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Publications

Publications by Maria Eduarda Almeida

2025

Culture-Dependent Bioprospecting of Halophilic Microorganisms from Portuguese Salterns

Authors
Almeida, E; Jackiewicz, A; Carvalho, MD; Lage, OM;

Publication
MICROORGANISMS

Abstract
Extreme hypersaline environments harbour a unique biodiversity capable of surviving in such habitats, including halophilic and halotolerant bacteria. Microbial adaptations to these environments comprehend two main strategies: the salt-in that involves a high intracellular concentration of salts (e.g., potassium), and the salt-out that relies on the accumulation of small organic compounds (e.g., glycine betaine and trehalose). These evolutionary haloadaptations, combined with natural population competitiveness, often promotes the production of distinctive antimicrobial compounds, highlighting hypersaline environments as promising rich sources of novel natural products with biotechnological potential. Aiming at enlarging the knowledge on the microbiota of two Portuguese salterns (Aveiro and Olh & atilde;o), microbial isolation was performed using salt and saline sediment samples. A total of 39 microbial isolates were obtained in a saline medium, affiliated with Bacillota, Pseudomonadota, Actinomycetota, and Rhodothermaeota and the archaeal phylum Euryarchaeota. All isolates are generally common in saline habitats, with most (79%) exhibiting a halotolerant profile. Regarding the presence of biosynthetic related genes, 28% of the isolates lacked type I genes for polyketide synthases or non-ribosomal peptide synthetases, 36% contained at least one of these genes, and 36% possessed both. This study provides evidence of the biotechnological potential of the microbiota from two Portuguese salterns.

2018

Current Screening Methodologies in Drug Discovery for Selected Human Diseases

Authors
Lage, OM; Ramos, MC; Calisto, R; Almeida, E; Vasconcelos, V; Vicente, F;

Publication
MARINE DRUGS

Abstract
The increase of many deadly diseases like infections by multidrug-resistant bacteria implies re-inventing the wheel on drug discovery. A better comprehension of the metabolisms and regulation of diseases, the increase in knowledge based on the study of disease-born microorganisms' genomes, the development of more representative disease models and improvement of techniques, technologies, and computation applied to biology are advances that will foster drug discovery in upcoming years. In this paper, several aspects of current methodologies for drug discovery of antibacterial and antifungals, anti-tropical diseases, antibiofilm and antiquorum sensing, anticancer and neuroprotectors are considered. For drug discovery, two different complementary approaches can be applied: classical pharmacology, also known as phenotypic drug discovery, which is the historical basis of drug discovery, and reverse pharmacology, also designated target-based drug discovery. Screening methods based on phenotypic drug discovery have been used to discover new natural products mainly from terrestrial origin. Examples of the discovery of marine natural products are provided. A section on future trends provides a comprehensive overview on recent advances that will foster the pharmaceutical industry.

2019

Selection of carbohydrate-active probiotics from the gut of carnivorous fish fed plant-based diets

Authors
Serra, CR; Almeida, EM; Guerreiro, I; Santos, R; Merrifield, DL; Tavares, F; Oliva Teles, A; Enes, P;

Publication
SCIENTIFIC REPORTS

Abstract
The gastrointestinal microbiota plays a critical role on host health and metabolism. This is particularly important in teleost nutrition, because fish do not possess some of the necessary enzymes to cope with the dietary challenges of aquaculture production. A main difficulty within fish nutrition is its dependence on fish meal, an unsustainable commodity and a source of organic pollutants. The most obvious sustainable alternatives to fish meal are plant feedstuffs, but their nutritive value is limited by the presence of high levels of non-starch polysaccharides (NSP), which are not metabolized by fish. The composition offish-gut microbial communities have been demonstrated to adapt when the host is fed different ingredients. Thus, we hypothesized that a selective pressure of plant-based diets on fish gut microbiota, could be a beneficial strategy for an enrichment of bacteria with a secretome able to mobilize dietary NSP. By targeting bacterial sporulating isolates with diverse carbohydrase activities from the gut of European sea bass, we have obtained isolates with high probiotic potential. By inferring the adaptive fitness to the fish gut and the amenability to industrial processing, we identified the best two candidates to become industrially valuable probiotics. This potential was confirmed in vivo, since one of the select isolates lead to a better growth and feed utilization efficiency in fish fed probiotic-supplemented plant-based diets, thus contributing for sustainable and more cost-effective aquaculture practices.

2019

Effects of dietary tryptophan and chronic stress in gilthead seabream (Sparus aurata) juveniles fed corn distillers dried grains with solubles (DDGS) based diets

Authors
Diogenes, AF; Teixeira, C; Almeida, E; Skrzynska, A; Costas, B; Oliva Teles, A; Peres, H;

Publication
AQUACULTURE

Abstract
Distillers' dried grains with solubles (DDGS) has low tryptophan (Trp) relatively to the branched-chain amino acids (BCAA) levels, and this may reduce transport of Trp through the blood-brain barrier due to competition for the same transport carrier. This may affect synthesis and release of serotonin, with negative consequences in stress tolerance. In the present study, it is hypothesized that a Trp/BCAA unbalance in high DDGS diets may impair the capacity of gilthead seabream (Sparus aurata) juveniles to cope with chronic stress induced by high stocking density. Three DDGS-based diets (30%DDGS+13%FM) were formulated and supplemented with Trp at 0, 0.13, and 0.25% of the diet and tested in triplicate, at two initial stocking densities (5 and 16 kg m(-3)), in a 2 x 3 total randomized factorial design. The growth trial was performed with 12 g fish and lasted 64 days. Irrespective of the diet, high stocking density reduced growth performance and feed intake, but not feed efficiency. Plasma protein, triglycerides, and cholesterol levels; whole-body lipid, hepatosomatic index, and liver glycogen; hepatic activity of key-enzymes of glycolysis and lipogenesis were also reduced. Moreover, plasma glucose level and hepatic activity of key-enzymes gluconeogenesis were increased. Irrespective of stocking density, diets supplementation with Trp did not affect growth and feed efficiency, but increased hepatic lipase activity and reduced liver lipids, plasma triglycerides and cholesterol levels, and hepatic activity of key-enzymes of amino acid catabolism. Moreover, dietary Trp supplementation restored plasma glucose levels of fish kept at high stocking density to levels similar to that of fish kept at low stocking density. Overall, present results indicate that high stocking density reduced growth performance without affecting feed efficiency of gilthead seabream. Dietary Trp supplementation did not counteract the negative effect of stocking density on growth performance but seemed to mitigate stress response of gilthead seabream juveniles kept at high stocking density.

2023

Actinobacteria from Arctic and Atlantic deep-sea sediments-Biodiversity and bioactive potential (vol 14, 1158441, 2023)

Authors
Ribeiro, I; Antunes, JT; Alexandrino, DAM; Tomasino, MP; Almeida, E; Hilario, A; Urbatzka, R; Leao, PN; Mucha, AP; Carvalho, MF;

Publication
FRONTIERS IN MICROBIOLOGY

Abstract
The deep-sea covers over 70% of the Earth’s surface and harbors predominantly uncharacterized bacterial communities. Actinobacteria are the major prokaryotic source of bioactive natural products that find their way into drug discovery programs, and the deep-sea is a promising source of biotechnologically relevant actinobacteria. Previous studies on actinobacteria in deep-sea sediments were either regionally restricted or did not combine a community characterization with the analysis of their bioactive potential. Here we characterized the actinobacterial communities of upper layers of deep-sea sediments from the Arctic and the Atlantic (Azores and Madeira) ocean basins, employing 16S rRNA metabarcoding, and studied the biosynthetic potential of cultivable actinobacteria retrieved from those samples. Metabarcoding analysis showed that the actinobacterial composition varied between the sampled regions, with higher abundance in the Arctic samples but higher diversity in the Atlantic ones. Twenty actinobacterial genera were detected using metabarcoding, as a culture-independent method, while culture-dependent methods only allowed the identification of nine genera. Isolation of actinobacteria resulted on the retrieval of 44 isolates, mainly associated with Brachybacterium, Microbacterium, and Brevibacterium genera. Some of these isolates were only identified on a specific sampled region. Chemical extracts of the actinobacterial isolates were subsequently screened for their antimicrobial, anticancer and anti-inflammatory activities. Extracts from two Streptomyces strains demonstrated activity against Candida albicans. Additionally, eight extracts (obtained from Brachybacterium, Brevibacterium, Microbacterium, Rhodococcus, and Streptomyces isolates) showed significant activity against at least one of the tested cancer cell lines (HepG2 and T-47D). Furthermore, 15 actinobacterial extracts showed anti-inflammatory potential in the RAW 264.4 cell model assay, with no concomitant cytotoxic response. Dereplication and molecular networking analysis of the bioactive actinobacterial extracts showed the presence of some metabolites associated with known natural products, but one of the analyzed clusters did not show any match with the natural products described as responsible for these bioactivities. Overall, we were able to recover taxonomically diverse actinobacteria with different bioactivities from the studied deep-sea samples. The conjugation of culture-dependent and -independent methods allows a better understanding of the actinobacterial diversity of deep-sea environments, which is important for the optimization of approaches to obtain novel chemically-rich isolates. Copyright © 2023 Ribeiro, Antunes, Alexandrino, Tomasino, Almeida, Hilário, Urbatzka, Leão, Mucha and Carvalho.

2018

Multiplex PCR identification and culture-independent quantification of Bacillus licheniformis by qPCR using specific DNA markers

Authors
Almeida, E; Serra, CR; Albuquerque, P; Guerreiro, I; Teles, AO; Enes, P; Tavares, F;

Publication
FOOD MICROBIOLOGY

Abstract
Probiotics benefits in fish farming have been usually inferred appraising the effects observed on the host and not through the direct assessment of probiotic dynamics in the host gut microbiota. To overcome this gap, quantitative PCR (qPCR) can be a powerful approach to study the bacterial dynamics in fish gut microbiota. The presented work proposes four B. licheniformis-specific DNA markers and details a qPCR method to track putative probiotics B. licheniformis on fish gut. The four B. licheniformis-specific DNA markers - BL5B (hypothetical protein BL00303), BL8A (serA2), BL13C (rfaB) and BL18A (ligD) - were selected and validated by PCR and multiplex-PCR with 20 B. licheniformis isolates and a broad range of non-target bacteria. To assess the dynamics of B. licheniformis in the digesta of farmed fish, a qPCR was validated using markers BL8A and BL18A and calibration curves obtained for both markers with digesta samples spiked with B. licheniformis cells showed a high correlation (R-2 > 0.99) over 6 log units (CFU/ reaction), and a limit of detection (LOD) as low as 247 CFUs/reaction. Furthermore, the consistent qPCR repeatability and reproducibility underline the specificity and reliability of the qPCR proposed. Ultimately, the possibility to monitor the dynamics of B. licheniformis probiotics in the gut microbiota of farmed fish might be instrumental to optimize best practices in aquaculture.

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