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Microorganisms
Volume 13
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Microorganisms, Volume 13, Issue 5 (May 2025) – 216 articles

Cover Story (view full-size image): This review systematically investigates the influence of microbes on internal regulatory factors governing CGA biosynthesis in plants. CGA is synthesized through four distinct metabolic pathways, with hormones, enzymes, and genes as key regulators. Notably, microbes enhance CGA biosynthesis by improving plant nutrient uptake, supplying essential hormones, regulating the expression of related enzymes and genes, and interacting with bacteria and fungi. View this paper
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27 pages, 1602 KiB  
Article
Biodegradation of Phenanthrene by Mycobacterium sp. TJFP1: Genetic Basis and Environmental Validation
by Shuyun Li, Jiazhen Liu and Ping Fang
Microorganisms 2025, 13(5), 1171; https://doi.org/10.3390/microorganisms13051171 (registering DOI) - 21 May 2025
Abstract
The development of efficient bioremediation technologies for polycyclic aromatic hydrocarbons contamination is a hot research topic in the environmental field. In this study, we found that the Mycobacterium sp., TJFP1, has the function of degrading low molecular weight PAHs, and further investigated its [...] Read more.
The development of efficient bioremediation technologies for polycyclic aromatic hydrocarbons contamination is a hot research topic in the environmental field. In this study, we found that the Mycobacterium sp., TJFP1, has the function of degrading low molecular weight PAHs, and further investigated its degradation characteristics using the PAH model compound phenanthrene as a target pollutant. The optimal growth and degradation conditions were determined by single-factor experiments to be 37 °C, pH 9.0, and an initial concentration of 100 mg/L phenanthrene. Under this condition, the degradation efficiency of phenanthrene reached 100% after 106 h of incubation, and the average degradation rate could reach 24.48 mg/L/day. Combined with whole genome sequencing analysis, it was revealed that its genome carries a more complete phenanthrene degradation pathway, including functional gene clusters related to the metabolism of PAHs, such as phd and nid. Meanwhile, intermediates such as phthalic acid were detected; it was determined that TJFP1 metabolizes phenanthrene via the phthalic acid pathway. Simulated contaminated soil experiments were also conducted, and the results showed that the removal rate of phenanthrene from the soil after 20 days of inoculation with the bacterial strain was about 3.7 times higher than that of the control group (natural remediation). At the same time from the soil physical and chemical properties and soil microbial community structure of two levels to explore the changes in different means of remediation, indicating that it can be successfully colonized in the soil, and as a dominant group of bacteria to play the function of remediation, verifying the environmental remediation function of the strains, for the actual inter-soil remediation to provide theoretical evidence. This study provides efficient strain resources for the bioremediation of PAH contamination. Full article
(This article belongs to the Section Microbial Biotechnology)
14 pages, 1316 KiB  
Article
Genetic Diversity in Phytoplasmas from X-Disease Group Based in Analysis of idpA and imp Genes
by Florencia Ivette Alessio, Vanina Aylen Bongiorno, Carmine Marcone, Luis Rogelio Conci and Franco Daniel Fernandez
Microorganisms 2025, 13(5), 1170; https://doi.org/10.3390/microorganisms13051170 - 21 May 2025
Abstract
Phytoplasmas of the X-disease group (16SrIII) are economically significant pathogens in South America, causing severe crop losses. Traditional classification based on the 16S rRNA gene has limitations in resolving closely related strains, prompting the exploration of alternative markers. This study focuses on the [...] Read more.
Phytoplasmas of the X-disease group (16SrIII) are economically significant pathogens in South America, causing severe crop losses. Traditional classification based on the 16S rRNA gene has limitations in resolving closely related strains, prompting the exploration of alternative markers. This study focuses on the immunodominant membrane proteins imp and idpA, which exhibit high variability and play crucial roles in host–pathogen interactions. Through molecular characterization of imp and idpA genes in 16SrIII subgroups, we identified significant genetic diversity and distinct evolutionary pressures. The imp gene, under positive selection, showed high variability in its hydrophilic extracellular domain, suggesting adaptation to host immune responses. In contrast, idpA exhibited strong negative selection, indicating functional conservation. Phylogenetic analyses revealed that imp and idpA provide higher resolution than the 16S rRNA gene, enabling finer differentiation within subgroups. These findings highlight the potential of imp and idpA as complementary markers for phytoplasma classification and diagnostics. Full article
(This article belongs to the Special Issue Phytoplasmas and Phytoplasma Diseases)
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26 pages, 753 KiB  
Review
Advances in Wastewater-Based Epidemiology for Pandemic Surveillance: Methodological Frameworks and Future Perspectives
by Weihe Zhu, Daxi Wang, Pengsong Li, Haohao Deng and Ziqing Deng
Microorganisms 2025, 13(5), 1169; https://doi.org/10.3390/microorganisms13051169 - 21 May 2025
Abstract
Wastewater-based epidemiology (WBE) has emerged as a transformative approach for community-level health monitoring, particularly during the COVID-19 pandemic. This review critically examines the methodological framework of WBE systems through the following three core components: (1) sampling strategies that address spatial–temporal variability in wastewater [...] Read more.
Wastewater-based epidemiology (WBE) has emerged as a transformative approach for community-level health monitoring, particularly during the COVID-19 pandemic. This review critically examines the methodological framework of WBE systems through the following three core components: (1) sampling strategies that address spatial–temporal variability in wastewater systems, (2) comparative performance of different platforms in pathogen detection, and (3) predictive modeling integrating machine learning approaches. We systematically analyze how these components collectively overcome the limitations of conventional surveillance methods through early outbreak detection, asymptomatic case identification, and population-level trend monitoring. While highlighting technical breakthroughs in viral concentration methods and variant tracking through sequencing, the review also identifies persistent challenges, including data standardization, cost-effectiveness concerns in resource-limited settings, and ethical considerations in public health surveillance. Drawing insights from global implementation cases, we propose recommendations for optimizing each operational phase and discuss emerging applications beyond pandemic response. This review highlights WBE as an indispensable tool for modern public health, whose methodological refinements and cross-disciplinary integration are critical for transforming pandemic surveillance from reactive containment to proactive population health management. Full article
(This article belongs to the Special Issue The Molecular Epidemiology of Infectious Diseases)
30 pages, 1272 KiB  
Article
Microbiological Profiles, Antibiotic Susceptibility Patterns and the Role of Multidrug-Resistant Organisms in Patients Diagnosed with Periprosthetic Joint Infection over 8 Years: Results from a Single-Center Observational Cohort Study from Romania
by Serban Dragosloveanu, Rares-Mircea Birlutiu, Bogdan Neamtu and Victoria Birlutiu
Microorganisms 2025, 13(5), 1168; https://doi.org/10.3390/microorganisms13051168 - 21 May 2025
Abstract
This study examines temporal patterns in pathogens isolated from prosthetic joint infection (PJI) cases and antimicrobial resistance patterns at a Romanian orthopedic center. We have conducted a retrospective cohort study that included 674 patients undergoing hip or knee replacement revision surgery between January [...] Read more.
This study examines temporal patterns in pathogens isolated from prosthetic joint infection (PJI) cases and antimicrobial resistance patterns at a Romanian orthopedic center. We have conducted a retrospective cohort study that included 674 patients undergoing hip or knee replacement revision surgery between January 2016 and December 2023. From these, 102 confirmed PJI cases requiring surgical intervention were selected for analysis. We isolated 27 microorganisms from acute PJI cultures and 82 from chronic PJIs. Staphylococcus epidermidis (33 cases, 30.3%; 95% CI 22.0–40.3) was the predominant pathogen, with coagulase-negative Staphylococci (22 cases, 20.18%; 95% CI 0.9–41.3) and Enterobacteriaceae (13 cases, 11.9%; 95% CI 6.4–18.3) also prevalent. Methicillin resistance was identified in 43.6% of coagulase-negative staphylococci and 45.5% of Staphylococcus aureus isolates. All Gram-positive isolates remained susceptible to vancomycin, linezolid, and tigecycline. Among Gram-negative bacilli, Klebsiella oxytoca and Proteus mirabilis showed resistance to third-generation cephalosporins, with phenotypic profiles suggestive of extended-spectrum β-lactamase (ESBL) production. All Escherichia coli, Enterobacter spp., and Citrobacter freundii strains were fully susceptible to tested agents, while Pseudomonas aeruginosa exhibited reduced susceptibility to ciprofloxacin, aztreonam, and imipenem. Among the isolated strains, 47 were multidrug-resistant (MDR), with Staphylococcus aureus accounting for the highest MDR count, including methicillin resistance. The distribution of microorganism types and MDR strains remained consistent throughout the study period, with no significant association between infection type and MDR strain presence or between infection site and microorganism presence except for a strong association between MDR strains and the type of microorganism (p < 0.05). The microbial profile and resistance patterns in PJIs have remained stable over eight years. Our observations do not suggest that MDR PJIs are more commonly acute cases, contrary to what has been highlighted in previous reports. The ongoing prevalence of MDR strains underscores the importance of targeted antimicrobial treatments based on local susceptibility profiles. Full article
(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)
22 pages, 2913 KiB  
Article
Comparative Analysis of PRV-1 in Atlantic Salmon and PRV-3 in Coho Salmon: Host-Specific Immune Responses and Apoptosis in Red Blood Cells
by Laura V. Solarte-Murillo, Sebastián Salgado, Tomás Gatica, Juan Guillermo Cárcamo, Thomais Tsoulia, Maria K. Dahle and Carlos Loncoman
Microorganisms 2025, 13(5), 1167; https://doi.org/10.3390/microorganisms13051167 - 21 May 2025
Abstract
Fish red blood cells (RBCs) are nucleated, transcriptionally active, and key players in both gas transport and immune responses. They are the primary targets of Orthoreovirus piscis (PRV), the etiological agent of heart and skeletal muscle inflammation (HSMI), which includes three genotypes (PRV-1, [...] Read more.
Fish red blood cells (RBCs) are nucleated, transcriptionally active, and key players in both gas transport and immune responses. They are the primary targets of Orthoreovirus piscis (PRV), the etiological agent of heart and skeletal muscle inflammation (HSMI), which includes three genotypes (PRV-1, PRV-2, and PRV-3), linked to circulatory disorders in farmed salmon. In Chile, PRV-3 affects the coho salmon (Oncorhynchus kisutch), but host–pathogen interactions remain poorly characterized. This study compared the interactions of PRV-3 in coho salmon and PRV-1 in Atlantic salmon (Salmo salar) using RBC infection models. RBCs were isolated from healthy juvenile salmon (n = 3) inoculated with either PRV-1 (Ct = 18.87) or PRV-3 (Ct = 21.86). Poly I:C (50 µg/mL) was used as a positive control for the antiviral response. Cells were monitored for up to 14 days post-infection (dpi). PRV-3 infection in coho salmon RBCs caused significant metabolic disruption, apoptosis from 7 dpi, and correlated with increasing viral loads. In contrast, PRV-1 infection in Atlantic salmon RBCs showed limited apoptosis and maintained cell viability. Coho salmon RBCs upregulated rig-i, mx, and pkr transcripts, indicating activation of the type I interferon pathway, whereas Atlantic salmon RBCs exhibited a more attenuated response. PRV-3 induced notable morphological changes in coho salmon RBCs, although neither PRV-3 nor PRV-1 caused hemolysis. These findings highlight species-specific differences in RBC responses to PRV infection and provide new insights into the pathogenesis of PRV-3 and PRV-1. Full article
(This article belongs to the Special Issue Animal Viral Infectious Diseases)
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16 pages, 4165 KiB  
Article
Establishment of a Sensitive and Visual Detection Platform for Viable Salmonella in Wastewater That Combines Propidium Monoazide with Recombinase Polymerase Amplification—CRISPR/Cas12a System
by Jiayin Liang, Xintian Sui, Yan Xu, Xiangqun Zheng and Lu Tan
Microorganisms 2025, 13(5), 1166; https://doi.org/10.3390/microorganisms13051166 - 21 May 2025
Abstract
Urban sewage, aquaculture wastewater, and medical wastewater are significant reservoirs and transmission sources of Salmonella. Rapid detection of Salmonella is crucial for effectively reducing the risk of disease transmission and safeguarding public health. Differentiating viable Salmonella from inactivated cells presents significant challenges, [...] Read more.
Urban sewage, aquaculture wastewater, and medical wastewater are significant reservoirs and transmission sources of Salmonella. Rapid detection of Salmonella is crucial for effectively reducing the risk of disease transmission and safeguarding public health. Differentiating viable Salmonella from inactivated cells presents significant challenges, affecting the accurate assessment of pathogen risks. Moreover, current detection methods face several limitations, including lengthy detection periods, high costs, and limited applicability, underscoring the need for rapid, sensitive, and visual detection diagnostic approaches. In this study, we combined propidium monoazide (PMA) with recombinase polymerase amplification (RPA) and clustered regularly spaced short palindromic repeats (CRISPR)/Cas12a systems to develop a rapid detection system for viable Salmonella targeting the fimY gene. DNA of viable Salmonella was amplified and visually detected within 60 min and dead cells were effectively excluded. We assessed the specificity and sensitivity of the PMA-RPA-CRISPR/Cas12a assay. The results showed that the assay had a high level of specificity, with no reactions observed with other pathogens. The application of PMA has no effect on the sensitivity of RPA-CRISPR/Cas12a technology and the visibility of the fluorescence reporting system. We successfully detected viable Salmonella in wastewater with a minimum detection limit of 101 CFU/mL. In summary, the PMA-RPA-CRISPR/Cas12a system developed in this study allows for the rapid and visual detection of viable Salmonella in wastewater at concentrations as low as 101 CFU/mL. By integrating PMA with the RPA-CRISPR/Cas12a technology, this system offers valuable technical support for the efficient, sensitive, and clear detection of viable Salmonella in wastewater. Full article
(This article belongs to the Special Issue Detection and Identification of Emerging and Re-Emerging Pathogens)
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13 pages, 2238 KiB  
Article
Impact of Phosphogypsum on Viability of Trichuris suis Eggs in Anaerobic Digestion of Swine Manure
by Olexandra Boyko, Viktor Brygadyrenko, Yelizaveta Chernysh, Viktoriia Chubur and Hynek Roubík
Microorganisms 2025, 13(5), 1165; https://doi.org/10.3390/microorganisms13051165 - 21 May 2025
Abstract
Waste from livestock farms contains various pathogens, including eggs and larvae of helminths—pathogens of parasitic diseases harmful to animals and humans. One of the methods for their effective processing to obtain biofertilizer and biofuel is anaerobic digestion, which requires further improvement to completely [...] Read more.
Waste from livestock farms contains various pathogens, including eggs and larvae of helminths—pathogens of parasitic diseases harmful to animals and humans. One of the methods for their effective processing to obtain biofertilizer and biofuel is anaerobic digestion, which requires further improvement to completely suppress the viability of pathogenic microorganisms in mesophilic conditions. To this end, the use of anaerobic digestion under sulfate reduction conditions to suppress pathogens using biogenic hydrogen sulfide is promising. Consequently, this study aims to study the effect of a sulfur-containing additive such as phosphogypsum on the disinfection of pig manure during anaerobic digestion. Egg mortality was already found to increase significantly compared to the control (80% and more), even at a minimum concentration of phosphogypsum (5%), on the fifth day of the experiment. At the same time, the maximum effect (100% mortality of Trichuris suis eggs) was recorded at a 10% concentration of phosphogypsum, starting from the 10th day of the study. Our experiment showed that changes in anaerobic digestion conditions using phosphogypsum could positively affect digestate disinfection. However, further research is needed to optimize the conditions of the process for an effective combination of disinfection with the production of environmentally safe organic fertilizers and high-quality biogas with a high level of methane. Full article
(This article belongs to the Special Issue Advances in Agro-Microbiology)
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16 pages, 5020 KiB  
Article
In Vitro Immune Response of Mononuclear Cells to Multidrug-Resistant Escherichia coli
by Berta Cuyàs, Elisabet Cantó, Elisabet Sanchez-Ardid, Elisenda Miró, Edilmar Alvarado-Tapias, Eva Román, Maria Poca, Ferran Navarro, Andreu Ferrero-Gregori, Maria Àngels Escorsell, Silvia Vidal and German Soriano
Microorganisms 2025, 13(5), 1164; https://doi.org/10.3390/microorganisms13051164 - 20 May 2025
Abstract
Infections caused by multidrug-resistant organisms (MDRO) are linked to poor outcomes, particularly in patients with cirrhosis. The underlying mechanisms are not fully understood and may involve a different immune response against MDRO. This study aimed to compare the in vitro immune response between [...] Read more.
Infections caused by multidrug-resistant organisms (MDRO) are linked to poor outcomes, particularly in patients with cirrhosis. The underlying mechanisms are not fully understood and may involve a different immune response against MDRO. This study aimed to compare the in vitro immune response between multidrug-resistant (MDR) Escherichia coli and antibiotic-susceptible E. coli strains. Surface protein extract and DNA extract were obtained from MDR E. coli (n = 6) and antibiotic-susceptible E. coli (n = 6) strains isolated from infected patients with cirrhosis. The extracts were used to stimulate in vitro peripheral blood mononuclear cells from healthy donors. After 48 h, cytokine levels (IFN-γ, IL-1β, IL-10, IL-12p70, MCP-1, IL-8, IL-6, MIP-1α, and MIP-1β) were measured. We observed no significant differences in cytokine production between MDR and susceptible strains. However, we identified notable interindividual variability in cytokine production for most of the cytokines studied. Only IFN-γ and IL-6 in surface extract and MCP-1 in DNA extract showed similar levels across all donors. We conclude that the cytokine profiles induced by MDR E. coli in vitro were similar to those in susceptible strains. These findings suggest that the poor prognosis associated with MDR E. coli infections is not due to a differential immune response but rather to other factors. Full article
(This article belongs to the Special Issue Bacterial Pathogenesis and Host Immune Responses)
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19 pages, 1214 KiB  
Article
Bioprotection with Saccharomyces cerevisiae: A Promising Strategy
by Fatima El Dana, Vanessa David, Raphaëlle Tourdot-Maréchal, Salem Hayar, Marie-Charlotte Colosio and Hervé Alexandre
Microorganisms 2025, 13(5), 1163; https://doi.org/10.3390/microorganisms13051163 - 20 May 2025
Abstract
Bioprotection in winemaking refers to the use of naturally occurring microorganisms—mainly non-Saccharomyces yeasts—to inhibit the growth of spoilage microbes and reduce the need for chemical preservatives like sulfur dioxide (SO2). Numerous studies have demonstrated the benefits of non-Saccharomyces as [...] Read more.
Bioprotection in winemaking refers to the use of naturally occurring microorganisms—mainly non-Saccharomyces yeasts—to inhibit the growth of spoilage microbes and reduce the need for chemical preservatives like sulfur dioxide (SO2). Numerous studies have demonstrated the benefits of non-Saccharomyces as bioprotectants. However, the use of Saccharomyces cerevisiae as a bioprotectant has been studied very little. Furthermore, it can offer many advantages for the production of sulfite-free wines. To test if S. cerevisiae could be used in bioprotection, we compared the ability of different strains to inhibit the growth of Brettanomyces bruxellensis and Hanseniaspora uvarum. Among the strains tested, the S. cerevisiae Sc54 strain isolated from the vineyard of the Bekaa plain was selected. To investigate its mechanisms of action, we analyzed its metabolite production, including acetic acid and ethanol. Taking into account the low levels of these metabolites and the lack of similar inhibition patterns in media supplemented with acetic acid and ethanol, it appears that other factors contribute to its antagonistic properties. Nutrient competition was ruled out as a factor, as the growth inhibition of B. bruxellensis and H. uvarum occurred rapidly within the first 24 h of co-culture. In this study, we explored the role of the S. cerevisiae killer toxin (Sc54Kt) as a bioprotective agent against H. uvarum and B. bruxellensis spoilage yeasts. Purification procedures with ethanol allowed the extraction of Sc54Kt, yielding two concentrations (0.185 and 0.5 mg/mL). Remarkably, semi-purified Sc54Kt exhibited inhibitory effects at both concentrations under winemaking conditions, effectively controlling the growth and metabolic activity of the target spoilage yeasts. Overall, these findings demonstrate that S. cerevisiae Sc54 not only exerts a strong bioprotective effect but also contributes to improving the quality of wine. The results suggest that S. cerevisiae Sc54 is a promising bioprotective agent for mitigating spoilage yeasts in winemaking, offering a natural and effective alternative to conventional antimicrobial strategies. Full article
(This article belongs to the Section Food Microbiology)
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23 pages, 4947 KiB  
Article
Anti-Biofilm Properties of Cell-Free Supernatant from Bacillus velezensis EA73 by In Vitro Study with Staphylococcus aureus
by Ziyao Tang, Muhammad Yousif, Samuel Kumi Okyere, Fei Liao, Siqi Peng, Lin Cheng, Feng Yang, Yuting Wang and Yanchun Hu
Microorganisms 2025, 13(5), 1162; https://doi.org/10.3390/microorganisms13051162 - 20 May 2025
Abstract
Endophytes are a potential source of novel bioactive antimicrobial compounds. A previous study showed that Bacillus velezensis EA73, an endophytic bacterium, has promising antibacterial activity against Staphylococcus aureus; however, the mechanisms associated with its activity have still not been investigated. Therefore, this [...] Read more.
Endophytes are a potential source of novel bioactive antimicrobial compounds. A previous study showed that Bacillus velezensis EA73, an endophytic bacterium, has promising antibacterial activity against Staphylococcus aureus; however, the mechanisms associated with its activity have still not been investigated. Therefore, this study was conducted to investigate the molecular mechanisms involved in the anti-biofilm activity of a cell-free supernatant (CFS) of B. velezensis EA73 against S. aureus. In this experiment, the biofilm-eliminating effects of a CFS of B. velezensis EA73 against S. aureus were examined in vitro. RT-qPCR was used to detect the changes in genes related to biofilm formation, whereas network pharmacology was used to predict the key targets and pathways of a cell-free supernatant of B. velezensis EA73 against S. aureus-mediated diseases. The minimum biofilm eradication concentration (MBEC) of the EA73 CFS against S. aureus was 1.28 × 10−3 g/mL. In addition, we observed that the EA73 CFS reduced bacterial adhesion and decreased extracellular proteins, polysaccharides, and the eDNA content in the biofilm and decreased the expression of biofilm-associated genes, such as icaA and sarA. The EA73 CFS had a significant effect on S. aureus biofilm eradication and hence can serve as a promising antibacterial reagent. Full article
(This article belongs to the Special Issue Antimicrobial and Anti-Biofilm Potentials of Plant Extracts, Natural Products and Their Formulations)
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17 pages, 5287 KiB  
Article
Diversity of Antifungal Properties in Bacterial Isolates from Different Plant Species Growing Across Uzbekistan
by Mukhlisa K. Shodmonova, Dono A. Muhammadova, Ilkham S. Aytenov, Marufbek Z. Isokulov, Tohir A. Bozorov, Daoyuan Zhang, Ozodbek S. Abduraimov, Sojida M. Murodova, Fazliddin A. Melikuziev, Bekhruz O. Ochilov and Sodir K. Meliev
Microorganisms 2025, 13(5), 1161; https://doi.org/10.3390/microorganisms13051161 - 20 May 2025
Abstract
Plant-associated bacteria play a crucial role in protecting plants from pathogens, yet the diversity and antagonistic potential of these bacteria across different plant species remain underexplored, especially in central Asia. To investigate the competitive dynamics between phytopathogenic fungi and plant-associated bacteria, we collected [...] Read more.
Plant-associated bacteria play a crucial role in protecting plants from pathogens, yet the diversity and antagonistic potential of these bacteria across different plant species remain underexplored, especially in central Asia. To investigate the competitive dynamics between phytopathogenic fungi and plant-associated bacteria, we collected stem and root samples from 50 plant species across nine regions of Uzbekistan. A total of 3355 bacterial isolates were obtained (1896 from roots and 1459 from shoots) and screened for antifungal activity against six fungal pathogens, resulting in 432 antagonistic isolates. These were identified through 16S rDNA sequencing, revealing 65 bacterial species across three phyla: Firmicutes, Proteobacteria, and Actinobacteria, predominantly in the respective families Bacillaceae, Pseudomonadaceae, and Caryophanaceae. The plant Salsola vvedenskii hosted the highest diversity of antagonists (26 species), while other species harbored fewer. Plant species showed strong associations with specific bacterial communities, with 14 plant species each hosting unique antagonists. Enzymatic profiling revealed functional diversity, with Bacillus species producing protease, cellulase, and lipase activities, while Pseudomonas species excelled in xylanase, glucanase, and cellobiase production. B. mojavensis 9r-29 stood out by producing all six enzymes. These findings underscore the ecological diversity and biocontrol potential of plant-associated bacteria in natural ecosystems, offering promising candidates for sustainable plant protection strategies. Full article
(This article belongs to the Section Environmental Microbiology)
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24 pages, 8199 KiB  
Article
Spatial Heterogeneity in Soil Microbial Communities Impacts Their Suitability as Bioindicators for Evaluating Productivity in Agricultural Practices
by Guoqiang Li, Xuanjing Li, Ting Jin, Muyilan Jiang, Peng Shi and Gehong Wei
Microorganisms 2025, 13(5), 1160; https://doi.org/10.3390/microorganisms13051160 - 20 May 2025
Abstract
Soil microorganisms are increasingly recognized as critical regulators of farmland soil fertility and crop productivity. However, the impacts of spatial heterogeneity in soil microbial communities on bioindicators for evaluating agricultural practices remain poorly understood and warrant further validation. Through field experiments, this study [...] Read more.
Soil microorganisms are increasingly recognized as critical regulators of farmland soil fertility and crop productivity. However, the impacts of spatial heterogeneity in soil microbial communities on bioindicators for evaluating agricultural practices remain poorly understood and warrant further validation. Through field experiments, this study investigated the differential effects of agricultural practice treatments on soil properties and bacterial communities between two main farmland soil compartments: intra-row and inter-row. Additionally, we explored the potential correlations between key taxa and soil properties, as well as maize biomass. Results revealed marked disparities in soil properties, bacterial community compositions, and co-occurrence network patterns between intra-row and inter-row soils. Agricultural practice treatments exerted significant impacts on bacterial community structures and network topological features in both intra-row and inter-row soils. Subsequent correlation analysis demonstrated strong relationships between soil properties and most keystone species. In addition, 42 and 41 indicator species were identified in intra-row and inter-row soils, respectively, including shared genera such as Solirubrobacter, Blastococcus, Iamia, Conexibacter, and Lysobacter. Notably, 22 key indicator species in intra-row soils displayed significant positive/negative correlations with maize biomass, whereas only 4 key indicator species showed negative correlations in inter-row soils. These findings highlight differential responses of bacterial communities to agricultural practices in distinct soil compartments. The intra-row soils harbored more bacterial taxa significantly associated with maize biomass, while the inter-row soils better reflected the effects of agricultural interventions. This study confirms the spatial variability of microbial communities as effective bioindicators for evaluating agricultural practice strategies. Identification of compartment-specific indicators provides novel microbiological insights into supporting precision agriculture practices. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 2099 KiB  
Article
Selection of Probiotics for Honey Bees: The In Vitro Inhibition of Paenibacillus larvae, Melissococcus plutonius, and Serratia marcescens Strain Sicaria by Host-Specific Lactobacilli and Bifidobacteria
by Buse Dengiz, Jiří Killer, Jaroslav Havlík, Pavel Dobeš and Pavel Hyršl
Microorganisms 2025, 13(5), 1159; https://doi.org/10.3390/microorganisms13051159 - 20 May 2025
Abstract
Host-specific Lactobacillus and Bifidobacterium species constitute the core microbiota of the honey bee digestive tract and are recognized for their probiotic properties. One of the properties of these bacteria is the inhibition of bacterial pathogens such as Paenibacillus larvae and Melissococcus plutonius, [...] Read more.
Host-specific Lactobacillus and Bifidobacterium species constitute the core microbiota of the honey bee digestive tract and are recognized for their probiotic properties. One of the properties of these bacteria is the inhibition of bacterial pathogens such as Paenibacillus larvae and Melissococcus plutonius, the causative agents of American and European foulbrood, respectively. Additionally, Serratia marcescens has emerged as a relevant opportunistic pathogen. Although several previously published studies have examined the inhibition of selected bacterial pathogens of bees by members of the bee physiological microbiota, none have simultaneously investigated the inhibition of multiple clinical isolates of P. larvae, M. plutonius, and S. marcescens using a wide range of bifidobacterial and lactobacilli strains isolated from various locations within a single country. Thus, this study evaluated the antimicrobial potential of Lactobacillus and Bifidobacterium strains against these pathogens, with a focus on strain-dependent inhibition. A total of 111 bacterial strains (62 Lactobacillus and 49 Bifidobacterium) were isolated from the digestive tracts of honey bees collected from eight sites across the Czech Republic. Using 16S rRNA gene sequencing, the isolates were classified and tested in vitro against four P. larvae isolates, one M. plutonius isolate, and the S. marcescens strain sicaria in modified BHI medium. Twenty-eight strains (~26%) exhibited strong inhibition (≥21 mm) against at least two P. larvae isolates, while 12 strains showed moderate inhibition (16–20 mm) against all four isolates. Inhibition of M. plutonius and S. marcescens was observed in three and twenty strains, respectively. The most effective strains belonged to Bifidobacterium asteroides, B. choladohabitans, B. polysaccharolyticum, Lactobacillus apis, L. helsingborgensis, L. kullabergensis, and L. melliventris. These results underscore the strain-dependent nature of antimicrobial activity and highlight the importance of selecting probiotic strains with broad-spectrum pathogen inhibition to support honey bee health. Full article
(This article belongs to the Special Issue Applied Gut Molecular Microbiology Technology)
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11 pages, 1751 KiB  
Systematic Review
Exploring the Effect of Enzyme and Protein-Containing Toothpaste on Gum Health: A Systematic Review
by Silvia D’Agostino and Marco Dolci
Microorganisms 2025, 13(5), 1158; https://doi.org/10.3390/microorganisms13051158 - 20 May 2025
Abstract
This systematic review critically evaluates the efficacy of enzyme- and protein-containing toothpastes in augmenting saliva’s inherent protective mechanisms. Adhering to PRISMA guidelines and having been registered under PROSPERO (CRD42024558854), a comprehensive literature search was conducted across PubMed, Web of Science, and Scopus, employing [...] Read more.
This systematic review critically evaluates the efficacy of enzyme- and protein-containing toothpastes in augmenting saliva’s inherent protective mechanisms. Adhering to PRISMA guidelines and having been registered under PROSPERO (CRD42024558854), a comprehensive literature search was conducted across PubMed, Web of Science, and Scopus, employing a PICO-structured query with the MeSH terms “enzymes”, “proteins”, and “toothpaste”. The inclusion criteria were restricted to in vivo human studies, published in English within the last 10 years, assessing the gingival effects of these toothpastes. Risk of bias was assessed using the Cochrane RoB 2.0 for randomized controlled trials (RCTs) and ROBINS-I for non-randomized controlled trials (N-RCTs). From an initial pool of 62 articles, three studies met the inclusion criteria: two RCTs exhibiting low to medium risk of bias and one N-RCT with low risk of bias. The analysis suggests that enzyme- and protein-enriched toothpastes may contribute to improved gingival health following 12 weeks and 12 months of use. However, the hypothesized effect against extrinsic black stains was not substantiated within the selected studies. These findings, while promising, are constrained by the limited number of included studies, necessitating further investigations to validate these observations and explore the broader implications of enzyme- and protein-based oral care formulations. Full article
(This article belongs to the Special Issue Oral Microbes and Human Health, Second Edition)
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16 pages, 2657 KiB  
Article
Evaluation of Growth Performance, Biochemical Composition, and Polyhydroxyalkanoates Production of Four Cyanobacterial Species Grown in Cheese Whey
by Eirini Sventzouri, Konstantinos Pispas, Georgia G. Kournoutou, Maria Geroulia, Eleni Giakoumatou, Sameh Samir Ali and Michael Kornaros
Microorganisms 2025, 13(5), 1157; https://doi.org/10.3390/microorganisms13051157 - 19 May 2025
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Abstract
Large-scale cultivation of cyanobacteria is often limited by the high cost of synthetic culture medium and the environmental impact of nutrient consumption. Cheese whey, a major agro-industrial waste product, is rich in organic and inorganic nutrients, making it a promising low-cost alternative for [...] Read more.
Large-scale cultivation of cyanobacteria is often limited by the high cost of synthetic culture medium and the environmental impact of nutrient consumption. Cheese whey, a major agro-industrial waste product, is rich in organic and inorganic nutrients, making it a promising low-cost alternative for microbial growth while addressing waste bioremediation. This study investigates the growth performance and the biochemical composition of four different cyanobacterial species (Phormidium sp., Synechocystis sp., Chlorogloeopsis fritschii, and Arthrospira platensis), cultivated in cheese whey (CW). Pretreated CW was used at 20% and 100% v/v concentrations. All species grew satisfactorily in both concentrations, reaching biomass above 4 g L−1 (in 100% v/v CW) and 2 g L−1 (in 20% v/v CW). The highest μmax value (0.28 ± 0.02 d−1) was presented by Synechocystis sp. grown in 20% CW. Waste bioremediation of both 20 and 100% v/v CW demonstrated effective nutrient removal, with COD removal exceeding 50% for most species, while total nitrogen (TN) and total phosphorus (TP) removals reached up to 33% and 32%, respectively. Biochemical composition analysis revealed high carbohydrate and protein content, while lipid content remained below 15% in all cases. Interestingly, C. fritschii accumulated 11% w/w polyhydroxyalkanoates (PHAs) during the last day of cultivation in 20% v/v CW. These findings highlight the potential of C. fritschii as a valuable candidate for integration into bioprocesses aimed at sustainable bioplastic production. Its ability to synthesize PHAs from agro-industrial waste not only enhances the economic viability of the process but also aligns with circular economy principles. This study is a primary step towards establishing a biorefinery concept for the cultivation of cyanobacterial species in cheese whey-based wastewater streams. Full article
(This article belongs to the Special Issue Biotechnology for Environmental Remediation)
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22 pages, 4236 KiB  
Article
Label-Free Flow Cytometry: A Powerful Tool to Rapidly and Accurately Assess the Efficacy of Chemical Disinfectants
by Andreea Pîndaru, Luminița Gabriela Măruțescu, Marcela Popa, Claude Lambert and Mariana-Carmen Chifiriuc
Microorganisms 2025, 13(5), 1156; https://doi.org/10.3390/microorganisms13051156 - 19 May 2025
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Abstract
A rapid and accurate evaluation of a chemical disinfectant’s bactericidal efficacy is crucial for ensuring effective infection control, preventing the spread of pathogens, and supporting the development of new disinfectant formulations. In this study, we report a rapid, label-free flow cytometry (FCM) protocol [...] Read more.
A rapid and accurate evaluation of a chemical disinfectant’s bactericidal efficacy is crucial for ensuring effective infection control, preventing the spread of pathogens, and supporting the development of new disinfectant formulations. In this study, we report a rapid, label-free flow cytometry (FCM) protocol for evaluating the bactericidal efficacy of disinfectants. Five commercial disinfectants (alcohols, oxidizing agents, and alkylating agents) were evaluated against type strains recommended by EN 13727+A2 and ten clinical strains. The label-free FCM method allowed the determination of disinfectant efficacy through assessment of scatter light profiles (FSC-H/SSC-H) and count differences. The label-free FCM provided the results in approximately 4 h and showed strong correlation with standard tests (91.4%, sensitivity 0.94 and specificity 0.98) that can take up to 48 h. Our results represent a proof-of-principle that label-free FCM can reliably assess the efficacy of chemical disinfectants, the same day, and substantially faster than the current growth-based methods. Additionally, the study highlights the potential of the FCM method for detecting the occurrence of viable but non-culturable bacteria following treatment with chlorine-based disinfectants. With its speed, accuracy, and capability to identify bacterial injuries at a single-cell level, the FCM method is a powerful tool for assessing the efficacy of new disinfectant formulations. Full article
(This article belongs to the Special Issue Antimicrobial Resistance: Challenges and Innovative Solutions)
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23 pages, 958 KiB  
Article
Impact of Temperature on the Biochemical Potential of Five Newly Isolated Strains of Microalgae Cultured in a Stirred Tank Reactor
by Panagiotis Dritsas and George Aggelis
Microorganisms 2025, 13(5), 1155; https://doi.org/10.3390/microorganisms13051155 - 18 May 2025
Viewed by 99
Abstract
The microalgal strains Picochlorum costavermella VAS2.5, Picochlorum oklahomense SAG4.4, Picochlorum oklahomense PAT3.2B, Microchloropsis gaditana VON5.3, and Nephroselmis pyriformis PAT2.7 were cultured in a Stirred Tank Reactor at 25 °C or 20 °C in modified artificial seawater and their biotechnological potential was assessed. VAS2.5, [...] Read more.
The microalgal strains Picochlorum costavermella VAS2.5, Picochlorum oklahomense SAG4.4, Picochlorum oklahomense PAT3.2B, Microchloropsis gaditana VON5.3, and Nephroselmis pyriformis PAT2.7 were cultured in a Stirred Tank Reactor at 25 °C or 20 °C in modified artificial seawater and their biotechnological potential was assessed. VAS2.5, VON5.3, and PAT2.7 were high in biomass production at both temperatures (i.e., 438.8–671.3 mg/L and 418.4–546.7 mg/L at 25 °C and 20 °C, respectively), though P. oklahomense strains grew only at 25 °C. The highest lipid percentage was recorded for the cultures of VAS2.5 (19.3 ± 0.7%) and VON5.3 (16.4 ± 1.5%) at 25 °C, notably rich in Δ5,8,11,14,17C20:5, while PAT2.7 proved a major producer of Δ9C16:1. The predominant lipid fraction was glycolipids and sphingolipids (41.3–57.4%) for VAS2.5, PAT2.7 at 25 °C and VON5.3 at 20 °C and neutral lipids (55.6–63.5%) in the other cultures, indicating the different effect of temperature on lipid synthesis of the various microalgae. Additionally, almost all strains stood out for their high protein content, exceeding 50% in the culture of PAT3.2B, but polysaccharide and pigment content were not high. The biochemical profiles of the isolates showcased their suitability for use primarily as feed additives in the aquaculture sector. Full article
(This article belongs to the Section Microbial Biotechnology)
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16 pages, 1398 KiB  
Article
Oral Microbiota Dysbiosis in Firefighters and the Potential Contributing Environmental and Lifestyle Factors Based on a Case-Control Study
by Sukanta S. Bhattacharya, Brijesh Yadav, Roman Jandarov, William A. Jetter and Jagjit S. Yadav
Microorganisms 2025, 13(5), 1154; https://doi.org/10.3390/microorganisms13051154 - 18 May 2025
Viewed by 382
Abstract
Epidemiological studies show firefighters have increased risks of cancer, diabetes, and cardiovascular disease. To explore links between occupational/environmental exposures and dysbiosis-associated health risks, this case-control study compared oral microbiota of age-matched firefighters (n = 13) and non-firefighters (n = 13) using next-generation sequencing. [...] Read more.
Epidemiological studies show firefighters have increased risks of cancer, diabetes, and cardiovascular disease. To explore links between occupational/environmental exposures and dysbiosis-associated health risks, this case-control study compared oral microbiota of age-matched firefighters (n = 13) and non-firefighters (n = 13) using next-generation sequencing. Firefighters exhibited significantly reduced overall microbial diversity (p ≤ 0.05) and compositional shifts. Firmicutes increased from 53.5% to 68.5%, and Bacteroidetes from 9.5% to 14.1%, while Proteobacteria decreased from 24.6% to 8.3%, and Fusobacteria from 3.3% to 1.1%. This resulted in a higher Firmicutes to Bacteroidetes ratio (5.63 vs. 4.89 in controls), indicating a pro-inflammatory oral microenvironment. At the family level, Streptococcaceae (45.1% to 60.3%) and Prevotellaceae (6.2% to 10.0%) increased, whereas Neisseriaceae (17.7% to 4.9%) and Fusobacteriaceae (2.1% to 0.8%) decreased. The genus Streptococcus dominated firefighters’ microbiota, rising from 45.1% to 60.3%. Diversity indices confirmed reduced microbial evenness and richness in firefighters. Metadata analysis linked frequent fire exposures to perturbations in Comamonadaceae and Carnobacteriaceae (p ≤ 0.05). Barbecue consumption, a source of polycyclic aromatic hydrocarbons, correlated with elevated Spirochaetaceae and Peptostreptococcaceae. This first report on oral dysbiosis in firefighters reveals significant alterations in microbiota abundance, diversity, and evenness, implying potential health risks for this group. Full article
(This article belongs to the Special Issue Exploring Microbial Dynamics in Oral Health and Disease: Periodontics, Implant Dentistry and Endodontics)
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16 pages, 1694 KiB  
Article
Synergistic Effect of Essential Oils and Rhamnolipid on Xanthomonas citri Subsp. citri
by Maria Olimpia Pereira Sereia, Eduarda Araujo dos Santos, Lucas Prado Leite, Raphael Culim Neves, Vítor Rodrigues Marin, Henrique Ferreira, Jonas Contiero and Daiane Cristina Sass
Microorganisms 2025, 13(5), 1153; https://doi.org/10.3390/microorganisms13051153 - 17 May 2025
Viewed by 212
Abstract
Citrus canker, caused by Xanthomonas citri subsp. citri, is a devastating disease that affects citrus production and trade worldwide. Traditional control methods, based on copper compounds, are effective but pose environmental and health risks due to their toxicity and potential for bioaccumulation. [...] Read more.
Citrus canker, caused by Xanthomonas citri subsp. citri, is a devastating disease that affects citrus production and trade worldwide. Traditional control methods, based on copper compounds, are effective but pose environmental and health risks due to their toxicity and potential for bioaccumulation. This study evaluates the synergistic potential of essential oils (EOs) and rhamnolipids as sustainable alternatives for disease management. Four EOS (citronella, palmarosa, geranium, and clove) were tested for their antibacterial activity. Citronella EO showed a 90% inhibitory concentration (IC 90) of 0.15% (v/v) and a minimum bactericidal concentration of 0.25% (v/v), while the other EOs showed IC 90 and bactericidal activity at 0.06% (v/v). Rhamnolipids (RHLs), biosurfactants produced by Pseudomonas aeruginosa, inhibited X. citri at a concentration of 0.3% (v/v). The combination of citronella EO and RHLs showed a synergistic effect, reducing the inhibitory concentration of citronella by 50% and that of RHLs by more than 90%. In addition, the combined formulation permeabilized more than 80% of bacterial membranes and reduced biofilm formation. In contrast, other oils tested in combination with rhamnolipid showed independent effects. These results indicate that EOs and rhamnolipids represent an environmentally safe strategy for the control of X. citri subsp. citri that overcomes the limitations of conventional methods while reducing environmental and health impacts. Full article
(This article belongs to the Special Issue Microbial Biotechnologies and Microorganism Interactions for Sustainable Agriculture)
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13 pages, 1333 KiB  
Article
The Clinical Profile of Pediatric M. pneumoniae Infections in the Context of a New Post-Pandemic Wave
by Mădălina Maria Merișescu, Gheorghiță Jugulete, Irina Dijmărescu, Anca Oana Dragomirescu and Larisa Mirela Răduț
Microorganisms 2025, 13(5), 1152; https://doi.org/10.3390/microorganisms13051152 - 17 May 2025
Viewed by 182
Abstract
Mycoplasma pneumoniae is an atypical bacterium with a tropism for the respiratory tract, but it can also cause numerous extrapulmonary involvements. The incidence of high rates varies in epidemiological waves, occurring at a frequency of 3–7 years. Since the end of 2023, an [...] Read more.
Mycoplasma pneumoniae is an atypical bacterium with a tropism for the respiratory tract, but it can also cause numerous extrapulmonary involvements. The incidence of high rates varies in epidemiological waves, occurring at a frequency of 3–7 years. Since the end of 2023, an increase in the incidence of M. pneumoniae infection cases has been noted internationally. We conducted a retrospective study of children hospitalized and confirmed with M. pneumoniae infection in our clinic during the last two epidemiological peaks. We retrieved data from the hospital database and divided the patients into two groups, corresponding to the years 2018–2019 and 2023–2024, respectively. Fisher’s exact test was used to compare the proportions. In the years 2023–2024, we observed a higher incidence of patients with respiratory failure (p = 0.032), pleural reaction (p = 0.016), and pulmonary consolidation (p = 0.016) compared to the group in the years 2018–2019. Gastrointestinal involvement was more frequent in the years 2018–2019 (p = 0.004). The incidence of other extrapulmonary complications did not show significant differences. Infection with M. pneumoniae has varied clinical manifestations. In patients with community-acquired pneumonia, even in cases of consolidation, the possibility of infection with M. pneumoniae must also be considered. Full article
(This article belongs to the Special Issue Current Challenges in Infectious Diseases Post COVID-19 Pandemic)
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21 pages, 1578 KiB  
Review
Programming Effects of Maternal Nutrition on Intestinal Development and Microorganisms of Offspring: A Review on Pigs
by Liang Hu, Fali Wu and Lianqiang Che
Microorganisms 2025, 13(5), 1151; https://doi.org/10.3390/microorganisms13051151 - 17 May 2025
Viewed by 127
Abstract
Intestinal development is a critical determinant of growth and overall health in pigs. Accumulating evidence underscores the significant influence of intestinal microbiota on essential physiological functions and systemic health. Dietary nutrients play a pivotal role in regulating both intestinal development and the composition [...] Read more.
Intestinal development is a critical determinant of growth and overall health in pigs. Accumulating evidence underscores the significant influence of intestinal microbiota on essential physiological functions and systemic health. Dietary nutrients play a pivotal role in regulating both intestinal development and the composition of intestinal microbiota. Optimal early-life nutrient provision ensures proper intestinal growth and functional maturation, with maternal nutrition emerging as a key factor shaping intestinal development during fetal and neonatal stages. This review synthesizes recent studies on maternal nutrient intake—encompassing protein, energy, carbohydrates, minerals, vitamins, probiotics, and prebiotics—and their effects on intestinal growth and health of offspring. Emerging multi-omics evidence has revealed that gestational and lactational nutrition dynamically coordinates offspring intestinal development through vertical microbial transmission and epigenetic mechanisms, such as DNA methylation and histone acetylation. These processes further regulate intestinal barrier maturation, mucosal immunity, and enteroendocrine signaling. Collectively, this review emphasizes that enhancing maternal nutrition can promote postnatal growth by enhancing intestinal development and early microbial colonization in piglets. Further research is crucial to determining the optimal nutritional strategies during the perinatal period. Full article
(This article belongs to the Section Microbiomes)
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15 pages, 2620 KiB  
Article
Hemolysin-like Protein of ‘Candidatus Phytoplasma Mali’ Is an NTPase and Binds Arabidopsis thaliana Toc33
by Kajohn Boonrod, Alisa Konnerth, Mario Braun and Gabi Krczal
Microorganisms 2025, 13(5), 1150; https://doi.org/10.3390/microorganisms13051150 - 17 May 2025
Viewed by 141
Abstract
‘Candidatus Phytoplasma mali’ is associated with apple proliferation, a devastating disease in fruit production. Using genome analysis, a gene encoding a hemolysin-like protein was identified. It was postulated that this protein could be an effector. However, the function of this protein is [...] Read more.
‘Candidatus Phytoplasma mali’ is associated with apple proliferation, a devastating disease in fruit production. Using genome analysis, a gene encoding a hemolysin-like protein was identified. It was postulated that this protein could be an effector. However, the function of this protein is unknown. It is shown that the hemolysin-like protein binds to a GTP binding protein, Toc33, of Arabidopsis thaliana in yeast two-hybrid analysis and that the Toc33-binding domain is located in the C-terminus of the domain of unknown function (DUF21) of the protein. The biochemical studies reveal that the protein can hydrolyze phosphate of purine and pyrimidine nucleotides. Transgenic Nicotiana benthamiana plants expressing the protein show no discernible change in phenotype. Phytoplasma have a much-reduced genome, lacking important genes for catabolic pathways or nucleotide production; therefore, the hemolysin-like protein plays a role in the uptake of plant nucleotides from their host and hydrolyzes these nucleotides for energy and their own biosynthesis. Full article
(This article belongs to the Special Issue Phloem Localized Insect Transmitted Bacteria Associated with Plant Diseases)
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18 pages, 585 KiB  
Article
Emergence of NDM-1- and OXA-23-Co-Producing Acinetobacter baumannii ST1 Isolates from a Burn Unit in Spain
by Elena Hidalgo, Jared Sotelo, María Pérez-Vázquez, Ángela Iniesta, Javier E. Cañada-García, Olga Valiente, Belén Aracil, David M. Arana and Jesús Oteo-Iglesias
Microorganisms 2025, 13(5), 1149; https://doi.org/10.3390/microorganisms13051149 - 16 May 2025
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Abstract
The global emergence of carbapenem-resistant Acinetobacter baumanii (CRAB) represents a significant public health threat. In the summer of 2022, a polyclonal CRAB outbreak occurred in our hospital, marking the first detection of an NDM-1 plus OXA-23 co-producing A. baumannii strain in Spain. The [...] Read more.
The global emergence of carbapenem-resistant Acinetobacter baumanii (CRAB) represents a significant public health threat. In the summer of 2022, a polyclonal CRAB outbreak occurred in our hospital, marking the first detection of an NDM-1 plus OXA-23 co-producing A. baumannii strain in Spain. The aim of this study was to phenotypically and genotypically characterize the clonal spread of NDM-1 and OXA-23 co-producing A. baumannii isolates and to describe the infection control measures implemented to contain the outbreak. Patients with multidrug-resistant A. baumannii isolates (July 2022–May 2023) were included in the study. Isolates were identified via MALDI-TOF, and antimicrobial susceptibility was tested using a broth microdilution method (DKMGN SensititreTM panels). Whole-genome sequencing was performed on 24 representative isolates. Phylogenetic analysis was performed using Ridom SeqSphere+ (cgMLST), while sequence typing was performed using ARIBA (Pasteur and Oxford schemes). A. baumannii isolates from the affected patients belonged to five different sequence types. The two main STs were ST1Pas/ST231Oxf (NDM-1- and OXA-23-co-producing), which accounted for 58%, and ST136Pas/ST406Oxf (OXA-23-producing), which accounted for 21%. All isolates were resistant to fluoroquinolones, trimethoprim/sulfamethoxazole, aminoglycosides, and carbapenems. In addition, 8% were resistant to colistin and 17% to cefiderocol. Finally, the affected patients were cohorted, and a thorough cleaning of the affected units was carried out. This study documents the clonal spread of an NDM-1- and OXA-23-co-producing A. baumannii strain in Spain, linked to a Libyan patient, highlighting the risk of cross-border spread. Although infection control measures successfully contained the outbreak, surveillance is essential as the incidence of CRAB infections is expected to increase. Full article
(This article belongs to the Special Issue Prevention and Treatment of Healthcare-Associated Infections)
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24 pages, 778 KiB  
Review
Eugenol Nanoparticles in Dental Composites: Literature Review of Antimicrobial, Anti-Inflammatory, and Clinical Applications
by Fatima Zahra Kamal, Alin Ciobica, Gabriel Dascalescu, Said Rammali, Mohamed El Aalaoui, Radu Lefter, Ioana Vata, Vasile Burlui and Bogdan Novac
Microorganisms 2025, 13(5), 1148; https://doi.org/10.3390/microorganisms13051148 - 16 May 2025
Viewed by 71
Abstract
The formation of microbial colonies and biofilms are common on dental restorations. This can lead to secondary caries. Another common complication is the post-operative inflammation noted in patients. The traditionally used dental composites are designed without the inherent components having antimicrobial and inflammatory [...] Read more.
The formation of microbial colonies and biofilms are common on dental restorations. This can lead to secondary caries. Another common complication is the post-operative inflammation noted in patients. The traditionally used dental composites are designed without the inherent components having antimicrobial and inflammatory properties. This has become a major challenge in current restorative dentistry applications. In order to address these challenges, a possible approach is to incorporate eugenol nanoparticles (NPs) into dental composites. This approach can offer dual therapeutic benefits since eugenol possess both antimicrobial and inflammatory properties. In fact, compared to synthetic antimicrobial agents, eugenol exhibits antibacterial activity not only against Streptococcus mutans but also against a range of oral pathogens. It also exhibits anti-inflammatory effects that can promote healing by reducing post-operative sensitivity. In spite of the above benefits, eugenol cannot be incorporated directly into dental materials. This is because eugenol is highly volatile and has poor water solubility. The encapsulation of eugenol in suitable nano-materials can overcome these limitations. In addition, it can enable the controlled and sustained release of desirable agents for long-term therapeutic action. In this review, we explore the mechanisms, advantages and potential clinical applications of dental composites containing NP integrated with eugenol. We highlight the advantages of having antimicrobial and anti-inflammatory functions in a single restorative material. At the same time, we acknowledge the need for more in-depth research to optimize NP formulations with eugenol that does not compromise the mechanical properties of dental materials. Based on a thorough literature review, we believe that this approach has much potential in restorative dentistry procedures that will aid therapeutic outcomes in the future. Full article
(This article belongs to the Special Issue Antimicrobial Properties of Nanoparticles)
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23 pages, 3484 KiB  
Article
In Silico Design, Optimization, and Evaluation of a Multi-Epitope Vaccine Targeting the Clostridium perfringens Collagen Adhesin Protein
by Dhiraj Chundru, Shailes Bhattrai, Madhusudan Timilsina, Hyun Lillehoj, Zhifeng Sun, Mostafa Ghanem and Charles Li
Microorganisms 2025, 13(5), 1147; https://doi.org/10.3390/microorganisms13051147 - 16 May 2025
Viewed by 93
Abstract
Necrotic enteritis (NE), caused by pathogenic Clostridium perfringens, poses a significant threat to global poultry health, with estimated annual losses exceeding USD 6 billion. The rising incidence of NE has been associated with the reduced use of antibiotic growth promoters, underscoring the [...] Read more.
Necrotic enteritis (NE), caused by pathogenic Clostridium perfringens, poses a significant threat to global poultry health, with estimated annual losses exceeding USD 6 billion. The rising incidence of NE has been associated with the reduced use of antibiotic growth promoters, underscoring the urgent need for alternative control measures such as vaccination. Collagen adhesin protein (CNA), a key virulence factor in NE pathogenesis, represents a promising vaccine target. The US Food and Drug Administration has begun phasing out animal testing requirements for biologics and monoclonal antibody drugs. In this study, a computational multi-epitope vaccine (MEV) targeting CNA was designed by integrating predicted Cluster of Differentiation (CD)4+ helper T lymphocyte (Th), CD8+ cytotoxic T lymphocyte (CTL), and B-cell epitopes. Bioinformatics tools were used to identify immunogenic, antigenic, and non-allergenic epitopes assembled into a 115-amino-acid peptide vaccine construct. The candidate demonstrated strong stability and solubility. In silico immune simulation predicted robust immune responses, including elevated IgG and IgM antibody levels, plasma cell proliferation, Th memory formation, and CTL activation, comparable to responses elicited by a full-length CNA. These findings support the potential of the designed peptide as one of the multiple effective NE vaccine components, offering a promising alternative to antibiotic-based approaches in poultry disease management. Full article
(This article belongs to the Special Issue Poultry Pathogens and Poultry Diseases, 2nd Edition)
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22 pages, 4707 KiB  
Article
The Impact of Litter from Different Belowground Organs of Phragmites australis on Microbial-Mediated Soil Organic Carbon Accumulation in a Lacustrine Wetland
by Chong Chen, Yong Wang, Liu Yang, Yongen Min, Keming Yue, Sitong Lu, Hongfeng Bian, Xue Wang and Leilei Zhang
Microorganisms 2025, 13(5), 1146; https://doi.org/10.3390/microorganisms13051146 - 16 May 2025
Viewed by 59
Abstract
Although belowground litter decomposition critically influences lacustrine wetland soil carbon dynamics, the organ-specific microbial mechanisms driving soil organic carbon (SOC) accumulation remain unclear. Existing research has predominantly focused on aboveground litter, leaving a significant gap in the understanding of how roots and rhizomes [...] Read more.
Although belowground litter decomposition critically influences lacustrine wetland soil carbon dynamics, the organ-specific microbial mechanisms driving soil organic carbon (SOC) accumulation remain unclear. Existing research has predominantly focused on aboveground litter, leaving a significant gap in the understanding of how roots and rhizomes differentially regulate carbon cycling through microbial community assembly and survival strategies. This study took Phragmites australis (a plant characteristic of lacustrine wetland) as the research object and examined how decomposing belowground litter from different organs affects microbial-mediated SOC accumulation through a one-year in situ field incubation in Jingyuetan National Forest Park, Changchun City, Jilin Province, China. Our findings reveal that root litter exhibited the highest decomposition rate, which was accelerated by intermittent flooding, reaching up to 1.86 times that of rhizome. This process enriched r-strategist microbial taxa, intensified homogeneous selection, and expanded niche width, directly promoting SOC accumulation. Rhizome litter decomposition enhanced dispersal limitation, promoted K-strategist microbial dominance, and indirectly modulated SOC through soil acidification. Mixed-litter treatments significantly enhanced SOC accumulation (up to three times higher than single-litter treatments) through synergistic nutrient release (non-additive effects < 0.04) and reinforced microbial network interactions. SOC accumulation varied significantly with the flooding regime as follows: non-flooded > intermittent flooding > permanent flooding. This study provides new insights into the microbially driven mechanisms of plant-organ-specific decomposition in the carbon cycling of wetland ecosystems. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 1627 KiB  
Article
The Temporal Trends of Mortality Due to Tuberculosis in Brazil: Tracing the Coronavirus Disease 2019 (COVID-19) Pandemic’s Effect Through a Bayesian Approach and Unmasking Disparities
by Reginaldo Bazon Vaz Tavares, Dulce Gomes, Thaís Zamboni Berra, Yan Mathias Alves, Antônio Carlos Vieira Ramos, Marcela Antunes Paschoal Popolin, André da Silva Abade, Nathalia Zini, Ariela Fehr Tártaro, Josilene Dália Alves, Fernanda Bruzadelli Paulino da Costa, Maria Eduarda Pagano Pelodan, Beatriz Fornaziero Vigato, Daniele de Moraes Pinheiro, Juliana Queiroz Rocha de Paiva, Clara Ferreira de Souza and Ricardo Alexandre Arcêncio
Microorganisms 2025, 13(5), 1145; https://doi.org/10.3390/microorganisms13051145 - 16 May 2025
Viewed by 66
Abstract
The COVID-19 pandemic disrupted tuberculosis (TB) control, increasing mortality and potentially worsening disparities. This study aimed to analyze the temporal trends of TB mortality in Brazil and to trace the COVID-19 pandemic’s effect using a Bayesian approach, focusing on nationwide data. An ecological [...] Read more.
The COVID-19 pandemic disrupted tuberculosis (TB) control, increasing mortality and potentially worsening disparities. This study aimed to analyze the temporal trends of TB mortality in Brazil and to trace the COVID-19 pandemic’s effect using a Bayesian approach, focusing on nationwide data. An ecological study of TB deaths recorded in the Mortality Information System (SIM) from 2012 to 2022 was conducted. Trends and percentage changes in the mortality were estimated. A Bayesian Structural Time Series model combined with an Autoregressive Integrated Moving Average model was used to assess the pandemic’s effect on TB. A total of 51,809 TB deaths were identified, with a mortality rate of 2.27 per 100,000. Higher rates were found among the elderly (6.86), indigenous populations (5.58), and black individuals (4.21). The Bayesian model estimated a 9.9% (CI 8.8–11%) increase in TB mortality due to COVID-19. The Midwest region showed the highest increase (30%, 25–35%). Females experienced a greater post-pandemic monthly increase (2.80%) in mortality than males (0.72%). The Bayesian analysis revealed a significant rise in TB mortality during the COVID-19 pandemic, with notable disparities affecting females, the elderly, the indigenous, and the black populations. These findings highlight the pandemic’s long-term impact on TB and stress the need for equity-focused, data-driven public health responses in Brazil. Full article
(This article belongs to the Special Issue Prevention, Treatment and Diagnosis of Tuberculosis, 2nd Edition)
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13 pages, 5440 KiB  
Article
Periplasmic Protein Mobility for Extracellular Electron Transport in Shewanella oneidensis
by Daobo Li, Xiaodan Zheng, Yonggang Yang and Meiying Xu
Microorganisms 2025, 13(5), 1144; https://doi.org/10.3390/microorganisms13051144 - 16 May 2025
Viewed by 46
Abstract
Extracellular electron transport (EET) supports the survival of specific microorganisms on the Earth’s surface by facilitating microbial respiration with diverse electron acceptors. A key aspect of EET is the organization of electron relays, i.e., multi-heme c-type cytochromes (MHCs), within the periplasmic space of [...] Read more.
Extracellular electron transport (EET) supports the survival of specific microorganisms on the Earth’s surface by facilitating microbial respiration with diverse electron acceptors. A key aspect of EET is the organization of electron relays, i.e., multi-heme c-type cytochromes (MHCs), within the periplasmic space of microbial cells. In this study, we investigated the mobility of periplasmic electron relays in Shewanella oneidensis MR-1, a model strain capable of EET, using in vivo protein crosslinking to the MHCs. First, we established that crosslinking efficiency correlates with the spatial proximity and diffusion coefficient of protein molecules through in vitro tests. Based on these findings, we identified distinct molecular behaviors of periplasmic MHCs, showing that the tetraheme flavocytochrome FccA, which also serves as a periplasmic fumarate reductase, forms protein complexes with limited motility, while the small tetraheme c-type cytochrome CctA remains discrete and mobile. Both MHCs contribute to EET for bioelectrochemical nitrate and nitrite reduction. These findings reveal dual mechanisms for organizing periplasmic electron relays in EET, advancing our understanding of microbial extracellular respiration. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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1 pages, 134 KiB  
Correction
Correction: Quan et al. Functional Characterization of a Novel SMR-Type Efflux Pump RanQ, Mediating Quaternary Ammonium Compound Resistance in Riemerella anatipestifer. Microorganisms 2023, 11, 907
by Heng Quan, Xiaowei Gong, Wenhui Wang, Fuying Zheng, Yongfeng Yu, Donghui Liu, Qiwei Chen and Yuefeng Chu
Microorganisms 2025, 13(5), 1143; https://doi.org/10.3390/microorganisms13051143 - 16 May 2025
Viewed by 47
Abstract
In the original publication [...] Full article
(This article belongs to the Section Veterinary Microbiology)
20 pages, 5150 KiB  
Article
Soil Microbial Adaptation and Biogeochemical Feedback in Degraded Alpine Meadows of the Qinghai–Tibetan Plateau
by Bingzhang Li, Quzhen Gesang, Yan Sun, Yuting Wang, Jibin Nan and Jun Xu
Microorganisms 2025, 13(5), 1142; https://doi.org/10.3390/microorganisms13051142 - 16 May 2025
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Abstract
Alpine meadows on the Qinghai–Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic [...] Read more.
Alpine meadows on the Qinghai–Tibetan Plateau are experiencing rapid degradation due to climate change and anthropogenic disturbances, leading to severe ecological consequences. In this study, we investigated the response of soil microbial communities and their metabolic functions across a degradation gradient using metagenomic sequencing and comprehensive soil physicochemical analysis in the city of Lhasa, China. Results showed that soil pH increased with degradation, while most nutrients, including different forms of nitrogen, phosphorus, and potassium, declined. pH, ammonium nitrogen, and organic matter were identified as key factors driving degradation dynamics. Microbial community composition shifted markedly, with distinct biomarker taxa emerging at different degradation levels. Network analysis revealed a progressive loss of microbial connectivity, with Actinobacteria dominance increasing in heavily degraded soils, while cross-phylum interactions weakened. Functional analysis of biogeochemical cycling genes showed that carbon, nitrogen, and phosphorus cycling were all disrupted by degradation, but each exhibited unique response patterns. These findings will extend our understanding of microbial-mediated soil processes under degradation and provide a scientific foundation for ecosystem management, conservation, and targeted restoration strategies in alpine meadows. Full article
(This article belongs to the Section Environmental Microbiology)
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