Microorganisms

14 pages, 1316 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

26 pages, 753 KiB

Open AccessReview

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

Open AccessArticle

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

Open AccessArticle

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)

► Show Figures

Figure 1

16 pages, 4165 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

13 pages, 2238 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

16 pages, 5020 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

19 pages, 1214 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

23 pages, 4947 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

17 pages, 5287 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

24 pages, 8199 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

17 pages, 2099 KiB

Open AccessArticle

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)

► Show Figures

Figure 1

11 pages, 1751 KiB

Open AccessSystematic 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)

► Show Figures

Figure 1

16 pages, 2657 KiB

Open AccessArticle

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

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 μ_max 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)

► Show Figures

Figure 1

22 pages, 4236 KiB

Open AccessArticle

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

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)

► Show Figures

Figure 1

23 pages, 958 KiB

Open AccessArticle

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

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 ^{Δ5,8,11,14,17}C20:5, 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)

► Show Figures

Figure 1

16 pages, 1398 KiB

Open AccessArticle

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

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)

► Show Figures

Figure 1

16 pages, 1694 KiB

Open AccessArticle

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

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)

► Show Figures

Figure 1

13 pages, 1333 KiB

Open AccessArticle

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

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)

► Show Figures

Figure 1

Journal Description

Microorganisms

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI