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dc.contributor.authorO’Donnell, Michelle M.
dc.contributor.authorRea, Mary C.
dc.contributor.authorShanahan, Fergus
dc.contributor.authorRoss, R. P.
dc.identifier.citationO’Donnell MM, Rea MC, Shanahan F and Ross RP (2018) The Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colon. Front. Microbiol. 9:1844. doi: 10.3389/fmicb.2018.01844en_US
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 highthroughput 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_US
dc.description.sponsorshipScience Foundation Ireland
dc.publisherFrontiers Media SAen_US
dc.relation.ispartofseriesFrontiers in Microbiology;Vol 9
dc.rightsAttribution-NonCommercial-ShareAlike 4.0 International*
dc.subjectfecal fermentationen_US
dc.subjectmini-fermentation systemen_US
dc.subjectbatch colon modelen_US
dc.titleThe Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colonen_US
dc.contributor.sponsorScience Foundation Irelanden_US
dc.source.journaltitleFrontiers in Microbiology

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