The Use of a Mini-Bioreactor Fermentation System as a Reproducible, High-Throughput ex vivo Batch Model of the Distal Colon

Frontiers in Microbiology
Michelle M O'DonnellR P Ross

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. Th...Continue Reading

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Citations

Apr 21, 2019·International Journal of Molecular Sciences·Irina TsitkoMaria Saarela
Jun 9, 2020·FEMS Microbiology Letters·Lorenzo NissenAndrea Gianotti
Jun 4, 2019·EBioMedicine·Leah Guthrie, Libusha Kelly
Nov 14, 2020·Current Opinion in Biotechnology·Michela Gambino, Lone Brøndsted
Apr 1, 2021·Microbes and Infection·Giuliano BayerDana J Philpott
Aug 15, 2021·Advanced Drug Delivery Reviews·Connor O'FarrellHannah Batchelor
Oct 1, 2021·Critical Reviews in Microbiology·Enriqueta Garcia-Gutierrez, Paul D Cotter

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Methods Mentioned

BETA
PCR

Software Mentioned

R phyloseq package
Adonis
SPSS PASW Statistics
SPSS
PyNAST
Permanova
QIIME
USEARCH
MiSeq

Related Concepts

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Bioreactors (ASM)

Bioreactors are important devices or systems that utilize living cells or enzymes for a chemical process. These devices carefully control and monitor the environment factors such as pH, nutrients level, and temperature, which can affect the yield in a given process. Discover the latest research here.