Search Results (4,232)

Members of the genus Rhizobium are best known for nitrogen-fixing symbioses with legumes, yet their diversity and evolutionary roles in non-legume hosts remain poorly explored, particularly in arid ecosystems. We report the isolation and characterization of strain AGC32, an endophytic bacterium obtained from surface-sterilized roots of the desert medicinal plant Peganum harmala collected in Moroccan drylands. Phylogenomic analyses placed AGC32 within the genus Rhizobium but clearly distinct from described species, with average nucleotide identity values below 96% and digital DNA–DNA hybridization values below 70%, supporting its designation as a novel species for which the name Rhizobium moroccans sp. nov. is proposed. Comparative genomics revealed extensive structural genome rearrangements relative to its closest sequenced relative, Rhizobium deserti, indicating a divergent evolutionary trajectory. The high-quality draft genome encodes metabolic pathways associated with adaptation to nutrient limitation and environmental stress, including complete allantoin utilization, polyphosphate metabolism, organic acid assimilation, and multiple systems involved in oxidative and osmotic stress tolerance. Phenotypic assays corroborated these genomic predictions, demonstrating the ability to metabolize diverse organic acids and carbohydrates and to express multiple plant growth–promoting traits, including nitrogen fixation and the solubilization of phosphorus, potassium, and silicon. Collectively, these findings expand the ecological and evolutionary diversity of Rhizobium, demonstrate its capacity to associate with non-legume medicinal plants in extreme environments, and highlight desert ecosystems as reservoirs of previously unrecognized microbial diversity with potential applications in sustainable agriculture in arid regions. Full article

Periodontitis is a chronic inflammatory disease driven by microbial dysbiosis and an exacerbated host immune response. This leads to progressive breakdown of periodontal tissues. Although scaling and root planing remains the standard treatment, its capacity to fully restore immune balance and host–microbiota homeostasis is limited. Probiotics have emerged as promising adjunctive strategies to modulate pathways involved in periodontal disease progression. This review aimed to evaluate current clinical evidence on the use of probiotics as adjuncts in periodontal therapy. The review followed the Scale for the Assessment of Narrative Review Articles criteria, applied exclusively as a reporting-quality framework. A literature search was conducted in MEDLINE via PubMed for manuscripts indexed through January/2026, using MeSH terms related to periodontitis and probiotics. Probiotics demonstrate potential as adjunctive agents in periodontal therapy, as evidenced by improvements in clinical parameters (probing depth, clinical attachment level, and/or bleeding on probing) reported in clinical studies. However, the findings remain heterogeneous across trials. Variability in probiotic strains, CFU concentrations, administration routes, and treatment durations highlights the need for standardized clinical protocols to improve comparability and reproducibility and better establish their clinical efficacy. Stronger, long-term evidence is required to standardize therapeutic protocols. Full article

Chemotherapy- and/or radiotherapy-induced oral mucositis (CRIOM) is a common complication in patients with head and neck cancer, driven largely by excessive proinflammatory cytokine signalling and treatment-associated bacterial dysbiosis. This narrative review synthesizes current mechanistic evidence and summarizes emerging therapeutic strategies targeting these pathways. Research indicates that elevated levels of IL-1β, IL-6, TNF, iNOS, and nitric oxide amplify tissue injury and ulceration, while disruption of oral and gut microbial communities, characterized by loss of beneficial commensals and enrichment of pathogenic taxa, further exacerbates mucosal inflammation. Anti-inflammatory agents, including pentoxifylline, atorvastatin, trans-caryophyllene, azilsartan, recombinant human IL-11, and low-level laser therapy have been shown in preclinical models to reduce cytokine levels and promote mucosal healing. Similarly, microbiome-targeted approaches, such as oral microbiota transplantation and multi-strain probiotic formulations, have demonstrated potential in restoring microbial balance and attenuating CRIOM severity, with current evidence including both preclinical and clinical studies. Overall, current findings highlight cytokine toxicity and dysbiosis as synergistic drivers of CRIOM and support anti-inflammatory and microbiome-modulating strategies as promising adjunctive approaches; however, further well-designed clinical studies are required to validate their efficacy and guide clinical translation. Full article

Optical density (OD)-based cell growth measurement is commonly used in high-throughput screening (HTS) during drug discovery or when deciphering the pharmaceutical mechanism of action. While resuspending the cells via a mixing step is often assumed to be necessary prior to OD measurement, its essentiality in HTS workflows has not been systematically verified. Here, through the measurement of the growth of several strains of the microbial yeast Schizosaccharomyces pombe cells, we compared the overall growth dynamics between samples that have been mixed and not mixed. Using statistical quantification by a two-tailed paired t-test followed by multiple comparison corrections, we concluded from the comparison of the doubling time of cells growing in the exponential phase that mixing did not significantly affect the biological interpretation compared to unmixed samples. Doubling time quantification between mixed and unmixed samples showed a difference of approximately 10% on average based on the assessment of the growth of eight strains. As such, if the experimental outcome can accommodate this level of variability, incorporating a mixing step before OD determination would not be necessary. These observations support the simplification of HTS processes, improving the cost efficacy and process efficiency of readouts, yet maintaining the accuracy of data acquisition. Full article

The aim of the study was to evaluate the biotechnological potential of thermophilic microorganisms isolated from chernozem soil during composting of poultry manure. The efficiency of the strains was determined by their effect on organic matter degradation, humification intensity, and nitrogen accumulation. The correlation between the quality indicators of the composting process was assessed with the gross values, taking into account the proportion of compost fractions. The strains were identified as: Aeribacillus pallidus KCTC 3564^T (cellulolytic), Neobacillus sedimentimangrovi FJAT-2464^T, Aeribacillus composti N.8^T, Caldifermentibacillus hisashii N-11^T (nitrogen fixers), Acinetobacter pittii CIP 70.29^T, and Pseudomonas plecoglossicida NBRC 103162^T (nitrifies). It was found that all the bacteria increase the proportion of small fractions by 19.0–19.9%. The gross content of humic acids increases under the influence of nitrifiers (15.5%) and nitrogen fixers (5.5%). The total nitrogen content increases under cellulolytics (13.8%) and nitrogen fixers (20.2%). The smallest fraction (≤0.25 mm) in nitrogen fixers and nitrifying variants has the greatest bioreclamation properties, by 16.4% (p < 0.001) and 12.9% (p < 0.001). Targeted microbial strains provide the direction of the transformation processes during biocomposting. It can also be concluded that assessing the quality of composting based on the fraction distribution can be a promising element of the biofermentation process monitoring. Full article

Peptaibols, predominantly secreted by Trichoderma species, are a class of linear peptides composed of five to twenty amino acid residues, synthesized non-ribosomally and enriched with α-amino isobutyric acid. These unique peptides appear to be highly effective in mediating the interactions between Trichoderma and plant pathogenic fungi. In this study, Ultra-Performance Liquid Chromatography–Quadrupole Time-Of-Flight Mass Spectrometry/Mass Spectrometry (UPLC-QTOF-MS/MS) technology was used to detect peptaibols profiles of Trichoderma strains during their interactions with the pathogen Fusarium graminearum. MS investigations of crude extracts derived from in vitro confrontations of Trichoderma atroviride T23 and its genetically modified counterparts, dual-culture assays of Mlae1, Mvel1, OElae1, and OEvel1 with F. graminearum were performed to shed light on the regulatory role of the velvet complex composed of LAE1&VEL1 in the synthesis of peptaibols during the microbial interaction. These results revealed intriguing variations in the total peptaibols produced during the interactions, as well as some differences in the specific peptaibol profiles between the confrontation and control tests. The overexpression strains, OElae1 and OEvel1, distinguished themselves by their proficiency in inducing long-residue peptaibols synthesis, attaining an impressive biocontrol index of up to 76%. The crude extracts containing peptaibols of OElae1 and OEvel1 demonstrated a capability to enhance cell membrane permeability and decrease DON toxin production in F. graminearum, and the crude extracts of OElae1 strains exhibited more effectiveness in reducing DON toxin production. In conclusion, the interaction with F. graminearum significantly impacted the peptaibol production in the examined Trichoderma strain, emphasizing the intricate interplay and reciprocal influence of genetic factors and environmental stimuli. Full article

Background/Objectives: Enterotoxigenic Escherichia coli (ETEC) is a leading cause of diarrheal illness worldwide, resulting in approximately 380,000 deaths annually, with significant morbidity in children and travelers to endemic regions. ETEC infection begins with the attachment of the bacterium to the small intestine via filamentous colonization factors (CF), followed by the production of heat-labile (LT) and heat-stable (ST) toxins that induce watery diarrhea. Targeting CF to prevent ETEC attachment is challenging due to strain heterogeneity. Methods: In previous studies, we developed a class-switched human monoclonal antibody, 68–90, expressed as secretory IgA (SIgA) in rice for cost-effective and stable storage. Rice-produced SIgA exhibited comparable binding efficiency to CfaE, a component of CF, compared to CHO-produced SIgA in vitro. Results: In this work, we showed that oral administration of 68–90 SIgA to Aotus nancymaae did not alter gut microbiome distribution or show signs of systemic exposure. Conclusions: These findings suggest that oral delivery of ETEC-specific SIgA is safe and does not disrupt the gut microbial population, highlighting its potential as an effective and targeted therapeutic strategy. Full article

Chronic kidney disease (CKD) is a progressive condition associated with metabolic disturbances, systemic inflammation, and the accumulation of gut-derived uremic toxins. Increasing evidence highlights the role of gut microbiota dysbiosis in the progression of CKD through the gut–kidney axis. Consequently, microbiome-targeted nutritional strategies, including probiotics, prebiotics, and synbiotics, have emerged as promising complementary approaches to modulate intestinal microbial composition and metabolic functions. This review summarizes and critically evaluates the current clinical evidence regarding the use of these interventions in CKD patients. Clinical studies indicate that supplementation with probiotics, prebiotics, and synbiotic formulations may promote beneficial shifts in the composition of the gut microbiota, enhance saccharolytic fermentation, and increase the production of short-chain fatty acids (SCFAs). These changes have been associated with reduced circulating levels of gut-derived uremic toxins such as indoxyl sulfate and p-cresyl sulfate, as well as with the attenuation of systemic inflammation and oxidative stress. However, available trials remain heterogeneous in terms of study design, probiotic strains, prebiotic substrates, dosing regimens, and patient populations, and are frequently limited by small sample sizes and short intervention durations. As a result, evidence for improvements in renal function and long-term clinical outcomes remains inconclusive. While synbiotics may offer theoretical advantages by combining microbial supplementation with targeted substrates that support microbial growth and metabolic activity, current evidence does not consistently demonstrate superior clinical efficacy. Overall, these interventions often improve surrogate biomarkers, but their effects on renal function and hard clinical outcomes remain uncertain. Larger, longer-duration multicenter randomized controlled trials with standardized formulations are needed to establish their clinical utility and to better elucidate microbiota–host interactions in CKD. Advancing this field may support the development of personalized microbiome-based therapeutic strategies aimed at modulating the gut–kidney axis and ultimately improving clinical outcomes in CKD patients. Full article

Environmental pH plays a critical role in microbial fermentation processes. Weizmannia coagulans attracts particular attention for exceptional acid tolerance and lactic acid productivity. Yet acidic stress impacts on its cell division regulation remain unclear. Here, a critical pH value (pH 4.20) for growth inhibition of the Gram-positive bacterium Weizmannia coagulans strain BC99 was first established. Transcriptomic analysis of metabolic pathways was then performed. The multi-layered regulatory network underlying acid stress-induced cell division was elucidated. Integrated transcriptomic and physiological analyses reveal that acid stress triggers multigene expression reprogramming. This drives core metabolic network reorganization, coordinately regulating division processes. RNA-seq analysis demonstrated acid stress triggered differential expression of division genes (FtsZ/Q downregulation), ATP synthase suppression, and peptidoglycan transport reduction, while enhancing membrane rigidification (Cfa) and magnesium homeostasis (CorA). The PhoPR dual-component system emerged as a central regulator, inhibiting septal assembly via RipA hydrolase and RpsU ribosomal suppression while rerouting carbon flux to glycolysis, elucidating bacterial acid adaptation mechanisms. Collectively, these adaptive changes prioritize cell survival over active proliferation under acidic conditions. This study provides molecular insights into how W. coagulans preserves viability under acid stress, offering a theoretical basis for optimizing its performance in probiotic applications. Full article

Background/Objectives: Atopic dermatitis (AD) is associated with gut dysbiosis linked to early-life antibiotic use and Staphylococcus aureus colonization. Gum Arabic (GA), a prebiotic, may modulate this dysbiosis and influence AD-related microbial balance. This study evaluated whether GA could support AD-associated probiotics-Lactobacillus casei, Bifidobacterium bifidum, and Bifidobacterium infantis-under amoxicillin- or azithromycin-containing conditions, examined the response of S. aureus under the same screening conditions, and developed GA-phospholipid-based semisolid carriers for topical application. Methods: Probiotic strains were cultured with 1–5% GA in the presence and absence of antibiotics, and viable cell counts were assessed. Sixteen topical formulations containing propylene glycol or isopropyl myristate in a hydrogenated phosphatidylcholine base were prepared and screened for rheological properties and galactose release using in vitro release testing (IVRT) and HPLC-UV. Results: GA at 1–2% concentrations promoted probiotic growth in antibiotic-free conditions. GA preserved B. infantis viability under azithromycin exposure in this in vitro screening model. For S. aureus, numerical CFU differences were observed between antibiotic-only and GA-containing conditions; however, the present screening design was not intended to determine antibiotic interaction outcomes. Formulations F14 (2% GA + 7% IPM) and F15 (3% GA + 7% IPM) exhibited optimal spreadability. IVRT showed that 6 h cumulative galactose release varied by formulation (F6 > F10 > F14 > F15). Conclusions: GA demonstrated dose-dependent prebiotic activity and preserved B. infantis viability under azithromycin exposure in this in vitro screening model. For S. aureus, the observed CFU differences between antibiotic-only and GA-containing conditions should be considered exploratory only and do not allow for conclusions regarding interference with antibiotic efficacy. Optimized GA-HPC systems with suitable rheological and release characteristics represent promising candidates for further preclinical investigation. Full article

The pathways governing the transformation of crop residues into humic acid (HA) remain incompletely understood because multiple biochemical routes may operate simultaneously during composting-like humification. In this study, a 30-day solid-state humification experiment was conducted by integrating physicochemical pretreatments, including steam explosion (SE) and ammonification coupled with steam explosion (SE-N), with a multi-fungal inoculation strategy involving Aspergillus niger, Candida spp., and Phanerochaete chrysosporium. Across three representative substrate–pretreatment systems and 81 experimental groups, the contents of lignocellulosic fractions, reducing sugars (RS), a UV-280-based soluble nitrogen-containing precursor index (operationally denoted as SNP), fulvic acid (FA), and HA were compared. The results showed that neither physicochemical pretreatment alone nor single-strain inoculation was sufficient to achieve substantial HA formation. SE mainly improved substrate accessibility and promoted carbon release, whereas ammonification provided essential nitrogen preloading for subsequent precursor coupling. In the saccharification-dominant treatment, RS reached 27.5%, but HA remained negligible. In the Candida-only treatment, the soluble nitrogen-containing precursor index increased markedly, yet HA formation was still minimal. By contrast, the highest HA yield (13.7%) was obtained under multi-fungal co-inoculation, particularly when nitrogen preloading by ammonification was combined with concurrent accumulation of carbon and aromatic precursors. The data suggest that lignin-targeting activity by P. chrysosporium was associated with the likely generation of phenolic and quinone-like intermediates that bridged the condensation of sugar- and nitrogen-derived compounds. Overall, the findings support a synergistic humification framework in which polysaccharide depolymerization, microbial nitrogen transformation, and lignin-derived aromatic precursor formation jointly contribute to HA accumulation, rather than a single linear pathway dominating the process. Full article

Construction and demolition activities generate over one-third of all waste produced within the European Union, with the largest fraction being mineral materials, and concrete representing up to 90% of this volume. In this context, the recycling of this type of waste is an important research topic with growing scientific and industrial relevance. While numerous studies have examined the influence of recycled concrete and other industrial waste on the technical performance of Portland cement-based composites, the antimicrobial resistance of these composites remains largely unexplored. Therefore, in this study we evaluate the effects of three different waste materials on the key properties of Portland cement mortar, as well as on its antimicrobial resistance; the investigated waste materials were fly ash (produced in thermal power plants), recycled concrete fines resulted from the mechanical processing of concrete waste generated in construction and demolition activities, as well as dried concrete slurry (a byproduct of concrete batching plants). The partial replacement of Portland cement with these concrete wastes slightly increased the mortar’s workability (up to 4.6%). However, it also led to an 11–12% reduction in compressive strength after 28 days of hardening. After 60 days of curing, the antimicrobial properties of these mortars were evaluated by assessing their effect on planktonic microbial growth and their anti-adherent capacity against the most common pathogenic strains (S. aureus, E. coli, P. aeruginosa, C. albicans, and C. parapsilosis). Antimicrobial assays were performed at two different concentrations of microbial suspensions, and the mortars exhibited significant antibiofilm properties against all strains, especially against E. coli. The study identified mortar formulations in which partial replacement of cement with construction, demolition, and industrial waste materials resulted in compressive strength and antimicrobial resistance comparable to those of conventional reference mortars. These findings highlight the potential to integrate recycled waste into Portland cement-based materials, supporting both structural integrity and microbial resistance and advancing sustainable construction practices. Full article

Kombucha is a fermented beverage produced using a symbiotic consortium of acetic acid bacteria and yeasts, often marketed for its health-promoting properties. However, probiotic bacteria in kombucha are typically present at inconsistent levels and may not remain viable during fermentation. In this study, three Lactobacillus strains (Lacticaseibacillus rhamnosus ATCC 53103 (L. rhamnosus), Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 (L. plantarum) and Lentilactobacillus hilgardii (L. hilgardii) isolate) were encapsulated in whey protein using the lyophilization method and added individually at the start of kombucha fermentation. Lactic acid bacteria (LAB)–enriched kombucha samples were evaluated for chemical composition (polyphenols, flavonoids, vitamin C and organic acids) and functional properties (antimicrobial, antiproliferative, antioxidant and anti-inflammatory activities) and compared to a traditionally obtained control kombucha, primarily demonstrating in vitro and experimental assessment. Encapsulation maintained LAB viability above 6–7 log CFU/mL throughout fermentation, producing kombucha with enhanced microbial stability. LAB–enriched samples exhibited increased L-lactic acid and antimicrobial activity. L. rhamnosus and L. hilgardii–enriched samples exhibited increased antiproliferative and anti-inflammatory activities, which may be associated with strain-dependent production of organic acids, polyphenol modulation and LAB-derived bioactive metabolites. Antioxidant activity varied depending on assay, and L. rhamnosus–enriched kombucha showed higher anti-inflammatory activity. These findings demonstrate that whey protein encapsulation can preserve LAB during fermentation, enhance specific bioactive properties and provide a platform for developing functional kombucha beverages with potential applications in the food industry. Full article

Polyhydroxyalkanoates (PHAs) are biodegradable microbial polyesters that represent a promising sustainable alternative to petroleum-based plastics. Salterns, hypersaline environments, are recognized as significant sources of halotolerant microorganisms that can produce PHAs in high-salinity conditions; however, Vietnamese saltern ecosystems have not been extensively investigated. This research aimed to isolate and initially characterize salt-tolerant bacteria capable of synthesizing PHAs from the Hon Khoi saltern in Khanh Hoa Province, Vietnam. A total of 37 halotolerant bacterial isolates were obtained, and potential PHA-producing strains were initially screened using Sudan Black B and Nile Blue A. TEM microscopy was then employed to confirm the existence of PHA granules. Furthermore, FTIR spectroscopy and GC–MS/MS spectrometry were utilized to analyze the chemical structure and monomer composition of the extracted polymers. Six isolates were identified as PHA-producing bacteria, including Salinivibrio sp. HK101 and HK116, Halomonas sp. HK105, Priestia sp. HK125 and HK142, and Bacillus sp. HK130. These strains exhibited growth across 3–10% NaCl and temperatures from 25 to 45 °C. Priestia sp. HK142 and Salinivibrio sp. HK101 exhibited the most substantial PHA accumulation, achieving 50.72 ± 1.83% and 42.07 ± 1.8% of DCW, respectively. These results indicate that the Hon Khoi saltern represents a promising source of halotolerant PHA-producing bacteria with potential relevance for future biopolymer production studies. Full article

Objective: The objective of this study is to evaluate the ability of silver oxide nanoparticle (Ag₂ONP)-functionalized high-efficiency particulate air (HEPA) filters and colloidal Ag₂ONP suspensions to inhibit biofilm formation by major respiratory pathogens causing infections at operating rooms. Background: Respiratory infections caused by bacterial pathogens such as Streptococcus pneumoniae, Pseudomonas aeruginosa and Staphylococcus species are often associated with the formation of biofilms, which confer increased resistance to antibiotics and host immune responses. Effective strategies to prevent biofilm formation on biological surfaces and in air filtration systems are urgently needed in clinical settings. Methods: The biofilm-forming ability of each bacterial strain was assessed by crystal violet microplate assay, viable count or confocal microscopy after prior incubation of the culture medium with Ag₂ONP-coated HEPA filter material or colloidal Ag₂ONP suspension. Results: Both silver-functionalized filters and silver nanoparticle suspensions significantly inhibited biofilm formation by S. pneumoniae and P. aeruginosa, with near-complete suppression observed. In the case of S. aureus and S. epidermidis, the silver nanoparticle suspension showed partial inhibition of biofilm development. Conclusions: Ag₂ONP-functionalized HEPA filters and colloidal Ag₂ONP suspensions effectively prevent biofilm formation by major respiratory pathogens, for both Gram-negative and Gram-positive bacteria. These materials show promise for integration with air filtration and surface coating systems to reduce microbial load and transmission in healthcare environments such as operating room facilities. Full article