{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,21]],"date-time":"2026-01-21T04:04:28Z","timestamp":1768968268541,"version":"3.49.0"},"reference-count":35,"publisher":"BMJ","issue":"11","funder":[{"name":"ERDF; FCT - Funda\u00e7\u00e3o para a Ci\u00eancia e a Tecnologia","award":["POCI-01-0145-ERDF-007746; UID\/IC\/4255\/2013"],"award-info":[{"award-number":["POCI-01-0145-ERDF-007746; UID\/IC\/4255\/2013"]}]}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["BMJ Open"],"published-print":{"date-parts":[[2019,11]]},"abstract":"<jats:sec><jats:title>Introduction<\/jats:title><jats:p>The gut microbiota plays a main role in the maintenance of host\u2019s health. Exposure to different conditions in early life contributes to distinct \u2018pioneer\u2019 bacterial communities in the intestine, which shape the newborn infant development. Newborn infants with congenital malformations of the gastrointestinal tract (CMGIT), necrotising enterocolitis (NEC) and spontaneous intestinal perforation (SIP) commonly require abdominal surgery and enterostomy. The knowledge about the colonisation of these newborns\u2019 intestine by microorganisms is scarce. This protocol is designed to explore the microbial colonisation over time of the proximal intestinal remnant in newborn infants who underwent surgery for CMGIT, NEC or SIP and require enterostomy.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods and analysis<\/jats:title><jats:p>The literature about microbiota colonisation in newborn infants with enterostomy was reviewed and an observational, longitudinal, prospective study was designed. The infants will be recruited at the Neonatal Intensive Care Unit of the Hospital Dona Estef\u00e2nia, Centro Hospitalar Universit\u00e1rio de Lisboa Central. Samples of the enterostomy effluent will be collected every 3 days, through 21 days after the first collection. The microorganisms colonising the proximal intestinal remnant will be identified using the 16S rRNA sequence analysis and a subset of microorganisms will be quantified using real-time PCR. This protocol may serve as basis for future observational and interventional studies on the modulation of the intestinal microbiota (eg, probiotics) on short and long-term outcomes in this population.<\/jats:p><\/jats:sec><jats:sec><jats:title>Ethics and dissemination<\/jats:title><jats:p>This study protocol was approved by the Ethics Committee of Centro Hospitalar Universit\u00e1rio de Lisboa Central (441\/2017) and by the Ethics Committee of NOVA Medical School, Universidade Nova de Lisboa (n\u00b050\/2018\/CEFCM). The results will be spread through peer-reviewed publications and presentations at international scientific meetings.<\/jats:p><\/jats:sec><jats:sec><jats:title>Trial registration number<\/jats:title><jats:p><jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"clintrialgov\" specific-use=\"clinicaltrial none\" xlink:href=\"NCT03340259\">NCT03340259<\/jats:ext-link>.<\/jats:p><\/jats:sec>","DOI":"10.1136\/bmjopen-2019-028916","type":"journal-article","created":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T18:08:41Z","timestamp":1680718121000},"page":"e028916","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":2,"title":["Colonisation of the proximal intestinal remnant in newborn infants with enterostomy: a longitudinal study protocol"],"prefix":"10.1136","volume":"9","clinical-trial-number":[{"clinical-trial-number":"nct03340259","registry":"10.18810\/clinical-trials-gov","type":"preResults"},{"clinical-trial-number":"nct03340259","registry":"10.18810\/clinical-trials-gov"}],"author":[{"given":"In\u00eas","family":"Barreiros Mota","sequence":"first","affiliation":[]},{"given":"Cl\u00e1udia","family":"Marques","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Faria","sequence":"additional","affiliation":[]},{"given":"Maria Teresa","family":"Neto","sequence":"additional","affiliation":[]},{"given":"Gon\u00e7alo","family":"Cordeiro-Ferreira","sequence":"additional","affiliation":[]},{"given":"Daniel","family":"Virella","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Pita","sequence":"additional","affiliation":[]},{"given":"Lu\u00eds","family":"Pereira-da-Silva","sequence":"additional","affiliation":[]},{"given":"Concei\u00e7\u00e3o","family":"Calhau","sequence":"additional","affiliation":[]}],"member":"239","published-online":{"date-parts":[[2019,11,24]]},"reference":[{"key":"2023040221290711000_9.11.e028916.1","doi-asserted-by":"publisher","DOI":"10.1016\/j.cell.2016.05.041"},{"key":"2023040221290711000_9.11.e028916.2","doi-asserted-by":"crossref","unstructured":"Stecher B . The roles of inflammation, nutrient availability and the commensal microbiota in enteric pathogen infection. Microbiol Spectr 2015;3.doi:10.1128\/microbiolspec.MBP-0008-2014","DOI":"10.1128\/microbiolspec.MBP-0008-2014"},{"key":"2023040221290711000_9.11.e028916.3","doi-asserted-by":"crossref","unstructured":"van den Elsen LWJ , Poyntz HC , Weyrich LS , et al . Embracing the gut microbiota: the new frontier for inflammatory and infectious diseases. Clin Trans Immunol 2017;6:e125.doi:10.1038\/cti.2016.91","DOI":"10.1038\/cti.2016.91"},{"key":"2023040221290711000_9.11.e028916.4","doi-asserted-by":"publisher","DOI":"10.1016\/j.clinthera.2016.02.003"},{"key":"2023040221290711000_9.11.e028916.5","doi-asserted-by":"crossref","unstructured":"Hill CJ , Lynch DB , Murphy K , et al . Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET cohort. Microbiome 2017;5.doi:10.1186\/s40168-016-0213-y","DOI":"10.1186\/s40168-017-0240-3"},{"key":"2023040221290711000_9.11.e028916.6","doi-asserted-by":"crossref","unstructured":"Arrieta M-C , Stiemsma LT , Amenyogbe N , et al . The intestinal microbiome in early life: health and disease. Front Immunol 2014;5:427.doi:10.3389\/fimmu.2014.00427","DOI":"10.3389\/fimmu.2014.00427"},{"key":"2023040221290711000_9.11.e028916.7","doi-asserted-by":"publisher","DOI":"10.1136\/archdischild-2012-302134"},{"key":"2023040221290711000_9.11.e028916.8","doi-asserted-by":"publisher","DOI":"10.1038\/pr.2015.54"},{"key":"2023040221290711000_9.11.e028916.9","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0152751"},{"key":"2023040221290711000_9.11.e028916.10","doi-asserted-by":"publisher","DOI":"10.1097\/ANC.0000000000000220"},{"key":"2023040221290711000_9.11.e028916.11","doi-asserted-by":"publisher","DOI":"10.1016\/j.earlhumdev.2011.12.027"},{"key":"2023040221290711000_9.11.e028916.12","first-page":"1","article-title":"Amin, MDA, Cleo Pappas, MLISb, Hari Iyengar, MDC, and Akhil Maheshwari MD","volume":"40","author":"Sachin","year":"2014","journal-title":"Short Bowel Syndrome in the Nicu"},{"key":"2023040221290711000_9.11.e028916.13","doi-asserted-by":"publisher","DOI":"10.1016\/j.jpeds.2016.10.053"},{"key":"2023040221290711000_9.11.e028916.14","doi-asserted-by":"crossref","first-page":"362","DOI":"10.1111\/j.1442-200X.2009.02963.x","article-title":"Early use of probiotics is important therapy in infants with severe congenital anomaly","volume":"52","author":"Kanamori","year":"2010","journal-title":"Pediatr Int"},{"key":"2023040221290711000_9.11.e028916.15","doi-asserted-by":"publisher","DOI":"10.4161\/gmic.28442"},{"key":"2023040221290711000_9.11.e028916.16","doi-asserted-by":"publisher","DOI":"10.1002\/mbo3.64"},{"key":"2023040221290711000_9.11.e028916.17","doi-asserted-by":"publisher","DOI":"10.1038\/ismej.2007.69"},{"key":"2023040221290711000_9.11.e028916.18","first-page":"1","article-title":"High-Fat diet-induced obesity rat model: a comparison between Wistar and Sprague-Dawley rat","volume":"5","author":"Marques","year":"2015","journal-title":"Adipocyte"},{"key":"2023040221290711000_9.11.e028916.19","doi-asserted-by":"publisher","DOI":"10.1038\/nprot.2006.142"},{"key":"2023040221290711000_9.11.e028916.20","doi-asserted-by":"publisher","DOI":"10.1038\/s41598-018-23276-8"},{"key":"2023040221290711000_9.11.e028916.21","doi-asserted-by":"publisher","DOI":"10.1128\/AEM.05605-11"},{"key":"2023040221290711000_9.11.e028916.22","doi-asserted-by":"crossref","unstructured":"Gosiewski T , Salamon D , Szopa M , et al . Quantitative evaluation of fungi of the genus Candida in the feces of adult patients with type 1 and 2 diabetes - a pilot study. Gut Pathog 2014;6:43.doi:10.1186\/s13099-014-0043-z","DOI":"10.1186\/s13099-014-0043-z"},{"key":"2023040221290711000_9.11.e028916.23","doi-asserted-by":"publisher","DOI":"10.1590\/S0212-16112012000100014"},{"key":"2023040221290711000_9.11.e028916.24","doi-asserted-by":"publisher","DOI":"10.1016\/j.micres.2009.03.003"},{"key":"2023040221290711000_9.11.e028916.25","doi-asserted-by":"publisher","DOI":"10.1128\/MMBR.00015-17"},{"key":"2023040221290711000_9.11.e028916.26","doi-asserted-by":"crossref","first-page":"747","DOI":"10.1016\/j.clinthera.2016.02.014","article-title":"The microbiome in necrotizing enterocolitis: a case report in twins and minireview","volume":"38","author":"Hourigan","year":"2016","journal-title":"Clin Ther"},{"key":"2023040221290711000_9.11.e028916.27","doi-asserted-by":"publisher","DOI":"10.1016\/j.clp.2017.01.005"},{"key":"2023040221290711000_9.11.e028916.28","doi-asserted-by":"publisher","DOI":"10.2217\/fmb.15.136"},{"key":"2023040221290711000_9.11.e028916.29","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nrgastro.2016.139","article-title":"The gut microbiota and gastrointestinal surgery","volume":"14","author":"Guyton","year":"2017","journal-title":"Nat Rev Gastroenterol Hepatol"},{"key":"2023040221290711000_9.11.e028916.30","doi-asserted-by":"crossref","first-page":"936.e1","DOI":"10.1016\/j.cmi.2015.06.003","article-title":"Preterm infant gut colonization in the neonatal ICU and complete restoration 2 years later","volume":"21","author":"Moles","year":"2015","journal-title":"Clin Microbiol Infect"},{"key":"2023040221290711000_9.11.e028916.31","doi-asserted-by":"publisher","DOI":"10.1097\/MPG.0000000000000913"},{"key":"2023040221290711000_9.11.e028916.32","doi-asserted-by":"publisher","DOI":"10.1038\/pr.2014.162"},{"key":"2023040221290711000_9.11.e028916.33","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.humic.2016.09.002","article-title":"Updating on gut microbiota and its relationship with the occurrence of necrotizing enterocolitis","volume":"4","author":"Hosny","year":"2017","journal-title":"Hum Microbiome J"},{"key":"2023040221290711000_9.11.e028916.34","doi-asserted-by":"crossref","first-page":"281","DOI":"10.3233\/NPM-16148","article-title":"Intestinal perforation in the premature infant","volume":"10","author":"Vongbhavit","year":"2017","journal-title":"J Neonatal Perinatal Med"},{"key":"2023040221290711000_9.11.e028916.35","doi-asserted-by":"crossref","unstructured":"Brower-Sinning R , Zhong D , Good M , et al . Mucosa-Associated bacterial diversity in necrotizing enterocolitis. PLoS One 2014;9:e105046.doi:10.1371\/journal.pone.0105046","DOI":"10.1371\/journal.pone.0105046"}],"container-title":["BMJ Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/syndication.highwire.org\/content\/doi\/10.1136\/bmjopen-2019-028916","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,5]],"date-time":"2023-04-05T18:08:57Z","timestamp":1680718137000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmjopen.bmj.com\/lookup\/doi\/10.1136\/bmjopen-2019-028916"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,11]]},"references-count":35,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2019,11,24]]},"published-print":{"date-parts":[[2019,11]]}},"alternative-id":["10.1136\/bmjopen-2019-028916"],"URL":"https:\/\/doi.org\/10.1136\/bmjopen-2019-028916","relation":{},"ISSN":["2044-6055","2044-6055"],"issn-type":[{"value":"2044-6055","type":"print"},{"value":"2044-6055","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,11]]}}}