Well established long ago for bacterial and fungal detection, Matrix-Assisted Laser Desorption/Ionization–Time of Flight (MALDI-TOF) technique is not so well established in the virology field, and taking care of its advantages (speed, precision and low cost), this can be a powerful method for viral identification. To explore the feasibility and potential of MALDI-TOF for viral detection, this study shows the development of an in-house spectral library including several uninfected cell cultures and cultures infected with different clinically relevant viruses, such as SARS-CoV-2. This library was applied to the identification of viral infections directly on cell cultures, assessing the ability of the technique to discriminate between infected and non-infected profiles. Additionally, bioinformatic analyses were conducted to evaluate the structure, specificity, and reproducibility of the in-house library, and to understand its strengths and limitations. Sensitivity and specificity of the method were estimated by testing multiple culture batches from selected viruses included in the library. Together, these results provide a deeper understanding of the performance and applicability of MALDI-TOF in the virological context, highlighting its potential as a valuable research platform and a prospective tool for clinical viral detection.

Hyphal systems have been essential for the morphoanatomical characterization of basidiomes and mycelia of aphyllophoroid fungi for taxonomic purposes. They have also been shown to influence the consistency of basidiomes. Recent developments in areas such as mycelium composite production as sustainable materials have redirected scientists’ attention to these structures, particularly regarding their material resistance, where complex hyphal systems enhance the properties of these composites. Compounds such as farnesol and octenol trigger growth and differentiation processes in many fungal groups, and laccases have been proposed as enzymes involved in these processes, given their roles in the synthesis of cell wall pigments and other cell wall components. Given the easily quantifiable differences in hyphal knots and dimitic mycelium between Fuscoporia torulosa and Inocutis tamaricis, we employed them as models to study their responses to these compounds, thereby helping fill the knowledge gap in the modulation of macrofungal mycelial differentiation. A variable effect was observed on laccase induction, while radial growth was reduced by octenol by up to 83% in F. torulosa and 65% in I. tamaricis, and by farnesol by up to 80% in I. tamaricis, showing slight effects on F. torulosa. Reductions of up to 100% were observed in the combination of high doses of both chemicals.

This study investigated the effectiveness of ethanol (70%, 3 min), Ultraviolet-C irradiation (6 and 12 min), and ultrasound (37 kHz, 15 min) for decreasing Candida albicans, Aspergillus brasiliensis, and Listeria innocua on Greek Kalamon table olives before brining. Ethanol demonstrated the greatest decreases (>2.80 log10 for C. albicans, >2.09 log10 for A. brasiliensis, and >3.79 log10 for L. innocua). UV-C had a time-dependent impact, with 12 min producing more inactivation than 6 min (1.30, 1.05, and 1.57 log10, respectively, for C. albicans, A. brasiliensis, and L. innocua). Ultrasound alone produced minimal reductions (<0.60 log10). Overall, ethanol outperformed Ultraviolet-C and ultrasound in the test settings, with Ultraviolet-C providing moderate, exposure-dependent decreases. These findings stimulate additional research into non-thermal therapies and their practical use in table olive processing.

Rhamnolipids (RL) are biosurfactants produced mainly by Pseudomonas aeruginosa strains that have environmental and industrial applications. However, their industrial-scale production still faces the challenge of improving the efficiency and cost-effectiveness of the process. The aim of this work was to optimize the cultivation conditions to increase the RL production by using Response Surface Methodology with key parameters of the process, such as oxygen level, agitation, temperature, nutrients, and residual frying oil as a low-cost carbon source. The optimized parameters were 3.04 g/L of nitrogen, 0.5 vvm of aeration and 180 rpm of agitation, with which 52.2 g/L was obtained in 168 h. The critical micellar concentration (CMC) of this RL was 3.14 g/L, and the Oil Spreading assay confirmed the presence of surface-active compounds in the purified RL that generated an average halo area of 2746.7 ± 72.0 mm2, which represents an increase of 2063.41% ± 28.36% compared to the negative control. These advances could contribute to more sustainable, cost-effective RL production, promoting its application in bioremediation processes and other industries.

High-quality bacterial genomes are essential for robust comparative genomics, reliable taxonomic assignment, and accurate pathogen and antimicrobial resistance (AMR) surveillance. Yet, public repositories still contain highly heterogeneous assemblies, and genome quality is often judged using single metrics in isolation. Here we develop an integrative Genome Quality Index (GQI) that combines four complementary metrics—including BUSCO single-copy completeness, contig number, N50, and unmapped read percentage—into a composite, interpretable score. We re-assembled and evaluated 474 pathogenic bacterial genomes submitted from South Korea using a standardized Illumina-based pipeline and validated the framework on an independent Enterobacteriaceae dataset (n = 5781). Species-level analyses and unsupervised clustering revealed pronounced variation in genome quality (one-way ANOVA, p < 1.05 × 10−33), with Cronobacter sakazakii and Listeria monocytogenes showing consistently high GQI scores, whereas Mycobacterium tuberculosis exhibited broad variability, including clear low-quality outliers. After log-transforming skewed variables, contig count and N50 remained strongly negatively correlated (r = −0.83), while BUSCO completeness showed moderate positive association with N50 and negative association with unmapped reads. GQI scores spanned 0.23–0.96, with most genomes clustering between 0.70 and 0.85. A Random Forest classifier trained on the four raw metrics predicted GQI-based quality tiers (low, medium, high) with 97% accuracy. From the top-decile genomes, we derived empirical thresholds like BUSCO ≥ 98.6%, contigs ≤ 30, N50 ≥ 1 Mb, and unmapped reads ≤ 0.82% that refine existing recommendations and provide actionable curation criteria. Our framework complements tools such as CheckM, gVolante, and Hybracter by offering a platform-agnostic composite scoring system that can be integrated into submission workflows and surveillance pipelines to systematically flag low-quality genomes and improve the reliability of microbial genomics.

Microorganisms are considered a potential source of biofertilizers for mobilizing nutrients from insoluble mineral potassium (K). This study was conducted to evaluate the effects of liquid potassium-solubilizing bacteria, Cereibacter sphaeroides M-Sl-09, Rhodopseudomonas thermotolerans M-So-11, and Rhodopseudomonas palustris M-So-14 (LPS-PNSB), on soil K content, plant K uptake, growth, and yield of hybrid maize cultivated on alluvial soil in the dyke-protected area of An Phu, An Giang, Vietnam. Results showed that the application of LPS-PNSB significantly improved exchangeable soil K from 0.428 to 0.460–0.470 meq 100 g−1, total plant K uptake from 181.5 to 205.8–259.4 kg ha−1, and yield from 11.1 to 12.2–12.6 ton ha−1, compared with the recommended 100% NPK fertilization. The addition of LPS-PNSB allowed a 100% reduction in K fertilizer compared with the recommended rate while still maintaining yield. Hybrid maize grain yield further increased when 100% recommended K was applied in combination with LPS-PNSB, surpassing the yield obtained with 100% K alone.

We hypothesized that Tuber melanosporum colonization enhances growth and photosynthetic performance in Corylus avellana seedlings. Forty-eight seedlings were assessed for root colonization (stereomicroscopy, ITS sequencing) and photosynthetic traits (Li-6800F) under short-term disturbed and undisturbed rhizosphere conditions. Mycorrhizal colonization was found in 97.9% of seedlings (47/48). The mean colonization was 33.1% (SD = 16.1), 16.7% of seedlings showed more than 50% colonization per seedling, and 65.0% showed more than 30% colonization per seedling. Colonization declined with root depth and correlated with seedling length (r = 0.371, p = 0.01). In disturbed roots, longer root length predicted higher Gsw (r = 0.60), PhiCO2 (r = 0.77), and PhiPSII (r = 0.70), while collar diameter negatively affected transpiration (r = −0.60). In undisturbed roots, collar-proximal colonization improved PhiPSII (r = 0.69, p = 0.02). Undisturbed seedlings showed ~2× higher CO2 assimilation, stomatal conductance, quantum yield, and transpiration. These findings confirm that T. melanosporum enhances seedling physiology, especially under undisturbed conditions.

The use of lactose-utilizing microalgae offers a sustainable and cost-effective approach for the bioconversion of dairy industry side-streams and the reduction in microalgae production costs. This work aims to improve the biomass productivity of the lactose-utilizing microalgal strain Graesiella emersonii MSCL 1718 in concentrated cheese whey permeate. It was demonstrated that the mixotrophic growth of the axenic G. emersonii culture resulted in a significantly higher biomass productivity in 20% permeate medium compared to the heterotrophic cultivation. Furthermore, supplementation of the permeate medium with iron, zinc, cobalt, and molybdenum resulted in 12.8%, 12.9%, 9.3%, and 28.9% significant increases (p < 0.05) in biomass synthesis, respectively, compared to the control permeate group. In the subsequent experiment, G. emersonii cultivated in molybdenum-supplemented permeate resulted in 0.34 ± 0.02 g/(L·d) biomass productivity and twofold higher lipid content (30.21 ± 1.29%) compared to the photoautotrophic control in defined synthetic medium. Analysis of the fatty acid composition revealed a twofold increase in saturated fatty acids, reaching 62.16% under mixotrophic cultivation in permeate, compared with the photoautotrophic control. Overall, concentrated cheese permeate proved to be a suitable medium for G. emersonii biomass production, supporting both enhanced growth and increased lipid accumulation.

The intestinal microbiota plays a crucial role in maintaining epithelial barrier integrity, while its impairment and the resulting inflammation contribute to numerous human pathologies. To preserve intestinal homeostasis, various probiotics are being developed; however, their selection and validation require accessible yet physiologically relevant models. We recently established a high-throughput Gut-on-Chip model comprising human epithelial (Caco-2) cells and peripheral blood mononuclear cells (PBMCs), demonstrating epithelial barrier disruption and pro-inflammatory cytokine secretion upon inflammation induction. The present study aimed to evaluate the feasibility of co-culturing anaerobic members of the human intestinal microbiota within this model and to assess their effects on inflammation-induced epithelial damage. We successfully co-cultured five intestinal anaerobic bacterial species in direct contact with the epithelial monolayer for two days. As proof of concept, we demonstrate that live Bacteroides thetaiotaomicron and its supernatant preserve epithelial barrier integrity and attenuate CCL2 secretion by Caco-2 cells. In contrast, Clostridium scindens did not prevent epithelial damage but suppressed CCL20 secretion, revealing a promising target for future studies. By recapitulating some of the key aspects of intestinal inflammation, we suggest that the current Gut-on-Chip model has potential as an easy-to-use platform for screening next-generation probiotics and live biotherapeutics with homeostatic and immunomodulatory properties.

In efforts to enhance the sensory profile of coffee, fermentation variations have been implemented, including extending the process for prolonged periods. Such practices create imbalances among the microbial groups involved and increase populations of filamentous fungi, compromising product safety. To identify the filamentous fungi present in fermentations for up to 192 h, coffee samples were collected from fermentations conducted under semi-anaerobic (SA) and self-induced anaerobic fermentation (SIAF) conditions. Microscopic, metabolic, and rDNA sequencing techniques were applied to identify the filamentous fungi. Relative abundance and taxonomic classification were obtained through High-Throughput Sequencing of the ITS region. In addition, the presence of Ochratoxin A (OTA) was evaluated through HPLC/FLD. The most abundant genera identified was Aspergillus in SA fermentations, and Fusarium in SIAFs both at 192 h. 3438 OTUs of filamentous fungi were obtained, distributed across 11 orders, 20 families, and 17 genera. The results suggest a greater presence of mycotoxin-producing genera in fermentations with longer processing times, particularly under semi-anaerobic conditions. However, OTA levels remained below 0.8 ppb (µg/kg). These findings provide essential information for microbiological control of fermentation, supporting the maintenance of product safety in subsequent stages and ensuring the safety of the final product.