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. 2018 Aug 10:9:1844.
doi: 10.3389/fmicb.2018.01844. eCollection 2018.

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

Michelle M O'Donnell  1   2 , Mary C Rea  2 , Fergus Shanahan  1   3 , R P Ross  1   2   4
Affiliations

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

Michelle M O'Donnell et al. Front Microbiol. .

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.

Keywords: batch colon model; fecal fermentation; micro-Matrix; microbiota; mini-fermentation system.

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Figures

FIGURE 1
FIGURE 1
The micro-Matrix fermentation system. (A) The micro-Matrix; (B) a micro-Matrix 24-well cassette; (C) an overview of two wells from the 24-well cassette; (D) a representation of a single well of the cassette including the DO and pH sensors and the temperature sensor.
FIGURE 2
FIGURE 2
Machine parameters logged over the first 20–40 min of the fermentation (A–C) and over the full 24 h fermentation period (D). (A) Percentage dissolved oxygen (DO%) (B) Temperature (C) pH (D) Liquid NaOH addition.
FIGURE 3
FIGURE 3
Alpha diversity indices (A) Simpson diversity index (B) Shannon diversity index. ∗∗∗∗P ≤ 0.0001.
FIGURE 4
FIGURE 4
Beta diversity plots. (A) Unweighted Unifrac distance; (B) Weighted Unifrac distance.
FIGURE 5
FIGURE 5
(A) Phylum level taxonomic diversity between cassettes and time-points. (B) Genus level taxonomic diversity between cassettes and time-points (w = well).
See this image and copyright information in PMC

References

    1. Alteri C. J., Mobley H. L. T. (2012). Escherichia coli physiology and metabolism dictates adaptation to diverse host microenvironments. Curr. Opin. Microbiol. 15 3–9. 10.1016/j.mib.2011.12.004 - DOI - PMC - PubMed
    1. Caporaso J. G., Bittinger K., Bushman F. D., DeSantis T. Z., Andersen G. L., Knight R. (2010). PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics 26 266–267. 10.1093/bioinformatics/btp636 - DOI - PMC - PubMed
    1. Edgar R. C., Haas B. J., Clemente J. C., Quince C., Knight R. (2011). UCHIME improves sensitivity and speed of chimera detection. Bioinformatics 27 2194–2200. 10.1093/bioinformatics/btr381 - DOI - PMC - PubMed
    1. Fehlbaum S., Chassard C., Haug M. C., Fourmestraux C., Derrien M., Lacroix C. (2015). Design and investigation of PolyFermS in vitro continuous fermentation models inoculated with immobilized fecal microbiota mimicking the elderly colon. PLoS One 10:e0142793. 10.1371/journal.pone.0142793 - DOI - PMC - PubMed
    1. Feria-Gervasio D., Denis S., Alric M., Brugère J.-F. (2011). In vitro maintenance of a human proximal colon microbiota using the continuous fermentation system P-ECSIM. Appl. Microbiol. Biotechnol. 91 1425–1433. 10.1007/s00253-011-3462-5 - DOI - PubMed