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 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.
Highlights
The use of batch and continuous fermentation systems has garnered a lot of attention in recent years as models to simulate the microbiota of the human gastrointestinal tract and in particular the human colon (Molly et al, 1993; Fooks and Gibson, 2003; Feria-Gervasio et al, 2011; Vamanu et al, 2013; Marzorati et al, 2014; Tanner et al, 2014; Fehlbaum et al, 2015)
The results demonstrate that the mini-fermentation system provides real-time monitoring of pH, %dissolved oxygen (DO) and liquid addition enabling the user to carefully monitor any changes between control samples and test conditions
We aimed to show that a mini-fermentation system could be used as a colon model
Summary
The use of batch and continuous fermentation systems has garnered a lot of attention in recent years as models to simulate the microbiota of the human gastrointestinal tract and in particular the human colon (Molly et al, 1993; Fooks and Gibson, 2003; Feria-Gervasio et al, 2011; Vamanu et al, 2013; Marzorati et al, 2014; Tanner et al, 2014; Fehlbaum et al, 2015). Mini-Fermentation Batch Colon Model models that can be truly used for high-throughput screening. The colon models are labor intensive to set-up and clean and often limited in the number of bioreactors available. The set-up and stabilization period of colon models can range from a couple of hours to a number of weeks (FeriaGervasio et al, 2011; Rea et al, 2011). Williams et al (2015) summarized the stabilization periods required or used with the different models (Williams et al, 2015) with stabilization periods of less than 48 h commonly used for batch fermentation systems. As with microbial cell cultivation and bio-processing, micro-bioreactors can be used to facilitate ex vivo colon modeling and the rapid screening of a variety of parameters
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