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Institute for Bioengineering and Biosciences
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ChiCoBionts: Chitinases from the Octocoral Microbiome

ChiCoBionts: Chitinases from the Octocoral Microbiome | iBB | Scoop.it

ChiCoBionts, a new FCT-funded research project, exploits the octocoral microbiome in the search for novel chitinases of relevance to global biogeochemical cycling, food waste management, and the smart production of added-value molecules. The project starts in January 2022, is funded with 50,000 euros, and aims to discover, express, and characterise novel chitinases and chitinolytic microbes with the potential to outperform current commercial enzymes and to foster the development of blue biotechnology for chitin waste. The ChiCoBionts team joins iBB scientists from BSRG and BERG, including Tina Keller-Costa (PI), Ângela Taipa (Co-PI), Carla de Carvalho and Rodrigo Costa, in addition to ITQB researcher Nuno Borges and collaborators from the University of Brussels, Belgium.

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Matilde Marques Wins Poster Prize at MICROBIOTEC21

Matilde Marques Wins Poster Prize at MICROBIOTEC21 | iBB | Scoop.it

PhD student Matilde Marques from DBE and iBB-BSRG received a Best Poster Prize for her video-poster presented at the Microbiotec21 web-conference. Matilde showed her work on metagenomics of viral communities in healthy and diseased octocorals. Matilde is a first year PhD student of the MIT Portugal program supervised by Rodrigo Costa and Tina Keller-Costa from IST and Raquel Peixoto from KAUST. Her thesis project focuses on developing microbiome therapy strategies to improve octocoral health. Congrats, Matilde!

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Insights into the Cultured Bacterial Fraction of Corals

Insights into the Cultured Bacterial Fraction of Corals | iBB | Scoop.it

Bacteria associated with coral hosts are diverse and abundant, with recent studies suggesting involvement of these symbionts in host resilience to anthropogenic stress. Combining published and unpublished data, a new article featuring iBB researchers Tina Keller-Costa and Rodrigo Costa among the authors provides a comprehensive overview of the diversity and function of culturable bacteria isolated from tropical, temperate, and cold-water corals. The study, published in the journal mSystems, compiles a total of 3,055 coral-associated isolates described in 52 reports from various laboratories around the world. The work presents a comparative genomic analysis of 74 strains and identifies signatures of potentially beneficial bacterium-coral symbioses among them. Such a resource is an important step in the selection of probiotic candidates, which are being investigated for promoting coral resilience and can potentially be applied in novel reef restoration and rehabilitation efforts. This genome and culture collection is available to the wider research community through the web site http://isolates.reefgenomics.org/ with the hope that many scientists across the globe will ask for access to these resources for future studies.

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Chitin Degradation and Use Across Marine Microbiomes

Chitin Degradation and Use Across Marine Microbiomes | iBB | Scoop.it

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.

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Probiotics in Fish Aquaculture

Probiotics in Fish Aquaculture | iBB | Scoop.it

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.

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Diverse Natural Product Biosynthesis Capacities in the Marine Bacterial Genus Aquimarina

Diverse Natural Product Biosynthesis Capacities in the Marine Bacterial Genus Aquimarina | iBB | Scoop.it

Aquimarina is a recently described bacterial genus of increasing research interest due to its high metabolic versatility and emerging role in the cycling of organic matter in marine ecosystems. Using comprehensive functional and comparative genomics, Sandra Godinho Silva, Tina Keller-Costa and Rodrigo Costa from BSRG-iBB revealed a previously underestimated number of gene clusters involved in the biosynthesis of natural products across several Aquimarina species, suggesting they are a promising target for the discovery of new bioactive compounds. The study, published in Environmental Microbiology, results from an extensive analysis of all the 26 Aquimarina genomes available to-date and uncovers 928 secondary metabolite biosynthetic gene clusters (BGCs) present in these genomes. Polyketide synthases, terpene synthases and non‐ribosomal peptide synthetases ranked as the most frequent BGCs encoding drug‐like candidates.

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Genomic Blueprints of Marine Sponge-prokaryote Symbiosis Revealed in Alphaproteobacteria

Genomic Blueprints of Marine Sponge-prokaryote Symbiosis Revealed in Alphaproteobacteria | iBB | Scoop.it

The role and relevance of low-abundance microbial populations – the so-called “rare biosphere” - in the environment is a matter of current debate in microbial ecology, with implications to our understanding of the functioning of host-microbiome interactions. Using marine sponges and their symbionts as a model system, iBB researchers and colleagues revealed that a complex consortium of low-abundant Alphaproteobacteria symbionts share diverse genomic attributes likely to improve host fitness through several mechanisms. These involve, but are not limited to, host cellular detoxification, provision of essential vitamins, nutritional exchange and chemical defense. The study, led by Rodrigo Costa from BSRG and published in Scientific Reports, suggests a role for the rare biosphere as reservoirs of host-beneficial traits and functional resilience in host-associated microbiomes.

 

Photo details: singleton (i.e., strain-specific) genes, core and pan-genomes across ten low abundance Alphaproteobacteria species cultivated from the marine sponge Spongia officinalis.

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Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth

Bioactive Secondary Metabolites from Octocoral-Associated Microbes—New Chances for Blue Growth | iBB | Scoop.it

Octocorals (Cnidaria, Anthozoa Octocorallia) are magnificent repositories of natural products with fascinating and unusual chemical structures and bioactivities of interest to medicine and biotechnology. Microorganisms associated with octocorals possess a widespread yet uncharted capacity to synthetize a broad range of these natural products. In this review article published in Marine Drugs, Inês Raimundo, Sandra Silva, Rodrigo Costa and Tina Keller-Costa from BSRG-iBB uncover a wide diversity of bioactive natural products, particularly alkaloids, cyclopeptides, terpenoids and polyketides, reported to date for octocoral-derived microbes, with remarkable antibacterial, antifungal, antiviral, antifouling and anticancer activities. Beyond providing an overview of these bioactive compounds, the authors reveal hundreds of putative secondary metabolite biosynthetic gene clusters across 15 genomes of bacteria isolated from octocorals in Portugal, highlighting their potential as sources of novel metabolites suitable for bioprospection studies. They finish by discussing how to harness this biotechnological potential using multidisciplinary laboratory experimentation. This review provides the scientific community with an integrated view of the current status of secondary metabolite biosynthesis by octocoral-associated microbes and the methodological challenges that are to be met in order to achieve a sustainable response to the urgent industrial demand for novel drugs and enzyme varieties from the blue economy sector.

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The Prokaryotic Consortium of the Gorgonian Coral Eunicella labiata

The Prokaryotic Consortium of the Gorgonian Coral Eunicella labiata | iBB | Scoop.it
Microbial communities inhabiting gorgonian corals provide hosts with nutrient provision and chemical defence. BSRG-iBB researchers led by Rodrigo Costa have found that the microbiome of the gorgonian Eunicella labiata is diverse, distinct from seawater, and rich in specific bacterial phylotypes. Furthermore, they have shown that many dominant E. labiata symbionts can be cultivated. Click on tilte to learn more about the research in FEMS Microbiology and Ecology.
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Special Issue: Coral Reef Ecology, Conservation, and Inspiration for Marine Drugs Development

Special Issue: Coral Reef Ecology, Conservation, and Inspiration for Marine Drugs Development | iBB | Scoop.it

Marine invertebrates together with a plethora of symbiotic and free-living algae, fungi and prokaryotes are amidst the most prolific producers of bioactive compounds in coral reefs and marine environments at large. Their natural products often show astounding structural novelty and complexity, facilitating chemically mediated behaviours and interspecies interactions from competition to cooperation. There is great potential for a minimally invasive and economically reliable exploitation of bioactive secondary metabolites from the highly diverse and chemically complex reef communities. iBB researchers Tina Keller-Costa and Rodrigo Costa (BSRG) are guest editing a special issue on Coral Reef Ecology, Conservation and Inspiration for Marine Drugs Development in the Journal Marine Drugs and cordially invite the scientific community to contribute original research or review articles on the role of natural products in coral reef ecology and conservation, organismal interactions and biotechnology.

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iBB Researcher Tina Keller-Costa Delivers Talk at the International Coral Reef Symposium

iBB Researcher Tina Keller-Costa Delivers Talk at the International Coral Reef Symposium | iBB | Scoop.it

In her talk at the 14th International Coral Reef Symposium, taking place online from 19-23 July 2021, Tina Keller-Costa presented her latest comparative metagenomics study on the functional features of the microbiomes of healthy and diseased octocoral tissue.  This conference, granted every 4 years by the International Coral Reef Society (ICRS), brings together 1300 scientists from 80 countries to discuss coral reef science, management, and conservation policies. The symposium is a key event to develop science-based solutions addressing the present and future challenges of coral reefs, which are globally exposed to unprecedented anthropogenic pressures.

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New Metagenomic Insights Into the Octocoral Microbiome

New Metagenomic Insights Into the Octocoral Microbiome | iBB | Scoop.it

Octocorals are marine invertebrates abundant in the Portuguese coast, which host complex microbiomes. Yet the functional relationship between host health and its symbiotic consortium has still to be determined. A new study from an international team led by iBB researchers Tina Keller-Costa and Rodrigo Costa employed comparative metagenomics to uncover the functional and phylogenetic features of the microbiomes of healthy tissue from three octocoral species from the Portuguese coast. The authors also explored how the octocoral microbiome shifts to a pathobiome state in one of the coral species. The study reveals that the octocoral microbiome is distinct from those of the environmental surroundings (that is, seawater and sediments), is host genus (but not species) specific, and undergoes complex structural changes in the transition to the dysbiotic state. Host-symbiont recognition, abiotic-stress response, micronutrient acquisition, and an antiviral defence arsenal comprising multiple restriction endonucleases, CRISPR/Cas systems, and phage lysogenization regulators are signatures of prokaryotic communities in octocorals. The authors argue that these features collectively contribute to the stabilization of host-microbe symbiosis in octocorals and constitute beneficial traits that can guide future studies on coral reef conservation and microbiome therapy. The article was published in the journal Microbiome.

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BSRG-iBB Researchers Participate in the 1st Microbiome PT Summit

BSRG-iBB Researchers Participate in the 1st Microbiome PT Summit | iBB | Scoop.it

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”.

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National Day of the Sea

National Day of the Sea | iBB | Scoop.it

This month we are celebrating the National Day of the Sea (Dia Nacional do Mar). On the 16th of November, BSRG members Nuno Borges, Ruben Silva, Patricia Paula and Tina Keller Costa showcased a bit of their work at the National Museum of Natural History and Science (Museu Nacional de História Natural e da Ciência) in Lisbon. On board they had activities for the youngest generation. The kids did handicrafts of corals, sponges, crabs and sea turtles and painted tiny bacterial symbionts. 

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Grant Awarded to iBB for the Sustainable Production of Bioactive Metabolites from the Sea

Grant Awarded to iBB for the Sustainable Production of Bioactive Metabolites from the Sea | iBB | Scoop.it

A new research project “SymbioReactor - Sustainable production of bioactive metabolites from microbial symbionts of marine sponges and corals” was recently awarded 178k EUR funding by the Fundo Azul programme from the Ministry of the Sea (Blue Biotechnology call 5/2017). SymbioReactor aims to uncover the antibacterial, antifungal and antitumor properties of an existing culture collection at BSRG-iBB comprising a yet uncharted panel of 1,000 bacterial symbionts from marine sponges and corals. The project’s overarching goal resides in the exploration of marine symbiotic communities to develop customized, effective tools that lead to the sustainable production of pharmacologically applicable metabolites from the seas. The project is headed by Rodrigo Costa and Tina Keller-Costa from BSRG-iBB and involves two public research institutions (University of Aveiro and Centro de Neurociências e Biologia Celular), an industrial partner (Biotrend) and an international consultant (Max Planck Institute for Chemical Ecology). It also counts with the support of the Centro Ciência Viva do Algarve and the Straw Patrol initiative for scientific dissemination.

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Twin Seminars on Soft Coral Microbiomes and Valorisation of Cellulosic Wastes

Twin Seminars on Soft Coral Microbiomes and Valorisation of Cellulosic Wastes | iBB | Scoop.it

The 3rd Edition of iBB seminars will start on the 13th May with short talks from Tina Keller Costa - "Bioactive compounds from soft coral microbiomes – new chances for blue growth?" and Teresa Cesário - "Circular economy: from cellulosic wastes to biochemical and biopolymers". Join us next monday (13h00 h, room VA.1, IST-Alameda) to learn more about Tina's and Teresa's research at BSRG and BERG.

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“The Wonders of the Marine Bacterial World” by iBB

“The Wonders of the Marine Bacterial World” by iBB | iBB | Scoop.it

Lisbon is celebrating 20 years of the Expo Event ("Expo98"). On the 22nd of May iBB members Prof. Rodrigo Costa, Dr. Tina Keller Costa, B.Sc. Inês Raimundo, M.Sc. Rúben Silva and undergrad student Carlos Clara will be participating in an exposition showing diverse subjects around ocean sciences (“O Mar de Alto a Baixo”). The team will focus on "the wonders of the marine bacterial world". They will show specimens of marine invertebrates, such as sponges and corals, which deeply interact with marine bacteria. Bioluminescence-, biofilm- and antibiotic-producing bacterial cultures will be exhibited to the wide audience.

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The Gorgonian Coral Microbiome: Diversity, Cultivability and Function

The Gorgonian Coral Microbiome: Diversity, Cultivability and Function | iBB | Scoop.it
Tina Keller, will be giving a talk entitled “The gorgonian coral microbiome: diversity, cultivability and function”, Monday the 19th June, at 12h30m, in room QA1.3, South Tower, IST (Alameda). Tina Keller is currently a Post-Doctoral Fellow at BSRG-iBB. The talk is included in the 2nd Edition of iBB seminars.

Photo details: Iciligorgia schrammi, NOAA, wikipedia, public domain.
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