Evaluation of compartmentalization systems to study microbial interactions

TL;DR

This paper compares different systems used to study yeast interactions in wine fermentation, finding that active exchange is the most versatile and efficient method.

Contribution

The study provides a comparative evaluation of compartmentalization systems for studying microbial interactions, emphasizing the importance of system choice for experimental outcomes.

Findings

The twin-bottles system showed very limited metabolite exchange.

Active exchange through hollow fiber cross-flow filtration devices was found to be the most versatile and efficient system.

Different systems have specific characteristics that make them suitable for different experimental objectives.

Abstract

With some exceptions, wine fermentation has increasingly relied on the use of Saccharomyces cerevisiae starters since the last decades of the past century. However, there is growing interest on the understanding of spontaneous wine fermentation, as well as on the use of complementary non-Saccharomyces wine starters. This in turn raises the question of the importance of interspecific interactions in winemaking and the underlying mechanisms. An important question about these interspecies recognition mechanisms is whether or not it is mediated by physical contact between yeast cells. To address this topic, different laboratories have developed diverse devices to cultivate at least two yeast species in the same growth medium without cell-to-cell contact between them. In this work, we compared four of the most popular systems and found that one of them (twin-bottles exchange through a flat membrane) showed very limited metabolite exchange. Among the other systems (Transwell, dialysis tube, or active exchange through hollow fiber cross-flow filtration devices), each one showed specific characteristics that made them more or less suitable, depending on the objectives of each experiment. The option showing the best versatility and efficiency was the use of active exchange. Our results highlight the importance of carefully characterizing the compartmentalization system when drawing conclusions about the impact of cell-to-cell contact in fermentation experiments.

The online version contains supplementary material available at 10.1038/s41598-025-32560-3.

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