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Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol
The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases. Bile samples will be collected in endoscopic retrograde cholangi...
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| Published in: | PloS one 2020-11, Vol.15 (11), p.e0242553-e0242553 |
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| creator | Nascimento, Fernanda Sayuri do Suzuki, Milena Oliveira Taba, João Victor de Mattos, Vitoria Carneiro Pipek, Leonardo Zumerkorn D'Albuquerque, Eugênia Machado Carneiro Iuamoto, Leandro Meyer, Alberto Andraus, Wellington Pinho, João Renato Rebello de Moura, Eduardo Guimarães Hourneaux Setubal, João Carlos Carneiro-D'Albuquerque, Luiz Augusto |
| description | The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.
Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.
The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.
NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426. |
| doi_str_mv | 10.1371/journal.pone.0242553 |
| format | article |
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Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.
The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.
NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0242553</identifier><identifier>PMID: 33211762</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Adult ; Antibiotics ; Bacteria ; Bile ; Bile - microbiology ; Biliary tract ; Biology and Life Sciences ; Biomarkers ; Case-Control Studies ; Cholangiopancreatography, Endoscopic Retrograde ; Colorectal cancer ; Composition ; Deoxyribonucleic acid ; Diagnosis ; Digestive system diseases ; Digestive System Diseases - microbiology ; Digestive tract ; Disease ; Diseases ; DNA ; DNA sequencing ; DNA, Bacterial - genetics ; Female ; Gastroenterology ; Gastrointestinal cancer ; Gastrointestinal tract ; Gene sequencing ; Genetic aspects ; Genomes ; Health aspects ; Health care ; Homeostasis ; Hospitals ; Humans ; Liver Transplantation ; Living Donors ; Male ; Medical prognosis ; Medicine ; Medicine and Health Sciences ; Metabolism ; Metabolites ; Metagenome ; Microbiomes ; Microbiota ; Microbiota (Symbiotic organisms) ; Microbiota - genetics ; Middle Aged ; Nucleotide sequence ; Pancreatic cancer ; Polyamines ; Protocol (computers) ; Registered Report Protocol ; Research and analysis methods ; Ribotyping ; RNA sequencing ; RNA, Bacterial - genetics ; RNA, Ribosomal, 16S - genetics ; rRNA 16S ; Transplantation ; Young Adult</subject><ispartof>PloS one, 2020-11, Vol.15 (11), p.e0242553-e0242553</ispartof><rights>COPYRIGHT 2020 Public Library of Science</rights><rights>2020 Nascimento et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2020 Nascimento et al 2020 Nascimento et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-5e4a01f54002c4018af143809143d134ee143b178f1f646fc13170561776c6b43</citedby><cites>FETCH-LOGICAL-c692t-5e4a01f54002c4018af143809143d134ee143b178f1f646fc13170561776c6b43</cites><orcidid>0000-0002-8408-0508 ; 0000-0001-5268-4668</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.proquest.com/docview/2462406314/fulltextPDF?pq-origsite=primo$$EPDF$$P50$$Gproquest$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.proquest.com/docview/2462406314?pq-origsite=primo$$EHTML$$P50$$Gproquest$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,25752,27923,27924,37011,37012,44589,53790,53792,74897</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33211762$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Alpini, Gianfranco D.</contributor><creatorcontrib>Nascimento, Fernanda Sayuri do</creatorcontrib><creatorcontrib>Suzuki, Milena Oliveira</creatorcontrib><creatorcontrib>Taba, João Victor</creatorcontrib><creatorcontrib>de Mattos, Vitoria Carneiro</creatorcontrib><creatorcontrib>Pipek, Leonardo Zumerkorn</creatorcontrib><creatorcontrib>D'Albuquerque, Eugênia Machado Carneiro</creatorcontrib><creatorcontrib>Iuamoto, Leandro</creatorcontrib><creatorcontrib>Meyer, Alberto</creatorcontrib><creatorcontrib>Andraus, Wellington</creatorcontrib><creatorcontrib>Pinho, João Renato Rebello</creatorcontrib><creatorcontrib>de Moura, Eduardo Guimarães Hourneaux</creatorcontrib><creatorcontrib>Setubal, João Carlos</creatorcontrib><creatorcontrib>Carneiro-D'Albuquerque, Luiz Augusto</creatorcontrib><title>Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.
Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.
The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.
NCT04391426. 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genetics</subject><subject>Middle Aged</subject><subject>Nucleotide sequence</subject><subject>Pancreatic cancer</subject><subject>Polyamines</subject><subject>Protocol (computers)</subject><subject>Registered Report Protocol</subject><subject>Research and analysis methods</subject><subject>Ribotyping</subject><subject>RNA sequencing</subject><subject>RNA, Bacterial - genetics</subject><subject>RNA, Ribosomal, 16S - genetics</subject><subject>rRNA 16S</subject><subject>Transplantation</subject><subject>Young Adult</subject><issn>1932-6203</issn><issn>1932-6203</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2020</creationdate><recordtype>article</recordtype><sourceid>PIMPY</sourceid><sourceid>DOA</sourceid><recordid>eNqNk--L0zAYx4so3nn6H4gWBNEXm_nVdL0Xwhz-KEwGd-obkZClT7eMrKlJKrf_3mzrHavcC1toQ_L5fp88T_IkyXOMxpjm-N3Gdq6RZtzaBsaIMJJl9EFyjgtKRpwg-vBkfJY88X6DUEYnnD9OziglGOecnCc30-ix89qntk6X2mjpdunXcna1WGobZKqbdA2tDPZDOS8XrWyUAxm0SivtQXrwqbLbVjqo0mAjKk1Y79IWbGsg_XkwOih_XabXoavikrPBKmueJo9qaTw86_8XyfdPH7_Nvozmi8_lbDofKV6QMMqASYTrjCFEFEN4ImvM6AQV8VthygDiYInzSY1rznitMMU5yjjOc674ktGL5OXRtzXWi75oXhDGCUOc4j1RHonKyo1ond7GGggrtThMWLcS0sWUDYgK8lpxKApcSEZyWSDgiE0qSrIYLKPR630frVtuoVLQBCfNwHS40ui1WNk_Iuc5j080eNMbOPu7Ax_EVnsFxsgGbHfYN8UITbI9-uof9P7semolYwK6qW2Mq_amYsoZITliOYrU-B4qvhVstYo3rNZxfiB4OxBEJsBNWMnOe1FeX_0_u_gxZF-fsMf75K3pgraNH4LsCCpnvXdQ3xUZI7FvkNtqiH2DiL5BouzF6QHdiW47gv4Fi2IIiA</recordid><startdate>20201119</startdate><enddate>20201119</enddate><creator>Nascimento, Fernanda Sayuri do</creator><creator>Suzuki, Milena Oliveira</creator><creator>Taba, João Victor</creator><creator>de Mattos, Vitoria Carneiro</creator><creator>Pipek, Leonardo Zumerkorn</creator><creator>D'Albuquerque, Eugênia Machado Carneiro</creator><creator>Iuamoto, Leandro</creator><creator>Meyer, Alberto</creator><creator>Andraus, Wellington</creator><creator>Pinho, João Renato Rebello</creator><creator>de Moura, Eduardo Guimarães Hourneaux</creator><creator>Setubal, João Carlos</creator><creator>Carneiro-D'Albuquerque, Luiz Augusto</creator><general>Public Library of Science</general><general>Public Library of Science (PLoS)</general><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>IOV</scope><scope>ISR</scope><scope>3V.</scope><scope>7QG</scope><scope>7QL</scope><scope>7QO</scope><scope>7RV</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TG</scope><scope>7TM</scope><scope>7U9</scope><scope>7X2</scope><scope>7X7</scope><scope>7XB</scope><scope>88E</scope><scope>8AO</scope><scope>8C1</scope><scope>8FD</scope><scope>8FE</scope><scope>8FG</scope><scope>8FH</scope><scope>8FI</scope><scope>8FJ</scope><scope>8FK</scope><scope>ABJCF</scope><scope>ABUWG</scope><scope>AEUYN</scope><scope>AFKRA</scope><scope>ARAPS</scope><scope>ATCPS</scope><scope>AZQEC</scope><scope>BBNVY</scope><scope>BENPR</scope><scope>BGLVJ</scope><scope>BHPHI</scope><scope>C1K</scope><scope>CCPQU</scope><scope>D1I</scope><scope>DWQXO</scope><scope>FR3</scope><scope>FYUFA</scope><scope>GHDGH</scope><scope>GNUQQ</scope><scope>H94</scope><scope>HCIFZ</scope><scope>K9.</scope><scope>KB.</scope><scope>KB0</scope><scope>KL.</scope><scope>L6V</scope><scope>LK8</scope><scope>M0K</scope><scope>M0S</scope><scope>M1P</scope><scope>M7N</scope><scope>M7P</scope><scope>M7S</scope><scope>NAPCQ</scope><scope>P5Z</scope><scope>P62</scope><scope>P64</scope><scope>PATMY</scope><scope>PDBOC</scope><scope>PIMPY</scope><scope>PQEST</scope><scope>PQQKQ</scope><scope>PQUKI</scope><scope>PRINS</scope><scope>PTHSS</scope><scope>PYCSY</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope><orcidid>https://orcid.org/0000-0002-8408-0508</orcidid><orcidid>https://orcid.org/0000-0001-5268-4668</orcidid></search><sort><creationdate>20201119</creationdate><title>Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol</title><author>Nascimento, Fernanda Sayuri do ; Suzuki, Milena Oliveira ; Taba, João Victor ; de Mattos, Vitoria Carneiro ; Pipek, Leonardo Zumerkorn ; D'Albuquerque, Eugênia Machado Carneiro ; Iuamoto, Leandro ; Meyer, Alberto ; Andraus, Wellington ; Pinho, João Renato Rebello ; de Moura, Eduardo Guimarães Hourneaux ; Setubal, João Carlos ; Carneiro-D'Albuquerque, Luiz Augusto</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c692t-5e4a01f54002c4018af143809143d134ee143b178f1f646fc13170561776c6b43</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2020</creationdate><topic>Adult</topic><topic>Antibiotics</topic><topic>Bacteria</topic><topic>Bile</topic><topic>Bile - 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Open Access: DOAJ - Directory of Open Access Journals</collection><jtitle>PloS one</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Nascimento, Fernanda Sayuri do</au><au>Suzuki, Milena Oliveira</au><au>Taba, João Victor</au><au>de Mattos, Vitoria Carneiro</au><au>Pipek, Leonardo Zumerkorn</au><au>D'Albuquerque, Eugênia Machado Carneiro</au><au>Iuamoto, Leandro</au><au>Meyer, Alberto</au><au>Andraus, Wellington</au><au>Pinho, João Renato Rebello</au><au>de Moura, Eduardo Guimarães Hourneaux</au><au>Setubal, João Carlos</au><au>Carneiro-D'Albuquerque, Luiz Augusto</au><au>Alpini, Gianfranco D.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2020-11-19</date><risdate>2020</risdate><volume>15</volume><issue>11</issue><spage>e0242553</spage><epage>e0242553</epage><pages>e0242553-e0242553</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The performance of the microbiota is observed in several digestive tract diseases. Therefore, reaching the biliary microbiota may suggest ways for studies of biomarkers, diagnoses, tests and therapies in hepatobiliopancreatic diseases.
Bile samples will be collected in endoscopic retrograde cholangiopancreatography patients (case group) and living liver transplantation donors (control group). We will characterize the microbiome based on two types of sequence data: the V3/V4 regions of the 16S ribosomal RNA (rRNA) gene and total shotgun DNA. For 16S sequencing data a standard 16S processing pipeline based on the Amplicon Sequence Variant concept and the qiime2 software package will be employed; for shotgun data, for each sample we will assemble the reads and obtain and analyze metagenome-assembled genomes.
The primary expected results of the study is to characterize the specific composition of the biliary microbiota in situations of disease and health. In addition, it seeks to demonstrate the existence of changes in the case of illness and also possible disease biomarkers, diagnosis, interventions and therapies in hepatobiliopancreatic diseases.
NCT04391426. Registered 18 May 2020, https://clinicaltrials.gov/ct2/show/NCT04391426.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>33211762</pmid><doi>10.1371/journal.pone.0242553</doi><tpages>e0242553</tpages><orcidid>https://orcid.org/0000-0002-8408-0508</orcidid><orcidid>https://orcid.org/0000-0001-5268-4668</orcidid><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 1932-6203 |
| ispartof | PloS one, 2020-11, Vol.15 (11), p.e0242553-e0242553 |
| issn | 1932-6203 1932-6203 |
| language | eng |
| recordid | cdi_plos_journals_2462406314 |
| source | Open Access: PubMed Central; Publicly Available Content Database |
| subjects | Adult Antibiotics Bacteria Bile Bile - microbiology Biliary tract Biology and Life Sciences Biomarkers Case-Control Studies Cholangiopancreatography, Endoscopic Retrograde Colorectal cancer Composition Deoxyribonucleic acid Diagnosis Digestive system diseases Digestive System Diseases - microbiology Digestive tract Disease Diseases DNA DNA sequencing DNA, Bacterial - genetics Female Gastroenterology Gastrointestinal cancer Gastrointestinal tract Gene sequencing Genetic aspects Genomes Health aspects Health care Homeostasis Hospitals Humans Liver Transplantation Living Donors Male Medical prognosis Medicine Medicine and Health Sciences Metabolism Metabolites Metagenome Microbiomes Microbiota Microbiota (Symbiotic organisms) Microbiota - genetics Middle Aged Nucleotide sequence Pancreatic cancer Polyamines Protocol (computers) Registered Report Protocol Research and analysis methods Ribotyping RNA sequencing RNA, Bacterial - genetics RNA, Ribosomal, 16S - genetics rRNA 16S Transplantation Young Adult |
| title | Analysis of biliary MICRObiota in hepatoBILIOpancreatic diseases compared to healthy people [MICROBILIO]: Study protocol |
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