Enzymes are acknowledged as effective catalysts, namely, on account of their selectivity, high turnover, and ability to operate under mild conditions. Despite these advantageous features, the industrial application of enzymes still lags behind their use on a laboratory scale. This pattern may be partly assigned to the intrinsic nature of enzymes: these biocatalysts have been optimized throughout the ages to be mostly active in aqueous media and to operate in environments where substrate and product concentrations are much lower than those required for industrial processes to be commercially feasible. In this Special Issue on “Biocatalysis, Enzyme, and Process Engineering”, guest edited by Pedro Fernandes and Carla de Carvalho (iBB-BERG) in Processes, several papers discuss the latest applications of enzymes.

Little is known about the structure and diversity of chitin-degrading microbial communities across marine niches. Researchers from BSRG-iBB, including PhD student Rúben Silva and former students Inês Raimundo (now a PhD student at KAUST) and Laurence Meunier (now a PhD student at University of Brussels), and led by Rodrigo Costa and Tina Keller-Costa have shed light on chitin processing within the microbiomes of marine sponges, octocorals, sediments, and seawater. The study, published in Microbiome, integrates cultivation-dependent and -independent approaches to unveil chitin degradation pathways across diverse marine bacteria. Functional metagenomics revealed that the marine sponge microbiome is rich in polysaccharide deacetylases, suggesting the ability of this consortium to convert chitin into its more biotechnologically versatile form - chitosan. The findings further suggest that chitin is processed via multiple mechanisms across marine micro-niches, favoring the hypothesis that inter-species microbial cross-feeding facilitates the co-existence of chitin users within the microbiomes of filter-feeding marine invertebrates. The study also reports on new chitinolytic enzymes from the genus Aquimarina that may find use in the blue biotechnology sector.

Cellular components that contribute to both pathogenesis and drug resistance are among the most promising drug targets in human pathogens. In this study, the uncharacterized drug:H+ antiporter CgTpo4 was shown to play a role in Candida glabrata virulence in the infection model G. mellonella. The underlying mechanism was demonstrated to include a role in AntiMicrobial Peptide (AMP) resistance, compatible with the observed immune response deployed by G. mellonella upon C. glabrata infection. These results, emerging from a collaboration between BSRG members, led by Miguel Cacho Teixeira and including Arsénio Fialho and Dalila Mil-Homens, were just published in International Journal of Molecular Sciences and are expected to contribute to design more suitable antifungal therapeutic strategies.

While Lactococcus lactis is traditionally associated with the fermented food industry, applications of these bacteria have been spreading to the pharmaceutical industry. The goal is to use L. lactis as cell factories for the production of added-value recombinant proteins and plasmid DNA (pDNA) for DNA vaccination, as a safer and industrially profitable alternative to the traditional Escherichia coli host. In a recent review in International Molecular Sciences, Sofia Duarte and Gabriel Monteiro from BERG-iBB critically systematize the plasmid replicons available for the production of pharmaceutical-grade pDNA and recombinant proteins by L. lactis. The work is funded by the LactoSynt project.

Six iBB researchers are among the most cited top scientists at the top 2% of their areas. Portugal is represented in this list compiled by Stanford University with 385 scientists affiliated to national institutions. The rankings are based upon a researcher’s citations for both a single year (2019) and cumulative across their careers. Titled “Updated science-wide author databases of standardized citation indicators,” the list uses algorithms that quantify and systematically rank individuals into consistent scientific fields. The scores are provided  with and without self-citations to lessen the impact of self-citations or the use of citation farms (small clusters of researchers massively citing each other’s work). Ranked within the careerlong citation impact list are these iBB researchers: Joaquim Cabral, Isabel Sá-Correia, Mário Berberan Santos, Miguel Prazeres, Carla Carvalho, also along with Carina Crucho in the
2017 single-year citations list.

Aquaculture is the fastest-growing sector in food production worldwide. BSRG-iBB researchers Nuno Borges, Tina Keller-Costa, PhD candidate Gracinda Sanches-Fernandes and Prof. Rodrigo Costa, together with colleagues from the University of Aveiro, have recently published a review in Annual Review of Animal Biosciences examining molecular studies of bacterial diversity, function, and host immunity modulation at early stages of fish development, where microbial infections cause important economic losses. The authors uncover host colonization and virulence factors from a synthetic assemblage of fish pathogens using comparative genomics and address the use of probiotics and paraprobiotics as disease-prevention strategies in fish larval and juvenile rearing. They also propose guidelines for future microbiome research of presumed relevance to fish larviculture.

João Carlos Silva and Frederico Castelo Ferreira from SCERG-iBB are guest-editing a special issue for the open-access journal “Polymers” entitled “Advanced Polymeric Scaffolds for Stem Cell Engineering and Regenerative Medicine”. Polymer scaffolds play a crucial role in tissue engineering and regenerative medicine applications since they can closely mimic the architecture of a native extracellular matrix (ECM) and improve the biological performance of cells both in vitro and in vivo. This Special Issue welcomes full research papers, communications and reviews on recent exciting developments of polymeric scaffolds for tissue engineering and regenerative medicine applications.

Saccharomyces boulardii has been widely used, for more than 50 years, as a human probiotic. Nonetheless, the molecular basis underlying its mode of action is scarcely understood. In this study, global gene expression analysis, resorting to Illumina- based RNA-sequencing, was conducted to analyze differential gene expression patterns in S. cerevisiae and S. cerevisiae var. boulardii in GI- tract like medium. Additionally, based on the construction of an S. cerevisiae var. boulardii database, a global comparison between gene promoter sequences in S. cerevisiae and S. cerevisiae var. boulardii strains was conducted. The obtained results shed light into the molecular basis of the differential probiotic phenotypes displayed by these two closely related yeasts. The knowledge gathered through this study, by a team led by Miguel Cacho Teixeira, BSRG-iBB, and Pedro T Monteiro, INESC-ID, and just published in Genomics, is expected to contribute to guide the design of more rationale, probiotic-based, therapeutic approaches.

The BIOTECnico PhD program will initiate a cycle of alumni seminars on the 19th of January 2021. Until the 30th of March, every 2 weeks, on Tuesdays at 4 pm, BIOTECnico alumni will deliver a 20 min presentation describing the main achievements of the PhD projects they developed at iBB, as well as their current professional activities and institution. The seminars will be delivered via zoom and the full list can be found here.

Vasco Bonifácio was invited to participate in the program “Explain me as if were 5 years old”, an IST initiative that consists of informal conversations about science for curious children and adults. In this program, which was broadcast live on Facebook on the afternoon of November 28, 2020, Vasco presented the session “Why do fireflies shine?”. In this session, chaired by Joana Lobo Antunes (Communication and Public Relations Office of IST), Vasco Bonifácio explained the phenomena of bioluminescence, chemiluminescence and phosphorescence and how these physical-chemical processes are related to research in the area of cancer treatment that he has been developing in recent years. There was also time to carry out live experiments, which delighted the young audience and to answer many questions! The program was recorded and is available on the program's website (Episode 12).

The attachment of bacteria and other microbes to natural and artificial surfaces leads to the development of biofilms, which can further cause nosocomial infections. Thus, an important field of research is the development of new materials capable of preventing the initial adhesion of pathogenic microorganisms. In this work, novel polymer/particle composite materials were developed and characterized with respect to their mechanical, chemical and surface properties. Both S. aureus and C. glabrata exhibit a reduced capacity to adhere to the newly developed nanomaterials used in this study, thus showing their potential for bio-medical applications. This study, led by researchers from LAAS-CNRS, Toulouse, and co-authored by Mafalda Cavalheiro and Miguel Cacho Teixeira from BSRG-iBB, was just published in Nanomaterials.

Microbiome research has grown considerably in the past few years, producing large amounts of data to address current and future societal challenges. ELIXIR, the European Infrastructure for Biological Data, and BioData.pt, the Portuguese node of Elixir, are assembling a national microbiome community to address these challenges and promote data findability, accessibility, interoperability, and reuse, as well as knowledge exchange, among Portuguese and European researchers. In this context, the 1st Microbiome Summit took place last February 4th 2021, and counted on contributions from several BSRG-iBB members, including doctorate researchers Nuno Borges and Tina Keller-Costa, PhD students Sandra Godinho Silva, Rúben Silva and Gracinda Sanches-Fernandes who all prepared short videos about their latest research, and Prof. Rodrigo Costa, who gave an invited talk entitled “The microbiome of marine sponges: diversity, function and biotechnology”.

Recent years have witnessed a growing interest in the use of biocatalysts in flow reactors. This merging combines the high selectivity and mild operation conditions typical of biocatalysis with enhanced mass transfer and resource efficiency associated to flow chemistry. Additionally, it provides a sound environment to emulate Nature by mimicking metabolic pathways in living cells and to produce goods through the systematic organization of enzymes towards efficient cascade reactions. Moreover, by enabling the combination of enzymes from different hosts, this approach paves the way for novel pathways. In a recent paper published in the journal Processes, Pedro Fernandes and Carla de Carvalho (iBB-BERG) review the recent developments within the scope of flow chemistry involving multi-enzymatic cascade reactions. The paper was published in the Special Issue  "Biocatalysis, Enzyme and Process Engineering" edited by both authors.

It is now known that a significant fraction of the total microbial diversity in nature exists at low abundance, which has given rise to an increasing number of studies on the so-called rare biosphere. With the fast-paced improvement of novel molecular technologies, surveys on the dynamics of the rare biosphere across the three domains of life (Bacteria, Archaea, Eukarya) and several environments are now possible. Importantly, this research field is transitioning from a taxonomy-driven to a functionally driven analysis, whereby the roles of rare microorganisms in boosting ecosystem functioning are addressed. In this context, a team formed by Prof. Rodrigo Costa (iBB-BSRG), Prof. Catarina Magalhães (CIIMAR-ECOBIOTEC), and PhD candidate Francisco Pascoal (Porto University), delineate the state of the art in our current knowledge of the microbial Rare Biosphere, highlighting the role of viruses in the regulation of low abundance microbial populations. The review article, published in FEMS Microbiology Ecology, also examines current concepts and methods employed in the study of the rare biosphere, integrating emerging knowledge of low abundance microorganisms into a larger ecological theory framework.

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.

Rogério Gaspar from BERG-iBB has been apointed Director of Regulation and Prequalification of the World Health Organization (WHO). The RPQ Department is part of the Access to Medicines and Health Products Division of WHO, which works with Member States and partners to improve the access to safe, quality assured, efficacious and affordable medicines and health products and to promote that these are used rationally. Rogério will inititate his new duties in Geneva in the early 2021. Read more here.