iBB

A new study from iBB, Instituto Superior Técnico, carried out within the scope of the FCT project “Mechanistic insights into adaptation and increased robustness to acetic acid and other weak acids toxicity in yeasts”, was published today in the journal Microbial Cell Factories. This study provides new biological knowledge of interest to gain further mechanistic insights into toxicity and tolerance to linear-chain monocarboxylic acids of increasing liposolubility and reports the first lists of tolerance genes, at the genome scale, for butyric and octanoic acids. These genes and biological functions are potential targets for synthetic biology approaches applied to promising yeast cell factories, towards more robust superior strains. This is a highly desirable phenotype to increase the economic viability of bioprocesses based on mixtures of volatiles/medium-chain fatty acids derived from low-cost biodegradable substrates or lignocellulose hydrolysates. The work was led by Prof. Isabel Sá-Correia and the two first co-authors are the PhD student of the Doctoral Programme in Biotechnology and Biosciences, Marta Mota, and the researcher with a MSc degree, Madalena Matos.

A new study from iBB, carried out within the scope of the Mobilizer Project Move2LowC, was published in the Journal of Fungi. The work describes the development, by adaptive laboratory evolution (ALE), of an evolved strain of the oleaginous yeast Rhodotorula toruloides more tolerant to the four major inhibitors present in lignocellulosic hydrolysates (LCH) (acetic acid, formic acid, hydroxymethylfurfural, and furfural). This outcome represents an advantage for the exploitation of promising lignocellulosic biomass feedstocks in bioprocesses envisaging the transition to a sustainable bio-based economy. In fact, the presence of toxic compounds in LCH is among the main barriers affecting the efficiency of lignocellulose-based fermentation processes, in particular hindering the production of intracellular lipids by oleaginous yeasts. These microbial oils are promising sustainable alternatives to vegetable oils for biodiesel production. The more protective role of the evolved strain cellular envelope (cell wall and plasma membrane) was demonstrated and the improved performance of this multi-tolerant strain for lipid production from a synthetic lignocellulosic hydrolysate medium, supplemented with those inhibitors, was confirmed. The work was led by Isabel Sá-Correia and the two first co-authors are the MSc student in Microbiology Mónica A. Fernandes, and the PhD student in Biotechnology and Biosciences Marta N. Mota. Dr. Nuno T. Faria has contributed with the lipid profile characterization.

As part of the celebrations of the International Microorganism Day (September 17th), the Academy of Sciences of Lisbon (ACL) and its Institute of Higher Studies, in collaboration with the Portuguese Society of Microbiology (SPM), organize, on the 18th September, Monday, an afternoon to promote Microbiology. The session includes talks by Isabel Sá-Correia who will moderate the colloquium, and Tinar Keller-Costa, both from DBE and iBB.

In the midst of the climate crisis, the colloquium's theme is: LIFE ON OUR PLANET DEPENDS ON MICROORGANISMS. The session is open and will take place, in a hybrid format, in the ACL session room, as well as on the Zoom platform. The session will take place in Portuguese, with the exception of the last talk which will be in English: SAVE THE MICROBES TO SAVE THE PLANET to be presented by the President of the International Union of Microbiological Societies (IUMS), it is a call to action to promote the development of sustainable solutions to control infectious agents, preserve global microbial diversity and healthy life on our planet.

The Blue Bioeconomy Pact led by Inovamar is one of the mobilizing agendas for corporate innovation recently funded by the European Union NextGenerationEU through the Portuguese Recovery and Resilience Plan (PRR). It consists of a consortium of 83 national entities including 53 companies of all dimensions, from large multinational corporations to small-medium enterprises and start-ups, and 30 R&D institutions. The project aims to develop the sustainable use of marine resources, creating 52 new products, processes and services across multiple sectors such as aquaculture, fisheries, food and feed, textiles, biomaterials and human health. The consortium will invest a total amount of 133 M€, of which 94 M€ are financed by the Recovery and Resilience Plan.

Instituto Superior Técnico is involved in four of the nine PBA work packages with 1.5 M€ of funding: WP1 – “Biomaterials”, WP4 – “Food”, WP5 – “Algae”, and WP9 – “The Portuguese Blue Biobank”. The project at IST is coordinated by Prof Rodrigo Costa from iBB and DBE and counts on expert contributions by Dr Teresa Cesário from iBB (WP1), Dr Tina Keller-Costa and Prof Isabel Sá-Correia from iBB (WP5 and WP9) and Prof Ana Clara Marques from CERENA and DEQ (WP4).

The December 16, 2022 Episode of 110 Stories | 110 Técnico objects is dedicated to Técnico’s first registered patent. That 1985´s  patent, entitled "PROCESS FOR THE PRODUCTION OF NATURAL SPARKLING WINES BY MEANS OF IMMOBILIZED YEAST" also belongs to the history of iBB. Indeed, iBB is the current research unit of the excellent lineage originating from the Laboratory of Biochemical Engineering/CEBQ-Center of Biological and Chemical Engineering. The first author was Júlio Maggiolly Novais, the founding director of that IST research unit. The other IST authors were Isabel Sá-Correia, Joaquim S Cabral and Manuela Cadete. In addition to IST, there were two other applicants: Instituto Superior de Agronomia (co-author: Prof Virgílio Loureiro) and Caves Raposeira LDA.
In this episode of the podcast, two of the authors intervened and explained the objectives and innovation related to the patent. The innovation consisted of immobilizing (sequestering in in an agar-agar gel) the yeast cells that carry out the secondary alcoholic fermentation in the bottle, typical of champagne production (to create the typical "bubbles" of CO2 gas). The objective was to make unnecessary the manual rotation of sparkling wine bottles, for three weeks, to remove the yeasts which, when free, accumulate in high concentrations making the drink very cloudy. During the podcast, it was also recalled the bottling carried out at Caves da Raposeira, applying the methods developed at the Técnico's laboratory to the reality of sparkling wine production. 

The YEASTRACT+ information system is a wide-scope computational tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in 11 yeast species of biotechnological or human health relevance. Its newest release, orchestrated by a large team led by Isabel Sá-Correia, Miguel Teixeira, from iBB, and Pedro Monteiro, from INESC-ID, has just described in the 2023 Nucleic Acids Research Database Issue, highlighting the availability of new regulatory-metabolic network modeling tools. These tools are expected to contribute to guide YEASTRACT+ users in the optimization of yeast cell factories of industrial relevance and the identification of new antifungal drug targets, to be used in advanced antifungal therapy. YEASTRACT+ is currently supported within the context of the Biodata.pt/Elixir.pt Research Infrastructure.

Protein kinases are essential as signal transductors for a proper cellular response to extracellular stimuli. A BSRG-iBB review paper, just published in Computational and Structural Biotechnology Journal gathers the available information regarding the NPR/Hal5 family of kinases in Saccharomyces cerevisiae and non-Saccharomyces species of clinical and biotechnological relevance. These kinases - for which information is scarce and scattered across scientific literature - are essential modulators of yeast nutrient availability responses and ion homeostasis. This publication has as first-author the PhD student Miguel Antunes of the IST PhD programme in Biotechnology and Biosciences and the FCT-DP BIOTECnico - and as a corresponding author his thesis supervisor, Professor Isabel Sá-Correia.

Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses. The cell wall is among the players whose biochemical and biophysical properties can be finely tuned as yeast cells encounter different stresses throughout the course of industrial bioprocesses. A new review article from BSRG-iBB provides a critical opinion and a comprehensive view on the current knowledge on the involvement of the cell wall in the adaptive response and tolerance of yeasts to multiple stresses of biotechnological relevance. A few successful attempts to improve stress tolerance through the manipulation of cell wall biosynthetic pathway are also described and the available information for some non-conventional yeast species included. The review article is co-authored by the PhD student of the IST PhD programme in Biotechnology and Biosciences Ricardo Ribeiro and the thesis supervisor, Prof. Isabel Sá-Correia. It was was published in the journal Frontiers in Microbiology (section: Microbial Physiology and Metabolism).

Exploration of yeast diversity for the sustainable production of biofuels, in particular biodiesel, is gaining momentum in recent years. A BSRG-iBB review paper, just published in the Journal of Fungi (Special Issue: Yeasts for a Sustainable Circular Bio-Based Economy), provides an overview of lipid production by oleaginous yeasts focusing on yeast diversity, metabolism, and other microbiological issues related to the toxicity and tolerance to multiple challenging stresses limiting bioprocess performance. Examples gathered from the literature showing the potential of different oleaginous yeasts/process conditions to produce oils for biodiesel from agro-forestry and industrial organic residues are also provided. This publication has as first-author the PhD student Marta N. Mota of the IST PhD programme in Biotechnology and Biosciences and as corresponding author her thesis supervisor, Professor Isabel Sá-Correia. Paula Múgica, from BIOREF—Collaborative Laboratory for Biorefineries, also contributed to the publication during her stay at BSRG-iBB for scientific training and collaboration in the execution of the Move2LowC project.

Together with Dr. Naseem A. Gaur, prof. Isabel Sá-Correia is organizing a special issue for The Journal of Fungi. This special issue is focused on the new circular bio-based economy. The development of large-scale bioprocesses for the bioconversion of biomass resources into environmentally friendly biofuels, chemicals, and materials is required to answer timeless societal challenges. Cost-effective microbial conversion processes of renewable feedstock into biofuels and biochemicals are of utmost importance for the establishment of a robust bioeconomy. Therefore, the transition to a sustainable bio-based economy requires further scientific research and innovation to reach those goals. Integrated yeast biorefinery processes have recently gained relevance in envisaging the conversion of forest and agro-industrial residues into environmentally friendly products currently produced by the petrochemical industry. For all these reasons, this is a very active and exciting area of R&D. Deadline for new manuscript submissions is August 31, 2022.

Marta Mota, a PhD student of the Instituto Superior Técnico, Universidade de Lisboa, PhD program in Biotechnology and Biosciences, (FCT doctoral programme in Applied and Environmental Microbiology (DP_AEM)), presented her work during the symposium on “Microbiotech for a Sustainable Future” of Microbiotec’ 21 Congress taking place online from 23-26 November. The presentation was entitled “Promising Genetic Determinants of Methanol Tolerance for Yeast Robustness Engineering for Biorefineries”. This work was performed in the Biological Sciences Research Group of iBB - Institute for Bioengineering and Biosciences, Instituto Superior Técnico, Universidade de Lisboa, under Professor Isabel Sá-Correia’s supervision.

If you missed the InternationalMicroorganismDay session at Academia das Ciências de Lisboa, you can now watch the full video of the symposium on YouTube: https://youtu.be/hOQqn-G8I18

The talks by Isabel Sá-Correia and Tina Keller-Costa, both from Departamento de Bioengenharia and iBB - Institute for Bioengineering and Biosciences, start at 07:00 min and 01h32 min, respectively.

The abstract book with contributions from all speakers of the session is available in Portuguese and English on the ACL website.

Massive representation of IBB at FEMS 2023, the largest Microbiology meeting in Europe, that took place in Hamburg, 9-13 July 2023. PhD students Sara Gomes (Poster entitled “Evolution of Burkholderia multivorans traits required for persistent infections of the cystic fibrosis lung”), Mirela Ferreira (Poster entitled “Characterization of multicellular aggregates formed by Burkholderia multivorans”), Marta Mota (Co-chairing the Industrial Microbiology and Bioeconomy Session and Offered Talk entitled “Candida boidinii, an oleaginous methylotrophic yeast species attractive as a platform for methanol-based biomanufacturing”), Miguel Antunes (Offered Talk entitled “The Hrk1 kinase as a modulator of ion homeostasis and acetic acid stress tolerance in yeast”) and Inês Costa (Offered Talk entitled “Candida glabrata’s genomic plasticity shapes the clinical evolution of biofilm formation”) have presented their work. Miguel Cacho Teixeira (Member of the Program Committee, Charing the Genetics and Genomics Session and Invited Talk entitled “Drug transporters in pathogenic yeasts: in the crossroad between drug resistance and pathogenesis”) and Isabel Sá-Correia (Co-chairing the Yeast strategies to resist relevant stresses in bioindustries and fungal biology and chemistry Session and Invited Talk entitled “Mechanisms underlying adaptation and tolerance to short-chain fatty acids in yeasts”) were also invited to participate. Altogether, all have enjoyed the conference and the chance to re/connect with colleagues and friends from the European microbiology community.

Organized at Instituto Superior Técnico by Isabel Sá-Correia and Jorge Leitão, a joint workshop of two FCT-funded doctoral programs in which  DBE and iBB participate or direct, AEM-Applied and Environmental Microbiology and BIOTECnico- Biotechnology and Biosciences, took place at the Zoom platform on February 15 (dedicated to AEM) and 16 (dedicated to BIOTECnico). The external supervisory committee (ESC) of the two programs were present and participated very actively. They are highly renowned academics in the areas of the PhD programs: Tom Coyne from Gent University, William de Vos from Wageningen University, Jack Pronk from Delft University, Prof Steve Oliver, University of  Cambridge, Michael Hoare, University College London. 

PhD students and alumni of both programs were present and program that we set up via Zoom allowed us to demonstrate the work carried out in terms of advanced training in the framework of BIOTECnico and AEM programs. The ESCs were very impressed about the way how “the two fabulous programs were designed and managed and built a culture that encourages PhD candidates to take initiative, grow and prosper.” Congratulations to the directive boards of both programs, the students, the alumni, and their supervisors and collaborators.

The Academic Jubilee of Isabel Sá-Correia, Distinguished Professor at the Departamento de Bioengenharia (DBE) and researcher at the iBB - Institute for Bioengineering and Biosciences will take place on the 7th February, at 5 p.m., in Instituto Superior Técnico congress centre.

Programme:
5 p.m. – Opening session – João Pedro Conde – Head of DBE
5.05 p.m. – Rogério Colaço – President of Técnico
5.10 p.m. – Jorge Pedrosa – Presidente da Sociedade Portuguesa de Microbiologia
5.15 p.m. – Joaquim Cabral – DBE
5.20 p.m. – Arsénio Fialho – DBE
5.25 p.m. – Jorge Leitão – DBE
5.30 p.m. – Isabel Sá-Correia – 30 min “As Ciências Biológicas numa Escola de Engenharia” (“Biological Sciences in a School of Engineering”)
6 p.m. – Luís Ferreira – Rector of Universidade de Lisboa
6.05 p.m. – Closing session and "Porto de Honra"

The video of a recent conference on the “Funding of Science”, included in the Cycle of Conferences – Challenges of Science in Contemporary Society, was published on the YouTube of Academia de Ciências de Lisboa. The session was chaired by Professor Isabel Sá-Correia from iBB - Institute for Bioengineering and Biosciences . This theme touches deeply the scientific community. Undoubtedly, the scientific and technological development of a country, an institution, a research group requires, in addition to adequate and coherent policies, very costly investments, very significant and continuous funding. But, even if the funding of science is obviously critical, this is not limited to the funds that are made available, to the % of the Gross domestic product (GDP) that governments and private institutions dedicate to research and there is a lot of material for reflection.
The cycle of conferences dedicated to Science challenges in contemporary society is promoted by the Instituto de Alto Estudos of ACL. 

Six researchers from @IBB have been ranked among the World’s Top 2% of most widely cited scientists in the 2022 List of outstanding researchers prepared by Elsevier BV, and Stanford University (USA).   

Carla Carvalho, Joaquim Cabral, Isabel Sá Correia,  Mário Berberan e Santos, Miguel Prazeres and Pedro Fonte were recognized for the impact throughout their careers, while Pedro Fernandes was recognized as one of the World’s Top 2%  influent scientist in his field.

The updated list is based on the Sep 01-2022 SCOPUS database, updated to the end of the citation year 2021 and analyses 22 scientific areas and 176 disciplines.

Overall, 93 researchers from Técnico were highlighted in the study.  Congratulations to all!

iBB held its Annual Workshop with the participation of 150 researchers and students. On past Friday, September 23, our community contributed with a rich and diversified program. Invited speakers, selected oral presentations by young researchers, and keynote lecturers from senior members and founders of Biological Sciences, Prof. Isabel Sá Correia, and of Biophysics, Prof. Manuel Prieto, at IST, made this event.

Bacterial pathogens belonging to the Vibrio genus such as Vibrio parahaemolyticus, Vibrio alginolyticus and Vibrio vulnificus are some of the most common and widespread disease-causing agents in the aquaculture industry, inducing severe losses in fish and shellfish production worldwide. In a Review Article published in Frontiers in Microbiology, iBB researchers Gracinda Sanches Fernandes, Isabel-Sá Correia and Rodrigo Costa performed a meta-analysis of vibriosis outbreaks reported for the economically valuable, model aquaculture fish gilthead seabream (Sparus aurata) in the Mediterranean zone. The study reveals the acquisition of multiple antibiotic resistance traits among pathogenic Vibrio species during the past 25 years. An increase in human infections caused by Vibrio pathogens of fish – either via seafood ingestion or wound colonization - has been documented in the recent literature, and it is believed to result from the synergistic interaction between the expansion of intensive fish farming across coastal ecosystems and global warming. Finally, the authors critically examine the potential, and review cases of success, of alternative methods to antibiotics use to suppress vibrio pathogens in aquaculture, including vaccines, phage therapy and probiotics supplementation. Diverse bacterial symbionts of fish suppress vibrio pathogens in experimental trials, suggesting that the natural fish microbiome may be a reservoir of biological control agents of interest in applied biotechnology.

Cláudia P. Godinho, a PhD researcher at BSRG-iBB, presented the work "The N.C.Yeastract and CommunityYeastract databases and tools: studying transcriptional regulation in non-conventional yeasts" during the Synthetic & Systems biology Symposium. Cláudia provided a guided exploration of the tools of the N.C.Yeastract database, which gathers all published regulatory associations and TF-binding sites for five yeast species of biotechnological potential. The potential of the database was also explained. The presentation was based in a recent MiniReview published this year in FEMS Yeast Research, resulting from collaborative work between the BSRG-iBB team coordinated by Isabel Sá-Correia and INESC-ID colleagues. Cláudia P. Godinho was also selected for presenting the International Microorganism Day initiative in the Teaching and Communicating in Science symposium. The purpose of the presentation, co-authored by Cláudia and Isabel Sá-Correia, was to report the results from IMD 2021 campaign and event, to promote IMD, and to provide an idea of the power of social media in Microbiology dissemination.