Institute for Health and Bioeconomy

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Publications

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome

Publication . Keller-Costa, Tina; Kozma, Lydia; Silva, Sandra G.; Toscan, Rodolfo; Gonçalves, Jorge Manuel Santos; Lago-Lestón, Asunción; Kyrpides, Nikos C.; Nunes da Rocha, Ulisses; Costa, Rodrigo

The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater. Results Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity. Conclusion This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large.

2022-09-22Journal article

Open Access

Insights into nanomedicine for head and neck cancer diagnosis and treatment

Publication . Viegas, Cláudia Sofia; Pereira, Daniela S. M.; Fonte, Pedro

Head and neck cancers rank sixth among the most common cancers today, and the survival rate has remained virtually unchanged over the past 25 years, due to late diagnosis and ineffective treatments. They have two main risk factors, tobacco and alcohol, and human papillomavirus infection is a secondary risk factor. These cancers affect areas of the body that are fundamental for the five senses. Therefore, it is necessary to treat them effectively and non-invasively as early as possible, in order to do not compromise vital functions, which is not always possible with conventional treatments (chemotherapy or radiotherapy). In this sense, nanomedicine plays a key role in the treatment and diagnosis of head and neck cancers. Nanomedicine involves using nanocarriers to deliver drugs to sites of action and reducing the necessary doses and possible side effects. The main purpose of this review is to give an overview of the applications of nanocarrier systems to the diagnosis and treatment of head and neck cancer. Herein, several types of delivery strategies, radiation enhancement, inside-out hyperthermia, and theragnostic approaches are addressed.

2022-03-11Journal article

Open Access

A guide to the use of bioassays in exploration of natural resources

Publication . Sabotič, Jerica; Bayram, Engin; Ezra, David; Gaudêncio, Susana P.; Haznedaroğlu, Berat Z.; Janež, Nika; Ktari, Leila; Luganini, Anna; Mandalakis, Manolis; Safarik, Ivo; Simes, Dina; Strode, Evita; Toruńska-Sitarz, Anna; Varamogianni-Mamatsi, Despoina; Varese, Giovanna Cristina; Vasquez, Marlen I.

Bioassays are the main tool to decipher bioactivities from natural resources thus their selection and quality are critical for optimal bioprospecting. They are used both in the early stages of compounds isolation/purification/ identification, and in later stages to evaluate their safety and efficacy. In this review, we provide a comprehensive overview of the most common bioassays used in the discovery and development of new bioactive compounds with a focus on marine bioresources. We present a comprehensive list of practical considerations for selecting appropriate bioassays and discuss in detail the bioassays typically used to explore antimicrobial, antibiofilm, cytotoxic, antiviral, antioxidant, and anti-ageing potential. The concept of quality control and bioassay validation are introduced, followed by safety considerations, which are critical to advancing bioactive compounds to a higher stage of development. We conclude by providing an application-oriented view focused on the development of pharmaceuticals, food supplements, and cosmetics, the industrial pipelines where currently known marine natural products hold most potential. We highlight the importance of gaining reliable bioassay results, as these serve as a starting point for application -based development and further testing, as well as for consideration by regulatory authorities.

2024Journal article

Open Access

Draft genome sequence of vibrio jasicida 20LP, an opportunistic bacterium isolated from fish larvae

Publication . Sanches-Fernandes, Gracinda M. M.; Califano, Gianmaria; Keller-Costa, Tina; Castanho, Sara; Soares, Florbela; Ribeiro, Laura; Pousão-Ferreira, Pedro; Mata, Leonardo; Costa, Rodrigo

We present the genome sequence of Vibrio jasicida 20LP, a bacterial strain retrieved from larvae of gilthead seabream (Sparus aurata), a highly valuable, model fish species in land-based aquaculture. Annotation of the V. jasicida 20LP genome reveals multiple genomic features potentially underpinning opportunistic associations with diverse marine animals.

2021-11Journal article

Open Access

Chitosan nanoparticles: a versatile platform for biomedical applications

Publication . Bashir, Showkeen Muzamil; Ahmed Rather, Gulzar; Patrício, Ana; Haq, Zulfiqar; Sheikh, Amir Amin; Shah, Mohd Zahoor ul Haq; Singh, Hemant; Khan, Azmat Alam; Imtiyaz, Sofi; Ahmad, Sheikh Bilal; Nabi, Showket; Rakhshan, Rabia; Hassan, Saqib; Fonte, Pedro

Chitosan is a biodegradable and biocompatible natural polymer that has been extensively explored in recent decades. The Food and Drug Administration has approved chitosan for wound treatment and nutritional use. Furthermore, chitosan has paved the way for advancements in different biomedical applications including as a nanocarrier and tissue-engineering scaffold. Its antibacterial, antioxidant, and haemostatic properties make it an excellent option for wound dressings. Because of its hydrophilic nature, chitosan is an ideal starting material for biocompatible and biodegradable hydrogels. To suit specific application demands, chitosan can be combined with fillers, such as hydroxyapatite, to modify the mechanical characteristics of pH-sensitive hydrogels. Furthermore, the cationic characteristics of chitosan have made it a popular choice for gene delivery and cancer therapy. Thus, the use of chitosan nanoparticles in developing novel drug delivery systems has received special attention. This review aims to provide an overview of chitosan-based nanoparticles, focusing on their versatile properties and different applications in biomedical sciences and engineering.

2022-09-20Journal article

Open Access