Polygenic analysis of the unique antibiotic potency of high acetic acid production and evaluation of other probiotic traits in Saccharomyces cerevisiae var. boulardii

The World Health Organisation (WHO) as well as the Food and Agricultural Organisation (FAO) define probiotics as live micro-organisms that confer a beneficial health effect on a host when they are administered in adequate quantities. Most probiotics are bacteria belonging to the genera Lactobacilli and Bifidobacteria. However, one of the most popular probiotics is the yeast Saccharomyces cerevisiae var. boulardii (S. boulardii).

The objective of my PhD project is to determine the polygenic basis of the probiotic properties in S. boulardii. To achieve this objective, we will use a genetic platform known as pooled-segregant whole-genome sequence analysis to dissect the polygenic basis of various phenotypes previously proposed as contributing to the ability of S. boulardii to act as a probiotic. 

One well-documented property of S. boulardii is its inability to sporulate. However, sporulation competency in yeast strains is essential for the pooled-segregant whole-genome sequence analysis methodology.  Therefore, the first part of this project will involve an exploration of various strategies that are aimed at restoring sporulation competency in S. boulardii.

Next, several wildtype S. boulardii and Saccharomyces cerevisiae (S. cerevisiae) Strains would be evaluated to determine strains that are superior in exhibiting the above-mentioned phenotypes. A haploid segregant of such strains that also exhibits a phenotype of interest (superior parent)  would be selected and used in genetic crosses with a haploid S. cerevisiae strain (inferior parent) that lacks such a phenotype, to initiate the pooled-segregant whole-genome sequence analysis methodology. Hybrids arising from such crosses would be sporulated to yield a large number of segregating progeny (segregants). These segregants would then be phenotyped to select a pool showing the trait of interest (superior pool) and a control pool (randomly selected or showing the same phenotype as the inferior parent). Whole genome DNA would next be isolated from the two pools and subjected to Next Generation Sequencing (NGS). An alignment of the sequence reads obtained for each pool against the genomic sequence of the inferior parent should indicate the genomic regions from the superior pool that are enriched with DNA mainly inherited from the Superior parent (S. boulardii). These regions, known as Quantitative Trait Loci (QTL), would be fine-mapped and studied further using functional genetic assays to identify the genetic determinants of the probiotic phenotype under investigation.