Class 2018
PhD Grant: PD/BD/142945/2018
PhD thesis
Promoting the use of Saccharomycodaceae yeasts in winemaking by leveraging genome-wide analyses
Supervisors
• Nuno Gonçalo Pereira Mira, Professor @ IST/ULisboa, PT
• Ana Alexandra Mendes-Ferreira, Professor @ Universidade de Trás-os-Montes e Alto Douro, Vila Real, PT
Collaborations
PhD Degree complete: Discussion on December 18, 2024
THESIS ABSTRACT
Wine has been produced and consumed by humans for centuries. At the heart of winemaking is the activity of fermenting yeasts, particularly Saccharomyces cerevisiae that leads vinification. The growing trend of using starter-cultures of other yeasts alongside S. cerevisiae aims to improve wine properties and create distinguishable products. Yeasts from the Saccharomycodacea family, specifically the sister genera Hanseniaspora and Saccharomycodes, are considered promising in this context. However, their utilization is hampered by the poor knowledge of their physiology and interaction mechanisms with S. cerevisiae. This thesis addresses these gaps through a combination of knowledge-gathering and application.
The first genome sequence of a Saccharomycodes ludwigii wine strain is described in Chapter II, facilitating comparative genomic analyses, both intra-species (Chapter III) and inter-species (Chapter V), against Hanseniaspora, providing insights into the physiology of Sd. ludwigii and the Saccharomycodacea family. Phenotypic profiling of Non-Saccharomyces isolates from grape musts in the Palmela winemaking area (Península de Setúbal region) enabled the identification of strain Hanseniaspora uvarum MJT198 (HuMJT198), based on its very high beta-glucosidase activity (Chapter IV.A). The combined use of HuMJT198 with S. cerevisiae produced wines with increased free terpenes, expanding the role of H. uvarum strains beyond modulation of secondary aroma. Exploring comparative genomics of HuMJT198 and other Hanseniaspora species beta-glucosidase-encoding genes were identified as contributors to this effect. Transcriptomic and metabolomic analyses revealed further interactions between HuMJT198 and S. cerevisiae at a molecular level (Chapter IV.B).
Altogether, the results described in this thesis supports the trend of exploring Non-Saccharomyces Yeasts as bio-flavourants in wine production but also other beverages, applying knowledge-driven and rational methods that improve the likelihood of success compared to the trial-and-error approaches currently in use.
RESUMO
A produção de vinho e o seu consumo acompanham o Ser Humano há vários séculos, com a atividade de leveduras fermentativas, como Saccharomyces cerevisiae, a liderar o processo de vinificação. A utilização de inóculos combinados de leveduras nativas e S. cerevisiae, é uma tendência crescente neste sector, ambicionando melhorar as propriedades do vinho e criando produtos distintos. Leveduras da família Saccharomycodaceae, particularmente dos géneros Hanseniaspora e Saccharomycodes, têm sido consideradas promissoras neste contexto. No entanto, o conhecimento limitado sobre a sua fisiologia e os mecanismos de interação com S. cerevisiae, restringe a sua utilização. Esta tese aborda estas lacunas, combinando investigação fundamental e aplicação prática.
No Capítulo III, é descrita a primeira sequência genómica de uma estirpe de Saccharomycodes ludwigii isolada de vinho, permitindo análises genómicas comparativas intraespécie (Capítulo III) e inter-espécies (Capítulo V), aprofundando a compreensão da fisiologia de Sd. ludwigii e da família Saccharomycodaceae. A fenotipagem de isolados Não-Saccharomyces obtidos de mostos da região vitivinícola da Península de Setúbal permitiu a identificação de estirpe Hanseniaspora uvarum (HuMJT198), pela sua elevada atividade de beta-glucosidase (Capítulo IVA). A utilização combinada de HuMJT198 com S. cerevisiae resultou em vinhos com maior concentração de terpenos livres, enaltecendo o papel das leveduras Hanseniaspora na modulação do aroma primário. A exploração genómica de HuMJT198 e outras espécies de Hanseniaspora identificou genes codificadores de beta-glucosidase como responsáveis por este efeito. Adicionalmente, análises transcriptómicas e
revelaram interações moleculares entre HuMJT198 e S. cerevisiae (Capítulo IVB).
No geral, os resultados desta tese apoiam a exploração de leveduras Não-Saccharomyces como agentes bioaromatizantes, aplicando métodos baseados emconhecimento, com maior probabilidade de sucesso face à abordagem empírica atualmente utilizada.
PUBLICATIONS
Papers
Tavares, M.J., Güldener, U., Mendes-Ferreira, A. et al. Genome sequencing, annotation and exploration of the SO2-tolerant non-conventional yeast Saccharomycodes ludwigii. BMC Genomics 22, 131 (2021). https://doi.org/10.1186/s12864-021-07438-z
Esteves, M., Barbosa, C., Vasconcelos, I., Tavares, M.J., Mendes-Faia, A., Mira, N.P., Mendes-Ferreira, A., Characterizing the potential of the Non-Convetional Yeast Saccharomycodes ludwigii UTAD17 in Winemaking. Microorganisms 7 (11), 478, 2019.
Tavares, M.J., Güldener, U., Esteves, M., Mendes-Faia, A., Mendes-Ferreira, A., Mira, N.P. Genome Sequence of the Wine Yeast Saccharomycodes ludwigii UTAD17. Microbiology Resource Announcements 7, 18, 2018.
Oral Communications
Tavares, M.J, Güldener, U., Tenreiro, R., Mendes-Faia, A., Mendes-Ferreira, A., Mira, N.P. “Unveiling the biology and physiology of the wine yeast Saccharomycodes ludwigii UTAD17 through the exploration of genomics data.” 7th Conference on Physiology of Yeasts and Filamentous Fungi. 24th-27th June 2019, Milan, Italy. (Flash Presentation)
Tavares, M.J, Güldener, U., Tenreiro, R., Mendes-Faia, A., Mendes-Ferreira, A., Mira, N.P. “Fostering the utilization of the Non-Saccharomyces yeast Saccharomycodes ludwigii UTAD17 as a co-adjuvant of fermented beverages through the exploration of comparative genomics data.” International Congress on Grapevine and Wine Science. 7th-9th November 2018 Logroño, Spain.
Poster Communications
Tavares, M.J, Güldener, U., Tenreiro, R., Mendes-Faia, A., Mendes-Ferreira, A., Mira, N.P. “Fostering the utilization of the Non-Saccharomyces yeast Saccharomycodes ludwigii UTAD17 as a co-adjuvant of fermented beverages through the exploration of comparative genomics data.” XXI Jornadas de Leveduras Professor Nicolau van Uden. 8th-9th June 2018, Braga, Portugal.
Tavares, M.J, Güldener, U., Tenreiro, R., Mendes-Faia, A., Mendes-Ferreira, A., Mira, N.P. “Unveiling the biology and physiology of the wine yeast Saccharomycodes ludwigii UTAD17 through the exploration of genomics data.” 7th Conference on Physiology of Yeasts and Filamentous Fungi. 24th-27th June 2019, Milan, Italy.
DOCTORAL PROGRAM (36 ECTS)
Curricular units:
• Bioentrepreneurship (6 ECTS)
• Outreach and Teaching Skills (6 ECTS)
• Microbiomes and Metagenomics (6 ECTS)
• Molecular and Cell Biophysics (6 ECTS)
• General Doctoral Training (6 ECTS)
• Advanced Experimental Techniques and methodologies (6 ECTS)
Advanced Courses
• Teaching STEM Students – Transformation Guide for teaching Assistants 1st Ed., by Academic Development Office, 10-12 September 2018, Instituto Superior Técnico, Lisbon, Portugal
Current Position:
International Affairs Officer @ ITQB NOVA