Microorganisms

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 (registering DOI) - 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)

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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 (registering DOI) - 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)

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21 pages, 1526 KiB

Open AccessReview

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 (registering DOI) - 17 May 2025

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)

15 pages, 2817 KiB

Open AccessArticle

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 (registering DOI) - 17 May 2025

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, 608 KiB

Open AccessArticle

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 (registering DOI) - 16 May 2025

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)

24 pages, 729 KiB

Open AccessReview

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

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)

23 pages, 3484 KiB

Open AccessArticle

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

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, 4813 KiB

Open AccessArticle

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

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)

17 pages, 1627 KiB

Open AccessArticle

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

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

Open AccessArticle

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

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

Open AccessCorrection

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

Abstract

In the original publication [...] Full article

(This article belongs to the Section Veterinary Microbiology)

20 pages, 5150 KiB

Open AccessArticle

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

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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10 pages, 381 KiB

Open AccessArticle

Retrospective Single-Center Study on the Epidemiological Characteristics of Influenza B Infections in Korea (2007–2024): Analysis of Sex, Age, and Seasonal Patterns

by Jeong Su Han, Yoo Na Chung and Jae Kyung Kim

Microorganisms 2025, 13(5), 1141; https://doi.org/10.3390/microorganisms13051141 - 16 May 2025

Abstract

Influenza B, a globally prevalent respiratory virus, particularly affects children, the elderly, and individuals with chronic diseases. This retrospective single-center study analyzed long-term epidemiological trends using 23,284 PCR test results from Dankook University Hospital, Cheonan-si, Republic of Korea, from 2007 to 2024. The [...] Read more.

Influenza B, a globally prevalent respiratory virus, particularly affects children, the elderly, and individuals with chronic diseases. This retrospective single-center study analyzed long-term epidemiological trends using 23,284 PCR test results from Dankook University Hospital, Cheonan-si, Republic of Korea, from 2007 to 2024. The data included inpatients and outpatients who presented with respiratory symptoms and underwent multiplex PCR testing. Unlike previous studies focusing on short-term outbreaks, this study examines extended trends and emerging seasonal patterns. Positivity rates were statistically analyzed by year, season, sex, age group, and the impact of COVID-19 (2020–2022). Significant annual differences (p < 0.001) occurred, with peaks in 2012 and 2018 and a sharp decline during 2020–2022. Children exhibited the highest positivity rate (2.40%), significantly higher than that of adults (2.24%) and the elderly (1.79%) (p < 0.05). Infections peaked in the winter (2.98%) and spring (3.95%), contrary to the belief that Influenza B peaks in winter only. Females had a higher positivity rate (2.13%) than males (1.70%) (p = 0.017). These findings provide novel insights into Influenza B epidemiology, emphasizing the need for prevention strategies beyond winter. The secondary spring peak suggests extending vaccination to early spring may improve influenza control, particularly among high-risk groups. Full article

(This article belongs to the Section Virology)

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11 pages, 3126 KiB

Open AccessArticle

Increased Expression of AbcA Efflux Pump Accelerated Resistance Development from Tolerance to Resistance Against Oxacillin in Staphylococcus aureus

by Xiaohui Yu, Miaomiao Liu, Pilong Liu, Zehua Hao, Lili Zhao and Xin Zhao

Microorganisms 2025, 13(5), 1140; https://doi.org/10.3390/microorganisms13051140 - 16 May 2025

Abstract

Bacterial tolerance, especially in Staphylococcus aureus (S. aureus), may arise under intermittent antibiotic regimens and act as a stepping stone toward resistance development. However, the transition from tolerance to resistance and its contributing factors remain poorly understood. This study explores the [...] Read more.

Bacterial tolerance, especially in Staphylococcus aureus (S. aureus), may arise under intermittent antibiotic regimens and act as a stepping stone toward resistance development. However, the transition from tolerance to resistance and its contributing factors remain poorly understood. This study explores the role of the efflux pump gene abcA in this process. abcA mutants (overexpression, knockout, and complementation) were constructed via homologous recombination. These strains were subjected to 21 cycles of intermittent exposure to oxacillin at 20× MIC, and the resistance evolution was monitored. Spontaneous mutation frequencies and survival abilities in these mutants were also measured to determine their involvement in resistance development. The abcA overexpression mutant exhibited a faster development of resistance compared to the wildtype strain. Conversely, the abcA knockout mutant maintained susceptibility to oxacillin, with no significant changes in the relative MIC. Increased mutation frequency and enhanced survival were observed in the overexpression strain, whereas both were reduced in the knockout. abcA overexpression significantly accelerated the development of oxacillin resistance in S. aureus by promoting spontaneous mutations and bacterial survival. Disrupting abcA may offer a novel strategy to prevent the evolution of antibiotic resistance. Full article

(This article belongs to the Collection Feature Papers in Antimicrobial Agents and Resistance)

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19 pages, 1310 KiB

Open AccessArticle

Irritable Bowel Syndrome with Diarrhea (IBS-D): Effects of Clostridium butyricum CBM588 Probiotic on Gastrointestinal Symptoms, Quality of Life, and Gut Microbiota in a Prospective Real-Life Interventional Study

by Francesco Di Pierro, Fabrizio Ficuccilli, Laura Tessieri, Francesca Menasci, Chiara Pasquale, Amjad Khan, Fazle Rabbani, Nazia Mumtaz Memon, Massimiliano Cazzaniga, Alexander Bertuccioli, Mariarosaria Matera, Ilaria Cavecchia, Martino Recchia, Chiara Maria Palazzi, Maria Laura Tanda and Nicola Zerbinati

Microorganisms 2025, 13(5), 1139; https://doi.org/10.3390/microorganisms13051139 - 15 May 2025

Abstract

Diarrhea-predominant irritable bowel syndrome (IBS-D) is a functional gastrointestinal disorder characterized by altered motility, abdominal pain, and dysbiosis—particularly reduced biodiversity and a lower abundance of butyrate-producing bacteria. Strategies that modulate the gut microbiota may offer therapeutic benefit. Clostridium butyricum (C. butyricum) [...] Read more.

Diarrhea-predominant irritable bowel syndrome (IBS-D) is a functional gastrointestinal disorder characterized by altered motility, abdominal pain, and dysbiosis—particularly reduced biodiversity and a lower abundance of butyrate-producing bacteria. Strategies that modulate the gut microbiota may offer therapeutic benefit. Clostridium butyricum (C. butyricum) CBM588 is a butyrate-producing probiotic with immunomodulatory properties and potential efficacy in treating gastrointestinal disorders. This pragmatic, prospective, open-label, single-arm interventional study assessed the clinical, microbial, and safety-related effects of an 8-week CBM588 supplementation, along with a low-fiber and low-residue diet, in 205 patients with IBS-D who attended Quisisana Nursing Home Hospital, Rome, Italy, between November 2024 and February 2025. The primary outcomes included the global symptom response, the Bristol Stool Scale (BSS), stool frequency, diarrhea episodes, abdominal pain (severity and frequency), bloating, bowel dissatisfaction, quality of life (QoL), safety, and treatment tolerability—measured using the IBS Symptom Severity Scale (IBS-SSS) and a standardized tolerability scale. CBM588, in patients treated with a low-fiber and low-residue diet, significantly improved all clinical endpoints, with a >80% reduction in diarrhea episodes; ~60% reductions in stool frequency and abdominal pain; and >50% improvements in bloating, bowel dissatisfaction, and QoL. Treatment was well tolerated (mean tolerability score 8.95 ± 0.88), with >95% adherence, and no serious adverse events were reported. The secondary outcomes included changes in gut microbiota. In a subset of patients, 16S rRNA gene sequencing showed increased α-diversity and enrichment of butyrate-producing genera (Agathobacter, Butyricicoccus, Coprococcus), which correlated with symptom improvement. Bloating increased in some patients, possibly related to fermentation activity. These findings support the C. butyricum CBM588 probiotic strain as a safe, well-tolerated, and microbiota-targeted intervention for IBS-D. Randomized controlled trials are warranted to confirm efficacy. Full article

(This article belongs to the Section Gut Microbiota)

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24 pages, 3183 KiB

Open AccessArticle

Deciphering the Language of Intestinal Microbiota Associated with Sepsis, Organ Failure, and Mortality in Patients with Alcohol-Related Acute-on-Chronic Liver Failure (ACLF): A Pioneer Study in Latin America

by Paula Alejandra Castaño-Jiménez, Tonatiuh Abimael Baltazar-Díaz, Luz Alicia González-Hernández, Roxana García-Salcido, Ksenia Klimov-Kravtchenko, Jaime F. Andrade-Villanueva, Kevin Javier Arellano-Arteaga, Mayra Paola Padilla-Sánchez, Susana Del Toro-Arreola and Miriam Ruth Bueno-Topete

Microorganisms 2025, 13(5), 1138; https://doi.org/10.3390/microorganisms13051138 - 15 May 2025

Abstract

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships [...] Read more.

ACLF is a severe stage of liver cirrhosis, characterized by multiple organ failure, systemic inflammation, and high short-term mortality. The intestinal microbiota (IM) influences its pathophysiology; however, there are currently no studies in Latin American populations. Therefore, we analyzed IM and its relationships with sepsis, organ failure, and mortality. In parallel, we quantified serum lipopolysaccharides as a marker of bacterial translocation. Fecal samples from 33 patients and 20 healthy controls (HCs) were obtained. The IMs were characterized by 16S-rRNA amplicon sequencing, the metagenomic functional predictive profiles were analyzed by PICRUSt2, and LPS quantification was performed by ELISA. Patients with ACLF showed significant alterations in alpha and beta diversity compared to the HCs. A strong dominance index accurately predicted 28-day and 90-day mortalities. The IMs showed a polarization toward Proteobacteria associated with increased LPS. The LPS correlated with clinical severity, organ dysfunction, and higher pathogenic taxa. The Klebsiella/Faecalibacterium ratio showed good performance in identifying sepsis (AUROC = 0.83). Furthermore, Morganella, Proteus, and Klebsiella were enriched in patients with multiorgan failure. Lactobacillus, Escherichia/Shigella, Veillonella, and Ruminococcus gnavus exhibited potential in predicting 28- and 90-day mortalities. The IM alterations in ACLF may be useful as clinical biomarkers of poor prognosis, primarily for mortality and sepsis. These findings are representative of western Mexico. Full article

(This article belongs to the Section Gut Microbiota)

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20 pages, 8074 KiB

Open AccessArticle

Effects of Short-Term Straw Return and Manure Fertilization on Soil Microorganisms and Soybean Yield in Parent Material of Degraded Black Soil in Northeast China

by Jiahua Ding, Zhao Li, Jiali Wu, Dalong Ma, Qiang Chen and Jianye Li

Microorganisms 2025, 13(5), 1137; https://doi.org/10.3390/microorganisms13051137 - 15 May 2025

Abstract

Soil erosion has caused the loss of black soil and exposed the soil parent material in the cultivated layer of sloping farmland in Northeast China. Straw return (STR) and manure fertilization (MF) are critical measures to improve soil quality and crop yield. However, [...] Read more.

Soil erosion has caused the loss of black soil and exposed the soil parent material in the cultivated layer of sloping farmland in Northeast China. Straw return (STR) and manure fertilization (MF) are critical measures to improve soil quality and crop yield. However, the effect of STR and MF on the soil properties of the parent material remains unclear. We conducted a 1-year pot experiment in the field using the soil parent material of degraded black soil to evaluate the effects of STR and MF on soil nutrients, microbial community, and soybean yield. We analyzed these effects using two treatments (STR and MF) in three soybean growth stages (seedling, flowering, and maturity) and a control group (CK). The MF treatment had higher α and β diversity of soil microbial than the CK during all soybean growth stages. Similarly, STR had higher soil microbial α diversity at the maturity stage and lower diversity at the seedling stage. Co-occurrence network analysis suggested that STR and MF increased the proportion of positively correlated edges in soil bacterial and fungal networks compared to the CK. Notably, the treatments enriched beneficial taxa, such as Schizothecium (fungi) and Massilia (bacteria), which are associated with organic matter decomposition and nitrogen cycling. STR and MF significantly improved soil organic matter, total nitrogen, and carbon-nitrogen ratio (p < 0.05). Structural equation modeling (SEM) revealed that STR and MF directly increased soybean yield. This effect was primarily mediated by the significantly higher soil organic matter, total carbon, total nitrogen, and carbon-to-nitrogen ratio in the treatments than in the CK (p < 0.05). In summary, STR and MF improved soil fertility and soil microbial community diversity of degraded black soil. This study provides scientific methods to improve the fertility of degraded black soil and increase soybean production in the short term. Full article

(This article belongs to the Special Issue Microorganisms: Climate Change and Terrestrial Ecosystems)

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20 pages, 7129 KiB

Open AccessArticle

High Genetic Diversity Among Bacillus cereus Isolates Contaminating Donated Milk at a Canadian Human Milk Bank

by Mathew Gene, Jennifer L. Guthrie, Kevin Li, Sarah Teatero, Aimee Paterson, Angel Li, Alain Doyen, Deborah Yamamura, Sarah Khan, Jocelyn A. Srigley, Debbie Stone, Deborah L. O’Connor, Susan Poutanen, Sharon Unger, Allison McGeer and Nahuel Fittipaldi

Microorganisms 2025, 13(5), 1136; https://doi.org/10.3390/microorganisms13051136 - 15 May 2025

Abstract

Bacillus cereus poses a persistent challenge for human milk banks (HMBs) due to its ability to survive Holder pasteurization (HoP; 62.5 °C for 30 min). To ensure neonatal safety, any milk found to be contaminated post-HoP must be discarded, which impacts milk supply [...] Read more.

Bacillus cereus poses a persistent challenge for human milk banks (HMBs) due to its ability to survive Holder pasteurization (HoP; 62.5 °C for 30 min). To ensure neonatal safety, any milk found to be contaminated post-HoP must be discarded, which impacts milk supply and adds to the operational demands of HMBs. In this study, we analyzed 688 B. cereus isolates from human milk (pre- and post-HoP), as well as from patient and environmental sources, to investigate human milk contamination by B. cereus at a Canadian HMB. Despite the limited temporal and geographic scope of the collection, the isolates exhibited remarkable genomic diversity, comparable to global B. cereus collections. Phylogenetic analysis at the core genome level revealed no clear clustering by isolate source, suggesting multifactorial pathways of B. cereus contamination. Isolates surviving HoP displayed gene variants linked to sporulation and cell wall integrity, suggesting a potential basis for HoP tolerance. Our findings emphasize that while genomic analyses offer major valuable insights, they alone are insufficient to address the complexities of B. cereus contamination in HMBs. Addressing this challenge will require combining genomic tools with robust monitoring systems, improved human milk-handling protocols, and pasteurization strategies better-suited to countering B. cereus resilience. Full article

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

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16 pages, 108763 KiB

Open AccessArticle

Observations of the Fine Structural Changes Associated with Merogony and Gametogony in Eimeria necatrix and Localization of Two Gametocyte Proteins

by Yu Zhu, Dandan Liu, Lele Wang, Qianqian Feng, Feiyan Wang, Nianyu Xue, Zhaofeng Hou, Jinjun Xu, Junjie Hu and Jianping Tao

Microorganisms 2025, 13(5), 1135; https://doi.org/10.3390/microorganisms13051135 - 15 May 2025

Abstract

Coccidian parasites possess complex life cycles involving asexual proliferation followed by sexual development, producing oocysts that are transmitted from host to host through feces, guaranteeing disease transmission. Eimeria necatrix is a highly pathogenic coccidian causing high mortality in birds. This study examined ultrastructural [...] Read more.

Coccidian parasites possess complex life cycles involving asexual proliferation followed by sexual development, producing oocysts that are transmitted from host to host through feces, guaranteeing disease transmission. Eimeria necatrix is a highly pathogenic coccidian causing high mortality in birds. This study examined ultrastructural changes occurring during the third merogony, microgametogenesis, and macrogametogenesis of E. necatrix. The third-generation meront contained eight merozoites, each with coccidian-specific features like conoid, rhoptries, micronemes, and dense granules. Microgametes had a nucleus, mitochondrion, two flagella, and a basal apparatus. Macrogametes surrounded by two membranes (M1 and M2), contained organelles like WFB1, WFB2, endoplasmic reticulum, mitochondria, and tubular structures. Oocyst wall formation began with M2 separating from M1 and forming a loose veil around the organism. The WFB1 fused together to form the outer layer of the oocyst wall between M1 and M2, while M4 formed beneath M1. The WFB2 fused with the M4 to discharge its contents external to M4, which fused together to form the inner layer of the oocyst wall. Immunogold electron microscopy co-localization result showed that EnGAM22 localized to WFB1 and the outer wall, while EnGAM59 localized to WFB2 and the inner wall, suggesting they are key structural components of the oocyst wall. Full article

(This article belongs to the Special Issue The Current View on Apicomplexan Parasites: Structure, Function, Evolution, 2nd Edition)

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12 pages, 247 KiB

Open AccessReview

Legionella in Hot Water Heat Pump (HWHP) Systems

by Jodi Brookes, Helena Senior, Rebecca J. Gosling, Duncan Smith and Margaret Wade

Microorganisms 2025, 13(5), 1134; https://doi.org/10.3390/microorganisms13051134 - 15 May 2025

Abstract

It is anticipated that by 2028 there will be a significant increase in the use of HWHP systems in Great Britain (GB). Such systems are considered a better, energy-efficient alternative to fossil fuel-based burners and furnaces, as they use electricity. There are concerns [...] Read more.

It is anticipated that by 2028 there will be a significant increase in the use of HWHP systems in Great Britain (GB). Such systems are considered a better, energy-efficient alternative to fossil fuel-based burners and furnaces, as they use electricity. There are concerns that these systems are susceptible to microbial contamination because they hold water at lower temperatures. In particular, the concern is regarding Legionella contamination, as it can potentially cause disease in the general public and those who are maintaining and replacing these systems. Therefore, this review was focused on understanding the potential risk posed by their increased use and maintenance requirements. This review was approached systematically but was not a full systematic review. There were 61 papers that were considered potentially relevant to the research questions. Of these, 40 papers were considered relevant to the topic of Legionella in HWHP and underwent full article assessment and data extraction. The remaining papers were considered useful for background information. The scope of this review established that Legionella are a known risk in hot water systems that can be carried over to HWHP systems, yet there is minimal evidence to suggest that the current control measures are being appropriately applied to reduce the risk of exposure. When considering countrywide legislation and guidance, it appears that the risk is considered lower in single- or multi-family homes that do not require a centralised system. This review included the assessment of information regarding the safety of working with HWHP systems with regards to maintenance and replacement. The authors found a lack of information regarding these safety concerns. This review is among the first to systematically evaluate the risks of Legionella contamination in HWHP systems. Full article

(This article belongs to the Special Issue Legionella pneumophila: A Microorganism with Thousand Faces, 2nd Edition)

29 pages, 455 KiB

Open AccessReview

Current Challenges in Yersinia Diagnosis and Treatment

by Bogna Grygiel-Górniak

Microorganisms 2025, 13(5), 1133; https://doi.org/10.3390/microorganisms13051133 - 15 May 2025

Abstract

Yersinia bacteria (Yersinia enterocolitica, Yersinia pseudotuberculosis) are commonly found in nature in all climatic zones and are isolated from food (mainly raw pork, unpasteurized milk, or contaminated water), soil, and surface water, rarely from contaminated blood. Yersinia infection occurs through sick or [...] Read more.

Yersinia bacteria (Yersinia enterocolitica, Yersinia pseudotuberculosis) are commonly found in nature in all climatic zones and are isolated from food (mainly raw pork, unpasteurized milk, or contaminated water), soil, and surface water, rarely from contaminated blood. Yersinia infection occurs through sick or asymptomatic carriers and contact with the feces of infected animals. The invasion of specific bacterial serotypes into the host cell is based on the type 3 secretion system (T3SS), which directly introduces many effector proteins (Yersinia outer proteins—Yops) into the host cell. The course of yersiniosis can be acute or chronic, with the predominant symptoms of acute enteritis (rarely pseudo-appendicitis or septicemia develops). Clinical and laboratory diagnosis of yersiniosis is difficult. The infection requires confirmation by isolating Yersinia bacteria from feces or other biological materials, including lymph nodes, synovial fluid, urine, bile, or blood. The detection of antibodies in blood serum or synovial fluid is useful in the diagnostic process. The treatment of yersiniosis is mainly symptomatic. Uncomplicated infections (diarrhea and abdominal pain) usually do not require antibiotic therapy, which is indicated in severe cases. Surgical intervention is undertaken in the situations of intestinal necrosis. Given the diagnostic and therapeutic difficulties, this review discusses the prevalence of Y. enterocolitica and Y. pseudotuberculosis, their mechanisms of disease induction (virulence factors and host response), clinical manifestations, diagnostic and preventive methods, and treatment strategies in the context of current knowledge and available recommendations. Full article

(This article belongs to the Special Issue Advances in Enteric Infections Research)

20 pages, 7176 KiB

Open AccessArticle

Gut Microbiota and Lipid Metabolism in Bullfrog Tadpoles: A Comparative Study Across Nutritional Stages

by Zhilong Wang, Pengxiang Liu, Jun Xie, Huirong Yang, Guangjun Wang, Kai Zhang, Rui Shu, Zhifei Li, Jingjing Tian, Hongyan Li, Wenping Xie, Wangbao Gong and Yun Xia

Microorganisms 2025, 13(5), 1132; https://doi.org/10.3390/microorganisms13051132 - 15 May 2025

Abstract

Our study investigated the growth-related metabolic changes and microbial community dynamics during the early feeding stage of bullfrog (Lithobates catesbeiana) tadpoles. In this research, we examined the changes in fat accumulation patterns, as well as the levels of biochemical and enzymatic [...] Read more.

Our study investigated the growth-related metabolic changes and microbial community dynamics during the early feeding stage of bullfrog (Lithobates catesbeiana) tadpoles. In this research, we examined the changes in fat accumulation patterns, as well as the levels of biochemical and enzymatic indicators and genes mRNA expression related to lipid metabolism across the endogenous, mixed, and exogenous nutritional stages of bullfrog tadpoles from a single mating pair. Simultaneously, we characterized the community structures of intestines, excreta, and water bodies during these stages using 16S rRNA high-throughput sequencing technology. Our findings reveal that fat accumulation in tadpole tissues gradually increases with the onset of feeding. Levels of alanine aminotransferase, aspartate aminotransferase, triacylglycerol, total cholesterol, non-esterified fatty acid, high-density lipoprotein cholesterol and low-density lipoprotein cholesterol show a significant increase in exogenous nutritional stages. The mRNA levels of lipid synthesis-related genes and lipid degradation-related genes increased gradually with the changes of nutritional stage. Significant differences were observed in microbial community characteristics among intestines, excreta, and water bodies across nutritional stages. Specifically, gut microbiota exhibited a lower similarity to water body microbiota but a higher similarity to excreta microbiota. Notably, the phyla Firmicutes and Actinobacteriota, and the genus Cetobacterium within the gut microbiota, increased with nutritional changes. A Spearman correlation analysis highlighted a significant correlation between gut microbiota composition and lipid metabolism markers, particularly a strong positive association between Cetobacterium and lipid-related parameters. These insights provide a theoretical foundation for nutritional interventions aimed at enhancing tadpole growth and survival rates. Full article

(This article belongs to the Special Issue Nutrition and Gut Microbiome)

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19 pages, 2253 KiB

Open AccessArticle

A Push–Pull Strategy to Enhance Biomass and Lipid Production in Nannochloropsis oculata

by Roxana Guadalupe Tamayo-Castañeda, Gloria Viviana Cerrillo-Rojas, Teodoro Ibarra-Pérez, Christophe Ndjatchi and Hans Christian Correa-Aguado

Microorganisms 2025, 13(5), 1131; https://doi.org/10.3390/microorganisms13051131 - 15 May 2025

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Abstract

The high demand for sustainable biodiesel feedstocks has led to the exploration of innovative strategies to enhance lipid productivity in microalgae. This study introduces a push–pull strategy to optimize lipid accumulation in Nannochloropsis oculata. The benzyl amino purine (BAP) and naphthalene acetic [...] Read more.

The high demand for sustainable biodiesel feedstocks has led to the exploration of innovative strategies to enhance lipid productivity in microalgae. This study introduces a push–pull strategy to optimize lipid accumulation in Nannochloropsis oculata. The benzyl amino purine (BAP) and naphthalene acetic acid (NAA) stimulation, acting as the ‘push’ component, significantly boost growth and nutrient stress tolerance. Meanwhile, the ‘pull’ component, nitrogen (N) deficiency, triggers lipid biosynthesis. A Box–Behnken design was employed to optimize the factors named BAP fraction (0–1), total phytohormone (PH) BAP/NAA mix dose (0–20 ppm), and N-concentration (0–50%). The combined BAP/NAA treatment significantly increased biomass (15% higher than the control) and mitigated N-stress with higher doses (20 ppm). Lipid yield surged from 12.4% to 38.87% under optimized conditions (23.25% N, 39.5 ppm NAA, and BAP fraction 0). The push–pull strategy contributed to boosting lipid synthesis and balancing biomass production. N-limitation and total PH dosage were the determining factors in this strategy. This work demonstrates the potential of the push–pull strategy in increasing lipid accumulation, offering a promising and optimistic solution for biodiesel production at scale from microalgae. By reducing dependence on fossil fuels, N. oculata emerges as a reliable feedstock for oil extraction and biodiesel. Full article

(This article belongs to the Special Issue The Application Potential of Microalgae in Green Biotechnology)

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12 pages, 254 KiB

Open AccessArticle

Comparative Assessment of Lower Urinary Tract Infections in Hospitalized Adults from Western Romania: A Retrospective Cohort with Microbiological Analysis

by Adela Benea, Mirela Turaiche, Ovidiu Rosca, Elena Hogea, Madalina-Ianca Suba, Norberth-Istvan Varga, Uday Shree Akkala Shetty, Daniel Porav-Hodade, Ileana Enatescu, Adrian Cosmin Ilie, Ciprian Rachieru, Daniel-Florin Lighezan, Oana Silvana Sarau and Cristian Andrei Sarau

Microorganisms 2025, 13(5), 1130; https://doi.org/10.3390/microorganisms13051130 - 14 May 2025

Viewed by 128

Abstract

Urinary tract infections (UTIs) remain a leading cause of healthcare-associated morbidity, particularly in patients with indwelling urinary catheters. This study aimed to compare catheter-associated (CAUTIs) and non-catheter-associated UTIs of the lower tract among hospitalized adults in Western Romania, identify potential predictors of prolonged [...] Read more.

Urinary tract infections (UTIs) remain a leading cause of healthcare-associated morbidity, particularly in patients with indwelling urinary catheters. This study aimed to compare catheter-associated (CAUTIs) and non-catheter-associated UTIs of the lower tract among hospitalized adults in Western Romania, identify potential predictors of prolonged hospital stay, and explore the interplay of inflammatory markers and clinical outcomes. We retrospectively examined 130 patients diagnosed with UTIs from 2020 to 2024. Demographic data, comorbidities, laboratory parameters (CRP, procalcitonin, fibrinogen, white blood cell counts), and microbiology results were assessed. Patients were divided into CAUTI (n = 72) and non-catheter UTI (n = 58) groups. CAUTI patients had a significantly longer mean hospital stay (13.9 ± 4.3 vs. 11.7 ± 3.8 days, p = 0.01). E. coli (29.2%), Klebsiella pneumoniae (18.5%), and mixed flora (11.5%) predominated overall, with Pseudomonas aeruginosa trending higher in CAUTIs (15.3% vs. 5.2%). Diabetic status correlated with higher CRP (54.7 ± 18.2 vs. 46.9 ± 15.7 mg/dL, p = 0.04) and increased intensive care unit (ICU) admission (23.5% vs. 9.4%, p = 0.03). In a subgroup of 65 patients, CRP demonstrated a moderate positive correlation with length of stay (r = 0.47, p = 0.02). Logistic regression indicated that CAUTI was associated with 2.3-fold higher odds of extended hospitalization (95% CI: 1.2–4.4, p = 0.02), adjusting for age, diabetes, and CRP levels. CAUTIs are linked to more resistant pathogens, longer hospitalizations, and potentially greater clinical complications. Diabetes further compounds risk, as reflected in higher inflammatory markers and ICU admissions. Full article

(This article belongs to the Section Medical Microbiology)

21 pages, 5503 KiB

Open AccessArticle

Comparative Genomic Analysis of Two Vibrio harveyi Strains from Larimichthys crocea with Divergent Virulence Profiles

by Kequan Wang, Chaozheng Zhang, Hetron Mweemba Munang’andu, Cheng Xu, Wenlong Cai, Xiaojun Yan and Zhen Tao

Microorganisms 2025, 13(5), 1129; https://doi.org/10.3390/microorganisms13051129 - 14 May 2025

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Abstract

Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality [...] Read more.

Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture. Full article

(This article belongs to the Section Veterinary Microbiology)

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13 pages, 1521 KiB

Open AccessArticle

Identification of Nigrospora oryzae Causing Leaf Spot Disease in Tomato and Screening of Its Potential Antagonistic Bacteria

by Jun Zhang, Fei Yang, Aihong Zhang, Qinggang Guo, Xiangrui Sun, Shangqing Zhang and Dianping Di

Microorganisms 2025, 13(5), 1128; https://doi.org/10.3390/microorganisms13051128 - 14 May 2025

Viewed by 92

Abstract

Tomato is a widely cultivated vegetable crop worldwide. It is susceptible to various phytopathogens, including fungi, bacteria, viruses, and nematodes. In 2024, an unknown leaf spot disease outbreak, characterized by distinct brown necrotic lesions on leaves, was observed in tomato plants in Yunnan [...] Read more.

Tomato is a widely cultivated vegetable crop worldwide. It is susceptible to various phytopathogens, including fungi, bacteria, viruses, and nematodes. In 2024, an unknown leaf spot disease outbreak, characterized by distinct brown necrotic lesions on leaves, was observed in tomato plants in Yunnan Province, China. Through rigorous pathogen isolation and the fulfillment of Koch’s postulates, it was proved that the fungal isolate could infect tomato leaves and cause typical symptoms. The pathogen isolated from tomato leaves was identified as Nigrospora oryzae based on its morphology and using a multilocus sequence analysis method with the internal transcribed spacer gene (ITS1), beta-tubulin gene (TUB2), and translation elongation factor 1-alpha gene (TEF1-α). This represents the first documented case of N. oryzae infecting tomatoes in the world. Given the damage caused by N. oryzae to tomato plants, we explored biocontrol methods. Through a dual-culture assay on PDA plates, Bacillus velezensis B31 demonstrated significant biocontrol potential, exhibiting strong antagonistic activity toward N. oryzae. In addition, we developed a polyethylene glycol (PEG)-mediated transformation system that successfully introduced pYF11-GFP into the protoplasts of N. oryzae. This achievement provides a foundation for future genetic manipulation studies of N. oryzae. Full article

(This article belongs to the Section Plant Microbe Interactions)

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16 pages, 1161 KiB

Open AccessReview

Acute Oak Decline-Associated Bacteria: An Emerging Worldwide Threat to Forests

by Alessandro Bene, Marzia Vergine, Giambattista Carluccio, Letizia Portaccio, Angelo Giovanni Delle Donne, Luigi De Bellis and Andrea Luvisi

Microorganisms 2025, 13(5), 1127; https://doi.org/10.3390/microorganisms13051127 - 14 May 2025

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Abstract

Acute oak decline (AOD) is a multifactorial disease that affects European oaks and represents a growing threat to forests. The disease results from a complex interaction between biotic and abiotic factors: the various environmental stresses, which vary depending on the area in question, [...] Read more.

Acute oak decline (AOD) is a multifactorial disease that affects European oaks and represents a growing threat to forests. The disease results from a complex interaction between biotic and abiotic factors: the various environmental stresses, which vary depending on the area in question, and generally increased by climate change, predispose trees to attack by opportunistic pathogens. Among them, we focused on a bacterial consortium associated with AOD, consisting mainly of Brenneria goodwinii, Gibbsiella quercinecans, Rahnella victoriana, and Lonsdalea britannica, which produce degrading enzymes that contribute to phloem necrosis and the development of stem bleeds and bark cracks. However, the role of other pathogens, such as fungi, cannot be ruled out, but instead could be contributory. The potential involvement of xylophagous insects is also being studied, particularly Agrilus biguttatus, which, although, frequently associated with the disease, has not been conclusively demonstrated to act as an active vector of the bacteria. Currently, disease management requires integrated approaches, including monitoring and other forestry strategies to increase forest resilience. Given the phenomenon’s complexity and the risk of the future expansion of that bacterial consortium, further research is necessary to understand the dynamics and to develop effective containment strategies of AOD-associated bacteria. Full article

(This article belongs to the Section Plant Microbe Interactions)

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35 pages, 2606 KiB

Open AccessReview

Advances in Diversity, Evolutionary Dynamics and Biotechnological Potential of Restriction-Modification Systems

by Chen Chen, Yue Zhang, Hao Wu, Jianjun Qiao and Qinggele Caiyin

Microorganisms 2025, 13(5), 1126; https://doi.org/10.3390/microorganisms13051126 - 14 May 2025

Viewed by 139

Abstract

Restriction–modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects [...] Read more.

Restriction–modification systems (RMS) are ubiquitous in prokaryotes and serve as primitive immune-like mechanisms that safeguard microbial genomes against foreign genetic elements. Beyond their well-known role in sequence-specific defense, RMS also contribute significantly to genomic stability, drive evolutionary processes, and mitigate the deleterious effects of mutations. This review provides a comprehensive synthesis of current insights into RMS, emphasizing their structural and functional diversity, ecological and evolutionary roles, and expanding applications in biotechnology. By integrating recent advances with an analysis of persisting challenges, we highlight the critical contributions of RMS to both fundamental microbiology and practical applications in biomedicine and industrial biotechnology. Furthermore, we discuss emerging research directions in RMS, particularly in light of novel technologies and the increasing importance of microbial genetics in addressing global health and environmental issues. Full article

(This article belongs to the Special Issue Using Microbial Functions to Improve Health, Technology, and Applications)

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18 pages, 869 KiB

Open AccessArticle

Comparison of In Vitro Methods for Assaying the Antibacterial Activity of a Mix of Natural Essential Oils Against Zoonotic Bacteria

by Karine Fayolle, Claire Girard, Pauline Lasfargues, Sahar Koteich and Sylvain Kerros

Microorganisms 2025, 13(5), 1125; https://doi.org/10.3390/microorganisms13051125 - 14 May 2025

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Abstract

With the increasing occurrence of bacterial resistance, it is now essential to look for new alternatives to protect the curative utilization of antibiotics within the One Health concept. Here, we adapt and optimize a broth microdilution method and compare it against the broth [...] Read more.

With the increasing occurrence of bacterial resistance, it is now essential to look for new alternatives to protect the curative utilization of antibiotics within the One Health concept. Here, we adapt and optimize a broth microdilution method and compare it against the broth macrodilution method for evaluating the antibacterial activity of a complex essential oils mix (EO mix) against four livestock pathogens: Escherichia coli, Bacillus cereus, Pseudomonas aeruginosa, and Staphylococcus aureus. Microdilution method performance (final volume well: 300 µL; inoculum: 1.0 × 10⁶ CFU/mL) was evaluated following CLSI recommendations, by comparing the MIC of each of the four strains with the MICs obtained with the macrodilution method (final volume tube: 2 mL; inoculum 1.0 × 10⁶ CFU/mL). Microdilution analysis was performed with an automated plate reader (Bioscreen C), and three bacterial growth parameters (OD max, lag phase, and growth rate) were calculated (DMFit curve-fitting software (v2.1; courtesy of the Institute of Food Research, Norwich, UK)). EO mix MICs were determined for E. coli, S. aureus, and B. cereus. Our results emphasize the importance of ensuring the accuracy of MIC results by performing three technical and three biological replicates, and combining OD max, lag phase, and growth rate to assess the impact of an EO mix at sub-MIC levels. Full article

(This article belongs to the Special Issue Advanced Research on Antimicrobial Activity of Natural Products)

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8 pages, 456 KiB

Open AccessCommunication

Microbiological Quality and Presence of Salmonella spp. in Broiler Carcasses with and Without Visible Gastrointestinal Contamination During Industrial Processing

by Bruno Leandro de Almeida Brito, Rafaela Assis Machado, João Luís Batista de Jesus, Francisco Yan Tavares Reis, Isabela Pádua Zanon, Monique Ribeiro Tiba Casas, Rodrigo Otávio Silveira Silva, Henrique César Pereira Figueiredo, Tadeu Chaves de Figueiredo, Marcelo Resende de Souza and Silvana de Vasconcelos Cançado

Microorganisms 2025, 13(5), 1124; https://doi.org/10.3390/microorganisms13051124 - 14 May 2025

Viewed by 97

Abstract

The industrial processing of broiler chickens has become increasingly automated to scale up meat production. However, certain procedures may cause rupture of the gastrointestinal tract, contaminating the products. The objective of this study was to evaluate the efficiency of the removal of visible [...] Read more.

The industrial processing of broiler chickens has become increasingly automated to scale up meat production. However, certain procedures may cause rupture of the gastrointestinal tract, contaminating the products. The objective of this study was to evaluate the efficiency of the removal of visible contaminated broiler carcasses from the slaughter line based on their microbiological quality compared to non-contaminated ones. Carcasses were analyzed for Escherichia coli and aerobic mesophilic microorganisms counts, as well as Salmonella spp. detection. Carcasses with gastrointestinal contamination had significantly higher counts of aerobic mesophilic microorganisms and E. coli than those without contamination. However, carcasses without visible contamination also showed high counts of bacteria, indicative of the hygiene and sanitary concerns during slaughter. Salmonella spp. were detected in both types of carcasses, with no significant difference in the frequency of positive samples. The most frequently identified serovar was Salmonella Minnesota. The most frequently detected bacteria were E. coli, Klebsiella pneumoniae, Citrobacter freundii, and Pseudomonas aeruginosa. In conclusion, both contaminated and non-contaminated carcasses exhibited high bacterial counts, including potentially pathogenic microorganisms, highlighting the need for post-evisceration steps to reduce microbial contamination. Full article

(This article belongs to the Special Issue Epidemiology, Prevention and Control of Foodborne Microbial Pathogens)

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