Fanny Claire Capri

This exploratory study compared gut microbiota composition and targeted detection of eight antimicrobial resistance genes (ARGs) among three geographically and ecologically distinct Sicilian populations: domestic pigs (DP), urban wild boars (WB-U), and sylvatic wild boars (WB-S). Ileal samples were collected from 36 animals (12 per group) and profiled by 16S rRNA gene (V3-V4) sequencing and PCR screening for β-lactam (blaTEM, blaCTX-M IV, blaOXA, blaSHV) and tetracycline (tetA, tetB, tetC, tetD). Firmicutes and Proteobacteria dominated all groups. DP showed high abundance of Psychrobacter and Pseudomonas, whereas Lactobacillus prevailed in WB-U; WB-S showed an intermediate profile. Community composition differed among groups (PERMANOVA, p = 0.001). Pairwise comparisons identified differences between DP and each WB group (p = 0.0015 for both), but not between WB-U and WB-S (p = 0.302). blaTEM detection frequencies were 83.3% in WB-U, 16.7% in WB-S, and 50.0% in DP, with a significant WB-U–WB-S difference (p = 0.0099). tetA was detected in 41.7% of DP and 33.3% of WB-U; tetC only in WB-U (25.0%). These findings provide baseline information of differences in gut microbiota composition and in the detection of selected ARGs, while informing future surveillance strategies at the wildlife–livestock–human interface.

Rare actinobacteria are promising sources of specialized metabolites, yet genome mining still prioritizes genomes encoding many biosynthetic gene clusters (BGCs) rather than clusters that are distant from characterized chemistry. Here, we describe the isolation of a novel Jiangella strain reported from a marine, animal-associated plastisphere and place its biosynthetic repertoire in the context of the whole genus, providing a genome-based prioritization of candidate biosynthetic targets. Digital DNA-DNA hybridization (57.8%) and OrthoANIu (94.65%) values against its closest relative, J. alba DSM 45237ᵀ, support its assignment as a candidate novel species, although formal species description will require additional phenotypic and chemotaxonomic characterization. antiSMASH predicted twelve BGCs, within the range observed across the genus (7–13), of which only one matched a characterized pathway, and the Biosynthetic Novelty Index of the genome was 865.3, the fourth highest among the twelve genomes analyzed. Across these genomes, 124 BGCs grouped into 70 gene cluster families, 74% of them strain-specific. Two families without any characterized representative, a lasso-peptide family and a RiPP recognition element-containing family, were instead conserved across a subclade, down to nearly identical precursor peptides. No antimicrobial activity was detected under the conditions tested. Genus-wide comparison therefore identifies conserved yet uncharacterized families as rational priorities that cluster counts alone would miss.

Rare actinobacteria are promising sources of specialized metabolites, yet genome mining still prioritizes genomes encoding many biosynthetic gene clusters (BGCs) rather than clusters that are distant from characterized chemistry. Here, we describe the isolation, for the first time, of a novel Jiangella strain reported from a marine, animal-associated plastisphere, and place its biosynthetic repertoire in the context of the whole genus. Digital DNA-DNA hybridization (57.8%) and OrthoANIu (94.65%) values against its closest relative, J. alba DSM 45237ᵀ, support its assignment as a candidate novel species. antiSMASH predicted twelve BGCs, within the range observed across the genus (7-13), of which only one matched a characterized pathway, and the Biosynthetic Novelty Index of the genome was 865.3, the fourth highest among the twelve genomes analyzed. Across these genomes, 124 BGCs grouped into 70 gene cluster families, 74% of them strain-specific. Two families without any characterized representative, a lasso-peptide family and a RiPP recognition element-containing family, were instead conserved across a subclade, down to nearly identical precursor peptides. No antimicrobial activity was detected under the conditions tested. Genus-wide comparison therefore identifies conserved yet uncharacterized families as rational priorities that cluster counts alone would miss.

Actinomycetes are among the richest sources of bioactive secondary metabolites in biotechnology, owing to their remarkable metabolic diversity. Although the genus Streptomyces has been extensively explored and has yielded many clinically important antibiotics, rare actinomycetes remain comparatively underinvestigated. In this study, Kitasatospora sp. SeTe27, isolated from uncontaminated soil in Sicily (Italy), was investigated for its antibacterial activity and fermentation-driven enhancement of secondary metabolite production. The strain inhibited Staphylococcus aureus ATCC 25923, prompting physiological and genomic analyses. Spore conditioning was evaluated in four media (R5A, GYM, TSB, and YEME) to enhance antibiotic production. Conditioned cultures exhibited markedly increased antibacterial activity in TSB and YEME, moderate production in R5A, and no detectable activity in GYM. Whole-genome sequencing revealed an 8.5 Mb genome (73.5% GC) containing 48 biosynthetic gene clusters (BGCs), including NRPS, PKS, terpene, and hybrid pathways. Several clusters showed high similarity to known antibiotic-associated BGCs, such as clifednamide- and phenazine-related pathways, while numerous orphan clusters indicated significant unexplored biosynthetic potential. These findings identify Kitasatospora sp. SeTe27 as a promising antimicrobial producer and demonstrate that spore conditioning in complex media is an effective strategy to enhance antibiotic production in rare actinomycetes.

Egg hatching success in sea turtle nests can be influenced by multiple abiotic and biotic factors. Although interest in nest microbiota as a determinant of embryo development and viability is increasing, its role has not yet been fully elucidated. In this study, we profiled the bacterial communities of four Caretta caretta nests on Lampedusa Island: Cala Pisana (P1 and P2) and Spiaggia dei Conigli (C1 and C2), which showed different hatching success rates (P1 = 85.2%, P2 = 1.1%, C1 = 1.1%, C2 = 0.0%). Using 16S rRNA gene (V3-V4) sequencing, we analyzed different sample types, including sand from inside and outside the nest chamber, eggshells, and inner membranes. Alpha diversity was highest in sand and lower in eggshells and inner membranes. β-diversity clearly separated the only successful nest (P1) from the others (P2, C1, and C2) (PERMANOVA p < 0.001). Across all nests, the dominant phyla were Proteobacteria, Firmicutes, Actinobacteriota, and Bacteroidota; notably, the Firmicutes/Bacteroidota (F/B) ratio was lowest in P1 compared with P2, C1, and C2. Nests with low hatching success were Firmicutes-dominated, enriched in Bacillus and Pseudomonas , and harbored hydrocarbon-degrading genera ( Pseudoxanthomonas and Devosia ), suggesting environmental influences. Opportunistic pathogens ( Ochrobactrum and Simkaniaceae), likely associated with vertical transmission, were detected exclusively in C1 and C2 nests. Overall, our findings highlight the potentially critical role of nest microbiota in reproductive success. Both vertical (maternal) and horizontal (environmental and anthropogenic) transmission appear to shape microbial composition, potentially affecting hatchling viability and offering useful insights for conservation monitoring.

The salt ponds of Trapani, Sicily, represent an extreme and under‐explored ecosystem characterised by varying salinity gradients and environmental conditions. These ponds, integral to traditional salt extraction, include cold, driving, hot and crystallizer ponds, each hosting diverse microbial communities. This study aimed to explore the biological and physical–chemical diversity of 11 ponds during the salt production season in Trapani. We conducted comprehensive physical–chemical characterizations, including measurements of pH, conductivity, viscosity, density, organic carbon and ion concentration. Microbial DNA was extracted from salt pond waters and subjected to metabarcoding of 16S rRNA genes to determine the diversity of archaea and bacteria. High‐throughput sequencing revealed significant variations in microbial communities across different pond types and seasons. Cold ponds showed a higher diversity of moderately halophilic organisms, while crystallizer and feeding ponds were dominated by extreme halophiles, particularly archaeal genus Halorubrum and Haloquadratum and bacterial genus Salinibacter . Statistical analyses indicated that environmental parameters, especially salinity and temperature, significantly influenced microbial community composition. Our findings enhance the understanding of microbial ecology in saline environments and highlight the potential of halophilic microorganisms. This study provides a foundation for future research into the functional roles of these microorganisms and their industrial applications.

Subclinical mastitis represents one of the most contagious diseases affecting animals involved in dairy production systems. Although coagulase-negative staphylococci (CoNSs) have been considered minor pathogens for many years, they have recently emerged as opportunistic pathogens in mastitis disorders. The objectives of this work were to assess the antimicrobial resistance profile and the ability to produce a biofilm in comparison with a reference strain and to search for genes related to biofilm production, antimicrobial resistance, and enterotoxins in 18 isolates of Staphylococcus species from the milk of sheep with subclinical mastitis, collected from different Sicilian farms. This knowledge is essential to provide basic information on the pathogenicity and virulence of staphylococcal species and their impact on animal health. All isolates were resistant to ampicillin, 88.8% to streptomycin, 77.7% to gentamicin, 44.4% to chloramphenicol, 27.7% to erythromycin, and 11.1% to tetracycline, and two isolates were strong biofilm producers. Antibiotic resistance gene profiling showed that 16.6% of isolates possess the blaZ gene, whereas the search of biofilm-associated genes revealed the occurrence of the sasC gene in 33.3% of isolates, the ica gene in 27.7%, and bap and agr (accessory gene regulator) genes in 16.6% of isolates. Altogether, the results of this study indicate that CoNSs can acquire virulence genes and could have a role as pathogens in subclinical mastitis.

Microbial communities provide essential information about host ecology and could be helpful as a tool to improve species conservation efforts. However, microbes can also infect and compromise the host development process and viability.Caretta carettais the most widespread marine turtle species in the Mediterranean basin and is the only species of sea turtle nesting along the Italian coasts. Little is known about the microbiota composition of the nest of sea turtles and its correlation with hatching failures. In this study, the microbial composition of two nests ofC. carettafeaturing different rates of hatching success from a nesting beach in Lampedusa (Italy) was analyzed and compared. The bacterial community was determined using culture-dependent methods and next-generation sequencing based on 16S rRNA gene metabarcoding analysis. Our results showed five dominant bacterial phyla (Proteobacteria, Bacteroidetes, Actinobacteria, Verrucomicrobia, and Firmicutes) and indicated different bacterial families (PseudomonadaceaeandBrucellaceae) as likely causes of hatching failures. Besides, our findings demonstrated the nests’ active role in modulating the sand’s bacterial communities. This study suggests microbiological analysis could be a valuable tool in monitoring nests to take preventive actions and reduce hatching failures.

Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that can be precursors of polyhydroxyalkanoate thermoplastic polyesters. The role of various operating parameters in VFA production has yet to be elucidated. This study aimed to correlate the levels of VFA yields with prokaryotic microbiota structures of sewage sludge in two sets of batch fermentations with an initial pH of 8 and 10. The sewage sludge used to inoculate the batch fermentations was collected from a Sicilian WWTP located in Marineo (Italy) as a case study. Gas chromatography analysis revealed that initial pH 10 stimulated chemical oxygen demands (sCOD) and VFA yields (2020 mg COD/L) in comparison with initial pH 8. Characterization of the sewage sludge prokaryotic community structures—analyzed by next-generation sequencing of 16S rRNA gene amplicons—demonstrated that the improved yield of VFA paralleled the increased abundance of fermenting bacteria belonging to Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes phyla and, conversely, the reduced abundance of VFA-degrading strains, such as archaeal methanogens.

Wastewater Treatment Plants (WWTPs) are complex systems characterized by interconnected chemical, physical, and biological processes. Considering the high amount of nutrients still present and the worldwide pollution, the conversion of WWTPs into Water Resource Recovery Facilities (WRRFs) or Wastewater Biorefineries (WWBRs) is a challenge to protect water quality, the environment, and thus, human health.In WWTPs, under specific operating conditions microbial fermentative products can be volatile fatty acids (VFAs) that can be precursors of polyhydroxyalkanoates (PHAs). The latter are thermoplastic polyesters with excellent properties considered an eco-friendly alternative to plastics.Although the role of various parameters in VFA production has been investigated, the studies on their effect on the microbial community are still in their infancy.The current study is further aimed at investigating comparatively the influence of two basic pH values (i.e. pH 8 and pH 10) on the structure of prokaryotic community residing in the activated sludge (AS) - collected from a Sicilian WWTP located in Marineo (Italy) as a case study - correlating the presence of prokaryotic taxa with the production of VFA in batch reactor fermentations. Gas chromatography analysis confirmed that a starting pH value of 10 positively affected chemical oxygen demands (sCOD) and VFA yields. The determination of the AS prokaryotic community structures, analyzed by next-generation sequencing of 16S rRNA encoding genes, demonstrated the effect of the pH on the abundance of members of some bacterial phyla, specifically Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes. Indeed, the pH 10 led to the increase in those bacterial strains known as VFA producers and the reduction of VFA degrading bacterial strains.The results of this study can give more insights into identifying parameters and specific microbial signatures for high yields of VFA production.