iBB

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.

Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract was associated to YEASTRACT+, a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. A recent Minireview published in FEMS Yeast Research aims to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on non-Saccharomyces species, exploring all the information and bioinformatics tools available in YEASTRACT +. Using simple and widely used examples, a guided exploitation is offered. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed. The Minireview is coauthored by a BSRG-iBB team coordinated by Isabel Sá-Correia and including Cláudia P. Godinho, Margarida Palma, Miguel C. Teixeira and the PhD students Miguel Antunes and Marta N. Mota, in collaboration with INESC-ID colleagues.

The role of the cell wall in yeast response and tolerance to stress is frequently neglected. A BSRG-iBB research paper just published in Scientific Reports, provides, for the first time, a comprehensive view of the alterations occurring at the cell wall in a yeast population adapting to sub-lethal stress induced by acetic acid. The results reveal changes to the cell wall polysaccharide composition and nanomechanical properties, as well as alterations in the transcript levels of key cell wall biosynthetic genes. This paper reinforces the notion that the adaptive yeast response to acetic acid involves coordinated alterations of the cell wall at the biophysical and molecular levels. The gathered knowledge is important for the design of superior industrial strains and for the efficient control of the deleterious activity of spoilage yeasts, particularly in the Food Industry. This research work is first-authored by the PhD student of the PhD programme in Biotechnology and Biosciences Ricardo Ribeiro (FCT_DP AEM fellowship), performed under the supervision of Isabel Sá-Correia. This collaborative study with Fábio Fernandes (BSIRG-iBB) and Mário S. Rodrigues and his team (BioISI, Faculty of Sciences, ULisboa), is also coauthored by Cláudia Godinho (posdoc researcher) and the PhD student Nuno Bourbon-Melo (FCT_DP BIOTECnico) from the BSRG-iBB team.

Methanol is a promising feedstock for metabolically competent yeast strains-based biorefineries. However, methanol toxicity can limit the productivity of these bioprocesses. For this reason, the identification of genes whose expression is required for maximum methanol tolerance is important for mechanistic insights and rational genomic manipulation to obtain more robust methylotrophic yeast strains. The chemogenomic analysis performed in this new BSRG-iBB study provided new valuable information on genes and potential regulatory networks involved in overcoming methanol toxicity in the model yeast Saccharomyces cerevisiae. The article was just published in the Journal of Fungi and belongs to the Special Issue “Yeast Biorefineries” (edited by Isabel Sá-Correia and Naseem A. Gaur). The article has as co-authors the PhD students of the IST Biotechnology and Biosciences PhD Programme ( FCT_DP Applied and Environmental Microbiology) Marta N. Mota (first  author) and Luís C. Martins, under Prof. Isabel Sá-Correia’s supervision. The gathered knowledge is an important starting point for the improvement of methanol tolerance in yeasts capable of catabolizing and copying with methanol concentrations present in promising bioeconomy feedstocks, including industrial residues.

During chronic respiratory infections of cystic fibrosis (CF) patients, bacteria adaptively evolve in response to the nutritional and immune environment. A research paper from iBB-BSRG researchers, just published in Frontiers in Microbiology (part of the Research Topic: Evolutionary Mechanisms of Infectious Diseases), contributes to the understanding of shared and species specific evolutionary patterns of B. cenocepacia and B. multivorans evolving in the same CF lung environment. Results support the idea that positive selection might be driven by the action of the host immune system, antibiotic therapy and low oxygen and iron concentrations. This research work, coordinated by Prof. Isabel Sá-Correia, results from the PhD thesis in Biotechnology and Biosciences (BIOTECnico program) of A. Amir Hassan. Dr. AA Hassan is currently working at the Laboratory of Microbiology, Department of Biochemistry and Microbiology, Ghent University, Belgium.

The Burkholderia cepacia complex (Bcc) bacteria are feared contaminants in pharmaceutical industries and cause nosocomial outbreaks, posing health threats to immunocompromised individuals and cystic fibrosis (CF) patients. In this study, the adaptation and survival of B. cepacia and B. contaminans isolates was investigated after long-term incubation in nutrient depleted saline solutions supplemented with increasing concentrations of the biocidal preservative benzalkonium chloride (BZK), recreating the storage conditions of pharmaceutical products. This study just published in the section Biosafety and Biosecurity of Frontiers in Bioengineering and Biotechnology is co-authored by several members of Isabel Sá-Correia team from iBB/BSRG. This study reveals mechanisms underlying the prevalence of Bcc bacteria as contaminants of aqueous pharmaceutical products containing BZK, which often lead to false-negative results during quality control and routine testing.

Pharmaceutical products contaminated with bacteria of the Burkholderia cepacia complex (Bcc) constitute a serious risk for patient ssffering from cystic fibrosis and Chronic granulomatous disease. Bcc infection also has been reported in immunocompromised individuals (e.g., cancer patients submitted to chemotherapy, HIV/AIDS patients, mechanically ventilated patients, and infants/the elderly). Over recent years, both sterile and nonsterile pharmaceutical products have been recalled from the market due to Bcc contamination and subsequent nosocomial outbreaks. In a review paper just published in Clinical Microbiology Reviews, the role of Bcc bacteria as a potential public health problem, the mechanisms behind their success as contaminants of pharmaceutical products, particularly in the presence of biocides, the difficulties encountered in their detection, and the preventive measures applied during manufacturing processes to control contamination with these objectionable microorganisms  are addressed. A summary of Bcc-related outbreaks in different clinical settings, due to contamination of diverse types of pharmaceutical products, is provided. The corresponding author Is Isabel Sá-Correia from iBB/BSRG and the first author is a recent graduate of the MSc in Biotechnology.

The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope computational tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in 10 yeast species of biotechnological or human health relevance. A large team led by Isabel Sá-Correia, Miguel Teixeira, from iBB, and Pedro Monteiro, from INESC-ID, has just released this new web-portal in the 2020 Nucleic Acids Research Database Issue and is compromised to continue its efforts to expand this resource, which is currently supported within the context of the Biodata.pt/Elixir.pt Research Infrastructure.

The non-conventional food spoiling yeast species Zygosaccharomyces bailii is remarkably tolerant to acetic acid, a highly important microbial inhibitory compound in Food Industry and Biotechnology. The study recently published in Scientific Reports, coordinated by Isabel Sá-Correia and Margarida Palma and first authored by the BIOTECnico PhD student Miguel Antunes, investigates the genomic transcription changes occurring during the early response of Z. bailii to acetic acid or copper stresses and uncovers the regulatory network activated under the bifunctional transcriptional factor ZbHaa1 control. This study provides valuable insights regarding Z. bailii adaptation mechanisms to acetic acid or copper stresses, ZbHaa1-dependent regulatory network, and the evolution of transcription factors and regulatory networks in pre- whole genome duplication (WGD) and post-WGD yeast species.

The ability of Saccharomyces cerevisiae to overcome the stress induced by cytotoxic compounds depends on the activity of plasma membrane transporters of the ABC superfamily, presumably through the questionable unspecific efflux of multiple drugs and xenobiotic compounds. A recent paper by iBB researchers provides new insights into the biological role of the ABC transporter of the pleiotropic drug resistance family of putative drug efflux pumps Pdr18, proposed to mediate ergosterol incorporation in plasma membrane. Pdr18 expression was found to help cells to counteract acetic acid-induced decrease of plasma membrane lipid order, increase the non-specific membrane permeability and decrease the transmembrane electrochemical potential. Results support the notion that Pdr18-mediated multistress resistance is linked to the status of plasma membrane lipid environment related with ergosterol content and the associated plasma membrane properties. The paper, published in Scientific Reports, results from the PhD project of Cláudia Godinho, advised by Prof. Isabel Sá-Correia from BSRG-iBB in collaboration with Fábio Fernandes and Sandra Pinto from BSIRG-iBB).

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.

Agro-industrial residues rich in pectin are generated in high amounts worldwide from the sugar industry or the industrial processing of fruits and vegetables. A recent paper by BSRG-iBB researchers, published in the Journal of Fungi (special issue “Yeast Biorefineries” (edited by Isabel Sá-Correia and Naseem Gaur), describes the optimization of the performance of Rhodotorula strains envisaging the use of the major carbon sources present in Sugar Beet Pulp (SBP) hydrolysates. SBP valorization through the production of lipids and carotenoids by the oleaginous red yeasts examined, supported by complete catabolism of the major carbon sources present, looks promising for industrial implementation. The work was conducted by the PhD student of the IST PhD Programme in Biotechnology and Biosciences Luís C. Martins (FCT_DP AEM programme fellowship) under the supervision of Isabel Sá-Correia. This work was developed in the context of the ERA-NET-Industrial Biotechnology-2 project, “YEASTPEC-Engineering of the yeast Saccharomyces cerevisiae for bioconversion of pectin-containing agro-industrial side-streams”.

There is a wide diversity of non-conventional yeast species, which often present distinctive metabolic properties and can therefore impart different flavours and aromas to beer. Because of this, brewers now regard non-conventional yeast species as a tool to differentiate their beers from other products in the market. In fact, some of these yeasts are already used to produce specific beer styles, such as lambics. A study recently published in Food Microbiology, coordinated by Dr. Margarida Palma and Prof. Isabel Sá-Correia and first authored by the BIOTECnico PhD student Nuno Melo, investigates how two non-conventional yeast species commonly found in wineries, Hanseniaspora guilliermondii and Hanseniaspora opuntiae, influence the volatile composition of beer. These two species, initially selected by a preliminary organoleptic evaluation, were found to modulate the aroma profile of beer, namely by increasing phenylethyl acetate concentration (‘rose’, ‘honey’ aroma). These findings highlight the importance of non-conventional yeasts in shaping the aroma profile of beer and suggest a role for Hanseniaspora spp. in improving it.

A new paper by researchers from iBB-BSRG describes, for the first time, the involvement of a plasma membrane multidrug/multixenobiotic resistance (MDR/MXR) ABC transporter in yeast thermotolerance. The expression of the ABC transporter Pdr18, required for pleotropic drug resistance and involved in ergosterol transport at the plasma membrane level, is related with decreased plasma membrane permeabilization induced by a supraoptimal growth temperature. Ergosterol biosynthesis and plasma membrane ergosterol content were implicated in yeast response and capacity to overcome stress induced by supraoptimal growth temperatures. These results support the notion that MDR/MXR transporters perform biological activities other than their accepted role as drug/xenobiotic exporters. Cláudia Godinho is the first author of this research work, coordinated by Isabel Sá-Correia and published in the journal Environmental Microbiology.

Pectin-rich agro-industrial residues generated worldwide from the industrial processing of fruits and vegetables,are feedstocks with potential for sustainable biorefineries. Although the most important yeast cell factory platform is Saccharomyces cerevisiae, this species cannot naturally catabolise the main sugars present in pectin-rich agro-industrial hydrolysates, in particular D-galacturonic acid and L-arabinose. However, there are non-conventional yeasts considered advantageous alternatives whenever they can express highly interesting metabolic pathways, natively assimilate a wider range of carbon sources or exhibit higher tolerance to relevant bioprocess-related stresses. For this reason, the interest in nonconventional yeasts is gaining momentum. A review published in Applied Microbiology and Biotechnology discusses major challenges and progress on the isolation, selection, sugar catabolism, metabolic engineering and use of nonconventional yeasts and S. cerevisiae-derived strains for the bioconversion of pectin-rich residue hydrolysates  Examples of value-added products synthesised by different yeasts using pectin-rich residues are also reviewed. The first author of this paper is the PhD student of the FCT Doctoral Program in Applied and Environmental Microbiology Luís C. Martins advised by Prof. Isabel Sá-Correia from iBB-BSRG.

Bacterial cell envelope plays a central role in cell physiology and the alteration of surface properties can implicate the variation of phenotypes that play a crucial role in the pathogenesis of infectious diseases, such as the resistance to antibiotics and other environmental stresses, biofilm formation, persistence of infection. However, the influence that Burkholderia cenocepacia adaptive evolution during long-term respiratory infection in cystic fibrosis (CF) patients has on cell wall morphology and mechanical properties is poorly understood. This study, just published in the journal Scientific Reports, has examined cell wall morphology and mechanical properties of three sequential B. cenocepacia clonal variants by Atomic Force Microscopy (AFM). Results reinforce the concept of the occurrence of phenotypic variation and adaptive evolution during chronic infection, also at the level of cell size, form, envelope topography and physical properties. This research work, coordinated by Prof. Isabel Sá-Correia from iBB-BSRG and IST, was the result of a national collaboration with the team of Dr. Mário S. Rodrigues from BioISI, Faculty of Sciences, Universidade de Lisboa, having the IST PhD student of the BIOTECnico program Amir Hassan, from iBB-BSRG, as first author of the publication.

Burkholderia cepacia complex (Bcc) bacteria can adapt to the hostile lung environment of cystic fibrosis (CF) patients leading to chronic infection. While it is unclear why different Bcc species/strains differ in their pathogenic potential, lipopolysaccharides (LPS) are considered a major virulence factor. The O-antigen (OAg) component of LPS is believed to modulate host-pathogen interaction and to be under selective pressure. A study recently published in Frontiers in Cellular and Infection Microbiology was performed to understand whether OAg loss can be considered a general phenomenon that affects immune evasion favoring chronic infection. A systematic retrospective and longitudinal screening was performed based on a collection of 357 isolates involving 21 different Bcc strains of six/seven Bcc species/lineages isolated from CF patients. These isolates were recovered from 1995 to 2016 from 19 CF patients under surveillance at Hospital de Santa Maria over the duration of chronic infection (ranging from 1.2 to 15.2 years). B. cenocepacia and B. multivorans showed a tendency to lose the OAg along chronic infection, with the switch frequency increasing with the duration of infection and level of lung function deterioration. For the first time, this study shows that the rarely found species B. cepacia and B. contaminans keep the OAg even during infections that last for 10 and 15 years. This research, coordinated by Prof. Isabel Sá-Correia and with the BIOTECnico PhD student Amir Hassan as first author, reinforces the relevance attributed to OAg-expression switch suggesting marked differences in the various Bcc species.

Several membrane transporters from the ATP-binding cassette (ABC) superfamily present in yeast genomes are implicated in multidrug/multixenobiotic resistance (MDR/MXR). This is the case of Pdr18, that confers tolerance to ethanol and acetic acid and several other toxicants in yeast and has a biological role attributed in ergosterol transport at the plasma membrane. A recently iBB-BSRG paper published in Frontiers in Genetics, Evolutionary and Genomic Microbiology section, reconstructs the evolutionary history of the encoding gene PDR18 and the paralogue gene SNQ2. This publication results from the PhD thesis in Biotechnology and Biosciences of Cláudia P. Godinho advised by Prof. Isabel Sá-Correia with collaboration of Paulo J. Dias and Elise Ponçot. By combining phylogenetic gene neighborhood analysis for 117 yeast genomes belonging to 29 species across the Saccharomycetaceae family, the gene duplication event was traced to the last common ancestor of the Saccharomyces genus yeasts. The fact that Snq2 and Pdr18 confer resistance to different sets of chemical compounds with little overlapping is consistent with the subfunctionalization and neofunctionalization of these gene copies. Remarkably, PDR18 is only found in Saccharomyces genus genomes.