Biology subjects

Di Cesare, F.

Publications and source records attributed to Di Cesare, F..

5 recordsLinked to original sources

bioRxiv2026

Laboratory evolution enhances resilience of a symbiont yeast and its honeybee host against agrochemical exposure

Yeasts are key microbial members of several ecosystems. Yet, the impact of widespread chemical pollutants on yeasts is only sparsely studied. Here we report the effect of >1000 chemical pollutants on fourteen diverse yeast species spanning the Saccharomycotina subphylum. Starmerella bombicola, a symbiont of various bee species, was the most sensitive and inhibited by several fungicides as well as by non-fungicides. To identify the molecular basis of this ultra-sensitivity, we selected resistant lineages against nine chemicals using adaptive laboratory evolution. Whole-genome-sequencing uncovered convergent evolution on YBP1, a key regulator of oxidative stress. Proteomic analysis confirmed the protective role of oxidative stress response pathways, including proteins encoded by horizontally transferred bacterial genes. We find that the evolved S. bombicola stably colonized the bee gut and ameliorated the negative effect of paclobutrazol, a plant hormone regulator, on gut microbes, sucrose responsiveness, and learning. Our findings demonstrate how laboratory evolution can be used to mitigate the negative impact of chemical pollutants on pollinators.

microbiology↗

bioRxiv2026

Diet-dependent mortality and cognitive impairment reveal species-specific vulnerabilities to a microbial biopesticide in social bees

The increasing use of microbial biopesticides in sustainable agriculture requires a deeper understanding of their potential impact on non-target pollinators. Although biocontrol agents are generally considered safer than synthetic pesticides, they may still cause subtle but ecologically relevant adverse effects on non-target organisms, especially when exposed to multiple stressors that are often overlooked in current risk assessment frameworks. Among these, nutritional stress, caused by habitat loss, fragmentation and reduced floral diversity, is becoming increasingly widespread. In this study, we investigated the lethal and sublethal effects of the bacterial biopesticide Bacillus velezensis (formerly B. amyloliquefaciens) strain QST713 at field-relevant concentrations on two key pollinators: Apis mellifera and Bombus terrestris. For the first time for a biopesticide, oral toxicity was assessed under environmental stress represented by diets with varying sugar concentrations (optimal and suboptimal) to identify potential synergistic effects on bee health. Sublethal effects were examined by studying learning performance and memory retention through a conditioning experiment under laboratory conditions. The results showed marked species-specific differences. While B. velezensis did not impact bee survival under realistic nutritional conditions, we observed a synergistic lethal effect in B. terrestris when biopesticide exposure was coupled with extreme nutritional stress (sugar deprivation). Similar species-specific differences emerged at the behavioral level: unlike A. mellifera, B. terrestris showed impaired visual learning and early long-term memory recall. Taken together, these results show that sublethal cognitive endpoints and multi-stressor contexts may reveal vulnerabilities not immediately evident through mortality-based assessments alone. Our findings also highlight the importance of including multiple pollinator species in risk assessment, as sensitivity to biopesticides might greatly vary among species.

animal behavior and cognition↗

bioRxiv2025

Gempipe: a tool for drafting, curating and analyzing pan and multi-strain genome-scale metabolic models.

Genome-scale metabolic models (GSMMs) can mechanistically explain phenotypic differences among closely-related bacterial strains. However, high-throughput multi-strain reconstructions of GSMMs are still challenging: reference-based methods inherit curated information while missing new contents; alternatively, (universe-based) reference-free methods could cover strain-specific reactions, but they disregard curated information. Ideally, references should be curated pan-GSMMs for species (or genus), but their reconstruction is extremely demanding, making them still rare in literature. Here Gempipe is presented, a computational tool streamlining the multi-strain reconstruction and analysis of GSMMs, going through the production of a pan-GSMM. Its reconstruction method is hybrid, as an optional reference GSMM is automatically expanded with extra reactions taken from a reference-free reconstruction. Gempipe also downloads, filters and annotates genomes; performs in-depth gene recovery; annotates models contents; predicts strain-specific capabilities. The companion programming interface includes functions ranging from the (pan-)GSMMs curation to the multi-strain analysis. Gempipe was validated using multi-strain datasets, showing improved accuracy when compared with state-of-the-art tools. Moreover, metabolic diversities within Limosilactobacillus reuteri were explored, grouping strains into metabolically coherent clusters and systematically predicting health-related metabolites biosynthesis. IMPORTANCEAvailable GSMM reconstruction tools present major limitations in the context of multi-strain modeling. Gempipe surpasses these limitations by implementing a novel, hybrid reconstruction strategy. Not only it produces more accurate strain-specific GSMMs, but also pan-GSMMs when the only available reference is a manually curated model for a single strain, which is currently the most common case. With the vast availability of genome sequences, the high-throughput, multi-strain GSMM reconstruction and analysis approach provided by Gempipe will facilitate large-scale studies of the exploration and bioprospecting of strain-level bacterial metabolic diversity, moving a step forward in strains screening and rational selection.

microbiology↗

bioRxiv2021

Comparison of two injectable anaesthetic protocols in Egyptian fruit bats (Rousettus aegyptiacus) undergoing gonadectomy

Egyptian fruit bats are experimental animals of increasing interest because they have been identified as a natural reservoir for several emerging zoonotic viruses. For this reason, bats could undergo different experimental procedures that require sedation or anaesthesia. Our aim was to compare the effects of two balanced anaesthetic protocols on sedation, cardiopulmonary variables and recovery in bats undergoing gonadectomy. Twenty bats were randomized into two groups; patients in group DK received intramuscular injection of dexmedetomidine (40 g kg-1) and ketamine (7 mg kg-1), whereas those in group DBM were anaesthetized with intramuscular dexmedetomidine (40 g kg-1), butorphanol (0.3 mg kg-1) and midazolam (0.3 mg kg-1). Time of induction, cardiopulmonary parameters and anaesthetic depth were measured. If anaesthesia plan was considered inadequate, fraction of inspired isoflurane was titrate-to-effect to achieve immobility. At the end of the surgery venous blood gas analysis was performed and intramuscular atipamezole (200 g kg-1) or atipamezole (200 g kg-1) and flumazenil (0.03 mg kg-1) was administered for timed and scored recovery phase. A significantly higher heart rate and peripheral oxygen saturation were recorded in DBM group (p = 0.001; p = 0.003 respectively), while respiratory rate was significantly lower than DK group (p = 0.001). All bats required isoflurane supplementation during surgery with no significant difference. No differences were observed in rectal temperature, induction and recovery times. Sodium and chlorine where significantly higher in DBM group (p = 0.001; p = 0.002 respectively). Recovery scores in group DK were significantly better than in group DBM (p = 0.034). Both protocols induced anaesthesia in Egyptian fruit bats with comparable sedative and cardiorespiratory effect. These drug combinations may be useful for minor procedures in bats, and they could be associated with inhalation anaesthesia in determining and maintaining a surgical anaesthetic plan.

zoology↗

bioRxiv2019

The personalized temporal dynamics of microbiome in the airways of cystic fibrosis patients

Although the cystic fibrosis (CF) lung microbiome has been characterized in several studies, little is still known about the functions harboured by those bacteria, and how they change with disease status and antibiotic treatment. The aim of this study was to investigate the taxonomic and functional temporal dynamics of airways microbiome in a cohort of CF patients. Multiple sputum samples were collected over 15 months from 22 patients with chronic P. aeruginosa infection, for a total of 79 samples. DNA extracted from samples was subjected to shotgun metagenomic sequencing allowing either strain-level taxonomic profiling and assessment of the functional metagenomic repertoire. High inter-patient taxonomic heterogeneity was found with short-term compositional changes during exacerbations and following antibiotic treatment. Each patient exhibited distinct sputum microbial communities at the taxonomic level, and strain-specific colonization of traditional CF pathogens, including P. aeruginosa, and emerging pathogens. Sputum microbiome was found to be extraordinarily resilient following antibiotic treatment, with rapid recovery of taxa and metagenome-associated gene functions. In particular, a large core set of genes, including antibiotic resistance genes, were shared across patients despite observed differences in clinical status or antibiotic treatment, and constantly detected in the lung microbiome of all subjects independently from known antibiotic exposure, suggesting an overall microbiome-associated functions stability despite taxonomic fluctuations of the communities. IMPORTANCEWhile the dynamics of CF sputum microbial composition were highly patient-specific, the overall sputum metagenome composition was stable, showing a high resilience along time and antibiotic exposure. The high degree of redundancy in the CF lung microbiome could testifies ecological aspects connected to the disease that were never considered so far, as the large core-set of genes shared between patients despite observed differences in clinical status or antibiotic treatment. Investigations on the actual functionality (e.g. by metatranscriptomics) of the identified core-set of genes could provide clues on genetic function of the microbiome to be targeted in future therapeutic treatments.

microbiology↗