Search Results (1,557)

This review explores the biofilm architecture and drug resistance of Enterococcus faecalis in clinical and environmental settings. The biofilm in E. faecalis is a heterogeneous, three-dimensional, mushroom-like or multilayered structure, characteristically forming diplococci or short chains interspersed with water channels for nutrient exchange and waste removal. Exopolysaccharides, proteins, lipids, and extracellular DNA create a protective matrix. Persister cells within the biofilm contribute to antibiotic resistance and survival. The heterogeneous architecture of the E. faecalis biofilm contains both dense clusters and loosely packed regions that vary in thickness, ranging from 10 to 100 µm, depending on the environmental conditions. The pathogenicity of the E. faecalis biofilm is mediated through complex interactions between genes and virulence factors such as DNA release, cytolysin, pili, secreted antigen A, and microbial surface components that recognize adhesive matrix molecules, often involving a key protein called enterococcal surface protein (Esp). Clinically, it is implicated in a range of nosocomial infections, including urinary tract infections, endocarditis, and surgical wound infections. The biofilm serves as a nidus for bacterial dissemination and as a reservoir for antimicrobial resistance. The effectiveness of first-line antibiotics (ampicillin, vancomycin, and aminoglycosides) is diminished due to reduced penetration, altered metabolism, increased tolerance, and intrinsic and acquired resistance. Alternative strategies for biofilm disruption, such as combination therapy (ampicillin with aminoglycosides), as well as newer approaches, including antimicrobial peptides, quorum-sensing inhibitors, and biofilm-disrupting agents (DNase or dispersin B), are also being explored to improve treatment outcomes. Environmentally, E. faecalis biofilms contribute to contamination in water systems, food production facilities, and healthcare environments. They persist in harsh conditions, facilitating the spread of multidrug-resistant strains and increasing the risk of transmission to humans and animals. Therefore, understanding the biofilm architecture and drug resistance is essential for developing effective strategies to mitigate their clinical and environmental impact. Full article

The ecological rice–eel co-culture system is not only beneficial for enhancing productivity and sustainability in agriculture but also plays a crucial role in promoting environmental health. In the present study, based on the long-term positioning trial of the rice–eel co-culture system that began in 2016 and was sampled in 2023, the effects of reduced nitrogen fertilizer application on soil physico-chemical properties and the bacterial community were investigated. Treatments included a conventional regular fertilization treatment (RT), rice–eel co-culture system regular fertilization (IT), and nitrogen-reduction 10%, 30%, and 50% fertilization treatments (IT90, IT70, and IT50). Our research demonstrated the following: (1) Compared to RT, IT significantly increased soil water-stable macroaggregates (R0.25), mean weight diameter (MWD), geometric mean diameter (GMD), and available phosphorus content, with the increases of 15.66%, 25.49%, 36.00%, and 18.42%, respectively. Among the nitrogen-reduction fertilization treatments, IT90 showed the most significant effect. Compared to IT, IT90 significantly increased R0.25, MWD, GMD, and available nitrogen content, with increases of 4.4%, 7.81%, 8.82%, and 28.89%, respectively. (2) Compared to RT, at the phylum level, the diversity of Chloroflexi was significantly increased under IT and IT50, and the diversity of Gemmatimonadota was significantly increased under IT90, IT70, and IT50. The diversity of Acidobacteriota was significantly higher in IT90 and IT70 compared to IT. It was shown that the rice–eel co-culture system and nitrogen fertilizer reduction could effectively improve the degradation capacity of organic matter and promote soil nitrogen cycling. In addition, redundancy analysis (RDA) identified total phosphorus, total nitrogen, and available nitrogen (p = 0.007) as the three most important environmental factors driving changes in the bacterial community. (3) The functional prediction analysis of soil microbiota showed that, compared to RT, the diversity of pathways related to biosynthesis (carbohydrate biosynthesis and cell structure biosynthesis) and metabolism (L-glutamate and L-glutamine biosynthesis) was significantly higher under IT70, IT90, IT, and IT50 (in descending order). However, the diversity of pathways associated with degradation/utilization/assimilation (secondary metabolite degradation and amine and polyamine degradation) was significantly lower under all the rice–eel co-culture treatments. In conclusion, the rice–eel co-culture system improved soil physicochemical properties and the soil microbial environment compared with conventional planting, and the best soil improvement was achieved with 10% less N fertilizer application. Full article

This study aimed to develop a functional powder using whey and milk matrices, leveraging the protective capacity of chia–alginate hydrogels and the advantages of electrohydrodynamic spraying (EHDA), a non-thermal technique suitable for encapsulating probiotic cells under stress conditions commonly encountered in food processing. A hydrogel matrix composed of chia seed mucilage and sodium alginate was used to form a biopolymeric network that protected probiotic cells during processing. The encapsulation efficiency reached 99.0 ± 0.01%, and bacterial viability remained above 9.9 log₁₀ CFU/mL after lyophilization, demonstrating the excellent protective capacity of the hydrogel matrix. Microstructural analysis using confocal laser scanning microscopy (CLSM) revealed well-retained cell morphology and homogeneous distribution within the hydrogel matrix while, in contrast, scanning electron microscopy (SEM) showed spherical, porous microcapsules with distinct surface characteristics influenced by the encapsulation method. Encapsulates were incorporated into beverages flavored with red fruits and pear and subsequently freeze-dried. The resulting powders were analyzed for moisture, protein, lipids, carbohydrates, fiber, and color determinations. The results were statistically analyzed using ANOVA and response surface methodology, highlighting the impact of ingredient ratios on nutritional composition. Raman spectroscopy identified molecular features associated with casein, lactose, pectins, anthocyanins, and other functional compounds, confirming the contribution of both matrix and encapsulants maintaining the structural characteristics of the product. The presence of antioxidant bands supported the functional potential of the powder formulations. Chia–alginate hydrogels effectively encapsulated L. reuteri, maintaining cell viability and enabling their incorporation into freeze-dried beverage powders. This approach offers a promising strategy for the development of next-generation functional food gels with enhanced probiotic stability, nutritional properties, and potential application in health-promoting dairy systems. Full article

Membrane bioreactors (MBRs) have been utilized for maricultural wastewater treatment, where high-salinity stress results in dramatic membrane fouling in the actual process. A microalgal–bacterial symbiotic system (MBSS) offers advantages for photosynthetic oxygen production, dynamically regulating the structure of extracellular polymeric substances (EPSs) and improving the salinity tolerance of bacteria and algae. This study centered on the mechanisms of membrane fouling mitigation via the microalgal–bacterial interactions in the MBSS, including improving the pollutant removal, optimizing the system parameters, and controlling the gel layer formation. Moreover, the contribution of electrochemistry to decreasing the inhibitory effects of high-salinity stress was investigated in the MBSS. Furthermore, patterns of shifts in microbial communities and the impacts have been explored using metagenomic technology. Finally, this review aims to offer new insights for membrane fouling mitigation in actual maricultural wastewater treatment. Full article

Bacterial nanocellulose (BNC) is a highly pure biopolymer with promising applications in the biomedical, food, and textile industries. However, the high production costs and low yields obtained in static conditions limit its scalability and industrial applications. This study addresses the sustainable production of BNC using a rotary disk bioreactor (RDB) and explores the use of grape pomace extract as an alternative carbon source for BNC production. Parameters such as the BNC production and biomass yield were evaluated using Komagataeibacter xylinus ATCC 53524 under different operational conditions (disk surface, rotation speed, and number of disks). The results showed that cellulose production increased using silicone-coated disks at 7–9 rpm (up to 2.72 g L⁻¹), while higher yields (5.23 g L⁻¹) were achieved when using grape pomace extract as the culture medium in comparison with conventional HS medium. FTIR and TGA characterizations confirmed that BNC obtained with grape pomace extract presents the same thermal and chemical characteristics than BNC produced with HS medium. This work provides insight into the feasibility of upscaling BNC production using a bioprocessing strategy, combining production in the RDB system and the use of an agro-industrial waste as a sustainable and cost-effective alternative. Full article

Acetate may act as a signaling molecule, regulating Paracin 1.7 production via quorum sensing (QS) in Lacticaseibacillus paracasei HD1.7. The “acetate switch” phenomenon requires mechanistic exploration to optimize Paracin 1.7 production. The “acetate switch” phenomenon delays with higher glucose levels (30 h, 36 h, and 96 h). Before the occurrence of the “acetate switch”, the ATP content increases and peaks at the “acetate switch” point and the NAD⁺/NADH ratio decreases, indicating energy changes. Moreover, the QS genes used for the pre-regulation of bacteriocin, such as prcKR, comCDE, were highly expressed. After the “acetate switch”, the ATP content decreased and the QS genes for the post-regulation of bacteriocin were highly expressed, such as rggs234 and sigma70-1/70-2. The “acetate switch” could act as an energy switch, regulating bacterial growth and QS genes. Before and after the “acetate switch”, some metabolic pathways were significantly altered according to the transcriptomic analysis by HD1.7 and HD1.7-Δpta. In this study, acetate was used as an input signal to regulate the two-component system, significantly influencing the bacteriocin expression system. And this study clarifies the roles of acetate, energy, and quorum sensing in promoting Paracin 1.7 production, providing a theoretical basis for optimizing the bacteriocin fermentation process of HD1.7. Full article

Background: Salivary pH plays a critical role in oral health by influencing enamel demineralization, buffering capacity, and the ecology of oral microbiota. Essential oils such as Origanum vulgare (oregano) possess well-documented antimicrobial properties that may reduce acidogenic bacterial activity. However, the effects of edible delivery systems like jellies on salivary pH modulation and their potential interactions with hormonal states remain poorly understood. Methods: This study evaluated the in vitro antimicrobial activity of an oregano-oil-based jelly formulation against standard bacterial (Staphylococcus aureus, Streptococcus pyogenes, and Escherichia coli) and fungal (Candida albicans) strains using the Kirby–Bauer disc diffusion method. Additionally, a human trial (n = 91) measured salivary pH before and after administration of the oregano-oil jelly. Participants were characterized by age, smoking status, menopausal status, and presence of menstruation. Multiple linear regression was used to identify predictors of final salivary pH. Results: The oregano-oil jelly demonstrated strong in vitro antimicrobial activity, with inhibition zones up to 8 mm for E. coli and C. albicans. In vivo, mean unstimulated salivary pH increased from 6.94 to 7.07 overall, indicating a mild alkalinizing effect. However, menstruating participants showed a significant decrease in final pH (from 7.03 to 6.78). Multiple regression identified menstruation as a significant negative predictor (β = −0.377, p < 0.001) and initial pH as a positive predictor (β = +0.275, p = 0.002). Menopausal status was not a significant predictor, likely due to the small sample size. Conclusions: Oregano-oil jellies may represent a promising natural approach to support oral health by increasing salivary pH and providing strong antimicrobial activity. However, physiological states such as menstruation can significantly modulate this response, underscoring the importance of personalized or phase-aware oral care strategies. Further studies with larger, diverse cohorts and controlled hormonal assessments are needed to validate these findings and optimize product formulations. Full article

Antimicrobial Resistance (AMR), i.e., the evolution of microbes to become resistant to chemicals used to control them, is a global public health concern that can make bacterial diseases untreatable. Inputs including antibiotics, metals, and biocides can create an environment in the agrifood chain that selects for AMR. Consumption of food represents a potential exposure route to AMR microbes and AMR genes (ARGs), which may be present in viable bacteria or on free DNA. Ready-to-eat (RTE) foods are of particular interest because they are eaten without further cooking, so AMR bacteria or ARGs that are present may be consumed intact. They also represent varied production systems (fresh produce, cooked meat, dairy, etc.). An evidence gap exists regarding the diversity and consumption of ARGs in RTE food, which this study begins to address. We sampled 1001 RTE products at retail sale in the UK, in proportion to their consumption by the UK population, using National Diet and Nutrition Survey data. Bacterial DNA content of sample extracts was assessed by 16S metabarcoding, and 256 samples were selected for metagenomic sequencing for identification of ARGs based on consumption and likely bacterial DNA content. A total of 477 unique ARGs were identified in the samples, including ARGs that may be involved in resistance to important antibiotics, such as colistin, fluoroquinolones, and carbapenems, although phenotypic AMR was not measured. Based on the incidence of ARGs in food types, ARGs are estimated to be present in a high proportion of average diets. ARGs were detected on almost all RTE food types tested (48 of 52), and some efflux pump genes are consumed in 97% of UK diets. Full article

The global antimicrobial resistance crisis demands innovative strategies to combat bacterial infections, including those caused by drug-sensitive pathogens that evade treatment through biofilm formation or metabolic adaptations. Here, we demonstrate that Squama Manitis extract (SME)—a traditional Chinese medicine component—exhibits broad-spectrum bactericidal activity against clinically significant pathogens, including both Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) species (MIC = 31.25 mg/mL), achieving significant reduction in bacterial viability within 24 h. Through integrated multi-omics analysis combining scanning electron microscopy and RNA sequencing, we reveal SME’s unprecedented tripartite mechanism of action: (1) direct membrane disruption causing cell envelope collapse, (2) metabolic paralysis through coordinated suppression of TCA cycle and fatty acid degradation pathways, and (3) inhibition of DNA repair systems (SOS response and recombination downregulation). Despite its potent activity, SME shows low cytotoxicity toward mammalian cells (>90% viability) and can penetrate Gram-negative outer membranes. These features highlight SME’s potential to address drug-resistant infections through synthetic lethality across stress response, energy metabolism, and DNA integrity pathways. While advocating for synthetic alternatives to endangered animal products, this study establishes SME as a polypharmacological template for resistance-resilient antimicrobial design, demonstrating how traditional knowledge and modern systems biology can converge to guide sustainable anti-infective development. Full article

Stipagrostis pennata is an important plant in desert ecosystems. Its seed-endophytic bacteria may play a critical role in plant growth and environmental adaptation processes. This study systematically analyzed the community composition and potential plant growth-promoting (PGP) functions of seed-endophytic bacteria associated with S. pennata. The results showed that while the overall diversity of bacterial communities from different sampling sites was similar, significant differences were observed in specific functional genes and species abundances. Nine endophytic bacterial strains were isolated from the seeds, among which Bacillus altitudinis strain L7 exhibited phosphorus solubilizing capabilities, nitrogen fixing, IAA production, siderophore generation, and multi-hydrolytic enzyme activities. Additionally, the genomic sequencing of L7 revealed the key genes involved in plant growth promotion and environmental adaptation, including Na⁺ efflux systems, K⁺ transport systems, compatible solute synthesis genes, and the gene clusters associated with nitrogen metabolism, IAA synthesis, phosphate solubilization, and siderophore synthesis. Strain L7 exhibits salt and osmotic stress tolerance while promoting plant growth, providing a promising candidate for desert microbial resource utilization and plant biostimulant development. Full article

Antimicrobial resistance is an escalating global threat that undermines the efficacy of modern antibiotics and places a substantial economic burden on healthcare systems—costing Europe alone over EUR 11.7 billion each year due to rising medical expenses and productivity losses. While genomics and transcriptomics have significantly advanced our understanding of the genetic foundations of resistance, they often fail to capture the dynamic, real-time adaptations that enable bacterial survival. Proteomics, particularly mass spectrometry-based strategies, bridges this gap by uncovering the functional protein-level changes that drive resistance, persistence, and tolerance under antibiotic pressure. In this review, we examine how proteomic approaches provide new insights into resistance mechanisms across various antibiotic classes, with a particular focus on β-lactams, aminoglycosides, and fluoroquinolones, highlighting clinically relevant pathogens, especially members of the ESKAPE group. Finally, we examine future directions, including the integration of proteomics with other omic technologies and the growing role of artificial intelligence in resistance prediction, paving the way for more predictive, personalized, and effective solutions to combat antimicrobial resistance. Full article

Sustainable agriculture requires replacing agrochemicals with environmentally friendly products. One alternative is bacterial inoculants with plant-growth-promoting (PGP) activity. Bacterial consortia offer advantages over single-strain inoculants, as they possess more PGP traits and allow the exploitation of bacterial synergies. Synthetic bacterial communities (SynComs) can be used as inoculants that are thoroughly characterized and assessed for efficiency and safety. Here, we describe the construction of a SynCom composed of seven bacterial strains isolated from the rhizosphere of tomato plants and other orchard vegetables. The strains were identified by 16S rDNA sequencing as Pseudomonas spp. (two isolates), Rhizobium sp., Ensifer sp., Microbacterium sp., Agromyces sp., and Chryseobacterium sp. The metagenome of the combined strains was sequenced, allowing the identification of PGP traits and the assembly of their individual genomes. These traits included nutrient mobilization, phytostimulation, and biocontrol. When inoculated into tomato plants in an agricultural soil, the SynCom caused minor effects in soil and rhizosphere bacterial communities. However, it had a high impact on the gene expression pattern of tomato plants. These effects were more significant at the systemic than at the local level, indicating a priming effect in the plant, as signaling through jasmonic acid and ethylene appeared to be altered. Full article

Background: Antimicrobial resistance (AMR) is increasingly acknowledged as a critical global challenge, posing serious risks to human and animal health and potentially disrupting poultry production systems. Commensal bacteria such as Staphylococcus spp., Enterococcus spp., and Escherichia coli may serve as important reservoirs and vectors of resistance genes. Objectives: This study aimed to assess the AMR profiles of bacterial strains isolated from industrial chicken farms in the Dél-Alföld region of Hungary, providing region-specific insights into resistance dynamics. Methods: A total of 145 isolates, including Staphylococcus spp., Enterococcus spp., and E. coli isolates, were subjected to minimum inhibitory concentration (MIC) testing against 15 antimicrobial agents, following Clinical and Laboratory Standards Institute (CLSI) guidelines. Advanced multivariate statistics, machine learning algorithms, and network-based approaches were employed to analyze resistance patterns and co-resistance associations. Results Multidrug resistance (MDR) was identified in 43.9% of Staphylococcus spp. isolates, 28.8% of Enterococcus spp. isolates, and 75.6% of E. coli isolates. High levels of resistance to florfenicol, enrofloxacin, and potentiated sulfonamides were observed, whereas susceptibility to critical antimicrobials such as imipenem and vancomycin remained largely preserved. Discussion: Our findings underscore the necessity of implementing region-specific AMR monitoring programs and strengthening multidisciplinary collaboration within the “One Health” framework with proper animal hygiene and biosecurity measures to limit the spread of antimicrobial resistance and protect both animal and human health. Full article

In order to achieve the efficient utilization of agricultural by-products and overcome the bottleneck of animal feed shortages in dry seasons, this study utilized corn stover (CS; Zea mays L.) as a material to systematically investigate the dynamic changes in the fermentation quality, bacterial community structure, and pathogenic risk of silage under different fermentation times (0, 3, 7, 15, and 30 days). CS has high nutritive value, including crude protein and sugar, and can serve as a carbon source and a nitrogen source for silage fermentation. After ensiling, CS silage (CSTS) exhibited excellent fermentation quality, characterized by relatively high lactic acid content, low pH, and ammonia nitrogen content within an acceptable range. In addition, neither propionic acid nor butyric acid was detected in any of the silages. CS exhibited high α-diversity, with Serratia marcescens being the dominant bacterial species. After ensiling, the α-diversity significantly (p < 0.05) decreased, and Lactiplantibacillus plantarum was the dominant species during the fermentation process. With the extension of fermentation days, the relative abundance of Lactiplantibacillus plantarum significantly (p < 0.05) increased, reaching a peak and stabilizing between 15 and 30 days. Ultimately, lactic acid bacteria dominated and constructed a microbial symbiotic network system. In the bacterial community of CSTS, the abundance of “potential pathogens” was significantly (p < 0.01) lower than that of CS. These results provide data support for establishing a microbial regulation theory for silage fermentation, thereby improving the basic research system for the biological conversion of agricultural by-products and alleviating feed shortages in dry seasons. Full article

Aromatic compounds are vital in both natural and synthetic chemistry, and they are traditionally sourced from non-renewable petrochemicals. However, plant biomass, particularly lignin, offers a renewable alternative source of aromatic compounds. Lignin, a complex polymer found in plant cell walls, is the largest renewable source of aromatic compounds, though its degradation remains challenging. Lignin can be chemically degraded through oxidation, acid hydrolysis or solvolysis. As an alternative, microorganisms, including fungi, could offer a sustainable alternative for breaking down lignin. The aromatic compounds released from lignin, by either microbial, chemical or enzymatic degradation, can be used by microorganisms to produce valuable compounds. Fungi possess unique enzymes capable of converting aromatic compounds derived from lignin or other sources into chemical building blocks that can be used in several industries. However, their aromatic metabolic pathways are poorly studied compared to bacterial systems. In the past, only a handful of genes and enzymes involved in the aromatic metabolic pathways had been identified. Recent advances in genomics, proteomics, and metabolic engineering are helping to reveal these metabolic pathways and identify the involved genes. This review highlights recent progress in understanding fungal aromatic metabolism, focusing on how Aspergillus niger converts plant-derived aromatic compounds into potentially useful products and the versatility of aromatic metabolism within the Aspergillus genus. Addressing the current knowledge gaps in terms of fungal pathways could unlock their potential for use in sustainable technologies, promoting eco-friendly production of chemical building blocks from renewable resources or bioremediation. Full article