Establishing a mucosal gut microbial community in vitro using an artificial simulator
The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human...
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| description | The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10-20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion. |
| doi_str_mv | 10.1371/journal.pone.0197692 |
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Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10-20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0197692</identifier><identifier>PMID: 30016326</identifier><language>eng</language><publisher>United States: Public Library of Science</publisher><subject>Agriculture ; Bioinformatics ; Biology and Life Sciences ; Chains ; Colon ; Communities ; Community structure ; Composition ; Digestive system ; Digestive tract ; Dynamic structural analysis ; Ecology and Environmental Sciences ; Fatty acids ; Food ; Functional foods & nutraceuticals ; Gastroenterology ; Gastrointestinal system ; Gastrointestinal tract ; Gene sequencing ; Health aspects ; Hepatology ; In vivo methods and tests ; Inoculation ; Inoculum ; Intestinal microflora ; Intestine ; Medicine and Health Sciences ; Methods ; Microbiota ; Microbiota (Symbiotic organisms) ; Microorganisms ; Mucosa ; Mucus ; Nutrition research ; RNA sequencing ; rRNA 16S ; Simulation ; Stability ; Synergistetes</subject><ispartof>PloS one, 2018-07, Vol.13 (7), p.e0197692-e0197692</ispartof><rights>COPYRIGHT 2018 Public Library of Science</rights><rights>This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication: https://creativecommons.org/publicdomain/zero/1.0/ (the “License”). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c692t-766129b5cab7a1c3fcddf004b58329daeec765e56db46192fb05ca0c1ba16bf53</citedby><cites>FETCH-LOGICAL-c692t-766129b5cab7a1c3fcddf004b58329daeec765e56db46192fb05ca0c1ba16bf53</cites><orcidid>0000-0003-3962-290X</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050037/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6050037/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,2102,2928,23866,27924,27925,53791,53793,79472,79473</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30016326$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><contributor>Blachier, François</contributor><creatorcontrib>Liu, LinShu</creatorcontrib><creatorcontrib>Firrman, Jenni</creatorcontrib><creatorcontrib>Tanes, Ceylan</creatorcontrib><creatorcontrib>Bittinger, Kyle</creatorcontrib><creatorcontrib>Thomas-Gahring, Audrey</creatorcontrib><creatorcontrib>Wu, Gary D</creatorcontrib><creatorcontrib>Van den Abbeele, Pieter</creatorcontrib><creatorcontrib>Tomasula, Peggy M</creatorcontrib><title>Establishing a mucosal gut microbial community in vitro using an artificial simulator</title><title>PloS one</title><addtitle>PLoS One</addtitle><description>The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. 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Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.</description><subject>Agriculture</subject><subject>Bioinformatics</subject><subject>Biology and Life Sciences</subject><subject>Chains</subject><subject>Colon</subject><subject>Communities</subject><subject>Community structure</subject><subject>Composition</subject><subject>Digestive system</subject><subject>Digestive tract</subject><subject>Dynamic structural analysis</subject><subject>Ecology and Environmental Sciences</subject><subject>Fatty acids</subject><subject>Food</subject><subject>Functional foods & nutraceuticals</subject><subject>Gastroenterology</subject><subject>Gastrointestinal system</subject><subject>Gastrointestinal tract</subject><subject>Gene sequencing</subject><subject>Health aspects</subject><subject>Hepatology</subject><subject>In vivo methods and tests</subject><subject>Inoculation</subject><subject>Inoculum</subject><subject>Intestinal 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Audrey</au><au>Wu, Gary D</au><au>Van den Abbeele, Pieter</au><au>Tomasula, Peggy M</au><au>Blachier, François</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Establishing a mucosal gut microbial community in vitro using an artificial simulator</atitle><jtitle>PloS one</jtitle><addtitle>PLoS One</addtitle><date>2018-07-17</date><risdate>2018</risdate><volume>13</volume><issue>7</issue><spage>e0197692</spage><epage>e0197692</epage><pages>e0197692-e0197692</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The Twin Simulator of the Human Intestinal Microbial Ecosystem (TWINSHIME®) was initially developed to study the luminal gut microbiota of the ascending (AC), transverse (TC), and descending (DC) colon regions. Given the unique composition and potential importance of the mucosal microbiota for human health, the TWINSHIME was recently adapted to simulate the mucosal microbiota as well as the luminal community. It has been previously demonstrated that the luminal community in the TWINSHIME reaches a steady state within two weeks post inoculation, and is able to differentiate into region specific communities. However, less is known regarding the mucosal community structure and dynamics. During the current study, the luminal and mucosal communities in each region of the TWINSHIME were evaluated over the course of six weeks. Based on 16S rRNA gene sequencing and short chain fatty acid analysis, it was determined that both the luminal and mucosal communities reached stability 10-20 days after inoculation, and remained stable until the end of the experiment. Bioinformatics analysis revealed the formation of unique community structures between the mucosal and luminal phases in all three colon regions, yet these communities were similar to the inoculum. Specific colonizers of the mucus mainly belonged to the Firmicutes phylum and included Lachnospiraceae (AC/TC/DC), Ruminococcaceae and Eubacteriaceae (AC), Lactobacillaceae (AC/TC), Clostridiaceae and Erysipelotrichaceae (TC/DC). In contrast, Bacteroidaceae were enriched in the gut lumen of all three colon regions. The unique profile of short chain fatty acid (SCFA) production further demonstrated system stability, but also proved to be an area of marked differences between the in vitro system and in vivo reports. Results of this study demonstrate that it is possible to replicate the community structure and composition of the gut microbiota in vitro. Through implementation of this system, the human gut microbiota can be studied in a dynamic and continuous fashion.</abstract><cop>United States</cop><pub>Public Library of Science</pub><pmid>30016326</pmid><doi>10.1371/journal.pone.0197692</doi><tpages>e0197692</tpages><orcidid>https://orcid.org/0000-0003-3962-290X</orcidid><oa>free_for_read</oa></addata></record> |
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| source | PLoS; Full-Text Journals in Chemistry (Open access); DOAJ Directory of Open Access Journals; PubMed Central; EZB Electronic Journals Library |
| subjects | Agriculture Bioinformatics Biology and Life Sciences Chains Colon Communities Community structure Composition Digestive system Digestive tract Dynamic structural analysis Ecology and Environmental Sciences Fatty acids Food Functional foods & nutraceuticals Gastroenterology Gastrointestinal system Gastrointestinal tract Gene sequencing Health aspects Hepatology In vivo methods and tests Inoculation Inoculum Intestinal microflora Intestine Medicine and Health Sciences Methods Microbiota Microbiota (Symbiotic organisms) Microorganisms Mucosa Mucus Nutrition research RNA sequencing rRNA 16S Simulation Stability Synergistetes |
| title | Establishing a mucosal gut microbial community in vitro using an artificial simulator |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-07T17%3A25%3A19IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-gale_plos_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Establishing%20a%20mucosal%20gut%20microbial%20community%20in%20vitro%20using%20an%20artificial%20simulator&rft.jtitle=PloS%20one&rft.au=Liu,%20LinShu&rft.date=2018-07-17&rft.volume=13&rft.issue=7&rft.spage=e0197692&rft.epage=e0197692&rft.pages=e0197692-e0197692&rft.issn=1932-6203&rft.eissn=1932-6203&rft_id=info:doi/10.1371/journal.pone.0197692&rft_dat=%3Cgale_plos_%3EA546778743%3C/gale_plos_%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=2071153169&rft_id=info:pmid/30016326&rft_galeid=A546778743&rft_doaj_id=oai_doaj_org_article_22ee76b0c196404dba31c4fee1cfb8ca&rfr_iscdi=true |