{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,3]],"date-time":"2026-10-03T04:19:52Z","timestamp":1791001192646,"version":"4.1.0"},"reference-count":38,"publisher":"Wiley","issue":"1","license":[{"start":{"date-parts":[[2019,4,29]],"date-time":"2019-04-29T00:00:00Z","timestamp":1556496000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/onlinelibrary.wiley.com\/termsAndConditions#vor"}],"funder":[{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["15\u201328745A AZV CR"],"award-info":[{"award-number":["15\u201328745A AZV CR"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003243","name":"Ministerstvo Zdravotnictv\u00ed Cesk\u00e9 Republiky","doi-asserted-by":"publisher","award":["15\u201327863A AZV CR"],"award-info":[{"award-number":["15\u201327863A AZV CR"]}],"id":[{"id":"10.13039\/501100003243","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100002367","name":"Chinese Academy of Sciences","doi-asserted-by":"publisher","award":["RVO 68378050"],"award-info":[{"award-number":["RVO 68378050"]}],"id":[{"id":"10.13039\/501100002367","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003335","name":"Ministry of Education, Youth and Science","doi-asserted-by":"publisher","award":["LM2015040"],"award-info":[{"award-number":["LM2015040"]}],"id":[{"id":"10.13039\/501100003335","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003335","name":"Ministry of Education, Youth and Science","doi-asserted-by":"publisher","award":["LQ1604"],"award-info":[{"award-number":["LQ1604"]}],"id":[{"id":"10.13039\/501100003335","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["aspenjournals.onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["J Parenter Enteral Nutr"],"published-print":{"date-parts":[[2020,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>The gut microbiome and metabolome may significantly influence clinical outcomes in patients with short bowel syndrome (SBS). The study aimed to describe specific metagenomic\/metabolomics profiles of different SBS types and to identify possible therapeutic targets.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>Fecal microbiome (FM), volatile organic compounds (VOCs), and bile acid (BA) spectrum were analyzed in parenteral nutrition (PN)\u2010dependent SBS I, SBS II, and PN\u2010independent (non\u2010PN) SBS patients.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>FM in SBS I, SBS II, and non\u2010PN SBS shared characteristic features (depletion of beneficial anaerobes, high abundance of <jats:italic>Lactobacilaceae<\/jats:italic> and <jats:italic>Enterobacteriaceae)<\/jats:italic>. SBS I patients were characterized by the abundance of oxygen\u2010tolerant microrganisms and depletion of strict anaerobes. Non\u2010PN SBS subjects showed markers of partial FM normalization. FM dysbiosis was translated into VOC and BA profiles characteristic for each SBS cohort. A typical signature of all SBS patients comprised high saturated aldehydes and medium\u2010chain fatty acids and reduced short\u2010chain fatty acid (SCFA) content. Particularly, SBS I and II exhibited low protein metabolism intermediate (indole, p\u2010cresol) content despite the hypothetical presence of relevant metabolism pathways. Distinctive non\u2010PN SBS marker was high phenol content. SBS patients\u2019 BA fecal spectrum was enriched by chenodeoxycholic and deoxycholic acids and depleted of lithocholic acid.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Environmental conditions in SBS gut significantly affect FM composition and metabolic activity. The common feature of diverse SBS subjects is the altered VOC\/BA profile and the lack of important products of microbial metabolism. Strategies oriented on the microbiome\/metabolome reconstitution and targeted delivery of key compounds may represent a promising therapeutic strategy in SBS patients.<\/jats:p><\/jats:sec>","DOI":"10.1002\/jpen.1595","type":"journal-article","created":{"date-parts":[[2019,4,29]],"date-time":"2019-04-29T06:42:34Z","timestamp":1556520154000},"page":"105-118","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":39,"title":["Microbiome and Metabolome Profiles Associated With Different Types of Short Bowel Syndrome: Implications for Treatment"],"prefix":"10.1002","volume":"44","author":[{"given":"Eva","family":"Budinska","sequence":"first","affiliation":[{"name":"RECETOX Faculty of Science Masaryk University  Brno Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jan","family":"Gojda","sequence":"additional","affiliation":[{"name":"2nd Department of Internal Medicine Kralovske Vinohrady University Hospital and 3rd Faculty of Medicine Charles University  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marie","family":"Heczkova","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Miriam","family":"Bratova","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Helena","family":"Dankova","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Petr","family":"Wohl","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hana","family":"Bastova","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vera","family":"Lanska","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Martin","family":"Kostovcik","sequence":"additional","affiliation":[{"name":"BIOCEV Institute of Microbiology AS CR  Vestec Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milan","family":"Dastych","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Internal Medicine University Hospital Brno  Brno Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michal","family":"Senkyrik","sequence":"additional","affiliation":[{"name":"Department of Gastroenterology and Internal Medicine University Hospital Brno  Brno Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jarmila","family":"Krizova","sequence":"additional","affiliation":[{"name":"3rd Department of Medicine, Department of Endocrinology and Metabolism General University Hospital and 1st Faculty of Medicine Charles University  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Milos","family":"Mraz","sequence":"additional","affiliation":[{"name":"2nd Department of Internal Medicine Kralovske Vinohrady University Hospital and 3rd Faculty of Medicine Charles University  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jaromir","family":"Hradecky","sequence":"additional","affiliation":[{"name":"University of Chemistry and Technology  Prague Czech Republic"},{"name":"Faculty of Forestry and Wood Sciences Czech University of Life Sciences  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jana","family":"Hajslova","sequence":"additional","affiliation":[{"name":"University of Chemistry and Technology  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6242-3488","authenticated-orcid":false,"given":"Martin","family":"Lenicek","sequence":"additional","affiliation":[{"name":"Institute of Medical Biochemistry and Laboratory Diagnostics 1st Faculty of Medicine Charles University  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kate\u0159ina","family":"Podzimkova","sequence":"additional","affiliation":[{"name":"Czech Centre for Phenogenomics  Vestec Czech Republic"},{"name":"Laboratory of Transgenic Diseases Institute of Molecular Genetics CAS  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karel","family":"Chalupsky","sequence":"additional","affiliation":[{"name":"Czech Centre for Phenogenomics  Vestec Czech Republic"},{"name":"Laboratory of Transgenic Diseases Institute of Molecular Genetics CAS  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Radislav","family":"Sedlacek","sequence":"additional","affiliation":[{"name":"Czech Centre for Phenogenomics  Vestec Czech Republic"},{"name":"Laboratory of Transgenic Diseases Institute of Molecular Genetics CAS  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2640-5084","authenticated-orcid":false,"given":"Monika","family":"Cahova","sequence":"additional","affiliation":[{"name":"Institute for Clinical and Experimental Medicine  Prague Czech Republic"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2019,4,29]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.clnu.2014.08.017"},{"key":"e_1_2_8_3_1","doi-asserted-by":"publisher","DOI":"10.1177\/0148607114520994"},{"key":"e_1_2_8_4_1","first-page":"224","article-title":"Microbiota is involved in post\u2010resection adaptation in humans with short bowel syndrome","author":"Gillard L","year":"2017","journal-title":"Front Physiol"},{"key":"e_1_2_8_5_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0054335"},{"key":"e_1_2_8_6_1","doi-asserted-by":"publisher","DOI":"10.4292\/wjgpt.v4.i4.97"},{"key":"e_1_2_8_7_1","doi-asserted-by":"publisher","DOI":"10.1038\/srep43326"},{"key":"e_1_2_8_8_1","doi-asserted-by":"publisher","DOI":"10.1113\/JP272476"},{"key":"e_1_2_8_9_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.05.041"},{"key":"e_1_2_8_10_1","doi-asserted-by":"publisher","DOI":"10.1194\/jlr.R500013-JLR200"},{"key":"e_1_2_8_11_1","doi-asserted-by":"publisher","DOI":"10.1097\/MOG.0000000000000057"},{"key":"e_1_2_8_12_1","doi-asserted-by":"publisher","DOI":"10.1038\/nmeth.f.303"},{"key":"e_1_2_8_13_1","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-009-4109-0"},{"key":"e_1_2_8_14_1","unstructured":"R: A language and environment for statistical computing[computer program]. Version. Vienna Austria: R Foundation for Statistical Computing."},{"key":"e_1_2_8_15_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005752"},{"key":"e_1_2_8_16_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.clnu.2016.09.028"},{"key":"e_1_2_8_17_1","doi-asserted-by":"publisher","DOI":"10.1111\/jgh.13806"},{"key":"e_1_2_8_18_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.biochi.2010.02.015"},{"key":"e_1_2_8_19_1","doi-asserted-by":"publisher","DOI":"10.1097\/MIB.0b013e31829a91f6"},{"issue":"3","key":"e_1_2_8_20_1","first-page":"153","article-title":"Oxidative stress biomarkers in exhaled breath of workers exposed to crystalline silica dust by SPME\u2010GC\u2010MS","volume":"16","author":"Jalali M","year":"2016","journal-title":"J Res Health Sci"},{"key":"e_1_2_8_21_1","doi-asserted-by":"publisher","DOI":"10.1080\/10715760400013763"},{"key":"e_1_2_8_22_1","doi-asserted-by":"publisher","DOI":"10.1111\/jam.12347"},{"key":"e_1_2_8_23_1","doi-asserted-by":"publisher","DOI":"10.1111\/1750-3841.13547"},{"key":"e_1_2_8_24_1","doi-asserted-by":"crossref","unstructured":"BansalT AlanizRC WoodTK JayaramanA.The bacterial signal indole increases epithelial\u2010cell tight\u2010junction resistance and attenuates indicators of inflammation.Proceedings of the National Academy of Sciences of the United States of America.2010;107(1):228\u2010233.","DOI":"10.1073\/pnas.0906112107"},{"key":"e_1_2_8_25_1","doi-asserted-by":"publisher","DOI":"10.1038\/npjbiofilms.2016.14"},{"key":"e_1_2_8_26_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2013.08.003"},{"key":"e_1_2_8_27_1","doi-asserted-by":"publisher","DOI":"10.4049\/jimmunol.1300016"},{"key":"e_1_2_8_28_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.immuni.2014.01.003"},{"key":"e_1_2_8_29_1","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.00630-07"},{"key":"e_1_2_8_30_1","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0080604"},{"key":"e_1_2_8_31_1","doi-asserted-by":"publisher","DOI":"10.1038\/nature18847"},{"key":"e_1_2_8_32_1","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2018.00013"},{"key":"e_1_2_8_33_1","doi-asserted-by":"publisher","DOI":"10.1017\/S0954422410000247"},{"key":"e_1_2_8_34_1","doi-asserted-by":"publisher","DOI":"10.1007\/s10620-013-2744-4"},{"key":"e_1_2_8_35_1","doi-asserted-by":"publisher","DOI":"10.1007\/BF02934085"},{"key":"e_1_2_8_36_1","doi-asserted-by":"publisher","DOI":"10.1016\/j.jhep.2014.06.025"},{"key":"e_1_2_8_37_1","doi-asserted-by":"publisher","DOI":"10.1152\/ajpgi.00256.2016"},{"key":"e_1_2_8_38_1","doi-asserted-by":"publisher","DOI":"10.1016\/S0261-5614(17)30397-7"},{"key":"e_1_2_8_39_1","doi-asserted-by":"publisher","DOI":"10.1136\/gut.2006.091108"}],"container-title":["Journal of Parenteral and Enteral Nutrition"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jpen.1595","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/onlinelibrary.wiley.com\/doi\/full-xml\/10.1002\/jpen.1595","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/aspenjournals.onlinelibrary.wiley.com\/doi\/pdf\/10.1002\/jpen.1595","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,10,19]],"date-time":"2025-10-19T14:13:32Z","timestamp":1760883212000},"score":1,"resource":{"primary":{"URL":"https:\/\/aspenjournals.onlinelibrary.wiley.com\/doi\/10.1002\/jpen.1595"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,4,29]]},"references-count":38,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,1]]}},"alternative-id":["10.1002\/jpen.1595"],"URL":"https:\/\/doi.org\/10.1002\/jpen.1595","archive":["Portico"],"relation":{},"ISSN":["0148-6071","1941-2444"],"issn-type":[{"value":"0148-6071","type":"print"},{"value":"1941-2444","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,4,29]]},"assertion":[{"value":"2018-12-21","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-04-08","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2019-04-29","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}