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18 pages, 7274 KiB  
Article
Functional Compression Fabrics with Dual Scar-Suppressing and Antimicrobial Properties: Microencapsulation Design and Performance Evaluation
by Lihuan Zhao, Changjing Li, Mingzhu Yuan, Rong Zhang, Xinrui Liu, Xiuwen Nie and Bowen Yan
J. Funct. Biomater. 2025, 16(8), 287; https://doi.org/10.3390/jfb16080287 - 5 Aug 2025
Abstract
Pressure therapy combined with silicone has a significant effect on scar hyperplasia, but limitations such as long-term wearing of compression garments (CGs) can easily cause bacterial infection, cleanliness, and lifespan problems of CGs caused by the tedious operation of applying silicone. In this [...] Read more.
Pressure therapy combined with silicone has a significant effect on scar hyperplasia, but limitations such as long-term wearing of compression garments (CGs) can easily cause bacterial infection, cleanliness, and lifespan problems of CGs caused by the tedious operation of applying silicone. In this study, a compression garment fabric (CGF) with both inhibition of scar hyperplasia and antibacterial function was prepared. A polydimethylsiloxane (PDMS)-loaded microcapsule (PDMS-M) was prepared with chitosan quaternary ammonium salt (HACC) and sodium alginate (SA) as wall materials and PDMS as core materials by the complex coagulation method. The PDMS-Ms were finished on CGF and modified with (3-aminopropyl)triethoxysilane (APTES) to obtain PDMS-M CGF, which was further treated with HACC to produce PDMS-M-HACC CGF. X-ray Photoelectron Spectroscopy(XPS) and Fourier transform infrared spectroscopy (FTIR) analysis confirmed the formation of covalent bonding between PDMS-M and CGF. The PDMS-M CGF exhibited antibacterial rates of 94.2% against Gram-negative bacteria Escherichia coli (E. coli, AATCC 6538) and of 83.1% against Gram-positive bacteria Staphylococcus aureus (S. aureus, AATCC 25922). The antibacterial rate of PDMS-M-HACC CGF against both E. coli and S. aureus reached 99.9%, with wash durability reaching grade AA for E. coli and approaching grade A for S. aureus. The finished CGF maintained good biocompatibility and showed minimal reduction in moisture permeability compared to unfinished CGF, though with decreased elastic recovery, air permeability and softness. The finished CGF of this study is expected to improve the therapeutic effect of hypertrophic scars and improve the quality of life of patients with hypertrophic scars. Full article
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24 pages, 1542 KiB  
Review
Genome-Editing Tools for Lactic Acid Bacteria: Past Achievements, Current Platforms, and Future Directions
by Leonid A. Shaposhnikov, Aleksei S. Rozanov and Alexey E. Sazonov
Int. J. Mol. Sci. 2025, 26(15), 7483; https://doi.org/10.3390/ijms26157483 (registering DOI) - 2 Aug 2025
Viewed by 121
Abstract
Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous [...] Read more.
Lactic acid bacteria (LAB) are central to food, feed, and health biotechnology, yet their genomes have long resisted rapid, precise manipulation. This review charts the evolution of LAB genome-editing strategies from labor-intensive RecA-dependent double-crossovers to state-of-the-art CRISPR and CRISPR-associated transposase systems. Native homologous recombination, transposon mutagenesis, and phage-derived recombineering opened the door to targeted gene disruption, but low efficiencies and marker footprints limited throughput. Recent phage RecT/RecE-mediated recombineering and CRISPR/Cas counter-selection now enable scar-less point edits, seamless deletions, and multi-kilobase insertions at efficiencies approaching model organisms. Endogenous Cas9 systems, dCas-based CRISPR interference, and CRISPR-guided transposases further extend the toolbox, allowing multiplex knockouts, precise single-base mutations, conditional knockdowns, and payloads up to 10 kb. The remaining hurdles include strain-specific barriers, reliance on selection markers for large edits, and the limited host-range of recombinases. Nevertheless, convergence of phage enzymes, CRISPR counter-selection and high-throughput oligo recombineering is rapidly transforming LAB into versatile chassis for cell-factory and therapeutic applications. Full article
(This article belongs to the Special Issue Probiotics in Health and Disease)
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23 pages, 1789 KiB  
Review
Multi-Enzyme Synergy and Allosteric Regulation in the Shikimate Pathway: Biocatalytic Platforms for Industrial Applications
by Sara Khan and David D. Boehr
Catalysts 2025, 15(8), 718; https://doi.org/10.3390/catal15080718 - 28 Jul 2025
Viewed by 392
Abstract
The shikimate pathway is the fundamental metabolic route for aromatic amino acid biosynthesis in bacteria, plants, and fungi, but is absent in mammals. This review explores how multi-enzyme synergy and allosteric regulation coordinate metabolic flux through this pathway by focusing on three key [...] Read more.
The shikimate pathway is the fundamental metabolic route for aromatic amino acid biosynthesis in bacteria, plants, and fungi, but is absent in mammals. This review explores how multi-enzyme synergy and allosteric regulation coordinate metabolic flux through this pathway by focusing on three key enzymes: 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase, chorismate mutase, and tryptophan synthase. We examine the structural diversity and distribution of these enzymes across evolutionary domains, highlighting conserved catalytic mechanisms alongside species-specific regulatory adaptations. The review covers directed evolution strategies that have transformed naturally regulated enzymes into standalone biocatalysts with enhanced activity and expanded substrate scope, enabling synthesis of non-canonical amino acids and complex organic molecules. Industrial applications demonstrate the pathway’s potential for sustainable production of pharmaceuticals, polymer precursors, and specialty chemicals through engineered microbial platforms. Additionally, we discuss the therapeutic potential of inhibitors targeting pathogenic organisms, particularly their mechanisms of action and antimicrobial efficacy. This comprehensive review establishes the shikimate pathway as a paradigmatic system where understanding allosteric networks enables the rational design of biocatalytic platforms, providing blueprints for biotechnological innovation and demonstrating how evolutionary constraints can be overcome through protein engineering to create superior industrial biocatalysts. Full article
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19 pages, 3813 KiB  
Article
An OSMAC Strategy for the Production of Antimicrobial Compounds by the Amazonian Fungi Talaromyces pinophilus CCM-UEA-F0414 and Penicillium paxilli CCM-UEA-F0591
by Cleudiane Pereira de Andrade, Caroline Dutra Lacerda, Raíssa Assímen Valente, Liss Stone de Holanda Rocha, Anne Terezinha Fernandes de Souza, Dorothy Ívila de Melo Pereira, Larissa Kirsch Barbosa, Cleiton Fantin, Sergio Duvoisin Junior and Patrícia Melchionna Albuquerque
Antibiotics 2025, 14(8), 756; https://doi.org/10.3390/antibiotics14080756 - 27 Jul 2025
Viewed by 321
Abstract
Background/Objectives: The emergence of antimicrobial resistance represents a critical global health threat, requiring the discovery of novel bioactive compounds. Fungi from Amazonian biodiversity are promising sources of secondary metabolites with potential antimicrobial activity. This study aimed to investigate the production of antimicrobial compounds [...] Read more.
Background/Objectives: The emergence of antimicrobial resistance represents a critical global health threat, requiring the discovery of novel bioactive compounds. Fungi from Amazonian biodiversity are promising sources of secondary metabolites with potential antimicrobial activity. This study aimed to investigate the production of antimicrobial compounds by two Amazonian fungal strains using the OSMAC (One Strain–Many Compounds) approach. Methods: Two fungal strains, Talaromyces pinophilus CCM-UEA-F0414 and Penicillium paxilli CCM-UEA-F0591, were cultivated under five distinct culture media to modulate secondary metabolite production. Ethyl acetate extracts were prepared and evaluated for antimicrobial activity against Gram-positive and Gram-negative bacteria, as well as pathogenic yeasts. Chemical characterization was performed using thin-layer chromatography (TLC), Fourier Transform Infrared Spectroscopy (FTIR), Ultraviolet–Visible (UV-Vis) spectroscopy, and Ultra-High-Performance Liquid Chromatography with Diode Array Detection (uHPLC-DAD). Results: The extracts exhibited significant antimicrobial activity, with minimum inhibitory concentrations (MICs) ranging from 78 to 5000 µg/mL. Chemical analyses revealed the presence of phenolic compounds, particularly caffeic and chlorogenic acids. Variations in the culture media substantially affected both the metabolite profiles and antimicrobial efficacy of the extracts. Conclusions: The OSMAC strategy effectively enhanced the metabolic diversity of the Amazonian fungal strains, leading to the production of bioactive metabolites with antimicrobial potential. These findings support the importance of optimizing culture conditions to unlock the biosynthetic capacity of Amazonian fungi as promising sources of antimicrobial agents. Full article
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16 pages, 2045 KiB  
Article
The Antimicrobial Activity of Silver Nanoparticles Biosynthesized Using Cymbopogon citratus Against Multidrug-Resistant Bacteria Isolated from an Intensive Care Unit
by Bianca Picinin Gusso, Aline Rosa Almeida, Michael Ramos Nunes, Daniela Becker, Dachamir Hotza, Cleonice Gonçalves da Rosa, Vanessa Valgas dos Santos and Bruna Fernanda da Silva
Pharmaceuticals 2025, 18(8), 1120; https://doi.org/10.3390/ph18081120 - 27 Jul 2025
Viewed by 353
Abstract
Objective: This study aimed to evaluate the in vitro efficacy of silver nanoparticles (AgNPs) synthesized by bioreduction using lemongrass (Cymbopogon citratus) essential oil against multidrug-resistant (MDR) bacteria isolated from an Intensive Care Unit (ICU). Methods: The essential oil was extracted and [...] Read more.
Objective: This study aimed to evaluate the in vitro efficacy of silver nanoparticles (AgNPs) synthesized by bioreduction using lemongrass (Cymbopogon citratus) essential oil against multidrug-resistant (MDR) bacteria isolated from an Intensive Care Unit (ICU). Methods: The essential oil was extracted and characterized by gas chromatography–mass spectrometry (GC-MS). Antioxidant activity was assessed using the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay, the 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay, and total phenolic content. AgNPs (3 mM and 6 mM silver nitrate) were characterized by UV-Vis spectroscopy, dynamic light scattering (DLS), zeta potential, transmission electron microscopy (TEM), and Fourier-transform infrared (FTIR) spectroscopy. Bacterial isolates were obtained from ICU surfaces and personal protective equipment (PPE). Results: The essential oil presented citral A, citral B, and β-myrcene as major components (97.5% of identified compounds). AgNPs at 3 mM showed smaller size (87 nm), lower Polydispersity Index (0.14), and higher colloidal stability (−23 mV). The 6 mM formulation (147 nm; PDI 0.91; −10 mV) was more effective against a strain of Enterococcus spp. resistant to all antibiotics tested. FTIR analysis indicated the presence of O–H, C=O, and C–O groups involved in nanoparticle stabilization. Discussion: The higher antimicrobial efficacy of the 6 mM formulation was attributed to the greater availability of active AgNPs. Conclusions: The green synthesis of AgNPs using C. citratus essential oil proved effective against MDR bacteria and represents a sustainable and promising alternative for microbiological control in healthcare environments. Full article
(This article belongs to the Special Issue Therapeutic Potential of Silver Nanoparticles (AgNPs), 2nd Edition)
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16 pages, 1319 KiB  
Review
Assessing the Divergent Soil Phosphorus Recovery Strategies in Domesticated and Wild Crops
by Mary M. Dixon and Jorge M. Vivanco
Plants 2025, 14(15), 2296; https://doi.org/10.3390/plants14152296 - 25 Jul 2025
Viewed by 362
Abstract
Plant-essential phosphorus (P) is a sparingly available mineral in soils. Phosphorus fertilizers—produced by the transformation of insoluble to soluble phosphates—are thus applied to agroecosystems. With advancements in commercial agriculture, crops have been increasingly adapted to grow in fertile environments. Wild crop relatives, however, [...] Read more.
Plant-essential phosphorus (P) is a sparingly available mineral in soils. Phosphorus fertilizers—produced by the transformation of insoluble to soluble phosphates—are thus applied to agroecosystems. With advancements in commercial agriculture, crops have been increasingly adapted to grow in fertile environments. Wild crop relatives, however, are adapted to grow in unfertilized soils. In response to these two conditions of P bioavailability (fertilized agroecosystems and unfertilized natural soils), domesticated crops and wild species employ different strategies to grow and develop. It is essential to understand strategies related to P acquisition that may have been lost to domestication, and here we present, for the first time, that across species, modern cultivars engage in physical (i.e., root morphological) mechanisms while their wild relatives promote ecological (i.e., root-microbial) mechanisms. Domesticated crops showcase shallower root system architecture and engage in topsoil foraging to acquire P from the nutrient-stratified environments common to fertilized agroecosystems. Wild species associate with P-cycling bacteria and AM fungi. This divergence in P recovery strategies is a novel delineation of current research that has implications for enhancing agricultural sustainability. By identifying the traits related to P recovery that have been lost to domestication, we can strengthen the P recovery responses by modern crops and reduce P fertilization. Full article
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20 pages, 4025 KiB  
Article
Genomic Analysis of Cadmium-Resistant and Plant Growth-Promoting Burkholderia alba Isolated from Plant Rhizosphere
by Luyao Feng, Xin Liu, Nan Wang, Zhuli Shi, Yu Wang, Jianpeng Jia, Zhufeng Shi, Te Pu and Peiwen Yang
Agronomy 2025, 15(8), 1780; https://doi.org/10.3390/agronomy15081780 - 24 Jul 2025
Viewed by 311
Abstract
Reducing the application of chemical fertilizers and remediating heavy metal pollution in soil are important directions in current agricultural research. Utilizing the plant-growth-promoting and remediation capabilities of bacteria can provide more environmentally friendly assistance to agricultural production. In this study, the Burkholderia alba [...] Read more.
Reducing the application of chemical fertilizers and remediating heavy metal pollution in soil are important directions in current agricultural research. Utilizing the plant-growth-promoting and remediation capabilities of bacteria can provide more environmentally friendly assistance to agricultural production. In this study, the Burkholderia alba YIM B08401 strain was isolated and identified from rhizospheric soil, subjected to whole-genome sequencing and analysis, and its Cd2+ adsorption efficiency and characteristics were confirmed using multiple experimental methods, including atomic absorption spectrometry (AAS), Fourier transform infrared spectroscopy (FTIR), and scanning electron microscopy with energy-dispersive X-ray spectroscopy (SEM-EDS). The results showed that the genome of strain YIM B08401 has a total length of 7,322,157 bp, a GC content of 66.39%, and predicts 6504 protein-coding sequences. It contains abundant functional genes related to nutrient conversion (phosphate solubilization, sulfur metabolism, zinc solubilization, siderophore production), plant hormone regulation (indole-3-acetic acid secretion, ACC deaminase production), phenolic acid degradation, root colonization, heavy metal tolerance, pathogen antagonism, and the production of antagonistic secondary metabolites. Additionally, strain YIM B08401 can specifically bind to Cd2+ through various functional groups on the cell surface, such as C-O-C, P=O, and O-H, enabling biosorption. In conclusion, strain YIM B08401 is an excellent strain with plant-growth-promoting, disease-resistant, and bioremediation capabilities, warranting further development as a biofertilizer for agricultural applications to promote green and sustainable agricultural development. Full article
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16 pages, 3181 KiB  
Article
Effects of Lactic Acid Bacteria Fermentation on the Release and Biotransformation of Bound Phenolics in Ma Bamboo Shoots (Dendrocalamus latiflorus Munro)
by Liangshi Zhang, Anping Li, Hemei Liu, Qifeng Mo and Zhengchang Zhong
Foods 2025, 14(15), 2573; https://doi.org/10.3390/foods14152573 - 23 Jul 2025
Viewed by 290
Abstract
Lactic acid bacteria fermentation has the potential to enhance the biological activity of bamboo shoot polyphenols. The aim of this study was to investigate the release pattern and biotransformation mechanism of bound phenols from bamboo shoots prepared by fermentation with Lactobacillus acidophilus, [...] Read more.
Lactic acid bacteria fermentation has the potential to enhance the biological activity of bamboo shoot polyphenols. The aim of this study was to investigate the release pattern and biotransformation mechanism of bound phenols from bamboo shoots prepared by fermentation with Lactobacillus acidophilus, Pediococcus pentosaceus, and Lactobacillus plantarum. The results showed that compared with unfermented controls, bound forms of vanillic acid, p-coumaric acid, and ferulic acid significantly decreased, while their free forms increased substantially after 6 d fermentation (p < 0.05). Quantitative analysis revealed particularly dramatic transformations for p-coumaric acid, which showed a 30–3000% increase in free form, and ferulic acid with a 203–359% increase in free form. Pediococcus pentosaceus demonstrated outstanding performance in bound phenol release and conversion, correlating with its higher β-glucosidase (0.67 U/g) and ferulic acid esterase (0.69 U/g) production. FITR, SEM, and IFM also demonstrated that LAB fermentation led to changes between free and bound phenols in bamboo shoots. These results demonstrate Pediococcus pentosaceus fermentation most effectively liberates bound phenolics, significantly improving their bioavailability for functional food applications. Full article
(This article belongs to the Section Food Microbiology)
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15 pages, 4484 KiB  
Article
Effects of Lanthanum-Modified Bentonite on Antibiotic Resistance Genes and Bacterial Communities in Tetracycline-Contaminated Water Environments
by Wanzhong Wang, Sijia Liang, Shuai Zhang, Daming Wei, Xueting Xu and Peng Zhang
Water 2025, 17(15), 2188; https://doi.org/10.3390/w17152188 - 22 Jul 2025
Viewed by 288
Abstract
Water environments and sediments are important reservoirs for antibiotic resistance genes (ARGs). Under the pressure of antibiotics, ARGs can transform between microorganisms. Lanthanum-modified bentonite (LMB) is a phosphorus passivation material with good prospects in water environment restoration. After a treatment with LMB, the [...] Read more.
Water environments and sediments are important reservoirs for antibiotic resistance genes (ARGs). Under the pressure of antibiotics, ARGs can transform between microorganisms. Lanthanum-modified bentonite (LMB) is a phosphorus passivation material with good prospects in water environment restoration. After a treatment with LMB, the phosphorus forms in water and sediments will change, which may have an impact on microorganisms and the transmission of ARGs. To investigate the effects of LMB and antibiotics on ARGs and bacterial communities in sediment and aquatic environments, LMB and tetracycline (Tet) were added individually and in combination to mixed samples of sediment and water. The results showed that the addition of either LMB or Tet increased the abundance of intI1 and tetA genes in both the sediment and water, with the Tet addition increasing ARGs to more than 1.5 times the abundance in the control group. However, when LMB and Tet were present simultaneously, the abundance of ARGs showed no significant difference compared to the control group. Tet and LMB also affected the bacterial community structure and function in the samples and had different effects on the sediment and water. A correlation analysis revealed that the potential host bacteria of the intI1 and tetA genes were unclassified_Geobacteraceae, Geothrix, Flavobacterium, Anaeromyxobacter, and Geothermobacter. These findings indicate that Tet or LMB may increase the dissemination of ARGs by affecting microbial communities, while LMB may reduce the impact of Tet through adsorption, providing a reference for the safety of the LMB application in the environment and its other effects (alleviating antibiotic pollution) in addition to phosphorus removal. Full article
(This article belongs to the Section Water Quality and Contamination)
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12 pages, 722 KiB  
Review
Bacteriophages: Potential Candidates for the Dissemination of Antibiotic Resistance Genes in the Environment
by Shahid Sher, Husnain Ahmad Khan, Zaman Khan, Muhammad Sohail Siddique, Dilara Abbas Bukhari and Abdul Rehman
Targets 2025, 3(3), 25; https://doi.org/10.3390/targets3030025 - 22 Jul 2025
Viewed by 484
Abstract
The invention of antibacterial agents (antibiotics) was a significant event in the history of the human race, and this invention changed the way in which infectious diseases were cured; as a result, many lives have been saved. Recently, antibiotic resistance has developed as [...] Read more.
The invention of antibacterial agents (antibiotics) was a significant event in the history of the human race, and this invention changed the way in which infectious diseases were cured; as a result, many lives have been saved. Recently, antibiotic resistance has developed as a result of excessive use of antibiotics, and it has become a major threat to world health. ARGs are spread across biomes and taxa of bacteria via lateral or horizontal gene transfer (HGT), especially via conjugation, transformation, and transduction. This review concerns transduction, whereby bacteriophages or phages facilitate gene transfer in bacteria. Bacteriophages are just as common and many times more numerous than their bacterial prey, and these phages are much more influential in controlling the population of bacteria. It is estimated that 25% of overall genes of Escherichia coli have been copied by other species of bacteria due to the HGT process. Transduction may take place via a generalized or specialized mechanism, with phages being ubiquitous in nature. Phage and virus-like particle (VLP) metagenomics have uncovered the emergence of ARGs and mobile genetic elements (MGEs) of bacterial origins. These genes, when transferred to bacteria through transduction, confer resistance to antibiotics. ARGs are spread through phage-based transduction between the environment and bacteria related to people or animals, and it is vital that we further understand and tackle this mechanism in order to combat antimicrobial resistance. Full article
(This article belongs to the Special Issue Small-Molecule Antibiotic Drug Development)
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20 pages, 6178 KiB  
Article
Time Evolution of Bacterial Resistance Observed with Principal Component Analysis
by Claudia P. Barrera Patiño, Mitchell Bonner, Andrew Ramos Borsatto, Jennifer M. Soares, Kate C. Blanco and Vanderlei S. Bagnato
Antibiotics 2025, 14(7), 729; https://doi.org/10.3390/antibiotics14070729 - 20 Jul 2025
Viewed by 411
Abstract
Background/Objectives: In recent work, we have demonstrated that principal component analysis (PCA) and Fourier Transformation Infrared (FTIR) spectra are powerful tools for analyzing the changes in microorganisms at the biomolecular level to detect changes in bacteria with resistance to antibiotics. Here biochemical [...] Read more.
Background/Objectives: In recent work, we have demonstrated that principal component analysis (PCA) and Fourier Transformation Infrared (FTIR) spectra are powerful tools for analyzing the changes in microorganisms at the biomolecular level to detect changes in bacteria with resistance to antibiotics. Here biochemical structural changes in Staphylococcus aureus were analyzed over exposure time with the goal of identifying trends inside the samples that have been exposed to antibiotics for increasing amounts of time and developed resistance. Methods: All studied data was obtained from FTIR spectra of samples with induced antibiotic resistance to either Azithromycin, Oxacillin, or Trimethoprim/Sulfamethoxazole following the evolution of this development over four increasing antibiotic exposure periods. Results: The processing and data analysis with machine learning algorithms performed on this FTIR spectral database allowed for the identification of patterns across minimum inhibitory concentration (MIC) values associated with different exposure times and both clusters from hierarchical classification and PCA. Conclusions: The results enable the observation of resistance development pathways for the sake of knowing the present stage of resistance of a bacterial sample. This is carried out via machine learning methods for the purpose of faster and more effective infection treatment in healthcare settings. Full article
(This article belongs to the Section Mechanism and Evolution of Antibiotic Resistance)
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36 pages, 6346 KiB  
Article
Thermoresponsive Effects in Droplet Size Distribution, Chemical Composition, and Antibacterial Effectivity in a Palmarosa (Cymbopogon martini) O/W Nanoemulsion
by Erick Sánchez-Gaitán, Ramón Rivero-Aranda, Vianney González-López and Francisco Delgado
Colloids Interfaces 2025, 9(4), 47; https://doi.org/10.3390/colloids9040047 - 19 Jul 2025
Viewed by 170
Abstract
The design of emulsions at the nanoscale is a significant application of nanotechnology. For spherical droplets and a given volume of dispersed phase, the nanometre size of droplets inversely increases the total area, A=3Vr, allowing greater contact with [...] Read more.
The design of emulsions at the nanoscale is a significant application of nanotechnology. For spherical droplets and a given volume of dispersed phase, the nanometre size of droplets inversely increases the total area, A=3Vr, allowing greater contact with organic and inorganic materials during application. In topical applications, not only is cell contact increased, but also permeability in the cell membrane. Nanoemulsions typically achieve kinetic stability rather than thermodynamic stability, so their commercial application requires reasonable resistance to flocculation and coalescence, which can be affected by temperature changes. Therefore, their thermoresponsive characterisation becomes relevant. In this work, we analyse this response in an O/W nanoemulsion of Palmarosa for antibacterial purposes that has already shown stability for one year at controlled room temperature. We now study hysteresis processes and the behaviour of the statistical distribution in droplet size by Dynamic Light Scattering, obtaining remarkable stability under temperature changes up to 50 °C. This includes a maintained chemical composition observed using Fourier Transform Infrared Spectroscopy and the preservation of antibacterial properties analysed through optical density tests on cultures and the Spread-Plate technique for bacteria colony counting. We obtain practically closed hysteresis curves for some tracers of droplet size distributions through controlled thermal cycles between 10 °C and 50 °C, exhibiting a non-linear behaviour in their distribution. In general, the results show notable physical, chemical, and antibacterial stability, suitable for commercial applications. Full article
(This article belongs to the Special Issue Recent Advances on Emulsions and Applications: 3rd Edition)
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10 pages, 558 KiB  
Communication
Carbon Sink Potential of Sulfur-Oxidizing Bacteria in Groundwater at Petroleum-Contaminated Sites
by Pingping Cai, Zhuo Ning and Min Zhang
Microorganisms 2025, 13(7), 1688; https://doi.org/10.3390/microorganisms13071688 - 18 Jul 2025
Viewed by 266
Abstract
Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough [...] Read more.
Groundwater at petroleum-contaminated sites typically exhibits elevated dissolved inorganic carbon (DIC) levels due to hydrocarbon biodegradation; however, our prior field investigations revealed an enigmatic DIC depletion anomaly that starkly contradicts this global pattern and points to an unrecognized carbon sink. In a breakthrough demonstration, this study provides the first experimental confirmation that sulfur-oxidizing bacteria (SOB) drive substantial carbon sequestration via a coupled sulfur oxidation autotrophic assimilation process. Through integrated hydrochemical monitoring and 16S rRNA sequencing in an enrichment culture system, we captured the complete DIC transformation trajectory: heterotrophic acetate degradation initially increased DIC to 370 mg/L, but subsequent autotrophic assimilation by SOB dramatically reduced DIC to 270 mg/L, yielding a net consumption of 85 mg/L. The distinctive pH dynamics (initial alkalization followed by acidification) further corroborated microbial regulation of carbon cycling. Critically, Pseudomonas stutzeri and P. alcaliphila were identified as the dominant carbon-fixing agents. These findings definitively establish that chemolithoautotrophic SOB convert DIC into organic carbon through a “sulfur oxidation-carbon fixation” coupling mechanism, overturning the conventional paradigm of petroleum-contaminated sites as perpetual carbon sources. The study fundamentally redefines natural attenuation frameworks by introducing microbial carbon sink potential as an essential assessment metric for environmental sustainability. Full article
(This article belongs to the Section Environmental Microbiology)
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19 pages, 4718 KiB  
Article
Assessment of Winery By-Products as Ingredients as a Base of “3S” (Safe, Salubrious, and Sustainable) Fermented Beverages Rich in Bioactive Anthocyanins
by Berta María Cánovas, Irene Pérez-Novas, Cristina García-Viguera, Raúl Domínguez-Perles and Sonia Medina
Foods 2025, 14(14), 2514; https://doi.org/10.3390/foods14142514 - 17 Jul 2025
Viewed by 508
Abstract
Oenological residues may cause environmental pollution when processing does not significantly reduce volume and/or harmful conditions. The lack of proper valorisation alternatives entails high disposal costs and resource inefficiency that jeopardise the sustainability and competitiveness of the industry. Interestingly, wine by-products are underappreciated [...] Read more.
Oenological residues may cause environmental pollution when processing does not significantly reduce volume and/or harmful conditions. The lack of proper valorisation alternatives entails high disposal costs and resource inefficiency that jeopardise the sustainability and competitiveness of the industry. Interestingly, wine by-products are underappreciated sources of multipurpose bioactive compounds, such as anthocyanins, associated with health benefits. Alternatively, transforming oenological by-products into valuable co-products will promote sustainability and thus, create new business opportunities. In this context, the present study has assessed the applicability of winery by-products (grape pomace and wine lees) as ingredients to develop new functional kombucha-analogous beverages “3S” (safe, salubrious, and sustainable) by the Symbiotic Culture of Bacteria and Yeast (SCOBY). Concerning the main results, during the kombucha’s development, the fermentation reactions modified the physicochemical parameters of the beverages, namely pH, total soluble solids, acetic acid, ethanol, and sugars, which remained stable throughout the monitored shelf-life period considered (21 days). The fermented beverages obtained exhibited high anthocyanin concentration, especially when using wine lees as an ingredient (up to 5.60 mg/L at the end of the aerobic fermentation period (10 days)) compared with the alternative beverages produced using grape pomace (1.69 mg/L). These findings demonstrated that using winery by-products for the development of new “3S” fermented beverages would provide a dietary source of bioactive compounds (mainly anthocyanins), further supporting new valorisation chances and thus contributing to the competitiveness and sustainability of the winery industries. This study opens a new avenue for cross-industry innovation, merging fermentation traditions with a new eco-friendly production of functional beverages that contribute to transforming oenological residues into valuable co-products. Full article
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20 pages, 1065 KiB  
Review
Microbial Genome Editing with CRISPR–Cas9: Recent Advances and Emerging Applications Across Sectors
by Chhavi Dudeja, Amish Mishra, Ansha Ali, Prem Pratap Singh and Atul Kumar Jaiswal
Fermentation 2025, 11(7), 410; https://doi.org/10.3390/fermentation11070410 - 16 Jul 2025
Viewed by 946
Abstract
CRISPR technology, which is derived from the bacterial adaptive immune system, has transformed traditional genetic engineering techniques, made strain engineering significantly easier, and become a very versatile genome editing system that allows for precise, programmable modifications to a wide range of microbial genomes. [...] Read more.
CRISPR technology, which is derived from the bacterial adaptive immune system, has transformed traditional genetic engineering techniques, made strain engineering significantly easier, and become a very versatile genome editing system that allows for precise, programmable modifications to a wide range of microbial genomes. The economies of fermentation-based manufacturing are changing because of its quick acceptance in both academic and industry labs. CRISPR processes have been used to modify industrially significant bacteria, including the lactic acid producers, Clostridium spp., Escherichia coli, and Corynebacterium glutamicum, in order to increase the yields of bioethanol, butanol, succinic acid, acetone, and polyhydroxyalkanoate precursors. CRISPR-mediated promoter engineering and single-step multiplex editing have improved inhibitor tolerance, raised ethanol titers, and allowed for the de novo synthesis of terpenoids, flavonoids, and recombinant vaccines in yeasts, especially Saccharomyces cerevisiae and emerging non-conventional species. While enzyme and biopharmaceutical manufacturing use CRISPR for quick strain optimization and glyco-engineering, food and beverage fermentations benefit from starter-culture customization for aroma, texture, and probiotic functionality. Off-target effects, cytotoxicity linked to Cas9, inefficient delivery in specific microorganisms, and regulatory ambiguities in commercial fermentation settings are some of the main challenges. This review provides an industry-specific summary of CRISPR–Cas9 applications in microbial fermentation and highlights technical developments, persisting challenges, and industrial advancements. Full article
(This article belongs to the Section Fermentation Process Design)
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