Microorganisms

18 pages, 2529 KB

Open AccessArticle

Unlocking the Potential of vB_EfaS_LOK1: A Newly Isolated Bacteriophage Against Enterococcus faecalis

by Laura Marcela Plata Suarez, Salvador Del Valle Balbuena, Isamar Leticia Becerra Mejía, Alejandra Aidee Loera Piedra, Cristina Domínguez Espinoza, Arantxa Monserrat Ángeles González, Araceli Contreras Rodríguez, Alejandra Aquino Andrade, Sergio Francisco Martínez Díaz and Ma. Guadalupe Aguilera Arreola

Microorganisms 2025, 13(10), 2414; https://doi.org/10.3390/microorganisms13102414 - 21 Oct 2025

Viewed by 541

Abstract

Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we [...] Read more.

Phage therapy has emerged as a promising alternative for combating infections caused by drug-resistant pathogens. Among these, Enterococcus faecalis remains a significant public health concern due to its persistence in clinical settings and frequent involvement in healthcare-associated infections (HAIs). In this study, we report the characterization of the lytic bacteriophage vB_EfaS_LOK1, isolated from urban sewage using E. faecalis strain IIH-74.4 as the host. Transmission electron microscopy revealed morphological features consistent with the phages formerly classified within the Siphoviridae family. The phage exhibited high thermal and pH stability, remaining viable up to 70 °C and within a pH range of 4–11. It displayed a latent period of 20 min and a burst size of 72 PFU/cell. Notably, vB_EfaS_LOK1 exhibited a narrow host range, lysing only the strain used for their isolation. Genomic analysis revealed a 41.2 kb double-stranded DNA genome devoid of known virulence or antibiotic resistance genes. Phylogenomic analysis classified the phage within the genus Efquatrovirus (Caudoviricetes), suggesting it represents a newly isolated bacteriophage species. Functional annotation identified genes related to DNA replication, host interaction, and bacterial lysis, including endolysins and holins with putative antimicrobial properties. Long-term stability assays demonstrated that tryptic soy broth (TSB) with CaCl₂/MgCl₂ at 4 °C maintained viability for at least 90 days. Collectively, these findings support the potential of vB_EfaS_LOK1 as a potential candidate for the development of phage-based therapies targeting E. faecalis. Full article

(This article belongs to the Special Issue New Trends in Medical Bacteriology: Diagnosis, Treatment and Prevention—Second Edition)

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18 pages, 2120 KB

Open AccessReview

Bacterial Extracellular Vesicles: An Emerging Concern in the Field of Environmental Contamination—Characterization, Impacts, and Response Strategies

by Yu Fu, Yaoqiang Shi, Zhijian Zhou, Yafei Huang, Yuzhu Song and Chao Li

Microorganisms 2025, 13(10), 2413; https://doi.org/10.3390/microorganisms13102413 - 21 Oct 2025

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Abstract

Bacterial extracellular vesicles (BEVs) are nanoscale membrane-bound structures secreted by prokaryotic cells and have recently gained considerable attention in environmental pollution research. By encapsulating virulence factors and antibiotic resistance genes (ARGs), BEVs can persist in aquatic, soil, and sedimentary environments, facilitating interspecies gene [...] Read more.

Bacterial extracellular vesicles (BEVs) are nanoscale membrane-bound structures secreted by prokaryotic cells and have recently gained considerable attention in environmental pollution research. By encapsulating virulence factors and antibiotic resistance genes (ARGs), BEVs can persist in aquatic, soil, and sedimentary environments, facilitating interspecies gene transfer, aggravating microbial contamination, and ultimately posing risks to ecosystem stability and human health. This review provides a comprehensive overview of BEVs’ formation mechanisms, structural composition, and spatial distribution. Particular attention is given to the environmental implications of BEVs, including their roles in mediating horizontal ARG transfer, delivering virulence genes and amplifying pathogenicity, and their emerging potential as environmental bioindicators, despite current analytical limitations in complex matrices. Nevertheless, three major research gaps remain: (i) the molecular mechanisms underlying BEV interactions with heavy metals and microplastics are poorly understood; (ii) field-based quantification and distribution data are still limited; and (iii) effective, targeted strategies for BEV removal or inactivation are lacking. Addressing these challenges will not only enhance our understanding of BEV-mediated environmental risks but also inform the development of advanced detection methods and remediation approaches for BEV-associated pollution. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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11 pages, 884 KB

Open AccessArticle

Essential Oils as a Novel Anti-Biofilm Strategy Against Salmonella Enteritidis Isolated from Chicken Meat

by Suzana Vidaković Knežević, Slobodan Knežević, Dubravka Milanov, Jelena Vranešević, Marko Pajić, Sunčica Kocić-Tanackov and Nedjeljko Karabasil

Microorganisms 2025, 13(10), 2412; https://doi.org/10.3390/microorganisms13102412 - 21 Oct 2025

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Abstract

Salmonella Enteritidis is a serious foodborne threat, being the most reported Salmonella serovar in the past several years. Biofilm formation contributes significantly to its persistence and resistance in food processing environments, making it harder to eliminate using conventional disinfectants. Recently, essential oils have [...] Read more.

Salmonella Enteritidis is a serious foodborne threat, being the most reported Salmonella serovar in the past several years. Biofilm formation contributes significantly to its persistence and resistance in food processing environments, making it harder to eliminate using conventional disinfectants. Recently, essential oils have emerged as promising natural alternatives due to their antimicrobial and anti-biofilm properties. In this study, the biofilm-forming ability of Salmonella Enteritidis, isolated from chicken meat, was evaluated under various nutrient conditions and temperatures. Furthermore, the anti-biofilm activity of essential oils derived from oregano, cinnamon, rosemary, clove, and thyme was assessed against strong and moderate biofilms formed by Salmonella Enteritidis. The isolates demonstrated the capacity to form biofilms in tryptic soy broth, meat broth, and Luria–Bertani broth at 37 °C, 15 °C, and 5 °C. All selected essential oils, at their minimum bactericidal concentrations, effectively reduced preformed biofilms by between 36.98% to 74.83%. The destructive effect of essential oils on Salmonella Enteritidis bacterial cells was further confirmed through scanning electron microscopy analysis. In conclusion, the selected essential oils exhibited promising anti-biofilm potential and may serve as effective natural agents for controlling biofilm-associated contamination by Salmonella Enteritidis. Full article

(This article belongs to the Special Issue Novel Antimicrobial Approaches in Biofilm Control in the Food Industry: Future Perspectives)

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39 pages, 3047 KB

Open AccessSystematic Review

Natural Molecules, Nutraceuticals, and Engineered Nanosystems: A Comprehensive Strategy for Combating Gardnerella vaginalis-Induced Bacterial Vaginosis

by Manoj Dalabehera, Abdulrahman Mohammed Alhudhaibi, Emad M. Abdallah, Tarek H. Taha, Shubham Chaudhari, Alka Kumari, Rudra Narayan Subudhi and Charul Rathore

Microorganisms 2025, 13(10), 2411; https://doi.org/10.3390/microorganisms13102411 - 21 Oct 2025

Viewed by 778

Abstract

Bacterial vaginosis (BV) is a highly prevalent vaginal infection characterized by a dysbiotic shift in the vaginal microbiota, with Gardnerella vaginalis acting as a principal pathogen. Despite its association with adverse reproductive outcomes, BV remains underexplored from both mechanistic and therapeutic standpoints. Standard [...] Read more.

Bacterial vaginosis (BV) is a highly prevalent vaginal infection characterized by a dysbiotic shift in the vaginal microbiota, with Gardnerella vaginalis acting as a principal pathogen. Despite its association with adverse reproductive outcomes, BV remains underexplored from both mechanistic and therapeutic standpoints. Standard antibiotic regimens frequently fail due to high recurrence rates driven by multidrug-resistant (MDR) G. vaginalis strains and biofilm formation. In response, natural compounds and nutraceuticals, owing to their intrinsic antibacterial, antibiofilm, and immunomodulatory properties, have emerged as promising candidates for alternative BV therapies. In this paper, we first compile and critically evaluate preclinical and clinical evidence on the efficacy of plant extracts, essential oils (EOs), probiotics, vitamins, proteins, fatty acids, and enzymes against G. vaginalis, emphasizing their mechanistic insights in restoring vaginal microbial balance. Next, we focus on the integration of these bioactive agents into engineered nanosystems, such as lipid-based nanoparticles (LNPs), polymeric carriers, and inorganic nanostructures, to overcome limitations related to solubility, stability, and targeted delivery. Nonetheless, comparative studies, combination therapies, and recent patent developments are discussed to highlight how naturally derived molecules can enhance antimicrobial potency and reduce cytotoxicity. In conclusion, these platforms demonstrate superior in vitro and in vivo efficacy, offering a paradigm shift in the management of BV. Key challenges include scalable manufacturing, regulatory approval, and comprehensive safety assessment. Future research should prioritize standardized nanoparticle (NP) synthesis, detailed pharmacokinetic and toxicity profiling, and well-designed clinical trials to validate nature-inspired, nanoengineered therapies against G. vaginalis-induced BV. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: Current Status and Future Directions (Second Edition))

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27 pages, 648 KB

Open AccessReview

Recent Advances in the Role of Bacteriophages in the Aetiology and Therapy of Vaginal Dysbiosis in the Form of Bacterial Vaginosis and the Prevention of Preterm Birth

by Ronald F. Lamont, Amaan Ali and Jan Stener Jørgensen

Microorganisms 2025, 13(10), 2410; https://doi.org/10.3390/microorganisms13102410 - 21 Oct 2025

Viewed by 457

Abstract

Bacterial vaginosis is more than a mild inconvenience for women and has been shown to be an important cause of morbidity and mortality in women through sexually transmitted infections, and in babies due to late miscarriage and preterm birth. The aetiology of bacterial [...] Read more.

Bacterial vaginosis is more than a mild inconvenience for women and has been shown to be an important cause of morbidity and mortality in women through sexually transmitted infections, and in babies due to late miscarriage and preterm birth. The aetiology of bacterial vaginosis remains unclear but there is increasing evidence to support sexual transmission as a cause. Preterm birth is a major cause of neonatal and perinatal mortality and morbidity worldwide and a huge cost on healthcare. The earlier bacterial vaginosis is detected in pregnancy, the greater the risk of an adverse outcome like preterm birth. Bacteriophages influence the vaginal microbiome, resulting in a eubiotic or dysbiotic state that may have implications on the prediction and prevention of preterm birth. We have provided the evidence to link vaginal dysbiosis in the form of bacterial vaginosis with the prediction and prevention of preterm birth. We have also explored the role of bacteriophages in bacterial vaginosis and the possibility of therapeutic interventions. Bacteriophages play an important role in the aetiology of vaginal dysbiosis and novel therapeutic interventions may help in the prediction and prevention of preterm birth through achieving vaginal eubiosis. Full article

(This article belongs to the Special Issue The Vaginal Microbiome in Health and Disease)

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15 pages, 4058 KB

Open AccessArticle

SpuA-Mediated Glycogen Metabolism Modulates Acid Stress Adaptation via Formic Acid and Amino Acid Utilization in Streptococcus pneumoniae

by Weichen Gong, Masayuki Ono, Xuefei Cheng, Yujiro Hirose, Keita Nishiyama, Haruki Kitazawa and Shigetada Kawabata

Microorganisms 2025, 13(10), 2409; https://doi.org/10.3390/microorganisms13102409 - 21 Oct 2025

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Abstract

Glycogen metabolism plays a key role in bacterial adaptation. In Streptococcus pneumoniae, the glycogen-degrading enzyme SpuA is widely conserved, but its physiological significance remains unclear. In this study, we investigated how SpuA affects bacterial growth and response to acid stress. We found [...] Read more.

Glycogen metabolism plays a key role in bacterial adaptation. In Streptococcus pneumoniae, the glycogen-degrading enzyme SpuA is widely conserved, but its physiological significance remains unclear. In this study, we investigated how SpuA affects bacterial growth and response to acid stress. We found that the spuA deletion strain (ΔspuA) produced more acidic metabolites under anaerobic conditions than the wild-type strain. In a mouse infection model, bronchoalveolar lavage fluid (BALF) from ΔspuA-infected mice was more acidic on day 1 post-infection, showing a lower bacterial load than wild-type infection—a finding consistent with the early growth delay observed in vitro—but the mutant later exhibited enhanced persistence at 72 h. ΔspuA strains also showed greater tolerance to formic acid and higher intake of serum amyloid A1 (SAA1), which may further contribute to their survival in acidic environments. Transcriptomic analysis revealed reduced utilization of certain amino acids, particularly cysteine, in ΔspuA strains. However, the addition of 0.05% (v/v) formic acid restored amino acid utilization in ΔspuA strains, and co-supplementation with formic acid and cysteine significantly enhanced ΔspuA growth in vitro. These findings suggest that in the absence of SpuA, S. pneumoniae shifts its metabolism toward formic acid production, which may act both as a metabolic signal and a stressor that influences bacterial gene expression. This shift is accompanied by increased expression of tRNAs and growth rescue, suggesting enhanced amino acid utilization capacity. Although our findings reveal a potential link between formic acid metabolism and amino acid utilization through tRNA regulation, further validation using metabolic flux analyses or targeted metabolomics will be required to confirm this relationship. These observations imply a metabolic adaptation that facilitates bacterial growth under low-oxygen, acidic conditions during infection. Our results also raise the possibility that SpuA plays a role in restraining bacterial overgrowth in the host, thereby promoting a more balanced coexistence between pathogen and host. Full article

(This article belongs to the Special Issue The Molecular Mechanisms Regulating Stress-Adaptive Responses in Bacteria)

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12 pages, 411 KB

Open AccessArticle

Tegoprazan–Amoxicillin Dual Therapy for Clarithromycin-Resistant Helicobacter pylori: A Feasibility Pilot Study

by Jun-Hyung Cho

Microorganisms 2025, 13(10), 2408; https://doi.org/10.3390/microorganisms13102408 - 21 Oct 2025

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Abstract

Tegoprazan (TPZ) has the potential to enhance Helicobacter pylori eradication. This study aimed to investigate the efficacy of TPZ–amoxicillin (TA) dual therapy against clarithromycin-resistant H. pylori strains. All H. pylori-positive patients were diagnosed by real-time polymerase chain reaction that can detect point [...] Read more.

Tegoprazan (TPZ) has the potential to enhance Helicobacter pylori eradication. This study aimed to investigate the efficacy of TPZ–amoxicillin (TA) dual therapy against clarithromycin-resistant H. pylori strains. All H. pylori-positive patients were diagnosed by real-time polymerase chain reaction that can detect point mutations causing clarithromycin resistance. Patients infected with clarithromycin-resistant H. pylori received TA dual therapy consisting of 50 mg TPZ twice daily and high-dose amoxicillin (3 g per day) for 2 weeks. A total of 57 patients received TA dual therapy. There was a significant difference in H. pylori eradication rates between the treatment-naïve (n = 40) and treatment-experienced (n = 17) groups in the intention-to-treat and per-protocol analyses (60.0% vs. 29.4%, p = 0.035 and 70.6% vs. 31.3%, p = 0.009, respectively). Compliance with the eradication regimen was 100%, with an 8% incidence of adverse events. Multivariate analysis revealed that treatment-naïve status was a significantly independent factor associated with H. pylori eradication success (odds ratio, 8.679; p = 0.007). In conclusion, the eradication efficacy of TA dual therapy against clarithromycin-resistant H. pylori strain infections was suboptimal in treatment-naïve patients. Notably, eradication rates were significantly lower in patients with a prior history of H. pylori treatment. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Bacterial Infection)

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17 pages, 1848 KB

Open AccessArticle

Vulnerability of Walnut Pruning Wounds to Fungal Trunk Pathogens and Seasonal Conidial Dynamics of Botryosphaeriaceae in the Maule Region, Chile

by Shehzad Iqbal, Iqra Mubeen, Mauricio Lolas, Ernesto Moya-Elizondo, Pedro Gundel, Samuel Ortega-Farias, William Campillay-Llanos and Gonzalo A. Díaz

Microorganisms 2025, 13(10), 2407; https://doi.org/10.3390/microorganisms13102407 - 21 Oct 2025

Viewed by 377

Abstract

Branch canker and dieback, caused by Botryosphaeriaceae and Diaporthaceae, is a major disease of walnut (Juglans regia L.) worldwide. In Chile, the impact of pruning wound age and timing on susceptibility to these pathogens in walnut trees remains poorly understood. During June–July [...] Read more.

Branch canker and dieback, caused by Botryosphaeriaceae and Diaporthaceae, is a major disease of walnut (Juglans regia L.) worldwide. In Chile, the impact of pruning wound age and timing on susceptibility to these pathogens in walnut trees remains poorly understood. During June–July (2023) and June–July (2024), this study assessed the effect of pruning wound age of the walnut cv. Chandler on infection by seven fungal species and simultaneously tracked seasonal conidial release of Botryosphaeriaceae spp. in the Maule Region, Chile. Lignified twigs were artificially inoculated at 1, 15, 30, and 45 days after pruning, and necrotic lesion lengths were measured six months post-inoculation. All fungal isolates caused significantly longer lesions than the control (p < 0.0001), with Diplodia mutila, Neofusicoccum nonquaesitum, and N. parvum being the most aggressive. At the same time, Dothiorella sarmentorum and Diaporthe species (Diaporthe australafricana, Di. foeniculina, and Di. patagonica) produced the smallest lesions. Susceptibility decreased with increasing wound age, with a significant interaction between fungal species and pruning wound age. Spore trapping of Botryosphaeriaceae revealed that dispersal was positively associated with rainfall (r = 0.81, p < 0.0001), relative humidity (r = 0.51 to 0.61, p < 0.05) and average temperature (r = 0.32 to 0.58, p < 0.05), but negatively or not significantly correlated with maximum temperature (r = −0.59 to −0.79, p > 0.05). These results demonstrate that rainfall or relative humidity, moderate conditions, and favor conidial release. At the same time, infection risk declines with wound age, underscoring the need to adjust pruning schedules and preventive strategies to reduce disease risk in walnut orchards. Full article

(This article belongs to the Special Issue Plant Pathogens: Monitoring, Identification and Biological Control, 2nd Edition)

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14 pages, 1581 KB

Open AccessArticle

Urobiome Signatures of Recurrent Urinary Tract Infections in Adolescent Pregnancy: A Longitudinal Study

by Carlos Daniel Mora-Vargas, Orly Grobeisen-Duque, Oscar Villavicencio-Carrisoza, Diana Angélica Aguilar-Ayala, Orlando Castellanos-Diaz, Maria Guadalupe Martinez-Salazar, Alejandro Rosas-Balan, Veronica Flores-Rueda, Moises Leon-Juarez, Mario Guzman-Huerta, Lisbeth Camargo-Marin, Maria Isabel Villegas-Mota, Veronica Zaga-Clavellina, Ma. Guadalupe Aguilera-Arreola and Addy Cecilia Helguera-Repetto

Microorganisms 2025, 13(10), 2406; https://doi.org/10.3390/microorganisms13102406 - 21 Oct 2025

Viewed by 298

Abstract

Adolescent pregnancy is a significant public health concern, with maternal and fetal risks compounded by pregnancy-related anatomical, hormonal, and urinary changes that predispose to urinary tract infections (UTIs). Alterations in the urinary microbiome may further influence infection susceptibility, yet little is known about [...] Read more.

Adolescent pregnancy is a significant public health concern, with maternal and fetal risks compounded by pregnancy-related anatomical, hormonal, and urinary changes that predispose to urinary tract infections (UTIs). Alterations in the urinary microbiome may further influence infection susceptibility, yet little is known about its role during adolescent pregnancy. This study analyzed the urinary microbiome of adolescent pregnant patients and its association with UTI and recurrent UTI (rUTI) across gestation. Healthy adolescents were enrolled in the first trimester and followed through subsequent trimesters, with urine samples collected at each visit for microbiological diagnosis. Patients were classified as healthy (34 samples), single UTI (22 samples), or rUTI (31 samples), and oxford-nanopore 16S rRNA sequencing was used to assess taxonomic composition, microbial diversity, and operational taxonomic units. Distinct trimester-specific patterns were observed, with Lactobacillus iners progressively increasing and L. kitasatonis emerging as a dominant taxon during adolescent pregnancy. Interestingly, rUTI cases showed persistent E. coli, reduced L. kitasatonis and L. ultunensis in the second trimester, and the appearance of Fannyhessea vaginae (Atopobium vaginae) in the third. These findings suggest a potential microbial signature of rUTI in adolescent pregnancy, underscoring the need for personalized preventive strategies and the establishment of microbiome-based clinical cutoffs. Full article

(This article belongs to the Special Issue The Microbiome of the Urinary Tract: A Balance Between Eubiosis and Dysbiosis)

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13 pages, 4259 KB

Open AccessArticle

Distinct Gut and Skin Microbiomes of a Carnivorous Caecilian Larva (Ichthyophis bannanicus) Show Ecological and Phylogenetic Divergence from Anuran Tadpoles

by Amrapali Prithvisingh Rajput, Dan Sun, Shipeng Zhou and Madhava Meegaskumbura

Microorganisms 2025, 13(10), 2405; https://doi.org/10.3390/microorganisms13102405 - 21 Oct 2025

Viewed by 916

Abstract

The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, [...] Read more.

The amphibian microbiome plays a vital role in host health, yet the bacterial communities of caecilians (Order: Gymnophiona) remain largely uncharacterised. We investigated this by providing the first characterisation of the gut and skin microbiome of larval Ichthyophis bannanicus, a carnivorous caecilian, using 16S rRNA gene metabarcoding. Our analyses show distinct communities between the faecal samples and skin, with significant enrichment of Laribacter in faeces and Flavobacterium on skin. Despite significant variation in their community structures, the core genera Escherichia-Shigella were shared between both regions, suggesting similar microbial exchange in the aquatic environments. Skin bacterial diversity exhibited relatively higher richness, but lower evenness than that of faeces. Further, the skin bacterial community exhibited more complex interactions, suggesting stronger resilience to changes. The relationships and interactions of skin and faecal bacterial communities suggest their interactive effects on the host’s overall health. Compared with anuran tadpoles, the I. bannanicus larval microbiome showed taxonomic overlap, but possessed certain unique core bacteria. This work on an understudied amphibian lineage is foundational, highlighting how diet, phylogeny, and aquatic environment shape microbial communities and informing future research into amphibian health and disease. Full article

(This article belongs to the Section Microbial Biotechnology)

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25 pages, 1385 KB

Open AccessReview

Harnessing Microalgae and Cyanobacteria for Sustainable Pesticide Biodegradation: Advances, Challenges, and Ecological Benefits

by Nurziya R. Akmukhanova, Sandugash N. Seiilbek, Bolatkhan K. Zayadan, Kenzhegul Bolatkhan, Ramina A. Bakytzhan, Gulzhaina S. Domash and Barry D. Bruce

Microorganisms 2025, 13(10), 2404; https://doi.org/10.3390/microorganisms13102404 - 21 Oct 2025

Viewed by 677

Abstract

Microalgae and cyanobacteria, as versatile photoautotrophic microorganisms, hold significant promise for mitigating soil and water pollution—particularly the removal of pesticides. This review examines their multifaceted roles in pesticide biodegradation, emphasizing how their metabolic capabilities simultaneously reduce environmental toxicity, enrich soil properties, and support [...] Read more.

Microalgae and cyanobacteria, as versatile photoautotrophic microorganisms, hold significant promise for mitigating soil and water pollution—particularly the removal of pesticides. This review examines their multifaceted roles in pesticide biodegradation, emphasizing how their metabolic capabilities simultaneously reduce environmental toxicity, enrich soil properties, and support beneficial microbiota. Cultivation in wastewater treatment systems further highlights their potential for cost-effective bioremediation, as these microbes degrade pesticides, recycle nutrients, break down organic pollutants, and generate biomass with value-added applications. Despite these advantages, implementing large-scale processes remains challenging. Key hurdles include optimizing growth parameters, preventing contamination, improving harvest efficiency, and designing robust bioreactors. Addressing these complexities demands interdisciplinary collaboration in strain selection, metabolic engineering, and process intensification. By capitalizing on microalgae and cyanobacteria’s adaptability and metabolic flexibility, we can develop more sustainable management strategies that reduce reliance on chemical inputs, foster soil health, and contribute to long-term ecological restoration. Ultimately, these microorganisms have the potential to reshape environmental stewardship by combining economic viability with broad-scale ecological benefits. Full article

(This article belongs to the Special Issue Microbial Metabolism and Application in Biodegradation)

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13 pages, 291 KB

Open AccessArticle

Agronomic Efficiency of a New Liquid Inoculant Formulated with a Mixture of Azospirillum brasilense Strains Ab-V5 and Ab-V6 in Corn (Zea mays L.)

by Ricardo Cancio Fendrich, Mayara Barbosa Silva and Ivanildo Evodio Marriel

Microorganisms 2025, 13(10), 2403; https://doi.org/10.3390/microorganisms13102403 - 21 Oct 2025

Viewed by 369

Abstract

Nitrogen fertilization is a critical factor in maize (Zea mays L.) production, as nitrogen is often the primary limiting nutrient. The use of microbial biostimulants has emerged as a promising strategy to enhance nitrogen use efficiency. This study assessed the field performance [...] Read more.

Nitrogen fertilization is a critical factor in maize (Zea mays L.) production, as nitrogen is often the primary limiting nutrient. The use of microbial biostimulants has emerged as a promising strategy to enhance nitrogen use efficiency. This study assessed the field performance of an industrially produced inoculant (Nodusoja™), formulated with Azospirillum brasilense strains Ab-V5 and Ab-V6, under contrasting soil and climatic conditions. The aim of this study is to assess the grain yield of maize cultivated in different edaphoclimatic conditions using the biostimulant, together with lower doses of topdressing fertilization. Field experiments were conducted across double cropping seasons in Sete Lagoas, Minas Gerais (19°28′ S; 44°15′ W), and Palmas, Tocantins (10°8′ S; 48°19′ W), Brazil, during the 2018, 2019, and 2021 harvests. Evaluated parameters included grain yield, shoot dry mass, and nitrogen content. The most pronounced effects were observed on productivity, with maximum grain yields of 8.76 and 9.05 t·ha⁻¹ recorded in the 2019 season, under inoculation without topdressed N and inoculation with 50% of the recommended N dose, respectively. By contrast, uninoculated treatments with 20, 60, and 120 kg N·ha⁻¹ yielded 6.41, 7.13, and 7.49 t·ha⁻¹, respectively. Statistical analyses demonstrated that inoculation with strains Ab-V5 and Ab-V6 increased maize grain yield by up to 40% when combined with 50% of the recommended nitrogen fertilization. These findings highlight the potential of Azospirillum-based inoculants to improve N use efficiency and reduce dependence on synthetic fertilizers in maize cultivation. Full article

(This article belongs to the Special Issue Plant Growth-Promoting Bacteria)

10 pages, 1294 KB

Open AccessArticle

Virulence and Resistance of Pseudomonas aeruginosa Isolated from Poultry in Brazil

by Fernanda Borges Barbosa, Maria J. Pons, Joaquim Ruiz, Yolanda Sáenz, Henrik Christensen and Terezinha Knöbl

Microorganisms 2025, 13(10), 2402; https://doi.org/10.3390/microorganisms13102402 - 21 Oct 2025

Viewed by 317

Abstract

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with infections in hospitalized and immunocompromised patients due to its virulence and antimicrobial resistance. In the poultry industry, it has been associated with hatchery mortality. This study aimed to characterize P. aeruginosa isolated from pipped [...] Read more.

Pseudomonas aeruginosa is an opportunistic pathogen commonly associated with infections in hospitalized and immunocompromised patients due to its virulence and antimicrobial resistance. In the poultry industry, it has been associated with hatchery mortality. This study aimed to characterize P. aeruginosa isolated from pipped eggs, one-day-old chicks, and broiler carcasses obtained from a slaughterhouse in São Paulo state, Brazil. Nineteen strains of P. aeruginosa were selected and their virulence genes were amplified via PCR. Clonality analysis was performed using BOX-PCR, and three strains were selected for whole-genome sequencing (WGS). All isolates carried aprA, plcH, plcN, lasA, lasB, lasI, lasR, rhlAB, and phzH. The exoA gene was detected in 73.7% of strains, while algD was present in 21.1%. The exoY and exoT genes were present in 94.7% of strains (18/19), whereas exoS was present in 47.4% (9/19). None of the isolates harbored the exoU gene. BOX-PCR and phylogenetic analyses revealed diverse clonal patterns. The sequenced strains were classified as O3 ST116, O2 ST1649, and O3 ST1744. The presence of virulence and antimicrobial resistance determinants in poultry-associated strains underscores the need for surveillance, as these isolates may represent a source for transmission of P. aeruginosa to humans. Our findings highlight the importance of monitoring P. aeruginosa within poultry production and emphasize the value of genomic approaches to understand its diversity, evolution, and public health risks. Full article

(This article belongs to the Special Issue Evolution and Spread of Drug-Resistant Pathogens)

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19 pages, 2329 KB

Open AccessArticle

Linking Soil Microbial Diversity to Nitrogen and Phosphorus Dynamics

by Bruna Arruda, Eduardo Mariano, Wilfrand Ferney Bejarano-Herrera, Fábio Prataviera, Elizabeth Mie Hashimoto, Fernando Ferrari Putti, Jéssica Pigatto de Queiroz Barcelos, Paulo Sergio Pavinato, Fernando Dini Andreote and Davey L. Jones

Microorganisms 2025, 13(10), 2401; https://doi.org/10.3390/microorganisms13102401 - 21 Oct 2025

Viewed by 360

Abstract

Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and [...] Read more.

Changes in the soil microbial community for studies of different novel communities can be promoted by different methodologies, among which soil autoclaving stands out as a quick and readily available tool. However, this procedure may also directly or indirectly alter nitrogen (N) and phosphorus (P) dynamics. The purposes of this study were as follows: (i) to characterize microbial activity after soil autoclaving through microbial ¹⁴CO₂-respiration; and (ii) to evaluate the effect of microbial manipulation and autoclaving on soil N and ³³P dynamics. For this, two sets of soil samples from two areas (forest and cultivated area) were used in the laboratory. Firstly, ¹⁴C-glucose was added to the soils and after 24 h five soil microbiomes were generated: AS (autoclaved soil), and AS re-inoculated with serial dilutions (w/v) prepared by successive mixing of soil suspensions in sterile deionized water obtaining 10⁻¹, 10⁻³, and 10⁻⁶, which generated the treatments AS + 10⁻¹, AS + 10⁻³, and AS + 10⁻⁶; and the treatment NS (non-autoclaved control), all incubated for 28 d. ¹⁴CO₂ emission was used to characterize microbial activity; additionally, N dynamics were assessed at the end of incubation. In a second assay, ³³P was applied to the soil before autoclaving and re-inoculation. Following further incubation (14 d), a ³³P chemical fractionation was performed. The following are based on the results: (i) ¹⁴CO₂ emission: microbial activity in the autoclaved soil is null, but after a reinoculation of AS + 10⁻¹ and AS + 10⁻³ soil dilution suspension, the ¹⁴CO₂-respiration is higher than in an NS. (ii) regarding the N dynamics, in autoclaved soils, the microbial levels increased N-NH₄⁺ concentration, with an evident increase in the AS + 10⁻³ and AS + 10⁻¹, and a reduction in the N-NO₃⁻ concentration in comparison to the NS. For ³³P, the autoclaving procedure itself reduced the ³³P lability, regardless of the levels of microbial community reinoculated. Full article

(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)

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23 pages, 6003 KB

Open AccessArticle

Biocontrol Potential, Plant Growth-Promotion, and Genomic Insights of Pseudomonas koreensis CHHM-1 Against Bacterial Canker in Actinidia arguta

by Mengqi Wang, Taiping Tian, Yue Wang, Ruoqi Liu, Shutian Fan, Mingjie Ma, Baoxiang Zhang, Jiaqi Li, Yanli Wang, Yiming Yang, Peilei Xu, Nan Shu, Wenpeng Lu, Bowei Sun, Manyu Wu, Hongyan Qin and Changyu Li

Microorganisms 2025, 13(10), 2400; https://doi.org/10.3390/microorganisms13102400 - 20 Oct 2025

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Abstract

In 2019, bacterial canker caused by Pseudomonas syringae pv. actinidiae was first identified in Actinidia arguta. This disease has led to significant yield reduction, plant mortality, and substantial economic losses in A. arguta cultivation. Its emergence poses a novel challenge to the [...] Read more.

In 2019, bacterial canker caused by Pseudomonas syringae pv. actinidiae was first identified in Actinidia arguta. This disease has led to significant yield reduction, plant mortality, and substantial economic losses in A. arguta cultivation. Its emergence poses a novel challenge to the sustainable global production of kiwifruit. Currently available treatments for bacterial canker caused by P. syringae pv. actinidiae are scarce. Moreover, the environmental toxicity of copper-based compounds and emerging antibiotic resistance issues necessitate the development of eco-friendly control strategies. Disease management strategies based on biocontrol bacteria have shown broad application prospects. In this study, the isolate CHHM-1 with significant antagonistic activity against P. syringae pv. actinidiae was isolated from the rhizosphere soil of healthy A. arguta. It was identified as Pseudomonas koreensis through 16S rRNA gene and whole-genome sequencing. Genomic analysis revealed that the isolate CHHM-1 harbors various genes related to biocontrol, plant growth promotion, and antibiotic resistance, suggesting strong environmental adaptability and functional potential. Furthermore, the strain exhibited multiple plant growth-promoting traits, such as nitrogen fixation, phosphate solubilization, siderophore production, and synthesis of indole-3-acetic acid (IAA). In vitro antagonism assays confirmed the strong antagonistic activity of the isolate CHHM-1 against P. syringae pv. actinidiae. A dual-culture plate assay showed an average inhibition zone of 4.36 cm, while preventive application on plants significantly reduced lesion length to 1.3 mm (vs. 6.2 mm control) in shoots and lesion area to 10% (vs. 80% control) in leaf discs. Further antibacterial tests revealed that its inhibitory mechanism is attributed to secreted antimicrobial substances. These findings provide a promising candidate for developing novel biopesticides to combat P. syringae pv. actinidiae variants, reduce chemical dependency, and foster sustainable A. arguta production. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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13 pages, 255 KB

Open AccessArticle

ST8 and ST72 Methicillin-Resistant S. aureus Bacteremia in Korea: A Comparative Analysis of Clinical and Microbiological Characteristics

by Yun Woo Lee, Ji-Hun Kim, So Yun Lim, Euijin Chang, Seongman Bae, Jiwon Jung, Min Jae Kim, Yong Pil Chong, Sung-Han Kim, Sang-Ho Choi, Sang-Oh Lee and Yang Soo Kim

Microorganisms 2025, 13(10), 2399; https://doi.org/10.3390/microorganisms13102399 - 20 Oct 2025

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Abstract

Methicillin-resistant Staphylococcus aureus (MRSA) remains a major cause of bloodstream infection worldwide. In Korea, sequence type (ST) 72 has predominated, whereas ST8, including the USA300 lineage, has recently emerged. Comparative data on these genotypes in MRSA bacteremia (MRSAB) are limited. We conducted a [...] Read more.

Methicillin-resistant Staphylococcus aureus (MRSA) remains a major cause of bloodstream infection worldwide. In Korea, sequence type (ST) 72 has predominated, whereas ST8, including the USA300 lineage, has recently emerged. Comparative data on these genotypes in MRSA bacteremia (MRSAB) are limited. We conducted a retrospective cohort study of adult patients with MRSAB admitted to a 2700-bed tertiary care hospital in Republic of Korea between July 2008 and December 2020. Clinical features and outcomes of patients with ST8 MRSA were compared with those of patients with ST72 MRSA. Among 1975 cases of S. aureus bacteremia, 998 (50.5%) were due to MRSA, including 327 (32.7%) ST72 and 23 (2.3%) ST8 isolates. Demographics and comorbidities were similar, though pneumonia appeared more frequent in ST8 cases without statistical significance. ST8 isolates exhibited greater resistance to ciprofloxacin and erythromycin and more frequent vancomycin E-test MICs ≥1 mg/L, while broth microdilution MICs were comparable. spa type distribution differed, with t324 predominating in ST72 and t008 in ST8. Management practices, persistent bacteremia, recurrence, and 30- and 90-day mortality did not differ significantly. In multivariable analysis, liver cirrhosis and Charlson comorbidity index >4, but not MRSA genotype, independently predicted 30-day mortality. These findings highlight the importance of continued surveillance of emerging ST8 clones. Full article

(This article belongs to the Section Medical Microbiology)

16 pages, 2545 KB

Open AccessArticle

Migration Characteristics of Manure-Derived Antibiotic-Resistant Bacteria in Vegetables Under Different Soil Types

by Tingting Song, Changxiong Zhu, Honghui Teng, Binxu Li, Shuang Zhong, Yan Qin, Jiawei He and Hongna Li

Microorganisms 2025, 13(10), 2398; https://doi.org/10.3390/microorganisms13102398 - 20 Oct 2025

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Abstract

The application of livestock manure can introduce antibiotic-resistant bacteria (ARB) into soil–vegetable systems, potentially shaping the antibiotic resistance profiles of plants. This study investigated the effects of manure containing chlortetracycline (CTC) on antibiotic resistance in pakchoi grown in three distinct soil types (black [...] Read more.

The application of livestock manure can introduce antibiotic-resistant bacteria (ARB) into soil–vegetable systems, potentially shaping the antibiotic resistance profiles of plants. This study investigated the effects of manure containing chlortetracycline (CTC) on antibiotic resistance in pakchoi grown in three distinct soil types (black soil, fluvo-aquic soil, and red soil). The results demonstrated that CTC-manure application significantly increased the relative abundance of CTC-resistant endophytic bacteria (CREB), with the magnitude of the increase following the order: black soil (235.43%) > fluvo-aquic soil (64.5%) > red soil (10.68%). Furthermore, the presence of CTC promoted the proliferation of Acinetobacter and increased the abundance of potential pathogens (such as Klebsiella, Rhodococcus, and Corynebacterium), thereby elevating the risk of antibiotic resistance transmission. Metabolomic analysis revealed that CTC induced the most substantial metabolic alterations in pakchoi grown in red soil. Correlation analysis indicated that the CREB community structure was primarily shaped by soil properties, including total nitrogen, total phosphorus, and organic matter, and was significantly correlated with indigenous soil ARB (Pseudomonas, Bacillus, and Stenotrophomonas). This study elucidates the mechanisms underlying manure-driven antibiotic resistance dissemination in vegetable production systems and offers a theoretical foundation for developing agricultural practices to mitigate associated risks. Full article

(This article belongs to the Special Issue Antimicrobial Resistance (AMR): From the Environment to Health)

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2 pages, 298 KB

Open AccessCorrection

Correction: Wu et al. Heterologous Expression and Enzymatic Properties of β-Glucuronidase from Clostridium perfringens and Its Application in Bilirubin Transformation. Microorganisms 2025, 13, 1043

by Qianlin Wu, Qing Guo, Fo Yang, Mengru Li, Yumeng Zhu, Binpeng Xu, Lu Zhao, Shanshan Zhang, Youyu Xie, Feng Li, Xiaomin Wu and Dayong Xu

Microorganisms 2025, 13(10), 2397; https://doi.org/10.3390/microorganisms13102397 - 20 Oct 2025

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Abstract

In the original publication [...] Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

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20 pages, 8470 KB

Open AccessArticle

Effects of the Wheat Crab Model and the Pond Culture Model on the Growth, Metabolism and Intestinal Microbiota of the Chinese Mitten Crab (Eriocheir sinensis)

by Min Yang, Jun Ling, Tong Li, Chengchen Yu, He Jiang and Tingshuang Pan

Microorganisms 2025, 13(10), 2396; https://doi.org/10.3390/microorganisms13102396 - 19 Oct 2025

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Abstract

This study investigated the influence of two distinct aquaculture systems, namely, the wheat-crab model (WCM) and pond culture (PC) model, on the growth, physiological well-being, and gut microbial structure of Chinese mitten crabs (Eriocheir sinensis). A total of 120 adult crabs [...] Read more.

This study investigated the influence of two distinct aquaculture systems, namely, the wheat-crab model (WCM) and pond culture (PC) model, on the growth, physiological well-being, and gut microbial structure of Chinese mitten crabs (Eriocheir sinensis). A total of 120 adult crabs were randomly selected from the two systems: 60 crabs from the WCM, including 30 females and 30 males, and 60 crabs from the PC model, also including 30 females and 30 males. The gonadosomatic index of female crabs in the WCM was notably higher than that of the other groups, while the hepatopancreatic index was significantly lower. Significant variations were not observed in final weight, fullness, or muscle yield between the WCM and PC groups. Biochemical evaluations indicated no substantial differences in antioxidant capabilities between the two systems; however, female crabs demonstrated increased critical antioxidant enzyme activity, such as for catalase and superoxide dismutase, and significantly elevated cholesterol levels. Additionally, the expression of the genes IL, ProPO, and Keap1 was significantly higher in the WCM group than the PC group, whereas the expression of ALF2, Myd88, and CncC did not significantly differ between the two cultivation methods. Non-targeted metabolomics analysis revealed notable distinctions in metabolite profiles between the two systems. Moreover, the WCM facilitated an increase in beneficial Firmicutes bacteria while reducing potentially harmful microorganisms, suggesting improved immune function in crabs raised under the WCM. In summary, female crabs reared in the WCM matured earlier and exhibited slightly better health conditions compared to those grown in the PC model. Full article

(This article belongs to the Special Issue Advances in Aquaculture and Microorganisms)

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23 pages, 3139 KB

Open AccessArticle

Microbial Communities and Physicochemical Properties of the Nile River Water in the Suez Canal Area

by Noha Elkayal, Samira Zakeer, Marwa Azab, Ali Abdellah and Sarah Shabayek

Microorganisms 2025, 13(10), 2395; https://doi.org/10.3390/microorganisms13102395 - 19 Oct 2025

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Abstract

Monitoring freshwater resources is crucial to drinking water quality. The Ismailia Canal supplies most freshwater to the Suez Canal area in Egypt. However, information on the freshwater microbiome is limited in this region. A total of 59 freshwater samples were collected. Along with [...] Read more.

Monitoring freshwater resources is crucial to drinking water quality. The Ismailia Canal supplies most freshwater to the Suez Canal area in Egypt. However, information on the freshwater microbiome is limited in this region. A total of 59 freshwater samples were collected. Along with determining the physicochemical properties of the samples, we used conventional methods to identify indicator bacteria. To overcome limitations of conventional culture, we employed high-throughput 16S rRNA gene sequencing, taxonomy profiling, and functional prediction to study uncultivated microbial communities. Total and fecal coliforms prevailed in 100% and 80% of samples, respectively. Predominant contaminants included E. coli, fecal streptococci, Pseudomonas aeruginosa, and Staphylococcus aureus. Taxonomic profiling revealed dominance of Proteobacteria and Actinobacteriota. Proteobacteria showed a positive correlation with Bacteroidetes and a negative correlation with Actinobacteria. Most samples had similar bacterial community structures, despite location-driven variability. Elevated bacterial loads were notable at the Qassasin district, which exhibited the highest relative abundance of genes associated with bacterial infections. This study provides key insights into the impact of freshwater microbiome on public health. Full article

(This article belongs to the Special Issue Water Microorganisms Associated with Human Health, 2nd Edition)

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13 pages, 829 KB

Open AccessArticle

Characterization of Metabolomic Response of Candida spp. to Heavy Metal Exposure

by Perla Nayeli Reyes-Sánchez, Jesús Alfonso Chairez-Ávila, Karol Karla García-Aguirre, Verónica Esparza-Cordero, María Fernanda Romo-García, Juan C. Medina-Llamas and Juan Ernesto López-Ramos

Microorganisms 2025, 13(10), 2394; https://doi.org/10.3390/microorganisms13102394 - 19 Oct 2025

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Abstract

As a result of anthropogenic activities, contaminants such as heavy metals have been introduced into the environment. Microorganisms, including Candida spp., have emerged as a viable alternative for their removal; however, the mechanism responsible for the removal process has not been fully characterized. [...] Read more.

As a result of anthropogenic activities, contaminants such as heavy metals have been introduced into the environment. Microorganisms, including Candida spp., have emerged as a viable alternative for their removal; however, the mechanism responsible for the removal process has not been fully characterized. This study aims to identify the secretome of Candida strains (C. albicans, C. glabrata, C. parapsilosis and C. tropicalis) contributing to their ability to withstand heavy metals. For this purpose, Candida spp. cultures were incubated at 28 °C under agitation for 72 h and exposed to different concentrations of Cd²⁺, Cu²⁺ and Zn²⁺. The cultures were then analyzed using GC-MS. In Candida spp. cultures exposed to heavy metals, 117 different compounds were identified compared with the control cultures. Among all Candida spp., 15 metabolites showed a fold change greater than two compared to the control conditions. These included hydrocarbons (3), fatty acids (5), aromatic compounds (5), a nonaromatic compound (1) and an organosiloxane (1), which were identified in the presence of heavy metals (Cd, Cu and Zn). Full article

(This article belongs to the Section Microbiomes)

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21 pages, 1015 KB

Open AccessArticle

Combating Foodborne MRSA: Identification and Silver Nanoparticle-Based Antibacterial Strategies with Antibiotic Synergy and Resistance Evolution Assessment

by Adil Abalkhail and Eman Marzouk

Microorganisms 2025, 13(10), 2393; https://doi.org/10.3390/microorganisms13102393 - 18 Oct 2025

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Abstract

Ready-to-eat (RTE) foods can carry antimicrobial-resistant pathogens; however, few studies link real-world surveillance to practical interventions. This study addressed this gap by estimating the prevalence of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) in ready-to-eat foods from Al-Qassim and [...] Read more.

Ready-to-eat (RTE) foods can carry antimicrobial-resistant pathogens; however, few studies link real-world surveillance to practical interventions. This study addressed this gap by estimating the prevalence of Staphylococcus aureus (S. aureus) and methicillin-resistant S. aureus (MRSA) in ready-to-eat foods from Al-Qassim and evaluating a rapid, orthogonal confirmation workflow (culture → MALDI-TOF MS → Vitek 2 → mecA/mecC PCR). The in vitro activity of citrate-stabilized silver nanoparticles (AgNPs) against food-derived MRSA was quantified, and synergy with oxacillin (primary) and ciprofloxacin (secondary) was examined. Silver-susceptibility stability was assessed over 20 days of sub-MIC serial passage, with attention to whether β-lactam co-exposure constrained drift. We surveyed 149 RTE products and paired the confirmation workflow with mechanistic tests of AgNPs as antibiotic adjuvants. S. aureus was recovered from 24.2% of products and MRSA from 6.7%, with higher recovery from animal-source matrices and street-vendor outlets. MALDI-TOF MS provided rapid species confirmation and revealed two reproducible low-mass peaks (m/z 3990 and 4125) associated with MRSA, supporting spectral triage pending molecular confirmation. Antimicrobial susceptibility testing showed the expected β-lactam split (MRSA oxacillin/cefoxitin non-susceptible; MSSA oxacillin-susceptible but largely penicillin-resistant), with last-line agents retained. Citrate-stabilized AgNPs displayed consistent potency against food-derived MRSA (MIC 8–32 µg/mL; MIC₅₀ 16; MIC₉₀ 32) and were predominantly bactericidal (MBC/MIC ≤ 4 in 90%). Checkerboards demonstrated frequent AgNP–oxacillin synergy (median fractional inhibitory concentration index [FICI] 0.37; 4–16-fold oxacillin MIC reductions) and additive-to-synergistic effects with ciprofloxacin (median FICI 0.63), translating time–kill assays into rapid, sustained bactericidal activity without antagonism. During sub-MIC evolution, silver MICs rose modestly (median two-fold) and often regressed off drug; oxacillin co-exposure limited drift. RTE foods therefore represent credible MRSA exposure routes. Integrating MALDI-assisted triage with automated AST enables scalable surveillance, and standardized AgNP formulations emerge as promising β-lactam adjuvants—pending in situ efficacy, safety, and residue evaluation. Full article

(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions, 2nd Edition)

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16 pages, 604 KB

Open AccessArticle

Helicobacter pylori-Mediated Injury: The Hidden Path to Gastric Hemorrhage and Neoplasia

by Sabrina-Nicoleta Munteanu, Ana-Maria Filip, Patrick-Lazăr-Dominik Chiciudean, Monica Pantea, Simona Mocan and Anca Elena Negovan

Microorganisms 2025, 13(10), 2392; https://doi.org/10.3390/microorganisms13102392 - 18 Oct 2025

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Abstract

Helicobacter pylori infection represents a well-established risk factor for the development of gastric carcinogenesis, yet reliable clinical or endoscopic predictors of infection remain poorly defined. Identifying non-invasive or endoscopic markers of this infection could improve early detection, which is crucial for effective prevention [...] Read more.

Helicobacter pylori infection represents a well-established risk factor for the development of gastric carcinogenesis, yet reliable clinical or endoscopic predictors of infection remain poorly defined. Identifying non-invasive or endoscopic markers of this infection could improve early detection, which is crucial for effective prevention and clinical management. This single-center study included 737 patients who underwent upper gastrointestinal endoscopy. We compared clinical, laboratory, and endoscopic features between H. pylori-positive and H. pylori-negative individuals. A total of 263 with H. pylori-positive gastric biopsies and 474 with H. pylori-negative biopsies were enrolled in our study. Cerebrovascular disease (9.51% vs. 5.51%, p = 0.04, OR = 1.80), type 2 diabetes mellitus (T2DM—22.05% vs. 15.86%, p = 0.04, OR 1.5), and alcohol consumption (18.96% vs. 9.3%, p = 0.00, OR = 2.28) were significantly more prevalent among H. pylori-positive patients. Heartburn was more commonly reported in H. pylori-negative individuals (23.77% vs. 15.38%, p = 0.01, OR = 0.58). Laboratory parameters showed no significant differences between groups. Regarding endoscopic findings, corporal erythema (26.92% vs. 16.17%, p = 0.00, OR = 1.91), corporal erosions (11.54% vs. 5.32%, p = 0.00, OR = 2.32), and submucosal hemorrhages (20.91% vs. 11.6%, p = 0.00, OR = 2.01) were associated with H. pylori infection. In the multivariate logistic regression models, alcohol consumption and corporal lesions remained independent predictors of H. pylori-associated gastritis, even after adjusting for age, sex, and PPI use. This study identifies alcohol consumption and specific corporal mucosal changes as novel, independent predictors of H. pylori infection. Heartburn was negatively associated with active H. pylori infection, while the rest of the symptoms did not predict infection or mucosal lesions. The laboratory parameters did not differ significantly between groups. These findings underscore the potential of targeted endoscopic evaluation and risk-based screening (particularly among T2DM and alcohol-consuming populations) to enhance early detection and management of H. pylori-associated disease. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Bacterial Infection)

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15 pages, 1337 KB

Open AccessArticle

Evaluation of Specific Torulaspora delbrueckii Fractions to Stimulate Malolactic Fermentation in Limiting Conditions

by Aitor Balmaseda, Paloma Toraño, Benjamin Leroux, José María Heras, Sibylle Krieger-Weber, Nicolas Rozès, Magali Deleris-Bou and Cristina Reguant

Microorganisms 2025, 13(10), 2391; https://doi.org/10.3390/microorganisms13102391 - 17 Oct 2025

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Abstract

Malolactic fermentation (MLF) is a bioprocess driven by lactic acid bacteria (LAB), which is desired in red and highly acidic white wines. Among all LAB, Oenococcus oeni is the main species in wine, followed by Lactiplantibacillus plantarum. The harsh conditions found in [...] Read more.

Malolactic fermentation (MLF) is a bioprocess driven by lactic acid bacteria (LAB), which is desired in red and highly acidic white wines. Among all LAB, Oenococcus oeni is the main species in wine, followed by Lactiplantibacillus plantarum. The harsh conditions found in wine—not only due to the low nutrient concentration but also the presence of antimicrobial compounds such as ethanol, high acidity, SO_2, and polyphenols—can compromise MLF performance. In recent years, the use of certain non-Saccharomyces yeasts, such as Torulaspora delbrueckii or Metschnikowia pulcherrima, as starter cultures for alcoholic fermentation, has emerged as a promising strategy to improve MLF. In this study, we evaluated the effect of four different fractions from a T. delbrueckii strain on MLF performance. First, the positive impact of this strain as a starter culture on O. oeni growth was confirmed; then, yeast-derived compounds were tested in different wines. Two fractions showed the most promising results in reducing MLF duration: the inactivated yeast fraction and the autolysate fraction. Those enhanced bacterial viability and promoted mannoprotein consumption. These findings highlight the potential of T. delbrueckii-derived compounds as enological tools to support MLF under restrictive wine conditions. Full article

(This article belongs to the Special Issue Wine Fermentation Microorganisms)

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18 pages, 3186 KB

Open AccessArticle

Preliminary Assessment of Mycobiome at Former Quarry Site That Hosts a Diverse and Abundant Orchid Population

by Viswambharan Sarasan, Dean Williams and Zoe Ringwood

Microorganisms 2025, 13(10), 2390; https://doi.org/10.3390/microorganisms13102390 - 17 Oct 2025

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Abstract

Former quarries offer unique opportunities for biodiversity restoration, yet their potential for orchid meadow creation remains underexplored. This study screened soils to study whether these habitats harbour key orchid-compatible fungi essential for orchid colonisation. We conducted comparative analyses of fungal community composition across [...] Read more.

Former quarries offer unique opportunities for biodiversity restoration, yet their potential for orchid meadow creation remains underexplored. This study screened soils to study whether these habitats harbour key orchid-compatible fungi essential for orchid colonisation. We conducted comparative analyses of fungal community composition across restored quarry sites using alpha and beta diversity metrics, NMDS ordinations, and regression models linking orchid abundance with fungal diversity. Using soil metabarcoding across four restored sites, the results showed that orchid abundance strongly correlated with fungal diversity, including mycorrhizal families such as Sebacinaceae and Thelephoraceae. The gorge-based site supported the highest orchid density and richest fungal assemblage. These findings demonstrate that former quarries can sustain the fungal networks required for orchid recruitment, providing a foundation for large-scale restoration strategies. Association analysis revealed that orchid abundance, though on a limited scale, is a strong predictor of fungal diversity, indicating that denser orchid populations support richer fungal communities. Despite its limited scale, this study demonstrates that former quarries can provide both the physical conditions and the fungal networks necessary for orchid establishment, offering a practical model for restoring orchid-rich meadows and enhancing biodiversity in former quarries. Full article

(This article belongs to the Section Plant Microbe Interactions)

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17 pages, 8320 KB

Open AccessArticle

ROS-Mediated Necroptosis Promotes Coxsackievirus B3 Replication and Myocardial Injury

by Junbo Huang, Yanjun Di, Qing Song, Zhiyun Cheng, Hao Wu, Mei Wu, Minjian He, Genrui Zhang, Fucai Wang and Lei Tong

Microorganisms 2025, 13(10), 2389; https://doi.org/10.3390/microorganisms13102389 - 17 Oct 2025

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Abstract

Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it [...] Read more.

Coxsackievirus B3 (CVB3) is a primary causative agent of viral myocarditis (VMC), which can lead to both acute and chronic cardiac inflammation accompanied by progressive heart failure and arrhythmias. Although CVB3 has been implicated in various forms of programmed cell death, whether it triggers necroptosis and the underlying mechanisms remains unclear. This study aimed to investigate the role and mechanism of CVB3-induced necroptosis and its effect on viral replication. Using both in vitro and in vivo models, we demonstrated that CVB3 infection significantly upregulates the expression of key necroptotic markers RIP1 and RIP3 in HeLa cells and mouse myocardial tissues. This upregulation was accompanied by elevated intracellular reactive oxygen species (ROS) levels and suppression of the Nrf2/HO-1 antioxidant pathway. Intervention with the necroptosis inhibitor Necrostatin-1 (Nec-1) or the ROS scavenger N-acetylcysteine (NAC) markedly attenuated cell death, suppressed viral replication, and ameliorated myocardial injury and inflammatory responses in infected mice. Mechanistically, CVB3 inhibits the Nrf2/HO-1 pathway, thereby inducing substantial ROS accumulation that promotes necroptosis. This effect can be reversed by NAC treatment. Our study reveals a novel mechanism through which CVB3 induces ROS-dependent necroptosis via the suppression of the Nrf2/HO-1 pathway, providing new insights into the pathogenesis of viral myocarditis and suggesting potential therapeutic strategies. Full article

(This article belongs to the Special Issue Viral Proteases in Viral Infection and Drug Development)

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24 pages, 432 KB

Open AccessArticle

Exploratory Temporal and Evolutionary Insights into the Filoviridae Family Through Multiprotein Phylogeny

by Thiago S. Messias, Kaique C. P. Silva, Narciso A. Vieira, Gislaine A. Querino, Elaine C. Marcos, Mateus J. de C. Stefani, Ana P. R. Battochio, Thaís M. Oliveira, Ivan S. Vieira, Aline S. Ibanes, Taylor E. T. Olivo, Edson C. de Melo, Silvia C. Arantes, Pedro C. R. da Luz, Maria G. R. Mengoa and Simone Soares

Microorganisms 2025, 13(10), 2388; https://doi.org/10.3390/microorganisms13102388 - 17 Oct 2025

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Abstract

Filoviruses are among the most lethal viral human pathogens known, with significant relevance to public health, yet their evolutionary history remains poorly resolved. This study applied a multiprotein molecular phylogenetic approach to investigate the evolutionary and temporal dynamics of the family Filoviridae. [...] Read more.

Filoviruses are among the most lethal viral human pathogens known, with significant relevance to public health, yet their evolutionary history remains poorly resolved. This study applied a multiprotein molecular phylogenetic approach to investigate the evolutionary and temporal dynamics of the family Filoviridae. Amino acid sequences from the proteome and seven individual proteins (NP, VP35, VP40, GP, VP30, VP24, L) were analyzed using MEGA 12, with RelTime inference anchored on uniform calibrations, and integration of epidemiological data (cases, fatalities, case fatality). The phylogenetic reconstructions revealed robust topologies for most proteins, though selective pressures on GP, VP30 and VP40 generated more variable patterns. Temporal inferences supported the classification of filoviruses into three groups: an ancestral lineage (>1 MYA, fish- and reptile-associated), an intermediate lineage (BCE–1 MYA, bat-associated), and a contemporary lineage (CE, ebolaviruses and marburgviruses). VP30 and VP40 showed consistent associations with epidemiological outcomes in Orthoebolavirus zairense, suggesting their interplay may underlie enhanced dispersal and virulence. Contrariwise, Orthoebolavirus restonense emerged as a natural counterpoint for comparison with other potential human pathogenic filoviruses. Taken together, these findings highlight that filoviral evolution is intrinsically linked not only to viral biology but also to the ecology and history of their hosts. Full article

(This article belongs to the Special Issue Advances in Viral Metagenomics)

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22 pages, 50770 KB

Open AccessArticle

Metagenomics and In Vitro Growth-Promoting Experiments Revealed the Potential Roles of Mycorrhizal Fungus Humicolopsis cephalosporioides and Helper Bacteria in Cheilotheca humilis Growth

by Yawei Liu, Yuhao Shang, Xin Wang, Xiao Li, Zhiming Yu, Zhanghui Zeng, Zhehao Chen, Lilin Wang, Taihe Xiang and Xiaoping Huang

Microorganisms 2025, 13(10), 2387; https://doi.org/10.3390/microorganisms13102387 - 17 Oct 2025

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Abstract

In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the [...] Read more.

In mycorrhizal symbiotic relationships, non-photosynthetic myco-heterotrophic plants are unable to supply photosynthates to their associated fungi. On the contrary, they rely on fungal carbon to sustain their own growth. Mycorrhizal fungi can mediate plant interactions with the rhizosphere microbiome, which contributes to the promotion of plant growth and nutrient uptake. However, the microbial community and key microbial species that function during the growth of the myco-heterotrophic plant Cheilotheca humilis remain unclear. In this study, we evaluated the microbial community associated with Cheilotheca humilis, which was confirmed via morphological characteristics typical of this plant species. Metagenomic analysis showed that the Afipia carboxidovorans was dominant at species level. Based on the LDA score, Bradyrhizobium ottawaense exhibited the higher abundance in the CH-B group (related to bud) while Afipia carboxidovorans was identified from the CH-F group (related to flower). Microbial co-occurrence networks showed that the Rhizobium genus, Herbaspirillum genus, and Cyanobacteriota were defined as core functional microbial species. To explore the potential microorganisms, metagenome-assembled genomes (MAGs) of the rhizosphere microbiome identified 14 medium- and high-quality MAGs, mainly involved in carbon fixation, nitrogen transformation, and phosphorus metabolism, possibly providing nutrients for the plant. Furthermore, a total of 67 rhizospheric and 66 endophytic microorganisms were isolated and obtained. In vitro experiments showed that the mycorrhizal helper bacteria (MHBs) Rhizobium genus and Pseudomonas genus possessed the ability of nitrogen fixation, phosphate solubilization, and siderophores production. Most importantly, the mycorrhizal fungus Humicolopsis cephalosporioides was obtained, which could potentially produce cellulase to supply carbohydrates for host. The findings suggest the mycorrhizal fungus Humicolopsis cephalosporioides and helper bacteria have great potential in the growth of the myco-heterotrophic plant Cheilotheca humilis. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere)

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16 pages, 821 KB

Open AccessReview

The Influence of Seasonal Variations in Clinical Trials Based on Gut Microbiota Studies

by Giovanna Cocomazzi, Concetta Panebianco, Annamaria Vallelunga, Daniele De Ruvo, Lino Del Pup, Serena Smeazzetto, Monica Antinori, Valeria Chimienti, Gabriele Maggio, Concetta Finocchiaro, Viviana Contu and Valerio Pazienza

Microorganisms 2025, 13(10), 2386; https://doi.org/10.3390/microorganisms13102386 - 17 Oct 2025

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Abstract

Seasonality is a key determinant in shaping the composition and function of the human gut microbiota, exerting its influence through multiple interconnected factors. These include seasonal variations in diet, environmental conditions (such as temperature, humidity, and sunlight exposure), behavioral patterns (physical activity, time [...] Read more.

Seasonality is a key determinant in shaping the composition and function of the human gut microbiota, exerting its influence through multiple interconnected factors. These include seasonal variations in diet, environmental conditions (such as temperature, humidity, and sunlight exposure), behavioral patterns (physical activity, time spent outdoors), and the incidence of seasonal infections. These changes are most visible in certain populations where food availability follows a seasonal pattern. Increasing evidence suggests that gut microbiota composition undergoes seasonal variations, which may have significant implications for human health. In patients with non-communicable chronic diseases (NCDs), where microbiota dysbiosis plays a crucial role in disease progression, understanding the seasonal effects on gut microbiota is essential. These dynamic changes impact the gut microbiota immune system interaction and may contribute to the onset or exacerbation of various diseases, including chronic inflammatory, metabolic, and autoimmune disorders. Most clinical trials on probiotics do not consider seasonality as a confounding variable, which could impact the interpretation of results and therapeutic efficacy, potentially biasing estimates of intervention efficacy or associations with disease. This review examines the current evidence on gut microbiota seasonality, discusses its potential bias, and outlines methodological considerations for future clinical trials. Full article

(This article belongs to the Section Environmental Microbiology)

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Open AccessArticle

Genome Analysis of Alginate-Degrading Bacterium Vibrio sp. 32415 and Optimization of Alginate Lyase Production

by Yi Zeng, Jia Xu, Zhongran Li, Rujie Wei, Haiyang Zhao, Liqin Sun and Chang Lu

Microorganisms 2025, 13(10), 2385; https://doi.org/10.3390/microorganisms13102385 - 16 Oct 2025

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Abstract

Vibrio sp. is one of the main producers of alginate lyase; however, most strains have problems such as low and unstable enzyme production. In this study, the enzyme production conditions of V. sp. 32415, a marine bacterium capable of producing extracellular alginate lyase, [...] Read more.

Vibrio sp. is one of the main producers of alginate lyase; however, most strains have problems such as low and unstable enzyme production. In this study, the enzyme production conditions of V. sp. 32415, a marine bacterium capable of producing extracellular alginate lyase, were optimized through Response Surface Design. The optimized medium was as follows: NaCl 12 g/L, FeSO₄·7H₂O 0.067 g/L, NH₄Cl 7 g/L, alginate 11 g/L, K₂HPO₄·3H₂O 4 g/L, MgSO₄·7H₂O 1 g/L. Under 28 °C, 160 rpm, 30 mL/300 mL liquid volume, and an initial pH 5.5 culture condition, the extracellular enzyme activity was 51.06 U/mL, which was 2.8 times higher compared with the activity before optimization. The optimal temperature, pH, and NaCl concentration for the extracellular alginate lyase were 37 °C, 8.0, and 0.1 M, respectively. The enzyme remained more than 80% of its original activity at 30 °C for 4 h. 1 mM Fe³⁺, Ca²⁺, K⁺, Mg²⁺, and Na⁺ enhance enzyme activity, with a preference for polyG blocks. V. sp. 32415 has two circular chromosomes and one circular plasmid. Chromosome 2 has two polysaccharide utilization loci. It utilizes alginate through the Scatter pathway. The results of this study provide theoretical and data support for understanding the production of extracellular alginate lyase by marine Vibrio and their metabolism and utilization of alginate. Full article

(This article belongs to the Section Microbial Biotechnology)

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Microorganisms, Volume 13, Issue 10 (October 2025) – 193 articles

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