Fungal biotechnology is crucial for generating high-value enzymes and fermentation products. Despite its industrial importance, major knowledge gaps in understanding fungal genomic variation, phenotypic diversity, and protein function prediction constrain biological innovation. While advancements in sequencing technologies have established data science as an integral component in driving developments in industrial fungal biotechnology, the inherent complexity of fungal genomes and incompatible repositories continue to limit comprehensive characterization of biological relationships and their translation into industrial applications. This review examines recent progress in non-graph methodologies applied to fungal biology. Genome annotation tools uncover genetic variation through homology-based approaches and enable functional annotation of sequence variants. Metric-based methods identify horizontal gene transfer events, while multivariate techniques characterize phenotypic variation across conditions. However, the increasing diversity, scale, and multimodal nature of fungal datasets require more integrative frameworks. Graph data science, a multivariate approach to model complex relationships as networks, offers opportunities to overcome these challenges. We discuss how graph-based methods enhance the detection of genomic structural variation and enable the modeling of molecular interactions. Furthermore, we outline how these approaches facilitate the exploration of complex fungal systems through multi-taxon, reference-free analyses, that integrate evolutionary signals, functional associations, and curated knowledgebases. By surveying available fungal resources and their taxonomic and ecological representations, we identify well-characterized genera, highlight underexplored taxa requiring further data generation, and pinpoint the ecological biases inherent in current sequencing efforts. Collectively, these advancements demonstrate how graph data science can accelerate fungal research and bridge fundamental discoveries and biotechnological applications.

Systematic study of genomic loci in Escherichia coli B and K12 for genomic integration: application in plasmid-free astaxanthin production.

Temperature effects on growth and biochemical composition of Chlorella vulgaris under heterotrophic cultivation.

Protein phase separation for enhanced production of 3-hydroxypropionate and polyhydroxybutyrate by Halomonas.

Engineering complex phenotypes in Halomonas bluephagenesis TD01 via large-fragment manipulation and multiplex base editing.

The research and development trends in the biosynthesis of 7-aminocephalosporanic acid based on patent analysis

Critical evaluation of the key mediators causing life-threatening symptoms during human anaphylaxis.

This study presents a transformative “one-pot” biorefinery approach for the simultaneous production of hyaluronic acid (HA) and polyhydroxybutyrate (PHB) using an engineered, non-pathogenic Halomonas bluephagenesis TD01 chassis. By leveraging the principles of Next-Generation Industrial Biotechnology (NGIB), a one-step fermentation process was developed in nutrient-rich 40-LBG-Y medium, achieving a balanced metabolic flux that yielded 1.99 g/L and high-molecular-weight (HMw) HA (9.6 × 106 Da) as the highest HA-Mw reported by heterogeneous bacteria, alongside intracellular PHB (0.68 to 1.6 g/L). A bioactive HA-PHB nanoparticle scaffold was fabricated, exhibiting a highly porous, interconnected 3D sponge-like architecture with a significant particle size shift from 12 nm to 450 nm, confirming successful polymer complexation. Antimicrobial evaluations revealed that the scaffold exhibited preliminary antimicrobial potential against representative Gram-positive and Gram-negative strains against Staphylococcus aureus, Klebsiella variicola, and Candida albicans. Notably, while Pseudomonas aeruginosa metabolically exploited purified HA, the integrated scaffold reversed this effect, providing preliminary antimicrobial potential by sterically hindering bacterial hyaluronidases. Furthermore, Halomonas-derived HA consistently outperformed Moringa oil and complex emulsions in preliminary tests against a wide range of pathogenic microbes. These results demonstrate that this dual-product platform provides a sustainable, cost-effective source of high-performance functional materials for advanced antimicrobial coatings and clinical wound management.

This study presents the results of a comprehensive investigation of the phytochemical profile and microscopic structure of leaf tissues of two species of the genus Kalanchoe: K. pinnata (serrated leaves) and K. blossfeldiana (rounded leaves). The total phenolic and flavonoid contents (TPC and TFC) were determined spectrophotometrically using the Folin–Ciocalteu method and the complex formation with AlCl3, respectively. Antioxidant activity was evaluated based on radical- scavenging capacity using the DPPH and ABTS assays. Optical microscopy of the leaf epidermis was employed to examine the distribution of secondary metabolites. A clear relationship was established between leaf morphology, solvent composition, and the yield of extracted bioactive compounds. Microscopic analysis revealed a pronounced accumulation of anthocyanins in the vacuoles of epidermal cells of K. blossfeldiana, which correlates with its high TPC (1.217 mg/g) and TFC (4.20 mg/g) in the 40% aqueous–ethanolic extract. In contrast, the epidermis of K. pinnata appeared optically transparent, consistent with a lower concentration of phenolic compounds. Biochemical analysis demonstrated substantial catalase activity in both species, with higher values observed for K. blossfeldiana (73 μmol H2O2·min-1·g-1). The highest radical-scavenging activity in the DPPH assay was recorded for the 70% aqueous–ethanolic extract of K. blossfeldiana (48.9%). The presence of anthocyanin pigments in the epidermis is suggested as a reliable visual indicator of elevated antioxidant potential. Overall, the findings indicate that both tissue organization and extractant polarity are key factors influencing the efficiency of bioactive compound extraction from plant material. In addition, Kalanchoe species are widely cultivated and readily available plant resources, which makes them economically attractive for the large-scale production of biologically active compounds. This accessibility enhances their potential for practical applications in pharmaceutical, cosmetic, and biotechnological industries.

Seaweed represents a potential sustainable carbon source for industrial biotechnology, yet the workhorse bacterium Corynebacterium glutamicum cannot naturally metabolize the deoxy sugars L-rhamnose and L-fucose, abundant in green and brown seaweed, respectively. Expanding its substrate range is crucial for sustainable bioprocessing, by enabling utilization of the available biomass. In this study, we engineered C. glutamicum to utilize L-rhamnose and L-fucose by introducing the Escherichia coli operons rhaBADM and fucIKUA, enabling growth on these sugars as sole carbon sources. To enhance growth, we evaluated various transport systems and identified the non-native fucose permease (FucP) as the most efficient for L-rhamnose uptake, and the native myo-inositol transporter 2 (IolT2) as optimal for L-fucose uptake. During L-rhamnose and L-fucose utilization, L-lactaldehyde is formed as a byproduct. We demonstrate that the native acetaldehyde dehydrogenase encoded by ald also exhibits lactaldehyde dehydrogenase activity, and that its overexpression enhances L-lactaldehyde utilization. Finally, cultivation on green and brown seaweed hydrolysates enabled the engineered strains to achieve increased biomass formation through consumption of the targeted deoxy sugars. This study expands the substrate spectrum of C. glutamicum through pathway engineering, transport optimization, and functional identification of a native lactaldehyde dehydrogenase. Growth and L-lysine production on seaweed hydrolysates highlights the potential of this approach for sustainable marine biomass valorization and bioproduction of value-added compounds.

Machine learning in applied microbiology, from data quality to model validation and implementation.

Revisiting risk-adjusted Net Present Value: a practical framework for biotechnology valuation.

Microbial fermentation plays a crucial role in industrial biotechnology, however, conventional and manual optimization methods often encounter challenges related to scalability and precision. Despite notable progress, a significant limitation in the current literature remains. Most studies address artificial intelligence or nanotechnology applications in isolation, which limits their ability to overcome multifaceted bottlenecks in real-time control and sustainable scale-up of fermentation processes. This review examines the transformative impact of convergence in artificial intelligence (AI) and nanotechnology on fermentation processes. AI tools, including neural networks, genetic algorithms and deep reinforcement learning, are employed to predict microbial behaviour, adjust conditions in real time and boost yields. Meanwhile, nanotechnology offers smart and innovative solutions, such as nano-carriers and sensors, for targeted microbial modulation and enzyme activation. The review underscores latest research done on AI-optimized fermentation and nanoparticle-assisted systems, showing their potential in streamlining high-throughput screening and scaling up production. Although fully integrated AI-nanotech fermentation systems are still in development, current research indicates significant potential across sectors like biofuels, food and pharmaceuticals. Synergistically, these innovations suggest a more intelligent and sustainable future for bio-manufacturing, one that aligns with circular bio-economy objectives and advances key United Nations Sustainable Development Goals.

Biosynthesis of succinic acid (SA) represents one of the largest sectors in industrial biotechnology for biochemicalproduction. Currently, the markets for fossil-derived and bio-based SA are comparable in scale, with the bio-based segment expanding particularly rapidly. In response to the growing demand for sustainable and renewable production routes, diverse types of lignocellulosic biomass have been employed as feedstocks. This chapter provides an overview of the microorganisms commonly used in SA production, including native producers such as Actinobacillus succinogenes, Anaerobiospirillum succiniciproducens, Basfia succiniciproducens, Mannheimia succiniciproducens, as well as engineered producers like Corynebacterium glutamicum, Escherichia coli, Saccharomyces cerevisiae, Yarrowia lipolytica, Kluyveromyces marxianus, and Issatchenkia orientalis. Their production performance, including titer, yield, and productivity, on conventional substrates such as glucose and on mixed sugars derived from lignocellulosic biomass is reviewed. The chapter concludes with a discussion of future prospects, highlighting the importance of integrating designed enzymes, robust strains, and fermentation optimization for sustainable SA production.

The demand for clean label thickening agents follows the trend in the food and biotechnology industries away from chemically derived hydrocolloids. Exopolysaccharides (EPS) from lactic acid bacteria (LAB) have the potential to meet this demand, as they are produced during fermentation and exhibit texturising functionality, making them promising candidates for applications where natural origin is valued. This study examined EPS fermentation process from Leuconostoc citreum CNTA 860 using a two-level fractional factorial design (2⁶⁻²) to assess interaction effects among six operational factors. Initial sucrose concentration was the main driver of EPS synthesis, although agitation and inoculum size also significantly influenced EPS productivity and viscosity development. Regression models reached high predictive performance (R² = 0.989; Predicted R² = 0.925 at 12 h), confirming model adequacy during early fermentation. Under optimized conditions (600 rpm, 150 g/L sucrose, C/N = 100, inoculum 10⁸ CFU/mL, 25 °C, no sucrose pulsing), EPS concentration reached 70 g/L and broth viscosity 8200 cP after 24 h, exceptionally high values for L. citreum fermentations. SEC-HPLC revealed that the presence of a 3.26–6.50 kDa glucan fraction (20–40 glucose units) strongly correlated with viscosity (r = 0.70, p<0.001). This approach provides a robust framework for scale-up and positions EPS from L. citreum CNTA 860 as promising biothickeners for food and biotechnology applications. • Time-resolved DoE linked process key variables to EPS structure and rheology • Initial sucrose and agitation jointly drove EPS concentration and viscosity • A 3.3–6.5 kDa glucan fraction (20–40 glucose units) governed viscosity development • Leuconostoc citreum CNTA 860 excelled in EPS production with thickening capacity • Optimal conditions yielded 70 g/L EPS and 8200 cP viscosity, highest for L. citreum

Evolution at the speed of fermentation.

Engineering the yeast Yarrowia lipolytica for biomanufacturing.

Toward a circular bioeconomy: bioproduction based on Halomonas grown on non-food feedstocks.

Non-agricultural feedstocks for next-generation biomanufacturing with yeasts.

Coastal ecosystems are dynamic environments characterized by strong seasonal variability in physicochemical parameters and biological communities. In the western Mediterranean, the Region of Murcia (southeastern Spain) is characterized by notable biodiversity and ecological heterogeneity, encompassing diverse habitats, including rocky shores, sandy beaches, seagrass meadows, and the Mar Menor, one of Europe’s largest hypersaline lagoons. Within these systems, marine yeasts play critical ecological roles in organic matter recycling and produce metabolites of biotechnological and medical interest. This study presents the first comprehensive survey of culturable marine yeasts from the Mediterranean coast of the Region of Murcia. From seawater and sediment samples, 415 strains were identified via internal transcribed spacer (ITS) and large subunit (LSU) rDNA sequencing, revealing 90 species across 44 genera, including 78 known taxa and 12 potentially novel ones. Most isolates were assigned to the phylum Ascomycota (62%), primarily distributed among the classes Pichiomycetes, Dothideomycetes, Saccharomycetes, and Dipodascomycetes, whereas Basidiomycota accounted for the remaining 38%, mainly comprising the classes Tremellomycetes and Microbotryomycetes. The genera most represented in both seawater and sediment were Rhodotorula and Candida, and approximately 10% of the isolates corresponded to stress-tolerant black yeast-like fungi (Aureobasidium spp., Hortaeawerneckii, Exophialaoligosperma, and Zalariaalba), a group notable for its taxonomic novelty and valuable biotechnological traits. Culturable yeast assemblages displayed pronounced spatiotemporal variability, with diversity generally increasing during milder seasons and in areas influenced by anthropogenic activity, suggesting the combined effect of natural gradients and human-driven alterations. Representative strains exhibited broad enzymatic capabilities, producing extracellular cellulases, proteases, xylanases, amylases, chitinases, and pectinases, underscoring their ecological role in organic matter turnover and nutrient cycling. The findings provide novel insights into the taxonomic composition and metabolic potential of marine yeasts recovered from the Mediterranean Sea and set the basis for their future exploitation in industrial and environmental biotechnology.