Saccharomyces species
Saccharomyces cerevisiae has a long-standing history of biotechnological applications, even before the dawn of modern biotechnology. The field is undergoing accelerated advancement with the recent systems and synthetic biology approaches (Ting et al. 2023).
The species designation of Saccharomyces boulardii was coined after a French agricultural engineer and microbiologist, Henri Boulard, who isolated the yeast in 1923 from lychee and mangosteen skins after observing that local populations in Indochina consumed fruit-based teas to treat cholera. The French pharmaceutical company Biocodex acquired the intellectual property rights of this S. boulardii strain in 1947 and registered it as S. boulardii CNCM I-745 in 1953 at the Pasteur Institute.
Currently, S. boulardii is the only probiotic yeast for the treatment of antibiotic-associated diarrhea and pediatric acute gastroenteritis, and has been clinically proven to be effective for acute and chronic digestive tract disorders, such as Clostridioides difficile–induced diarrhea, traveler’s diarrhea, irritable bowel syndrome (IBS), and Crohn’s disease. Collective genetic findings suggest that S. boulardii is not a distinct species but rather a strain of S. cerevisiae, with the correct nomenclature being Saccharomyces cerevisiae var. boulardii. For conciseness, S. cerevisiae var. boulardii will be abbreviated as Sb and S. cerevisiae as Sc.
Currently, our group is attempting bioengineering of Saccharomyces cerevisiae and S. boulardii with a protease to detoxify gluten in bakery and as a functional probiotic, respectively. This will add to an enzyme therapy option for people with coeliac disease or gluten sensitivity.
The species designation of Saccharomyces boulardii was coined after a French agricultural engineer and microbiologist, Henri Boulard, who isolated the yeast in 1923 from lychee and mangosteen skins after observing that local populations in Indochina consumed fruit-based teas to treat cholera. The French pharmaceutical company Biocodex acquired the intellectual property rights of this S. boulardii strain in 1947 and registered it as S. boulardii CNCM I-745 in 1953 at the Pasteur Institute.
Currently, S. boulardii is the only probiotic yeast for the treatment of antibiotic-associated diarrhea and pediatric acute gastroenteritis, and has been clinically proven to be effective for acute and chronic digestive tract disorders, such as Clostridioides difficile–induced diarrhea, traveler’s diarrhea, irritable bowel syndrome (IBS), and Crohn’s disease. Collective genetic findings suggest that S. boulardii is not a distinct species but rather a strain of S. cerevisiae, with the correct nomenclature being Saccharomyces cerevisiae var. boulardii. For conciseness, S. cerevisiae var. boulardii will be abbreviated as Sb and S. cerevisiae as Sc.
Currently, our group is attempting bioengineering of Saccharomyces cerevisiae and S. boulardii with a protease to detoxify gluten in bakery and as a functional probiotic, respectively. This will add to an enzyme therapy option for people with coeliac disease or gluten sensitivity.
Bioengineering of Saccharomyces boulardii as live biotherapeutics
Bioengineering of Yeasts with neprosin for gluten detoxification
In this study, neprosin from N. rafflesiana (NrNpr1) was recombinantly expressed with chicken lysozyme signal peptide in the baker’s yeast Saccharomyces cerevisiae expression host. The culture media of the bioengineered S. cerevisiae can degrade pure gliadin substrate and gliadin in wheat flour. The live yeast culture was demonstrated to degrade gliadin in wheat flour dough. The purified rNrNpr1 enzyme was successfully characterized to have an optimal pH of 2.5, optimal temperature of 50°C, thermal tolerance of 0-65°C, and can digest all immunogenic epitopes in α-gliadin 33-mer when tested in vitro. ELISA test proved that rNrNpr1 can detoxify 0.75 mg/mL gliadin to a gluten-free level (<20 ppm) after 6 hours of incubation.
Highlights
- The first characterization of neprosin from Nepenthes rafflesiana in Saccharomyces cerevisiae
- Bioengineered S. cerevisiae is capable of constitutively expressing and secreting recombinant neprosin into culture medium
- Purified recombinant neprosin can detoxify immunogenic 33-mer in α-gliadin
- Concentrated culture medium exhibits gliadin degradation activity in wheat flour
- Live yeast culture can degrade gliadin in wheat dough
Molecular Genetics and Probiotic Mechanisms of Saccharomyces cerevisiae var. boulardii
Saccharomyces cerevisiae var. boulardii (Sb) is a S. cerevisiae (Sc) strain that has been widely used in the treatment of gastrointestinal diseases due to its unique probiotic properties. The key genomic differences that distinguish Sb from Sc include the tetrasomy of chromosome XII, the absence of intact transposon-yeast (Ty) elements, and variations in the copy number of specific genes. These genomic variations may contribute to enhanced thermotolerance, increased acid resistance, and elevated acetate production, collectively supporting its probiotic functions.
Recent findings further suggest that Sb may serve as a potential adjuvant therapy for brain disorders by modulating the gut–brain axis (GBA) to attenuate neuroinflammation. With continued multidisciplinary research, Sb is well-positioned to advance the biotherapeutic landscape. This review aims to synthesize recent advances in the genetics and probiotic mechanisms of Sb, with particular emphasis on its modulatory effects on the GBA.
Recent findings further suggest that Sb may serve as a potential adjuvant therapy for brain disorders by modulating the gut–brain axis (GBA) to attenuate neuroinflammation. With continued multidisciplinary research, Sb is well-positioned to advance the biotherapeutic landscape. This review aims to synthesize recent advances in the genetics and probiotic mechanisms of Sb, with particular emphasis on its modulatory effects on the GBA.
Mechanisms of probiotic yeast Sb in maintaining gut health
Luminal action: Sb enhances concentrations of gut SCFAs directly via fermentation of dietary fiber and indirectly via synbiotic interactions with bacterial probiotics. One of the SCFAs produced is acetate, which has antimicrobial properties that help inhibit pathogen growth. Sb also secretes serine protease, PHO8 phosphatase, and kinase/transporter. The serine protease cleaves C. difficile toxins A and B, while the PHO8 phosphatase desphosphorylates the E. coli endotoxin lipopolysaccharide (LPS). The secreted kinase prevents chloride secretion in diarrhea caused by Vibrio cholerae.
Trophic effect: Sb secretes polyamines such as spermine and spermidine that have signaling effects towards gut epithelial cells to enhance the synthesis of digestive enzymes and transporters.
Mucosal action: Sb exerts anti-inflammatory effects through interference with NF-κB and MAPK pathways.
Luminal action: Sb enhances concentrations of gut SCFAs directly via fermentation of dietary fiber and indirectly via synbiotic interactions with bacterial probiotics. One of the SCFAs produced is acetate, which has antimicrobial properties that help inhibit pathogen growth. Sb also secretes serine protease, PHO8 phosphatase, and kinase/transporter. The serine protease cleaves C. difficile toxins A and B, while the PHO8 phosphatase desphosphorylates the E. coli endotoxin lipopolysaccharide (LPS). The secreted kinase prevents chloride secretion in diarrhea caused by Vibrio cholerae.
Trophic effect: Sb secretes polyamines such as spermine and spermidine that have signaling effects towards gut epithelial cells to enhance the synthesis of digestive enzymes and transporters.
Mucosal action: Sb exerts anti-inflammatory effects through interference with NF-κB and MAPK pathways.
Bioengineering of Probiotic Yeast Saccharomyces boulardii for Advanced Biotherapeutics
Saccharomyces cerevisiae var. boulardii (Sb), a subspecies of S. cerevisiae (Sc), is widely recognized for its probiotic properties. Recently, Sb has attracted growing interest as a chassis organism for engineered live biotherapeutics and advanced microbiome therapies.
To the best of our knowledge, earlier reviews have largely emphasized its clinical applications, safety profile, and probiotic mechanisms. This review uniquely consolidates recent advances in genetic modification, metabolic engineering, and synthetic biology strategies applied to Sb for therapeutic use. Together, these synthetic biology advancements position Sb as a promising and versatile platform for next-generation microbiome-based therapeutics and expanding applications in human health and food biotechnology.
To the best of our knowledge, earlier reviews have largely emphasized its clinical applications, safety profile, and probiotic mechanisms. This review uniquely consolidates recent advances in genetic modification, metabolic engineering, and synthetic biology strategies applied to Sb for therapeutic use. Together, these synthetic biology advancements position Sb as a promising and versatile platform for next-generation microbiome-based therapeutics and expanding applications in human health and food biotechnology.
systems and synthetic biology studies of Saccharomyces cerevisiae
In this review, we highlight recent findings in the field, focusing on omics studies of S. cerevisiae to investigate its stress tolerance across different industries. The latest advancements in S. cerevisiae systems and synthetic biology approaches for the development of genome-scale metabolic models (GEMs) and molecular tools such as multiplex Cas9, Cas12a, Cpf1, and Csy4 genome-editing tools, modular expression cassette with optimal transcription factors, promoters, and terminator libraries, as well as metabolic engineering.
Omics data analysis is key to identifying exploitable native genes/proteins/pathways in S. cerevisiae, enabling the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
Omics data analysis is key to identifying exploitable native genes/proteins/pathways in S. cerevisiae, enabling the optimization of heterologous pathway implementation and fermentation conditions. Through systems and synthetic biology, various heterologous compound productions that require non-native biosynthetic pathways in a cell factory have been established via different strategies of metabolic engineering integrated with machine learning.
From exploratory omics to translational research with precision biotechnological development
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References
Intellectual Property
Grants
- Ting T-Y, Lee W-J, Goh H-H* (2025) Bioengineering of probiotic yeast Saccharomyces boulardii for advanced biotherapeutics. ACS Synthetic Biology 14 (9), 3275–3292. https://doi.org/10.1021/acssynbio.5c00236 (Q1, IF:3.8)
- Ting T-Y, Lee W-J, Goh H-H* Molecular genetics and probiotic mechanisms of Saccharomyces cerevisiae var. boulardii. Probiotics and Antimicrobial Proteins Accepted 18 Jun 2025 https://doi.org/10.1007/s12602-025-10634-y
- Ting T-Y, Lee W-J, Ramzi, AB, Goh H-H* Bioengineered Saccharomyces cerevisiae with neprosin for gluten detoxification. Journal of Future Foods Accepted 21 Jan 2025 https://doi.org/10.1016/j.jfutfo.2025.01.008
- Ting T-Y, Li YD, Bunawan H, Ramzi AB & Goh H-H* (2023) Current advancements in systems and synthetic biology studies of Saccharomyces cerevisiae. Journal of Bioscience and Bioengineering 135(4):259-265. https://doi.org/10.1016/j.jbiosc.2023.01.010 (Q3, IF:3.185)
Intellectual Property
- Patent Filed [UI2024005827] Utility Innovation: LIVE BIOENGINEERED YEAST FOR GLUTEN DETOXIFICATION (Bioengineered yeast with enzyme from Nepenthes rafflesiana for gluten detoxification), 07/10/2024, UKM.IKB.800-4/1/5204
Grants
- FORMULATION OF ENGINEERED BAKER`S YEAST WITH RECOMBINANT NEPROSIN FOR GLUTEN-SAFE BAKERY - Research University Grant: GUP-2024-092 [1 Nov 2024 – 31 Oct 2026]
- INVESTIGATION ON THE OVEREXPRESSION OF NEPROSIN FROM NEPENTHES RAFFLESIANA IN SACCHAROMYCES CEREVISIAE FOR GLUTEN DETOXIFICATION - Fundamental Research Grant Scheme: FRGS/1/2024/STG01/UKM/02/5 [1 Aug 2024 – 31 Jul 2027]
Collaborators / Researchers
- Dr Ahmad Bazli Ramzi
- Dr ZALIFAH BINTI MOHD KASIM (FST, Food Science)
- LEE WEI JING (2024)
- Dr TING TIEK YIK (2020-2024), Structure-function analysis of neprosin from Nepenthes species and characterisation in Saccharomyces cerevisiae
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