Biology subjects

Ricciardi, A.

Publications and source records attributed to Ricciardi, A..

12 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

Automated and parallelized microfluidic generation of large and precisely-defined lipid nanoparticle libraries

Building on the success of lipid nanoparticles (LNPs) in vaccines, LNPs are being developed for a broad set of therapeutic applications by changing both the structures of the lipids used to formulate each LNP and their relative proportions. Because lipid synthesis and in vivo screening have been parallelized using combinatorial chemistry and LNP barcoding respectively, the manual and sequential microfluidic formulation of LNPs has become the rate-limiting step in the discovery process. In this work, we present a high-throughput, automated microfluidic platform capable of generating large, precisely-defined LNP libraries in parallel at a rate of one distinct formulation every three seconds. Each formulation is defined by varying the reagent flow ratios into one of eight microscale mixers using litho-graphically encoded fluidic resistors and dynamically controlled external pressure supplies. The microfluidic chip is integrated with custom frobotic plate handling for the rapid collection of each distinct formulation. Using this platform, we produce a library of 96 formulations, which we profile physicochemically and evaluate in terms of both in vitro and in vivo transfection.

bioengineering↗

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↗

bioRxiv2025

Plug-and-play assembly of biodegradable ionizable lipids for potent mRNA delivery and gene editing in vivo

mRNA-based gene editing therapeutics offer the potential to permanently cure diseases but are hindered by suboptimal delivery platforms. Here, we devise a robust combinatorial chemistry for plug-and-play assembly of diverse biodegradable ionizable lipids and identify a lead candidate that produces superior lipid nanoparticles for various gene editing tools delivery in vivo. Our study highlights the utility of this synthetic approach and the generality of this platform for potent in vivo gene editing.

bioengineering↗

bioRxiv2024

Solution biophysics identifies lipid nanoparticle non-sphericity, polydispersity, and dependence on internal ordering for efficacious mRNA delivery

Designing lipid nanoparticle (LNP) delivery systems with specific targeting, potency and minimal side effects is crucial for their clinical use. However, traditional characterization methods, such as dynamic light scattering, cannot accurately quantify physicochemical properties of LNPs and how they are influenced by the lipid composition and mixing method. Here we structurally characterize polydisperse LNP formulations by applying emerging solution-based biophysical methods that have higher resolution and provide biophysical data beyond size and polydispersity. These techniques include sedimentation velocity analytical ultracentrifugation, field-flow fractionation followed by multi-angle light scattering, and size-exclusion chromatography in-line with synchrotron small-angle X-ray scattering. We show that LNPs have intrinsic polydispersity in size, RNA loading, and shape, which depends on both the formulation technique and lipid composition. Lastly, we predict LNP transfection in vitro and in vivo by examining the relationship between mRNA translation and physicochemical characteristics. Solution-based biophysical methods will be essential for determining LNP structure-function relationships, facilitating the creation of new design rules for LNPs.

bioengineering↗

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

Spatiotemporal changes in genetic diversity and structure of a recent fish invasion in eastern North America

Introduced and geographically expanding populations experience similar eco-evolutionary challenges, including founder events, genetic bottlenecks, and novel environments. Theory predicts that reduced genetic diversity resulting from such genetic phenomena limits the colonization success of introduced populations. We examined an invasive population of a Eurasian freshwater fish, Tench (Tinca tinca), that has been expanding geographically in eastern North America for three decades. Using genomic data, we evaluated evidence for single versus multiple introductions and the connectivity of the population across the entire range in which it has been spreading. Tench exhibited low levels of genetic diversity, a lack of marked population subdivision across time and space, and evidence of a recent genetic bottleneck. These results suggest that the invasion stemmed from a single introduction, consistent with the reported invasion history. Furthermore, the large genetic neighbourhood size and weak within-population genetic substructure suggest high connectivity across the invaded range, despite the large area occupied, and no evidence of substantial diminution of genetic diversity from the invasion core to the margins. As eradicating the species within a ~112 km radius would be necessary to prevent recolonization, eradicating Tench is likely not feasible at watershed--and possibly local--scales. Management should instead focus on reducing abundance in priority conservation areas to mitigate adverse impacts. Our study supports the argument that introduced populations can thrive despite recent bottlenecks and low levels of genetic diversity, and it suggests that landscape heterogeneity and population demographics can generate variability in spatial patterns of genetic diversity within a single range expansion.

genomics↗

bioRxiv2022

In utero delivery of miRNA induces epigenetic alterations and corrects pulmonary pathology in congenital diaphragmatic hernia

Structural fetal diseases, such as congenital diaphragmatic hernia (CDH) can be diagnosed prenatally. Neonates with CDH are healthy in utero as gas exchange is managed by the placenta, but impaired lung function results in critical illness from the time a baby takes its first breath. During fetal development, lungs are capable of remarkable growth and the fetus does not yet require lung function for gas exchange. MicroRNA (miR) 200b and its downstream targets in the TGF{beta} pathway are critically involved lung branching morphogenesis. Here we characterize the expression of miR200b and the TGF{beta} pathway at different gestational times using a rat model of CDH. Fetal rats with CDH are deficient in miR200b at gestational day 18. We demonstrate that NPs loaded with miR200b given systemically to fetal rats result in changes in the TGF{beta} pathway; these epigenetic changes improve lung size, lung morphology, and lung vascularization. This is the first demonstration of in utero epigenetic therapy to improve lung growth and development in a pre-clinical model. With refinement, this technique could be applied to fetal cases of CDH or other forms of impaired lung development in a minimally invasive fashion. eTOC SynopsisIn utero treatment with NPs loaded with miR200b improves lung development in a rat model of CDH. miR200b treatment epigenetic changes in the TGF{beta}, leads to larger lungs with more airspace and favorable pulmonary vascular remodeling. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/482144v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@3531caorg.highwire.dtl.DTLVardef@57ff5aorg.highwire.dtl.DTLVardef@13d6ee9org.highwire.dtl.DTLVardef@3cb3d8_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

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

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↗

bioRxiv2019

Consequences of consumer origin and omnivory on stability in experimental food web modules

O_LIFood web stability, a fundamental characteristic of ecosystems, is influenced by the nature and strength of species interactions. Theory posits that food webs are stabilized by omnivory and disrupted by novel consumers.\nC_LIO_LITo test the effects of secondary consumer origin and trophic level on basal resource stability, we constructed crayfish-snail-algae modules using four congeneric species of crayfish (Faxonius spp.), two from native populations (F. propinquus and F. virilis) and two from non-native populations (F. limosus and F. rusticus). We performed surgical manipulations of crayfish feeding structures to create omnivore food web and predator food chain modules. We compared the temporal stability of these modules using measures of the coefficient of variation of the basal resource (benthic algae).\nC_LIO_LIConsistent with theoretical and empirical predictions, food web modules with omnivory had the lowest coefficient of variation. However, contrary to prediction, we did not find consistently higher coefficients of variation in modules with non-native species. Rather, across species, we found the lowest coefficient of variation in modules with one of the non-native species (F. rusticus) and one native species (F. virilis), owing to stronger interactions between these crayfish species and their snail and algal food resources.\nC_LIO_LIThe results suggest that omnivory is indeed stabilizing and that very weak interactions or very low attack rates of the consumer on the basal resource can be unstable. Thus, we demonstrate that omnivores may have different impacts than predators when introduced into a novel ecosystem, differences that can supersede the effect of species identity.\nC_LI

ecology↗

bioRxiv2018

Challenges and perspectives of functional sodium imaging (fNaI)

Brain function has been investigated via the blood oxygenation level dependent (BOLD) effect using magnetic resonance imaging (MRI) for the past decades. Advances in sodium imaging offer the unique chance to access signal changes directly linked to sodium ions (23Na) flux across the cell membrane, which generates action potentials, hence signal transmission in the brain. During this process 23Na transiently accumulates in the intracellular space. Here we show that quantitative functional sodium imaging (fNaI) at 3T is potentially sensitive to 23Na concentration changes during finger tapping, which can be quantified in grey and white matter regions key to motor function. For the first time, we measured a 23Na concentration change of 0.54 mmol/l in the ipsilateral cerebellum, 0.46 mmol/l in the contralateral primary motor cortex, 0.27 mmol/l in the corpus callosum and -11 mmol/l in the ipsilateral primary motor cortex, suggesting that fNaI is sensitive to distributed functional alterations. Open issues persist on the role of the glymphatic system in maintaining 23Na homeostasis, the role of excitation and inhibition as well as volume distributions during neuronal activity. Hemodynamic and physiological signal recordings coupled to realistic models of tissue function will be critical to understand the mechanisms of such changes and contribute to meeting the overarching challenge of measuring neuronal activity in vivo.

neuroscience↗