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The Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colon
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2018-08-10
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O’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.2018.01844
Abstract
Ex 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.