The use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex-vivo batch model of the distal colon

dc.contributor.authorO'Donnell, Michelle M.
dc.contributor.authorRea, Mary C.
dc.contributor.authorShanahan, Fergus
dc.contributor.authorRoss, R. Paul
dc.contributor.funderScience Foundation Ireland
dc.description.abstractEx vivo colon fermentation systems are highly versatile as models for analyzing gastrointestinal tract microbiota composition and functionality. Ex vivo colon models range in size and functionality from bench-top micro fermenters to large units housed in individualized cabinets. The length of set-up time (including stabilization periods) for each fermentation system can range from hours to weeks to months. The aim of this study was to investigate a single-use cassette mini-fermentation system as a reproducible batch model of the colon. The online data log from the cassettes (triplicate wells across four different cassettes, n = 12) was sensitive enough to identify real-time changes in pH, temperature, dissolved oxygen or liquid addition (sodium hydroxide) during the runs which could be addressed if an alarm set-point was triggered. The alpha diversity indices also showed little variation between cassettes with the samples clustering around the mean. The weighted beta diversity PCoA analysis illustrated that 95% of the variance between the samples was accounted for by the time-point and not the fermentation run/cassette used. The variation in taxonomic diversity between cassettes was limited to less than 20 out of 115 genera. This study provides evidence that micro-bioreactors provide some very attractive advantages as batch models for the human colon. We show for the first time the use of the micro-Matrix a 24-well sophisticated parallel controlled cassette-based bioreactors as a batch colon model. We demonstrated a high level of reproducibility across fermentation cassettes when used in conjunction with a standardized fecal microbiota. The machine can operate 24 individual fermentations simultaneously and are relatively cost effective. Based on next generation sequencing analysis, the micro-bioreactors offer a high degree of reproducibility together with high-throughput capacity. This makes it a potential system for large screening projects that can then be scaled up to large fermenters or human/animal in vivo experiments.en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.identifier.citationO’Donnell, M. M., Rea, M. C., Shanahan, F. and Ross, R. P. (2018) 'The use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex-vivo batch model of the distal colon', Frontiers in Microbiology, 9, 1844 (9pp). doi: 10.3389/fmicb.2018.01844en
dc.identifier.journaltitleFrontiers in Microbiologyen
dc.publisherFrontiers Mediaen
dc.relation.projectinfo:eu-repo/grantAgreement/SFI/SFI Research Centres/12/RC/2273/IE/Alimentary Pharmabiotic Centre (APC) - Interfacing Food & Medicine/
dc.rights© 2018, O'Donnell, Rea, Shanahan and Ross. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.en
dc.subjectFecal fermentationen
dc.subjectMini-fermentation systemen
dc.subjectBatch colon modelen
dc.titleThe use of a mini-bioreactor fermentation system as a reproducible, high-throughput ex-vivo batch model of the distal colonen
dc.typeArticle (peer-reviewed)en
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