhances differentiation, mucus-formation and structural 3d organization of intestinal epithelial cells in vitro","volume":"10","author":"Lindner","year":"2021","journal-title":"Cells"},{"key":"2023060914235560500_bib180","first-page":"430","article-title":"Is jejunostomy output nutrient or waste in short bowel syndrome? Experience from six cases","volume":"25","author":"Liu","year":"2016","journal-title":"Asia Pac J Clin Nutr"},{"key":"2023060914235560500_bib181","doi-asserted-by":"crossref","first-page":"630","DOI":"10.1016\/j.ebiom.2019.10.002","article-title":"A single faecal microbiota transplantation modulates the microbiome and improves clinical manifestations in a rat model of colitis","volume":"48","author":"Lleal","year":"2019","journal-title":"EBioMedicine"},{"key":"2023060914235560500_bib182","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3389\/fimmu.2020.00587","article-title":"The paneth cell: the curator and defender of the immature small intestine","volume":"11","author":"Lueschow","year":"2020","journal-title":"Front Immunol"},{"key":"2023060914235560500_bib183","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.01438-14","article-title":"Differential modulation by Akkermansia muciniphila and Faecalibacterium prausnitzii of host peripheral lipid metabolism and histone acetylation in mouse gut organoids","volume":"5","author":"Lukovac","year":"2014","journal-title":"MBio"},{"key":"2023060914235560500_bib184","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-64703-z","article-title":"Human microbiota-transplanted C57BL\/6 mice and offspring display reduced establishment of key bacteria and reduced immune stimulation compared to mouse microbiota-transplantation","volume":"10","author":"Lundberg","year":"2020","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib195","doi-asserted-by":"crossref","first-page":"229","DOI":"10.1530\/JOE-12-0468","article-title":"The sorting of proglucagon to secretory granules is mediated by carboxypeptidase E and intrinsic sorting signals","volume":"217","author":"McGirr","year":"2013","journal-title":"J Endocrinol"},{"key":"2023060914235560500_bib185","doi-asserted-by":"crossref","first-page":"148","DOI":"10.3389\/fgene.2015.00148","article-title":"Systematic genome assessment of B-vitamin biosynthesis suggests cooperation among gut microbes","volume":"6","author":"Magn\u00fasd\u00f3ttir","year":"2015","journal-title":"Front Genet"},{"key":"2023060914235560500_bib186","first-page":"37","article-title":"SCFA: mechanisms and functional importance in the gut","volume-title":"Proceedings of the Nutrition Society","author":"Martin-Gallausiaux","year":"2021"},{"key":"2023060914235560500_bib187","doi-asserted-by":"crossref","first-page":"458","DOI":"10.1016\/j.chom.2018.03.011","article-title":"Small intestine microbiota regulate host digestive and absorptive adaptive responses to dietary lipids","volume":"23","author":"Martinez-Guryn","year":"2018","journal-title":"Cell Host Microbe"},{"key":"2023060914235560500_bib188","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.idairyj.2013.03.010","article-title":"Casein hydrolysate and derived peptides stimulate mucin secretion and gene expression in human intestinal cells","volume":"32","author":"Mart\u00ednez-Maqueda","year":"2013","journal-title":"Int Dairy J"},{"key":"2023060914235560500_bib189","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1111\/j.1742-7843.2005.pto960202.x","article-title":"Gastric juice: a barrier against infectious diseases","volume":"96","author":"Martinsen","year":"2005","journal-title":"Basic Clin Pharmacol Toxicol"},{"key":"2023060914235560500_bib190","doi-asserted-by":"crossref","DOI":"10.1186\/1471-2180-14-133","article-title":"The HMITM module: a new tool to study the host-microbiota interaction in the human gastrointestinal tract in vitro","volume":"14","author":"Marzorati","year":"2014","journal-title":"BMC Microbiol"},{"key":"2023060914235560500_bib191","doi-asserted-by":"crossref","first-page":"2688","DOI":"10.1039\/C5LC00392J","article-title":"A four-organ-chip for interconnected long-term co-culture of human intestine, liver, skin and kidney equivalents","volume":"15","author":"Maschmeyer","year":"2015","journal-title":"Lab Chip"},{"key":"2023060914235560500_bib192","doi-asserted-by":"crossref","first-page":"e0129076","DOI":"10.1371\/journal.pone.0129076","article-title":"Gastrointestinal pH and transit time profiling in healthy volunteers using the IntelliCap system confirms ileo-colonic release of ColoPulse tablets","volume":"10","author":"Maurer","year":"2015","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib193","doi-asserted-by":"crossref","first-page":"16","DOI":"10.3390\/microorganisms4010016","article-title":"Extensive intestinal resection triggers behavioral adaptation, intestinal remodeling and microbiota transition in short bowel syndrome","volume":"4","author":"Mayeur","year":"2016","journal-title":"Microorganisms"},{"key":"2023060914235560500_bib194","doi-asserted-by":"crossref","first-page":"e54335","DOI":"10.1371\/journal.pone.0054335","article-title":"Faecal D\/L lactate ratio is a metabolic signature of microbiota imbalance in patients with short bowel syndrome","volume":"8","author":"Mayeur","year":"2013","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib196","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1038\/s41591-020-1024-z","article-title":"Engineering transplantable jejunal mucosal grafts using patient-derived organoids from children with intestinal failure","volume":"26","author":"Meran","year":"2020","journal-title":"Nat Med"},{"key":"2023060914235560500_bib197","doi-asserted-by":"crossref","first-page":"147","DOI":"10.2527\/jas.2008-1560","article-title":"Ileal microbiota of growing pigs fed different dietary calcium phosphate levels and phytase content and subjected to ileal pectin infusion","volume":"88","author":"Metzler-Zebeli","year":"2010","journal-title":"J Anim Sci"},{"key":"2023060914235560500_bib198","doi-asserted-by":"crossref","first-page":"50","DOI":"10.1016\/j.tim.2011.11.002","article-title":"The pig: a model for human infectious diseases","volume":"20","author":"Meurens","year":"2012","journal-title":"Trends Microbiol"},{"key":"2023060914235560500_bib199","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1002\/stem.1655","article-title":"Adult stem cells in the small intestine are intrinsically programmed with their location-specific function","volume":"32","author":"Middendorp","year":"2014","journal-title":"Stem Cells"},{"key":"2023060914235560500_bib200","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1093\/femsec\/fiab111","article-title":"Nutrient load acts as a driver of gut microbiota load, community composition and metabolic functionality in the simulator of the human intestinal microbial ecosystem","volume":"97","author":"Minnebo","year":"2021","journal-title":"FEMS Microbiol Ecol"},{"key":"2023060914235560500_bib201","first-page":"1079","article-title":"Characterization of fasted-state human intestinal fluids collected from duodenum and jejunum","volume":"58","author":"Moreno\u00a0MP\u00a0de\u00a0la","year":"2006","journal-title":"J Pharm Pharmacol"},{"key":"2023060914235560500_bib202","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1042\/BST20200338","article-title":"Advances in modelling the human microbiome-gut-brain axis in vitro","volume":"49","author":"Moysidou","year":"2021","journal-title":"Biochem Soc Trans"},{"key":"2023060914235560500_bib203","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1159\/000524023","article-title":"The compositional structure of the small intestinal microbial community via balloon-assisted enteroscopy","volume":"103","author":"Nagasue","year":"2022","journal-title":"Digestion"},{"key":"2023060914235560500_bib204","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-40182-9","article-title":"Effects of bowel preparation on the human gut microbiome and metabolome","volume":"9","author":"Nagata","year":"2019","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib205","doi-asserted-by":"crossref","first-page":"28","DOI":"10.3389\/fnut.2018.00028","article-title":"Gut microbiome composition in non-human primates consuming a Western or Mediterranean diet","volume":"5","author":"Nagpal","year":"2018","journal-title":"Front Nutr"},{"key":"2023060914235560500_bib206","doi-asserted-by":"crossref","first-page":"13734","DOI":"10.1111\/nmo.13734","article-title":"Normative values for region-specific colonic and gastrointestinal transit times in 111 healthy volunteers using the 3D-transit electromagnet tracking system: influence of age, gender, and body mass index","volume":"32","author":"Nandhra","year":"2020","journal-title":"Neurogastroenterol Motil"},{"key":"2023060914235560500_bib207","doi-asserted-by":"crossref","first-page":"G1368","DOI":"10.1152\/ajpgi.00135.2010","article-title":"The steroid glycoside H.g.-12 from Hoodia gordonii activates the human bitter receptor TAS2R14 and induces CCK release from HuTu-80 cells","volume":"299","author":"Nev\u00e9","year":"2010","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib208","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-021-01069-y","article-title":"Diet, obesity, and the gut microbiome as determinants modulating metabolic outcomes in a non-human primate model","volume":"9","author":"Newman","year":"2021","journal-title":"Microbiome"},{"key":"2023060914235560500_bib209","doi-asserted-by":"crossref","first-page":"1171","DOI":"10.1136\/gut.34.9.1171","article-title":"Disturbed gastric emptying in the short bowel syndrome. Evidence for a \u201ccolonic brake\u201d","volume":"34","author":"Nightingale","year":"1993","journal-title":"Gut"},{"key":"2023060914235560500_bib210","doi-asserted-by":"crossref","first-page":"574","DOI":"10.1038\/s41586-020-2724-8","article-title":"Homeostatic mini-intestines through scaffold-guided organoid morphogenesis","volume":"585","author":"Nikolaev","year":"2020","journal-title":"Nature"},{"key":"2023060914235560500_bib211","doi-asserted-by":"crossref","first-page":"1381","DOI":"10.1007\/s00702-016-1612-8","article-title":"Prevalence of small intestinal bacterial overgrowth in Chinese patients with Parkinson\u2019s disease","volume":"123","author":"Niu","year":"2016","journal-title":"J Neural Transm"},{"key":"2023060914235560500_bib212","first-page":"1","article-title":"A primary human macrophage-enteroid co-culture model to investigate mucosal gut physiology and host-pathogen interactions","volume":"7","author":"Noel","year":"2017","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib213","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1016\/j.cgh.2005.10.002","article-title":"Short bowel syndrome and intestinal failure: consensus definitions and overview","volume":"4","author":"O\u2019Keefe","year":"2006","journal-title":"Clin Gastroenterol Hepatol"},{"key":"2023060914235560500_bib214","doi-asserted-by":"crossref","first-page":"1697","DOI":"10.3390\/cells9071697","article-title":"In silico evaluation of putative S100B interacting proteins in healthy and IBD gut microbiota","volume":"9","author":"Orsini","year":"2020","journal-title":"Cells"},{"key":"2023060914235560500_bib215","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-030-05240-9","volume-title":"Lower Gastrointestinal Tract Surgery: Laparoscopic Procedures","author":"Parker","year":"2019"},{"key":"2023060914235560500_bib216","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/srep40248","article-title":"A fibrolytic potential in the human ileum mucosal microbiota revealed by functional metagenomic","volume":"7","author":"Patrascu","year":"2017","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib217","doi-asserted-by":"crossref","first-page":"160","DOI":"10.1016\/j.humpath.2005.10.001","article-title":"Prognostic value of mucins in the classification of ampullary carcinomas","volume":"37","author":"Paulsen","year":"2006","journal-title":"Hum Pathol"},{"key":"2023060914235560500_bib218","first-page":"1","article-title":"A large-scale survey of the postmortem human microbiome, and its potential to provide insight into the living health condition","volume":"8","author":"Pechal","year":"2018","journal-title":"Sci Reports"},{"key":"2023060914235560500_bib219","doi-asserted-by":"crossref","first-page":"1451","DOI":"10.1038\/s12276-021-00606-x","article-title":"Biobanking of human gut organoids for translational research","volume":"53","author":"Perrone","year":"2021","journal-title":"Exp Mol Med"},{"key":"2023060914235560500_bib220","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/nri3608","article-title":"Intestinal epithelial cells: regulators of barrier function and immune homeostasis","volume":"14","author":"Peterson","year":"2014","journal-title":"Nat Rev Immunol"},{"key":"2023060914235560500_bib221","doi-asserted-by":"crossref","first-page":"1371","DOI":"10.1007\/s00383-021-04948-5","article-title":"Fecal microbiome alterations in pediatric patients with short bowel syndrome receiving a rotating cycle of gastrointestinal prophylactic antibiotics","volume":"37","author":"Phyo","year":"2021","journal-title":"Pediatr Surg Int"},{"key":"2023060914235560500_bib222","doi-asserted-by":"crossref","first-page":"165","DOI":"10.14309\/ajg.0000000000000501","article-title":"ACG Clinical guideline: small intestinal bacterial overgrowth","volume":"115","author":"Pimentel","year":"2020","journal-title":"Am J Gastroenterol"},{"key":"2023060914235560500_bib223","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1016\/j.clnu.2014.08.017","article-title":"ESPEN endorsed recommendations: definition and classification of intestinal failure in adults","volume":"34","author":"Pironi","year":"2015","journal-title":"Clin Nutr"},{"key":"2023060914235560500_bib224","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1016\/j.clnu.2016.01.020","article-title":"ESPEN guidelines on chronic intestinal failure in adults","volume":"35","author":"Pironi","year":"2016","journal-title":"Clin Nutr"},{"key":"2023060914235560500_bib225","doi-asserted-by":"crossref","first-page":"1633","DOI":"10.1111\/j.1572-0241.2006.00710.x","article-title":"Candidates for intestinal transplantation: a multicenter survey in Europe","volume":"101","author":"Pironi","year":"2006","journal-title":"Am J Gastroenterol"},{"key":"2023060914235560500_bib226","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1016\/j.ijantimicag.2013.12.008","article-title":"In vitro activity of rifaximin against isolates from patients with small intestinal bacterial overgrowth","volume":"43","author":"Pistiki","year":"2014","journal-title":"Int J Antimicrob Agents"},{"key":"2023060914235560500_bib227","doi-asserted-by":"crossref","first-page":"4253","DOI":"10.1126\/sciadv.aat4253","article-title":"Transistor in a tube: a route to three-dimensional bioelectronics","volume":"4","author":"Pitsalidis","year":"2018","journal-title":"Sci Adv"},{"key":"2023060914235560500_bib228","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1007\/s00253-017-8616-7","article-title":"Propionibacterium spp.\u2014source of propionic acid, vitamin B12, and other metabolites important for the industry","volume":"102","author":"Piwowarek","year":"2018","journal-title":"Appl Microbiol Biotechnol"},{"key":"2023060914235560500_bib229","doi-asserted-by":"crossref","first-page":"110459","DOI":"10.1016\/j.foodres.2021.110459","article-title":"Prediction of in-vitro glycemic responses of biscuits in an engineered small intestine system","volume":"147","author":"Priyadarshini","year":"2021","journal-title":"Food Res Int"},{"key":"2023060914235560500_bib230","first-page":"gutjnl","article-title":"Advancing human gut microbiota research by considering gut transit time","volume":"0","author":"Proch\u00e1zkov\u00e1","year":"2022","journal-title":"Gut"},{"key":"2023060914235560500_bib231","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1111\/j.1574-6968.2002.tb11467.x","article-title":"The microbiology of butyrate formation in the human colon","volume":"217","author":"Pryde","year":"2002","journal-title":"FEMS Microbiol Lett"},{"key":"2023060914235560500_bib232","doi-asserted-by":"crossref","first-page":"4633","DOI":"10.1038\/s41596-021-00589-z","article-title":"Intestinal organoid cocultures with microbes","volume":"16","author":"Puschhof","year":"2021","journal-title":"Nat Protoc"},{"key":"2023060914235560500_bib233","doi-asserted-by":"crossref","first-page":"537","DOI":"10.1111\/asj.12946","article-title":"Dietary protein level affects nutrient digestibility and ileal microbiota structure in growing pigs","volume":"89","author":"Qiu","year":"2018","journal-title":"Anim Sci J"},{"key":"2023060914235560500_bib235","doi-asserted-by":"crossref","first-page":"1526","DOI":"10.1053\/j.gastro.2020.06.090","article-title":"AGA clinical practice update on small intestinal bacterial overgrowth: expert review","volume":"159","author":"Quigley","year":"2020","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib234","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11894-019-0671-z","article-title":"The spectrum of Small Intestinal Bacterial Overgrowth (SIBO)","volume":"21","author":"Quigley","year":"2019","journal-title":"Curr Gastroenterol Rep"},{"key":"2023060914235560500_bib236","first-page":"85","article-title":"Liver disease symptoms in non-alcoholic fatty liver disease and small intestinal bacterial overgrowth","volume":"56","author":"Rafiei","year":"2018","journal-title":"Rom J Intern Med"},{"key":"2023060914235560500_bib237","doi-asserted-by":"crossref","first-page":"1736","DOI":"10.1111\/j.1462-2920.2009.01900.x","article-title":"Development and application of the human intestinal tract chip, a phylogenetic microarray: analysis of universally conserved phylotypes in the abundant microbiota of young and elderly adults","volume":"11","author":"Rajili\u0107-Stojanovi\u0107","year":"2009","journal-title":"Environ Microbiol"},{"key":"2023060914235560500_bib238","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.autneu.2009.07.007","article-title":"Gut chemosensing: interactions between gut endocrine cells and visceral afferents","volume":"153","author":"Raybould","year":"2010","journal-title":"Auton Neurosci"},{"key":"2023060914235560500_bib239","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1016\/j.cmet.2011.12.019","article-title":"G-protein-coupled receptors in intestinal chemosensation","volume":"15","author":"Reimann","year":"2012","journal-title":"Cell Metab"},{"key":"2023060914235560500_bib240","doi-asserted-by":"crossref","first-page":"1900053","DOI":"10.1002\/aisy.201900053","article-title":"Ingestible osmotic pill for in vivo sampling of gut microbiomes","volume":"1","author":"Rezaei\u00a0Nejad","year":"2019","journal-title":"Adv Intell Syst"},{"key":"2023060914235560500_bib241","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1038\/ajg.2017.46","article-title":"Hydrogen and methane-based breath testing in gastrointestinal disorders: the North American consensus","volume":"112","author":"Rezaie","year":"2017","journal-title":"Am J Gastroenterol"},{"key":"2023060914235560500_bib242","doi-asserted-by":"crossref","first-page":"530","DOI":"10.1097\/MCG.0000000000000803","article-title":"Small-intestinal bacterial overgrowth is associated with concurrent intestinal inflammation but not with systemic inflammation in Crohn\u2019s disease patients","volume":"52","author":"Ricci","year":"2018","journal-title":"J Clin Gastroenterol"},{"key":"2023060914235560500_bib243","doi-asserted-by":"crossref","first-page":"673","DOI":"10.1002\/jps.24603","article-title":"Characterization of human duodenal fluids in fasted and fed state conditions","volume":"105","author":"Riethorst","year":"2015","journal-title":"J Pharm Sci"},{"key":"2023060914235560500_bib245","doi-asserted-by":"crossref","first-page":"907","DOI":"10.1038\/mi.2015.121","article-title":"Antigen sampling by intestinal M cells is the principal pathway initiating mucosal IgA production to commensal enteric bacteria","volume":"9","author":"Rios","year":"2016","journal-title":"Mucosal Immunol"},{"key":"2023060914235560500_bib244","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-021-86980-y","article-title":"A toolbox for the comprehensive analysis of small volume human intestinal samples that can be used with gastrointestinal sampling capsules","volume":"11","author":"Rios-Morales","year":"2021","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib246","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.bpg.2013.03.018","article-title":"Ex vivo systems to study host-microbiota interactions in the gastrointestinal tract","volume":"27","author":"Roeselers","year":"2013","journal-title":"Best Pract Res Clin Gastroenterol"},{"key":"2023060914235560500_bib247","doi-asserted-by":"crossref","first-page":"1052","DOI":"10.1016\/j.bbalip.2013.02.009","article-title":"Identification of amino acids in human colipase that mediate adsorption to lipid emulsions and mixed micelles","volume":"1831","author":"Ross","year":"2013","journal-title":"Biochim Biophys Acta Mol Cell Biol Lipids"},{"key":"2023060914235560500_bib248","doi-asserted-by":"crossref","first-page":"118","DOI":"10.3390\/nu3010118","article-title":"Folate production by probiotic bacteria","volume":"3","author":"Rossi","year":"2011","journal-title":"Nutrients"},{"key":"2023060914235560500_bib249","doi-asserted-by":"crossref","first-page":"313","DOI":"10.1038\/nri2515","article-title":"The gut microbiota shapes intestinal immune responses during health and disease","volume":"9","author":"Round","year":"2009","journal-title":"Nat Rev Immunol"},{"key":"2023060914235560500_bib250","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12915-020-00860-x","article-title":"Spatial and temporal modulation of enterotoxigenic E. coli H10407 pathogenesis and interplay with microbiota in human gut models","volume":"18","author":"Roussel","year":"2020","journal-title":"BMC Biol"},{"key":"2023060914235560500_bib251","doi-asserted-by":"crossref","first-page":"367","DOI":"10.1016\/j.ejps.2012.02.025","article-title":"Human small intestinal and colonic tissue mounted in the Ussing chamber as a tool for characterizing the intestinal absorption of drugs","volume":"46","author":"Rozehnal","year":"2012","journal-title":"Eur J Pharm Sci"},{"key":"2023060914235560500_bib253","doi-asserted-by":"crossref","first-page":"G792","DOI":"10.1152\/ajpgi.00074.2006","article-title":"Colocalization of the \u03b1-subunit of gustducin with PYY and GLP-1 in L cells of human colon","volume":"291","author":"Rozengurt","year":"2006","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib254","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-019-09964-7","article-title":"Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders","volume":"10","author":"Saffouri","year":"2019","journal-title":"Nat Commun"},{"key":"2023060914235560500_bib255","doi-asserted-by":"crossref","first-page":"158","DOI":"10.3945\/jn.108.092023","article-title":"Cell and molecular aspects of human intestinal biotin absorption","volume":"139","author":"Said","year":"2009","journal-title":"J Nutr"},{"key":"2023060914235560500_bib256","doi-asserted-by":"crossref","first-page":"1762","DOI":"10.1053\/j.gastro.2011.07.050","article-title":"Long-term expansion of epithelial organoids from human colon, adenoma, adenocarcinoma, and Barrett\u2019s epithelium","volume":"141","author":"Sato","year":"2011","journal-title":"Gastroenterology"},{"key":"2023060914235560500_bib258","doi-asserted-by":"crossref","first-page":"1050","DOI":"10.1002\/biot.201000214","article-title":"Metabolism of green tea catechins by the human small intestine","volume":"5","author":"Schantz","year":"2010","journal-title":"Biotechnol J"},{"key":"2023060914235560500_bib259","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.42693","article-title":"Extensive transmission of microbes along the gastrointestinal tract","volume":"8","author":"Schmidt","year":"2019","journal-title":"Elife"},{"key":"2023060914235560500_bib260","doi-asserted-by":"crossref","first-page":"214","DOI":"10.1016\/j.ejpb.2016.09.009","article-title":"Resolving the physiological conditions in bioavailability and bioequivalence studies: comparison of fasted and fed state","volume":"108","author":"Schneider","year":"2016","journal-title":"Eur J Pharm Biopharm"},{"key":"2023060914235560500_bib261","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1080\/19490976.2018.1474321","article-title":"The enteric microbiota regulates jejunal Paneth cell number and function without impacting intestinal stem cells","volume":"10","author":"Schoenborn","year":"2019","journal-title":"Gut Microbes"},{"key":"2023060914235560500_bib262","doi-asserted-by":"crossref","first-page":"e142","DOI":"10.1038\/ctg.2015.69","article-title":"Long-term teduglutide for the treatment of patients with intestinal failure associated with short bowel syndrome","volume":"7","author":"Schwartz","year":"2016","journal-title":"Clin Transl Gastroenterol"},{"key":"2023060914235560500_bib263","doi-asserted-by":"crossref","DOI":"10.1128\/mSphere.00126-19","article-title":"Spatial and temporal analysis of the stomach and small-intestinal microbiota in fasted healthy humans","volume":"4","author":"Seekatz","year":"2019","journal-title":"Msphere"},{"key":"2023060914235560500_bib264","doi-asserted-by":"crossref","first-page":"1770","DOI":"10.1007\/s10620-020-06556-0","article-title":"Breath test or duodenal aspirate for small intestinal bacterial overgrowth: still no breath of fresh air","volume":"66","author":"Shah","year":"2021","journal-title":"Dig Dis Sci"},{"key":"2023060914235560500_bib265","doi-asserted-by":"crossref","first-page":"2000250","DOI":"10.1002\/mnfr.202000250","article-title":"Stimulation of gastric transit function driven by hydrolyzed casein increases small intestinal carbohydrate availability and its microbial metabolism","volume":"64","author":"Shen","year":"2020","journal-title":"Mol Nutr Food Res"},{"key":"2023060914235560500_bib266","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1016\/S0002-9610(05)81226-7","article-title":"Intraoperative tissue oximetry in the human gastrointestinal tract","volume":"159","author":"Sheridan","year":"1990","journal-title":"Am J Surg"},{"key":"2023060914235560500_bib267","doi-asserted-by":"crossref","first-page":"4636","DOI":"10.3748\/wjg.v20.i16.4636","article-title":"Combined probiotic bacteria promotes intestinal epithelial barrier function in interleukin-10-gene-deficient mice","volume":"20","author":"Shi","year":"2014","journal-title":"World J Gastroenterol"},{"key":"2023060914235560500_bib268","doi-asserted-by":"crossref","first-page":"1","DOI":"10.14309\/ctg.0000000000000073","article-title":"Characterization of proximal small intestinal microbiota in patients with suspected small intestinal bacterial overgrowth: a cross-sectional study","volume":"10","author":"Shin","year":"2019","journal-title":"Clin Transl Gastroenterol"},{"key":"2023060914235560500_bib269","doi-asserted-by":"crossref","first-page":"e143","DOI":"10.1038\/ctg.2015.54","article-title":"The effects of bowel preparation on microbiota-related metrics differ in health and in inflammatory bowel disease and for the mucosal and luminal microbiota compartments","volume":"7","author":"Shobar","year":"2016","journal-title":"Clin Transl Gastroenterol"},{"key":"2023060914235560500_bib270","first-page":"100127","article-title":"A compendium of predicted growths and derived symbiotic relationships between 803 gut microbes in 13 different diets","volume":"3","author":"Singh","year":"2022","journal-title":"Curr Res Microb Sci"},{"key":"2023060914235560500_bib271","first-page":"299","article-title":"Short-chain fatty acid transporters: role in colonic homeostasis","volume":"8","author":"Sivaprakasam","year":"2018","journal-title":"Compr Physiol"},{"key":"2023060914235560500_bib272","first-page":"3","article-title":"Caco-2 cells, biopharmaceutics classification system (BCS) and biowaiver","volume":"54","author":"Smetanov\u00e1","year":"2011","journal-title":"Acta Med"},{"key":"2023060914235560500_bib273","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1046\/j.1365-201X.1998.0248f.x","article-title":"Integrity and metabolism of human ileal mucosa in vitro in the Ussing chamber","volume":"162","author":"S\u00f6derholm","year":"1998","journal-title":"Acta Physiol Scand"},{"key":"2023060914235560500_bib274","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s40168-019-0628-3","article-title":"Taxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome","volume":"7","author":"Song","year":"2019","journal-title":"Microbiome"},{"key":"2023060914235560500_bib275","doi-asserted-by":"crossref","first-page":"1260","DOI":"10.1038\/ijo.2016.46","article-title":"Influence of Roux-en-Y gastric bypass on plasma bile acid profiles: a comparative study between rats, pigs and humans","volume":"40","author":"Spinelli","year":"2016","journal-title":"Int J Obes"},{"key":"2023060914235560500_bib276","first-page":"93","article-title":"Nutrition communication about low FODMAP diet in irritable bowel syndrome (IBS) and small intestinal bacterial overgrowth (SIBO) in Thai healthcare practitioners","volume":"4","author":"Srisukthaveerat","year":"2021","journal-title":"Bioact Compd Heal Dis"},{"key":"2023060914235560500_bib277","doi-asserted-by":"crossref","first-page":"e113","DOI":"10.1002\/cpim.113","article-title":"Co-culture system of human enteroids\/colonoids with innate immune cells","volume":"131","author":"Staab","year":"2020","journal-title":"Curr Protoc Immunol"},{"key":"2023060914235560500_bib278","doi-asserted-by":"crossref","first-page":"104989","DOI":"10.1016\/j.ejps.2019.104989","article-title":"A higher throughput and physiologically relevant two-compartmental human ex vivo intestinal tissue system for studying gastrointestinal processes","volume":"137","author":"Stevens","year":"2019","journal-title":"Eur J Pharm Sci"},{"key":"2023060914235560500_bib279","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1007\/978-1-0716-0338-3_16","article-title":"Establishing human intestinal enteroid\/organoid lines from preterm infant and adult tissue","volume":"2121","author":"Stewart","year":"2020","journal-title":"Methods Mol Biol"},{"key":"2023060914235560500_bib280","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1093\/femsec\/fiz096","article-title":"Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota","volume":"95","author":"Stolaki","year":"2019","journal-title":"FEMS Microbiol Ecol"},{"key":"2023060914235560500_bib281","doi-asserted-by":"crossref","first-page":"27","DOI":"10.1007\/s00535-017-1371-9","article-title":"Meta-analysis: proton pump inhibitors moderately increase the risk of small intestinal bacterial overgrowth","volume":"53","author":"Su","year":"2018","journal-title":"J Gastroenterol"},{"key":"2023060914235560500_bib282","doi-asserted-by":"crossref","first-page":"677","DOI":"10.1002\/jpen.1704","article-title":"Repeated metabolic balance studies in patients with short bowel syndrome","volume":"44","author":"Sun","year":"2020","journal-title":"J Parenteral Enteral Nutr"},{"key":"2023060914235560500_bib283","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12866-017-1059-6","article-title":"The human jejunum has an endogenous microbiota that differs from those in the oral cavity and colon","volume":"17","author":"Sundin","year":"2017","journal-title":"BMC Microbiol"},{"key":"2023060914235560500_bib284","first-page":"71","article-title":"Enteral feeding and its impact on the gut immune system and intestinal mucosal barrier","volume":"10","author":"Szefel","year":"2015","journal-title":"Prz Gastroenterol"},{"key":"2023060914235560500_bib285","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.soard.2014.09.016","article-title":"Bowel length: measurement, predictors, and impact on bariatric and metabolic surgery","volume":"11","author":"Tacchino","year":"2015","journal-title":"Surg Obes Relat Dis"},{"key":"2023060914235560500_bib286","doi-asserted-by":"crossref","first-page":"915","DOI":"10.1016\/j.xphs.2015.11.035","article-title":"Application of a human intestinal epithelial cell monolayer to the prediction of oral drug absorption in humans as a superior alternative to the Caco-2 cell monolayer","volume":"105","author":"Takenaka","year":"2016","journal-title":"J Pharm Sci"},{"key":"2023060914235560500_bib287","doi-asserted-by":"crossref","first-page":"108633","DOI":"10.1016\/j.celrep.2020.108633","article-title":"A constant pool of Lgr5+ intestinal stem cells is required for intestinal homeostasis","volume":"34","author":"Tan","year":"2021","journal-title":"Cell Rep"},{"key":"2023060914235560500_bib288","doi-asserted-by":"crossref","first-page":"151","DOI":"10.3389\/fcimb.2020.00151","article-title":"Current sampling methods for gut microbiota: a call for more precise devices","volume":"10","author":"Tang","year":"2020","journal-title":"Front Cell Infect Microbiol"},{"key":"2023060914235560500_bib289","doi-asserted-by":"crossref","first-page":"5643","DOI":"10.1128\/JB.185.18.5643-5647.2003","article-title":"Lactobacillus reuteri CRL1098 produces cobalamin","volume":"185","author":"Taranto","year":"2003","journal-title":"J Bacteriol"},{"key":"2023060914235560500_bib290","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.stem.2016.01.001","article-title":"Replacement of lost Lgr5-positive stem cells through plasticity of their enterocyte-lineage daughters","volume":"18","author":"Tetteh","year":"2016","journal-title":"Cell Stem Cell"},{"key":"2023060914235560500_bib291","doi-asserted-by":"crossref","first-page":"2826","DOI":"10.1158\/0008-5472.CAN-08-4466","article-title":"GPR109A is a G-protein-coupled receptor for the bacterial fermentation product butyrate and functions as a tumor suppressor in colon","volume":"69","author":"Thangaraju","year":"2009","journal-title":"Cancer Res"},{"key":"2023060914235560500_bib292","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1038\/nature10408","article-title":"A reserve stem cell population in small intestine renders Lgr5-positive cells dispensable","volume":"478","author":"Tian","year":"2011","journal-title":"Nature"},{"key":"2023060914235560500_bib293","doi-asserted-by":"crossref","first-page":"732","DOI":"10.3390\/nu12030732","article-title":"\u03b1-Linolenic acid-rich diet influences microbiota composition and villus morphology of the mouse small intestine","volume":"12","author":"Todorov","year":"2020","journal-title":"Nutrients"},{"key":"2023060914235560500_bib294","doi-asserted-by":"crossref","first-page":"348","DOI":"10.21037\/atm.2020.02.40","article-title":"Variation in small bowel transit time on capsule endoscopy","volume":"8","author":"Tominaga","year":"2020","journal-title":"Ann Transl Med"},{"key":"2023060914235560500_bib296","doi-asserted-by":"crossref","first-page":"1441","DOI":"10.1016\/j.cell.2020.08.027","article-title":"Diet diurnally regulates small intestinal microbiome-epithelial-immune homeostasis and enteritis","volume":"182","author":"Tuganbaev","year":"2020","journal-title":"Cell"},{"key":"2023060914235560500_bib297","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/1757-4749-5-35","article-title":"Time-dependent post mortem changes in the composition of intestinal bacteria using real-time quantitative PCR","volume":"5","author":"Tuomisto","year":"2013","journal-title":"Gut Pathog"},{"key":"2023060914235560500_bib298","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-020-71939-2","article-title":"Compositional and functional differeances of the mucosal microbiota along the intestine of healthy individuals","volume":"10","author":"Vaga","year":"2020","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib299","doi-asserted-by":"crossref","first-page":"S660","DOI":"10.14309\/01.ajg.0000707300.36404.b6","article-title":"The first advanced network analysis of the small bowel microbiome in Small Intestinal Bacterial Overgrowth (SIBO) reveals that Escherichia and Klebsiella are disruptive to network integrity: data from the REIMAGINE study","volume":"115","author":"Valiente-Banuet","year":"2020","journal-title":"Am J Gastroenterol"},{"key":"2023060914235560500_bib314","first-page":"305","article-title":"The Simulator of the Human Intestinal Microbial Ecosystem (SHIME\u00ae)","volume-title":"The Impact of Food Bioactives on Health: In Vitro and Ex Vivo Models","author":"van\u00a0de\u00a0Wiele","year":"2015"},{"key":"2023060914235560500_bib31","doi-asserted-by":"crossref","first-page":"e83418","DOI":"10.1371\/journal.pone.0083418","article-title":"Comparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem","volume":"8","author":"Van\u00a0den\u00a0Bogert","year":"2013","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib87","doi-asserted-by":"crossref","first-page":"241","DOI":"10.1146\/annurev.physiol.010908.163145","article-title":"Stem cells, self-renewal, and differentiation in the intestinal epithelium","volume":"71","author":"Van\u00a0Der\u00a0Flier","year":"2009","journal-title":"Annu Rev Physiol"},{"key":"2023060914235560500_bib107","doi-asserted-by":"crossref","first-page":"375","DOI":"10.3389\/fcell.2020.00375","article-title":"Congruence of transcription programs in adult stem cell-derived jejunum organoids and original tissue during long-term culture","volume":"8","author":"van\u00a0der\u00a0Hee","year":"2020","journal-title":"Front Cell Dev Biol"},{"key":"2023060914235560500_bib257","doi-asserted-by":"crossref","first-page":"520","DOI":"10.1016\/j.gie.2013.03.170","article-title":"A novel ingestible electronic drug delivery and monitoring device","volume":"78","author":"van\u00a0der\u00a0Schaar","year":"2013","journal-title":"Gastrointest Endosc"},{"key":"2023060914235560500_bib151","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1007\/BF00702340","article-title":"The human intestinal cell lines Caco-2 and LS174T as models to study cel-type specific mucin expression","volume":"13","author":"van\u00a0Klinken","year":"1996","journal-title":"Glycoconjugate J"},{"key":"2023060914235560500_bib295","first-page":"1","article-title":"Fermentation kinetics of selected dietary fibers by human small intestinal microbiota depend on the type of fiber and subject","volume":"64","author":"Van\u00a0Trijp","year":"2020","journal-title":"Mol Nutr Food Res"},{"key":"2023060914235560500_bib300","doi-asserted-by":"crossref","first-page":"507","DOI":"10.1038\/nature24460","article-title":"Quantitative microbiome profiling links gut community variation to microbial load","volume":"551","author":"Vandeputte","year":"2017","journal-title":"Nature"},{"key":"2023060914235560500_bib301","first-page":"1287","article-title":"Evidence-based recommendations of the Andalusian group for nutrition reflection and investigation (Garin) for the management of adult patients with short bowel syndrome","volume":"38","author":"V\u00edlchez-L\u00f3pez","year":"2021","journal-title":"Nutr Hosp"},{"key":"2023060914235560500_bib302","doi-asserted-by":"crossref","first-page":"4736","DOI":"10.1038\/s41598-018-23198-5","article-title":"Species level description of the human ileal bacterial microbiota","volume":"8","author":"Villmones","year":"2018","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib303","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-022-05723-9","article-title":"Investigating the human jejunal microbiota","volume":"12","author":"Villmones","year":"2022","journal-title":"Sci Rep"},{"key":"2023060914235560500_bib304","doi-asserted-by":"crossref","first-page":"920","DOI":"10.1126\/science.aao2774","article-title":"Patient-derived organoids model treatment response of metastatic gastrointestinal cancers","volume":"359","author":"Vlachogiannis","year":"2018","journal-title":"Science"},{"key":"2023060914235560500_bib305","first-page":"1","article-title":"Drug use in patients with short bowel syndrome and intestinal failure","volume":"69","author":"Vorre","year":"2022","journal-title":"Dan Med J"},{"key":"2023060914235560500_bib306","doi-asserted-by":"crossref","first-page":"897","DOI":"10.1177\/2050640619852255","article-title":"Composition of the mucosa-associated microbiota along the entire gastrointestinal tract of human individuals","volume":"7","author":"Vuik","year":"2019","journal-title":"Unit Eur Gastroenterol J"},{"key":"2023060914235560500_bib307","doi-asserted-by":"crossref","first-page":"77","DOI":"10.3390\/ani10010077","article-title":"From mice to monkeys? Beyond orthodox approaches to the ethics of animal model choice","volume":"10","author":"Walker","year":"2020","journal-title":"Animals"},{"key":"2023060914235560500_bib308","doi-asserted-by":"crossref","first-page":"2261","DOI":"10.1242\/dev.135400","article-title":"Generation of intestinal surface: an absorbing tale","volume":"143","author":"Walton","year":"2016","journal-title":"Development"},{"key":"2023060914235560500_bib309","doi-asserted-by":"crossref","first-page":"219","DOI":"10.1016\/j.femsec.2005.03.012","article-title":"Comparison of bacterial diversity along the human intestinal tract by direct cloning and sequencing of 16S rRNA genes","volume":"54","author":"Wang","year":"2005","journal-title":"FEMS Microbiol Ecol"},{"key":"2023060914235560500_bib310","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1111\/apt.13329","article-title":"Regional gastrointestinal transit and pH studied in 215 healthy volunteers using the wireless motility capsule: influence of age, gender, study country and testing protocol","volume":"42","author":"Wang","year":"2015","journal-title":"Aliment Pharmacol Ther"},{"key":"2023060914235560500_bib311","doi-asserted-by":"crossref","first-page":"542","DOI":"10.1038\/s41579-022-00712-1","article-title":"Carbohydrate-active enzymes (CAZymes) in the gut microbiome","volume":"20","author":"Wardman","year":"2022","journal-title":"Nat Rev Microbiol"},{"key":"2023060914235560500_bib312","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.ejps.2014.07.003","article-title":"A new approach to predict human intestinal absorption using porcine intestinal tissue and biorelevant matrices","volume":"63","author":"Westerhout","year":"2014","journal-title":"Eur J Pharm Sci"},{"key":"2023060914235560500_bib313","doi-asserted-by":"crossref","DOI":"10.7554\/eLife.37138","article-title":"Human gut bacteroides capture vitamin B12 via cell surface-exposed lipoproteins","volume":"7","author":"Wexler","year":"2018","journal-title":"Elife"},{"key":"2023060914235560500_bib315","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3390\/nu14163382","article-title":"Efficacy of an irritable bowel syndrome diet in the treatment of small intestinal bacterial overgrowth: a narrative review","volume":"14","author":"Wielgosz-Grochowska","year":"2022","journal-title":"Nutrients"},{"key":"2023060914235560500_bib316","first-page":"4083","article-title":"Two novel mucin genes down-regulated in colorectal cancer identified by differential display","volume":"59","author":"Williams","year":"1999","journal-title":"Cancer Res"},{"key":"2023060914235560500_bib317","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1006\/bbrc.1999.1001","article-title":"The MUC3 gene encodes a transmembrane mucin and is alternatively spliced","volume":"261","author":"Williams","year":"1999","journal-title":"Biochem Biophys Res Commun"},{"key":"2023060914235560500_bib318","doi-asserted-by":"crossref","first-page":"18327","DOI":"10.1074\/jbc.M008850200","article-title":"MUC13, a novel human cell surface mucin expressed by epithelial and hemopoietic cells","volume":"276","author":"Williams","year":"2001","journal-title":"J Biol Chem"},{"key":"2023060914235560500_bib319","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/j.jcmgh.2018.05.004","article-title":"A high-throughput organoid microinjection platform to study gastrointestinal microbiota and luminal physiology","volume":"6","author":"Williamson","year":"2018","journal-title":"Cell Mol Gastroenterol Hepatol"},{"key":"2023060914235560500_bib320","doi-asserted-by":"crossref","first-page":"235","DOI":"10.1097\/00004836-200603000-00015","article-title":"Colonic health: fermentation and short chain fatty acids","volume":"40","author":"Wong","year":"2006","journal-title":"J Clin Gastroenterol"},{"key":"2023060914235560500_bib321","doi-asserted-by":"crossref","DOI":"10.1186\/1471-230X-11-145","article-title":"Gastric transit and small intestinal transit time and motility assessed by a magnet tracking system","volume":"11","author":"Wors\u00f8e","year":"2011","journal-title":"BMC Gastroenterol"},{"key":"2023060914235560500_bib322","doi-asserted-by":"crossref","first-page":"543","DOI":"10.2527\/jas.2011-4001","article-title":"Effect of dietary phytic acid on performance and nutrient uptake in the small intestine of piglets","volume":"90","author":"Woyengo","year":"2012","journal-title":"J Anim Sci"},{"key":"2023060914235560500_bib323","doi-asserted-by":"crossref","first-page":"1419","DOI":"10.1080\/00365521.2019.1694067","article-title":"Small intestinal bacterial overgrowth is associated with diarrhea-predominant irritable bowel syndrome by increasing mainly Prevotella abundance","volume":"54","author":"Wu","year":"2019","journal-title":"Scand J Gastroenterol"},{"key":"2023060914235560500_bib324","doi-asserted-by":"crossref","DOI":"10.3389\/fcimb.2021.734416","article-title":"Improved metabolite prediction using microbiome data-based elastic net models","volume":"11","author":"Xie","year":"2021","journal-title":"Front Cell Infect Microbiol"},{"key":"2023060914235560500_bib325","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1186\/s12876-021-01630-x","article-title":"Clinical efficacy of fecal microbiota transplantation for patients with small intestinal bacterial overgrowth: a randomized, placebo-controlled clinic study","volume":"21","author":"Xu","year":"2021","journal-title":"BMC Gastroenterol"},{"key":"2023060914235560500_bib326","doi-asserted-by":"crossref","first-page":"10758","DOI":"10.1039\/D0FO02252G","article-title":"Effects of dietary fibre and protein content on intestinal fibre degradation, short-chain fatty acid and microbiota composition in a high-fat fructose-rich diet induced obese G\u00f6ttingen Minipig model","volume":"11","author":"Xu","year":"2020","journal-title":"Food Funct"},{"key":"2023060914235560500_bib327","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1155\/2015\/659018","article-title":"Differential expression of MUC12, MUC16, and MUC20 in patients with active and remission ulcerative colitis","volume":"2015","author":"Yamamoto-Furusho","year":"2015","journal-title":"Mediators Inflamm"},{"key":"2023060914235560500_bib328","doi-asserted-by":"crossref","DOI":"10.1128\/spectrum.00343-22","article-title":"The lumenal microbiota varies biogeographically in the gastrointestinal tract of rhesus macaques","volume":"10","author":"Yan","year":"2022","journal-title":"Microbiol Spectr"},{"key":"2023060914235560500_bib329","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.chom.2015.01.015","article-title":"Biogeography of the intestinal mucosal and lumenal microbiome in the rhesus macaque","volume":"17","author":"Yasuda","year":"2015","journal-title":"Cell Host Microbe"},{"key":"2023060914235560500_bib330","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/S0022-2275(20)33335-6","article-title":"The bile acid-inducible baiF gene from Eubacterium sp. strain VPI 12708 encodes a bile acid-coenzyme A hydrolase","volume":"40","author":"Ye","year":"1999","journal-title":"J Lipid Res"},{"key":"2023060914235560500_bib331","doi-asserted-by":"crossref","first-page":"G258","DOI":"10.1152\/ajpgi.00282.2020","article-title":"Fluid shear stress enhances differentiation of jejunal human enteroids in Intestine-Chip","volume":"320","author":"Yin","year":"2021","journal-title":"Am J Physiol Gastrointest Liver Physiol"},{"key":"2023060914235560500_bib332","article-title":"Mucosal microbiota and metabolome along the intestinal tract reveal a location-specific relationship","volume":"5","author":"Yuan","year":"2020","journal-title":"Host Microbe Biol"},{"key":"2023060914235560500_bib333","doi-asserted-by":"crossref","first-page":"e0215351","DOI":"10.1371\/journal.pone.0215351","article-title":"The bacterial communities of the small intestine and stool in children with short bowel syndrome","volume":"14","author":"Zeichner","year":"2019","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib334","article-title":"Spatial heterogeneity and co-occurrence of mucosal and luminal microbiome across swine intestinal tract","volume":"9","author":"Zhang","year":"2018","journal-title":"Front Microbiol"},{"key":"2023060914235560500_bib335","first-page":"117441","article-title":"The dynamic distribution of porcine microbiota across different ages and gastrointestinal tract segments","volume":"10","author":"Zhao","year":"2015","journal-title":"PLoS ONE"},{"key":"2023060914235560500_bib336","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1097\/MCG.0000000000000814","article-title":"Probiotics for preventing and treating small intestinal bacterial overgrowth","volume":"51","author":"Zhong","year":"2017","journal-title":"J Clin Gastroenterol"},{"key":"2023060914235560500_bib337","doi-asserted-by":"crossref","first-page":"295","DOI":"10.1016\/j.aninu.2020.11.012","article-title":"Gut microbiota absence and transplantation affect growth and intestinal functions: an investigation in a germ-free pig model","volume":"7","author":"Zhou","year":"2021","journal-title":"Anim Nutr"},{"key":"2023060914235560500_bib338","doi-asserted-by":"crossref","first-page":"1415","DOI":"10.1038\/ismej.2011.212","article-title":"The human small intestinal microbiota is driven by rapid uptake and conversion of simple carbohydrates","volume":"6","author":"Zoetendal","year":"2012","journal-title":"ISME J"}],"container-title":["FEMS Microbiology Reviews"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/femsre\/advance-article-pdf\/doi\/10.1093\/femsre\/fuad022\/50356027\/fuad022.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsre\/article-pdf\/47\/3\/fuad022\/50530456\/fuad022.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/femsre\/article-pdf\/47\/3\/fuad022\/50530456\/fuad022.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,12,12]],"date-time":"2023-12-12T23:04:18Z","timestamp":1702422258000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/femsre\/article\/doi\/10.1093\/femsre\/fuad022\/7165754"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2023,5]]},"references-count":337,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2023,5,19]]}},"URL":"https:\/\/doi.org\/10.1093\/femsre\/fuad022","relation":{},"ISSN":["1574-6976"],"issn-type":[{"value":"1574-6976","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2023,5]]},"published":{"date-parts":[[2023,5]]},"article-number":"fuad022"}}