Biology subjects

Parente, E.

Publications and source records attributed to Parente, E..

7 recordsLinked to original sources

bioRxiv2025

A survey of bacterial and fungal communities of table olives.

Table olives are produced from a large number of olive varieties subjected to different trade preparations, resulting in a highly heterogeneous family of fermented foods. To characterise the diversity of bacterial and fungal communities and its relationship with variety, ripeness, and trade preparation, we surveyed 363 samples from 40 producers across 6 countries, combining physicochemical measurements, viable counts, and amplicon-based metagenomics. This is the largest survey of table olive microbial communities to date and includes the first culture-independent characterisation of microbial communities for several Italian PDO and non-PDO varieties, most notably Oliva di Gaeta. The contrast between alkali-treated and naturally fermented olives was the dominant structuring factor, with HALAB (Halophilic and Alkalophilic Lactic Acid Bacteria) and other halophiles enriched in alkali-treated varieties and a diverse array of Lactobacillaceae and Pseudomonadota characterising naturally fermented olives. Despite these consistent signals, striking variability was observed within the same variety and even within the same producer, driven by stochastic colonization events, house microbiota, and the widespread use of small fermentation vessels. This variability obscured variety-specific microbial signatures and prevented reliable discrimination of Italian PDO varieties from similar non-PDO counterparts using amplicon-based approaches. The ecological and taxonomic complexity documented here, encompassing bacterial and fungal genera with largely untapped starter and flavour potential, provides the foundation for the development of variety-specific microbiome-based starter cultures. HighlightsO_LIWe report a metataxonomic survey of microbial communities in 363 table olive samples C_LIO_LIAlkali treatment and natural fermentation drive distinct microbial community structures C_LIO_LIHouse microbiota and stochastic colonization generate high within-variety variability C_LIO_LIMicrobiome data provide ecological foundations for olive microbiome-based starters C_LI

microbiology↗

bioRxiv2025

Determining the core bacterial and fungal genera in table olive fermentations.

Table olives are among the most ancient and important fermented foods of the Mediterranean basin. Their production is still strongly related to traditional practices, and the lack of thermal treatments, the reliance on natural contamination and selective factors (NaCl, pH, occurrence of phenolics, etc.) determine the dynamics of the microbial community. Lactic acid bacteria (LAB) and yeasts have a pivotal role in table olive microbial communities, but several halophilic and alkalophilic microorganisms may also contribute, positively or negatively, to the quality and safety of this fermented vegetable. We have use metataxonomic data extracted from the FoodMicrobionet database to provide quantitative insights on the structure of bacterial and fungal microbial communities of table olives and to identify core genera in different trade preparations. Celerinatantimonas and Lactiplantibacillus were the most prevalent genera among bacteria, followed by several LAB, halophilic and alkalophilic lactic acid bacteria (HALAB) and Gram negatives, including non-halophilic species. Similarly, 3 fungal genera (Pichia, Candida, and Wickerhamomyces) were the most abundant and prevalent among fungi. The distribution of both bacteria and fungi varied significantly in different olive varieties, among olives, brines and contact surfaces or materials, and at different production stages, and no clear grouping related to the combination of ripeness and trade preparation was found, although HALAB were characteristically abundant in Spanish style green olives. Addition of starter cultures affected the composition and dynamics of microbial communities to a variable extent. HighlightsO_LIData from 16 metataxonomic studies on table olives, including 833 samples, were combined. C_LIO_LIEnhanced metadata facilitated the comparison among different studies. C_LIO_LIComposition of the microbiota of table olives was highly variable. C_LIO_LICelerinatantimonas and Lactiplantibacillus dominated the core bacterial microbiota. C_LIO_LIPichia, Candida, and Wickermahomyces were the most prevalent among fungi. C_LI

microbiology↗

bioRxiv2024

Bezafibrate treatment rescues neurodevelopmental and neurodegenerative defects in 3D cortical organoid model of MAPT frontotemporal dementia

INTRODUCTIONThe intronic MAPT mutation IVS10+16 is linked to familiar frontotemporal dementia, causing hyperphosphorylation and accumulation of tau protein, resulting in synaptic and neuronal loss and neuroinflammation in patients. This mutation disrupts MAPT gene splicing, increasing exon 10 inclusion and leading to an imbalance of 3R and 4R Tau isoforms. METHODSWe generated patterned cortical organoids from isogenic control and mutant human iPSC lines. Nanostring gene expression analysis immunofluorescence and calcium imaging recordings were used to study the impact of the MAPT IVS10+16 mutation on neuronal development and function. RESULTSTau mutant cortical organoids showed altered mitochondrial function and gene expression related to neuronal development, with synaptic markers and neuronal activity reduction. Bezafibrate treatment, which restored mitochondrial content, rescued synaptic functionality and tau physiology. DISCUSSIONThese findings suggest that targeting mitochondrial function with bezafibrate could potentially reverse tau-induced neurodevelopmental deficits, highlighting its therapeutic potential for tauopathies like FTD. HIGLIGHTSO_LIThe IVS 10+16 MAPT mutation significantly disrupts cortical differentiation and synaptic maturation, evidenced by downregulated genes associated with synapses and neuronal development. C_LIO_LITau-mutant cortical organoids exhibit mitochondrial dysfunction, with fewer and smaller mitochondria alongside with tau hyperphosphorylation and aggregation, which further contribute to neuronal damage and disease progression. C_LIO_LITreatment with bezafibrate effectively normalizes mitochondrial parameters, enhances neuronal integrity and synaptic maturation, and restores network functionality, showcasing its promise as a therapeutic strategy for tauopathies. C_LIO_LIThe 3D in vitro disease model used in this study proves valuable for studying tauopathies and testing new drugs, effectively mimicking key aspects of tau-related neurodegeneration. C_LI RESEARCH IN CONTEXTO_LISystematic Review: We searched PubMed, Google Scholar, and Web of Science for studies on the MAPT IVS10+16 mutations impact on tauopathies, focusing on neuronal development, synaptic function, and mitochondrial involvement. Key terms included "MAPT IVS10+16 mutation," "tauopathy," "neuronal development," "synaptic function," and "mitochondrial function." C_LIO_LIInterpretation: Our findings reveal that the MAPT IVS10+16 mutation disrupts mitochondrial function altering gene expression related to neuronal development, synaptic structures, impairing neuronal and glial maturation. Bezafibrate treatment restored mitochondrial content, synaptic functionality, and tau physiology in mutant-derived cortical organoids, suggesting it as a potential therapeutic strategy for tauopathies. C_LIO_LIFuture Directions: Future research should investigate the molecular mechanisms underlying the bezafibrates therapeutic effect and its long-term efficacy and safety in vivo, in humanized mouse models. Additionally, the possibility to combine bezafibrate with other therapeutic agents used to treat tauopathies will be worth to assess. C_LI

neuroscience↗

bioRxiv2022

Metataxonomic insights in the distribution of Lactobacillaceae in foods and food environments

Members of the family Lactobacillaceae, which now includes species formerly belonging to the genera Lactobacillus and Pediococcus, but also Leuconostocaceae, are of foremost importance in food fermentations and spoilage, but also as components of animal and human microbiota and as potentially pathogenic microorganisms. Knowledge of the ecological distribution of a given species and genus is important, among other things, for the inclusion in lists of microorganisms with a Qualified Presumption of Safety or with beneficial use. The objective of this work is to use the data in FoodMicrobionet database to obtain quantitative insights (in terms of both abundance and prevalence) on the distribution of these bacteria in foods and food environments. We first explored the reliability of taxonomic assignments using the SILVA v138.1 reference database with full length and partial sequences of the 16S rRNA gene for type strain sequences. Full length 16S rRNA gene sequences allow a reasonably good classification at the genus and species level in phylogenetic trees but shorter sequences (V1-V3, V3-V4, V4) perform much worse, with type strains of many species sharing identical V4 and V3-V4 sequences. Taxonomic assignment at the genus level of 16S rRNA genes sequences and the SILVA v138.1 reference database can be done for almost all genera of the family Lactobacillaceae with a high degree of confidence for full length sequences, and with a satisfactory level of accuracy for the V1-V3 regions. Results for the V3-V4 and V4 region are still acceptable but significantly worse. Taxonomic assignment at the species level for sequences for the V1-V3, V3-V4, V4 regions of the 16S rRNA gene of members of the family Lactobacillaceae is hardly possible and, even for full length sequences, and only 49.9% of the type strain sequences can be unambiguously assigned to species. We then used the FoodMicrobionet database to evaluate the prevalence and abundance of Lactobacillaceae in food samples and in food related environments. Generalist and specialist genera were clearly evident. The ecological distribution of several genera was confirmed and insights on the distribution and potential origin of rare genera (Dellaglioa, Holzapfelia, Schleiferilactobacillus) were obtained. We also found that combining Amplicon Sequence Variants from different studies is indeed possible, but provides little additional information, even when strict criteria are used for the filtering of sequences.

microbiology↗

bioRxiv2022

FoodMicrobionet v4: a large, integrated, open and transparent database for food bacterial communities

With the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods. Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1,684 environmental samples and 8,467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249). Using data in FoodMicrobionet we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level. Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data). Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.

microbiology↗

bioRxiv2021

L-type calcium channel blocker increases VEGF concentrations in retinal cells and human serum

ObjectiveVascular endothelial growth factor (VEGF) plays a key role in diabetic retinopathy (DR). L-type calcium channel blockers (LTCCBs) have been widely used as antihypertensive medication (AHM), but their association with VEGF and DR is still unclear. Therefore, we explored the effect of LTCCBs compared to other AHMs on VEGF concentrations in retinal cells and human serum. Furthermore, we evaluated the association between the use of LTCCBs and the risk of severe diabetic eye disease (SDED). Research design and methodsMuller cells (MIO-M1) were cultured as per recommended protocol and treated with LTCCBs and other AHMs. VEGF secreted from cells were collected at 24 hours intervals. In an interventional study, 39 individuals received LTCCBs or other AHM for four weeks with a four-week wash-out placebo period between treatments. VEGF was measured during the medication and placebo periods. Finally, we evaluated the risk of SDED associated with LTCCB usage in 192 individuals from the FinnDiane Study in an oberservational setting. ResultsIn the cell cultures, medium VEGF concentration increased time-dependently after amlodipine (p<0.01) treatment, but not after losartan (p>0.01), or lisinopril (p>0.01). Amlodipine, but no other AHM, increased serum VEGF concentration (p<0.05) during the interventional clinical study. The usage of LTCCB was not associated with the risk of SDED in the observational study. ConclusionsLTCCB increases VEGF concentrations in retinal cells and human serum. However, the usage of LTCCBs does not appear to be associated with SDED in adults with type 1 diabetes.

pharmacology and toxicology↗

bioRxiv2021

Microbial association networks in cheese: a meta-analysis

Interactions among starter and non-starter microorganisms (starter bacteria, naturally occurring or intentionally added non-starter bacteria, yeasts and filamentous fungi, spoilage and pathogenic microorganisms and, finally bacteriophages and even arthropods) deeply affect the dynamics of cheese microbial communities and, as a consequence, multiple aspects of cheese quality, from metabolites affecting the taste, aroma and flavour, to body, texture and colour. Understanding and exploiting microbial interactions is therefore key to managing cheese quality. This is true for the simplest systems (fresh cheeses produced from pasteurized milk using defined starters composed solely of Lactic Acid Bacteria) and the more so for complex, dynamic systems, like surface ripened cheese produced from raw milk, in which a dynamic succession of diverse microorganisms is essential for obtained the desired combination of sensory properties while guaranteeing safety. Positive (commensalism, protocooperation) and negative (competition, amensalism, predation and parasitism) among members of the cheese biota have been reviewed multiple times. Although the complex, multidimensional datasets generated by multi-omic approaches to cheese microbiology and biochemistry are ideally suited for the representation of biotic and metabolic interactions as networks, network science concepts and approaches are rarely applied to cheese microbiology. In this review we first illustrate concepts relevant to the description of microbial interaction networks using network science concepts. Then, we briefly review methods used for the inference and analysis of microbial association networks and their potential use in the interpretation of the cheese interactome. Since these methods can only be used for mining microbial associations, a review of the experimental methods used to confirm the nature of microbial interactions among cheese microbes. Finally, we demonstrate the potential of microbial association network inference by mining metataxonomic data stored in the public database DairyFMBN, a specialized version of FoodMicrobionet which collates data on 74 metataxonomic studies on dairy products. Microbial association networks were inferred from 34 studies on cheese with up to 4 different methods and the results discussed to evaluate several aspects (choice of method, level of taxonomic resolution for the analysis, network, node and edge properties) which provide insight on the usefulness of this approach as explorative tool in the detection of microbial interactions in cheese. HighlightsO_LIApproaches for inference of association networks from metataxonomic data were reviewed C_LIO_LIA metastudy on association networks in cheese was carried out using 34 recent studies C_LIO_LIInference method and taxonomic resolution should be chosen carefully C_LIO_LISPIEC-EASI may be used as a conservative method for microbial association inference C_LIO_LIEdge and node properties support the formulation of testable hypotheses for microbial interactions C_LI

microbiology↗