You seem to have javascript disabled. Please note that many of the page functionalities won't work as expected without javascript enabled.

Search for Articles:

Title / Keyword

Author / Affiliation / Email

Journal

Article Type

Advanced Search

Section

Special Issue

Volume

Issue

Number

Page

Logical OperatorOperator

Search Text

Search Type

In Utero Exposure to 2,3,7,8-Tetrachlorodibenzo-p-dioxin Impairs the Ability of Mice to Clear a Pseudomonas aeruginosa Infection in Adulthood
Nematophagous Fungi Occurrence: Prediction Using Bioclimatic Variables
Genomic Insights into Plant Growth-Promoting Traits of Lysinibacillus fusiformis and Bacillus cereus from Rice Fields in Panama
Tick Dispersal and Borrelia Species in Ticks from Migratory Birds: Insights from the Asinara National Park, Sardinia, Italy

Journal Description

Microbiology Research

Microbiology Research is an international, scientific, peer-reviewed open access journal published monthly online by MDPI (from Volume 11 Issue 2-2020).

Open Access— free for readers, with article processing charges (APC) paid by authors or their institutions.
High Visibility: indexed within Scopus, ESCI (Web of Science), Embase, and other databases.
Rapid Publication: manuscripts are peer-reviewed and a first decision is provided to authors approximately 20.7 days after submission; acceptance to publication is undertaken in 2.9 days (median values for papers published in this journal in the first half of 2025).
Recognition of Reviewers: APC discount vouchers, optional signed peer review, and reviewer names published annually in the journal.

Impact Factor: 2.2 (2024); 5-Year Impact Factor: 2.1 (2024)

Imprint Information Journal Flyer Open Access ISSN: 2036-7481

Latest Articles

15 pages, 2159 KiB

Open AccessArticle

Selection and Evaluation of Phosphate-Solubilizing Fungal Consortia Inoculated into Three Varieties of Coffea arabica Under Greenhouse Conditions

by Yamel del Carmen Perea-Rojas, Rosa María Arias and Rosario Medel-Ortíz

Microbiol. Res. 2025, 16(7), 162; https://doi.org/10.3390/microbiolres16070162 (registering DOI) - 17 Jul 2025

Phosphorus-solubilizing fungi represent a viable alternative to traditional fertilizers for use in coffee cultivation. The aim of this work was to select fungal consortia with a high phosphorus-solubilizing capacity for application to three varieties of coffee plants under greenhouse conditions. The research comprised [...] Read more.

Phosphorus-solubilizing fungi represent a viable alternative to traditional fertilizers for use in coffee cultivation. The aim of this work was to select fungal consortia with a high phosphorus-solubilizing capacity for application to three varieties of coffee plants under greenhouse conditions. The research comprised three phases: Firstly, solubilizing strains were identified morphologically and molecularly. Secondly, compatibility tests were carried out to select combinations of phosphorus-solubilizing fungi. The selection of the consortia was evaluated based on their phosphorus-solubilizing capacity, and the consortia with the solubilizing activity were chosen for application to coffee plants. In the greenhouse phase, three coffee varieties were inoculated; the treatments involved single, dual, and triple inoculation, as well as a control without fungi. Five species were identified: Fusarium crassum, F. irregulare, Leptobacillium leptobactrum, Penicillium brevicompactum, and Trichoderma spirale, plus one strain of Absidia sp. The in vitro phase of the study revealed that 11 consortia demonstrated compatibility, and their phosphorus solubilization capacity and phosphatase activity were evaluated. As a result, four consortia with high phosphorus solubilization capacity were selected for inoculation on coffee plants. The greenhouse phase results showed that the three coffee varieties inoculated in consortia showed higher phosphorus availability in the substrate and significant growth. Full article

► Show Figures

Graphical abstract

27 pages, 3370 KiB

Open AccessReview

Sourdough Fermentation and Gluten Reduction: A Biotechnological Approach for Gluten-Related Disorders

by Ricardo H. Hernández-Figueroa, Aurelio López-Malo and Emma Mani-López

Microbiol. Res. 2025, 16(7), 161; https://doi.org/10.3390/microbiolres16070161 - 17 Jul 2025

Sourdough fermentation has emerged as a promising biotechnological approach to reducing gluten content and modifying gluten proteins in wheat-based products. This review assesses the current scientific literature on the enzymatic degradation and hydrolysis of gluten during lactic acid bacteria (LAB) sourdough fermentation. It [...] Read more.

Sourdough fermentation has emerged as a promising biotechnological approach to reducing gluten content and modifying gluten proteins in wheat-based products. This review assesses the current scientific literature on the enzymatic degradation and hydrolysis of gluten during lactic acid bacteria (LAB) sourdough fermentation. It explores implications for individuals with gluten-related disorders, including celiac disease, non-celiac gluten sensitivity and intolerance, as well as irritable bowel syndrome (IBS). In addition, LAB sourdough effect on fermentable oligo-, di-, monosaccharides and polyols (FODMAPs), amylase-trypsin inhibitors (ATIs), and phytate are revised. Selected homo- and heterofermentative LAB are capable of degrading gluten proteins, especially the polypeptides derived from the action of native cereal proteases. Mixed cultures of LAB degrade gluten peptides more effectively than monocultures. However, LAB sourdough is not sufficient to remove the toxic peptides to the minimal level (<20 ppm). This goal is achieved only if sourdough is combined with fungal proteases during sourdough fermentation. LAB sourdough directly contributes to lower FODMAPs but not ATIs and phytate. Phytate is reduced by the endogenous cereal phytases activated at acidic pHs (pH < 5.0), conditions generated during sourdough fermentation. ATIs are also lowered by endogenous cereal proteases instead of LAB proteases/peptidases. Despite LAB sourdough not fully degrading the gluten or directly reducing the ATIs and phytate, it participates through peptidases activity and acidic pH that trigger the action of endogenous cereal proteases and phytases. Full article

► Show Figures

Figure 1

14 pages, 736 KiB

Open AccessArticle

Sfm Fimbriae Play an Important Role in the Pathogenicity of Escherichia coli CE129

by Yang Yang, Mingliang Chen, Zixin Han, Congrui Zhu, Ziyan Wu, Junpeng Li and Guoqiang Zhu

Microbiol. Res. 2025, 16(7), 160; https://doi.org/10.3390/microbiolres16070160 - 16 Jul 2025

Avian pathogenic Escherichia coli (APEC) is highly infective in poultry, causing significant economic losses to the poultry industry. As an extraintestinal pathogenic strain, adherence is a critical step in the infection. The functions of several adhesins, including type I, P, and Curli fimbriae, [...] Read more.

Avian pathogenic Escherichia coli (APEC) is highly infective in poultry, causing significant economic losses to the poultry industry. As an extraintestinal pathogenic strain, adherence is a critical step in the infection. The functions of several adhesins, including type I, P, and Curli fimbriae, have been extensively studied. However, the roles of other adhesins, like Sfm, remain largely unexplored. Sfm is widely present in E. coli. Although the Sfm cluster is an ortholog of the fim gene cluster of Salmonella type I fimbriae, the biological function of Sfm in APEC has not yet been elucidated. To investigate whether Sfm in APEC CE129 plays a role in virulence, in this study, we constructed recombinant strains by expressing Sfm in the fimbriae-deficient strain SE5000. Additionally, a CE129 sfmA mutant strain was constructed. The resulting changes in adherence, biofilm formation, resistance to macrophage phagocytosis, and resistance to serum bactericidal ability were observed. The adherence ability of CE129ΔsfmA was reduced by 41%. HD-11 cells demonstrated a 30% increase in the phagocytosis of CE129ΔsfmA, and a 50% reduction in SE5000 (pBR322-sfm). The sfm deletion mutant showed a 23.9% reduction in the resistance to serum bactericidal ability, while SE5000 (pBR322-sfm) displayed a 32% increase. SE5000 (pBR322-sfm) exhibited a 34% increase in biofilm formation, and CE129ΔsfmA demonstrated a 21% decrease. Real-time PCR was employed to examine the impact of Sfm deletion on the transcription level of key virulence factors (fimA, fliC, papC, tsh, ompA, and iss). The results indicated that Sfm in CE129 is closely associated with bacterial adherence and survivability, contributing to biofilm formation and influencing the expression of key virulence factors. This study yields initial insight into the functional roles of Sfm in APEC and provides a foundation for the effective control of E. coli in the poultry industry. Full article

13 pages, 892 KiB

Open AccessArticle

Comparative Evaluation of Recombinant Chlamydia abortus and Chlamydia trachomatis Major Outer Membrane Proteins for Diagnosing Human Chlamydial Infection

by Fernando M. Guerra-Infante, María J. de Haro-Cruz, Marcela López-Hurtado, Miguel A. De la Rosa-Ramos, Efrén Díaz-Aparicio and Beatriz Arellano-Reynoso

Microbiol. Res. 2025, 16(7), 159; https://doi.org/10.3390/microbiolres16070159 - 9 Jul 2025

Chlamydia trachomatis infection is a public health problem. Serological tests can determine the disease burden and serve as a biomarker for identifying patients with infertility due to tubal obstruction. However, cross-reactions between chlamydial species have been reported, which causes problems with diagnosis. A [...] Read more.

Chlamydia trachomatis infection is a public health problem. Serological tests can determine the disease burden and serve as a biomarker for identifying patients with infertility due to tubal obstruction. However, cross-reactions between chlamydial species have been reported, which causes problems with diagnosis. A real-time PCR commercial test for the detection of endocervical infection and two ELISAs with the recombinant major outer membrane protein (rMOMP) from C. trachomatis and C. abortus as antigens were used to diagnose both infections. The prevalence of endocervical infection by C. trachomatis was 7.77%, and that of IgG antibodies against C. trachomatis and C. abortus was 31.1% and 10.7%, respectively. The ELISA with C. trachomatis rMOMP showed a sensitivity of 75% and a specificity of 72.5%. The lowest sensitivity (25%) and high specificity (76.8%) were obtained with anti-C. abortus rMOMP ELISAs. A low cross-reactivity of 7% between ELISA tests was observed. Conclusion. The recombinant MOMP ELISA could help identify women who had contact with C. trachomatis or C. abortus and could be a tool to lower the costs of performing molecular testing on all patients attending an infertility clinic. Full article

(This article belongs to the Special Issue Host–Microbe Interactions in Health and Disease)

► Show Figures

Graphical abstract

16 pages, 2299 KiB

Open AccessReview

Intestinal Microeukaryotes in Fish: A Concise Review of an Underexplored Component of the Microbiota

by Jesús Salvador Olivier Guirado-Flores, Estefanía Garibay-Valdez, Diana Medina-Félix, Francisco Vargas-Albores, Luis Rafael Martínez-Córdova, Yuniel Mendez-Martínez and Marcel Martínez-Porchas

Microbiol. Res. 2025, 16(7), 158; https://doi.org/10.3390/microbiolres16070158 - 8 Jul 2025

The intestinal microbiota of fish is predominantly composed of prokaryotic microorganisms, with research historically focused on bacteria. In contrast, the role of microeukaryotic organisms in the fish gut remains largely unexplored. This review synthesizes current knowledge on the diversity, ecology, and potential functions [...] Read more.

The intestinal microbiota of fish is predominantly composed of prokaryotic microorganisms, with research historically focused on bacteria. In contrast, the role of microeukaryotic organisms in the fish gut remains largely unexplored. This review synthesizes current knowledge on the diversity, ecology, and potential functions of intestinal microeukaryotes, particularly fungi and protozoans, in teleost fish. Fungi, especially Ascomycota and Basidiomycota phyla members, are consistently identified across species and may contribute to digestion, immune modulation, and microbial homeostasis. Protists, though often viewed as pathogens, also exhibit potential commensal or immunoregulatory roles, including the modulation of bacterial communities through grazing. Other eukaryotic taxa, including metazoan parasites, microalgae, and zooplankton, are commonly found as transient or diet-derived members of the gut ecosystem. While many of these organisms remain poorly characterized, emerging evidence suggests they may play essential roles in host physiology and microbial balance. The review highlights the need for improved detection methodologies, functional studies using gnotobiotic and in vitro models, and multi-kingdom approaches to uncover fish gut microeukaryotes’ ecological and biotechnological potential. Full article

► Show Figures

Figure 1

16 pages, 1097 KiB

Open AccessReview

Beyond Fish Pathogens: A Comprehensive Overview of Aeromonas salmonicida

by Xiaotong Qin, Zhongduo Li, Jinglan Guo, Feng Bai and Xiaodong Ling

Microbiol. Res. 2025, 16(7), 157; https://doi.org/10.3390/microbiolres16070157 - 8 Jul 2025

Aeromonas salmonicida is an age-old fish pathogen widely distributed in seawater and freshwater environments that causes significant economic losses to the global aquaculture industry. Genetic mutations and the emergence of thermophilic strains are factors in the continuous expansion of A. salmonicida’s host [...] Read more.

Aeromonas salmonicida is an age-old fish pathogen widely distributed in seawater and freshwater environments that causes significant economic losses to the global aquaculture industry. Genetic mutations and the emergence of thermophilic strains are factors in the continuous expansion of A. salmonicida’s host range. Beyond infecting fish, A. salmonicida poses a potential threat to mammalian and human health. This review synthesizes recent global research advances concerning A. salmonicida, encompassing strain characteristics, genomic features, virulence factors, and pathogenic mechanisms, as well as the clinical manifestations in infected fish and mammals, and discusses prevention and treatment methods. Particular emphasis is placed on evaluating the potential prophylactic roles of Chinese herbs and bacteriophages against A. salmonicida infection. Furthermore, the review provides perspectives on future research directions, diagnostics, and disease management, informed by contemporary domestic and international studies on this pathogen. Full article

► Show Figures

Graphical abstract

12 pages, 732 KiB

Open AccessArticle

Bacteremia Outbreak Due to Achromobacter xylosoxidans in Hospitalized COVID-19 Patients

by Magdalini Tsekoura, Georgios Petridis, Konstantinos Koutsouflianiotis, Styliani Pappa, Anna Papa and Konstantina Kontopoulou

Microbiol. Res. 2025, 16(7), 156; https://doi.org/10.3390/microbiolres16070156 - 8 Jul 2025

Background: Hospitalized COVID-19 patients are particularly vulnerable to secondary bacterial infections, which can significantly worsen clinical outcomes. The aim of the study was to identify the cause of bacteremia in a group of hospitalized COVID-19 patients and find out the source of the [...] Read more.

Background: Hospitalized COVID-19 patients are particularly vulnerable to secondary bacterial infections, which can significantly worsen clinical outcomes. The aim of the study was to identify the cause of bacteremia in a group of hospitalized COVID-19 patients and find out the source of the outbreak to prevent further spread. Methods: Pathogen identification in blood cultures and sensitivity testing were carried out using the automated VITEK2 system. A total of 110 samples were tested; these were collected from patients’ colonization sites and from surfaces, materials and fluids used in the setting. Furthermore, multilocus sequence typing (MLST) and next-generation sequencing (NGS) were employed to characterize the isolates. Results: Achromobacter xylosoxidans was detected in the blood of nine hospitalized patients and in cotton used for disinfection; all isolates presented an identical antibiotic resistance pattern, and all carried the bla_OXA-114 gene which is intrinsic to this species. Infection control measures were implemented promptly. With one exception, all patients recovered and were discharged in good health. Conclusions: This outbreak underscores the urgent need for investigation and control of hospital infections, as bacteremia is associated with increased morbidity, mortality, hospitalization time, and cost. It also highlights the importance of close collaboration among healthcare professionals. Full article

► Show Figures

Figure 1

17 pages, 2474 KiB

Open AccessArticle

Localization of a Cardiolipin Synthase in Helicobacter pylori and Its Impact on the Flagellar Sheath Proteome

by Doreen Nguyen, Nathan East, Vincent J. Starai and Timothy R. Hoover

Microbiol. Res. 2025, 16(7), 155; https://doi.org/10.3390/microbiolres16070155 - 7 Jul 2025

Helicobacter pylori, which colonizes the human gastric mucosa, uses a cluster of polar, sheathed flagella to swim across the mucous layer of the stomach. The function and biogenesis of the H. pylori flagellar sheath are poorly understood. Cardiolipin is a phospholipid that [...] Read more.

Helicobacter pylori, which colonizes the human gastric mucosa, uses a cluster of polar, sheathed flagella to swim across the mucous layer of the stomach. The function and biogenesis of the H. pylori flagellar sheath are poorly understood. Cardiolipin is a phospholipid that accumulates in regions of the membrane that have negative curvature, such as the cell pole, cell septum, and flagellar sheath. The final step in cardiolipin biosynthesis is catalyzed by cardiolipin synthase. H. pylori has at least two cardiolipin synthases, one of which is cardiolipin synthase C (ClsC). Bioinformatic analysis revealed that homologs of H. pylori ClsC are restricted to Helicobacter species that have sheathed flagella and the ClsC homologs are predicted lipoproteins. Fluorescence microscopy revealed that a ClsC super-folder green fluorescent protein localized to the cell pole and cell septum in H. pylori G27. Comparing the proteomes of isolated sheathed flagella from the H. pylori B128 wild type and a clsC::cat mutant, we identified five proteins that were absent in the mutant flagellum preparations. One of the proteins was FaaA, an autotransporter that localizes to the flagellar sheath. These findings suggest that the localization of FaaA and possibly other proteins to the flagellar sheath is dependent on ClsC. Full article

► Show Figures

Figure 1

18 pages, 1473 KiB

Open AccessPerspective

Virus-First Theory Revisited: Bridging RNP-World and Cellular Life

by Francisco Prosdocimi and Savio Torres de Farias

Microbiol. Res. 2025, 16(7), 154; https://doi.org/10.3390/microbiolres16070154 - 7 Jul 2025

The virus-first theory presents a model in which viral lineages emerged before cells. This proposal aims to give the theory greater relevance by offering a plausible evolutionary framework that explains both (i) the origin of viruses from prebiotic chemistry and (ii) how viruses [...] Read more.

The virus-first theory presents a model in which viral lineages emerged before cells. This proposal aims to give the theory greater relevance by offering a plausible evolutionary framework that explains both (i) the origin of viruses from prebiotic chemistry and (ii) how viruses contributed to the emergence of cells. Here, we propose that viruses should be understood as a distinct class of ribonucleoprotein (RNP) systems, some of which evolved directly from the RNP-world. In our model, simple progenotes produced capsid-like particles through the evolution of a single gene encoding a self-assembling peptide. This allowed the formation of icosahedral shells around RNA genomes, as observed today in certain viral families whose capsids consist of ~60 identical subunits derived from a single gene product. These early capsids enabled mobility and protection, representing key intermediates toward biological complexity. Over time, some of those populations acquired additional peptides and evolved more elaborate architectures. Finally, the incorporation of lipid-binding domains in those capsid-like peptides allowed the formation of proteolipidic membranes akin to those found in modern cells. This model provides a gradualistic and logically coherent evolutionary path from the RNP-world to the emergence of cellular life, emphasizing the foundational role of viruses in early evolution. Full article

► Show Figures

Figure 1

17 pages, 2220 KiB

Open AccessArticle

Soil Prokaryotic Diversity Responds to Seasonality in Dehesas, Modulated by Tree Identity and Canopy Effect

by José Manjón-Cabeza, Mercedes Ibáñez, María José Leiva, Cristina Chocarro, Anders Lanzén, Lur Epelde and Maria Teresa Sebastià

Microbiol. Res. 2025, 16(7), 153; https://doi.org/10.3390/microbiolres16070153 - 5 Jul 2025

Dehesas are mosaics of open grassland and standalone trees that are diversity reservoirs. However, they have recently faced abandonment and intensification, being replaced by plantations of fast-growing trees or subject to encroachment. Following a change in dehesa communities and structure, a change in [...] Read more.

Dehesas are mosaics of open grassland and standalone trees that are diversity reservoirs. However, they have recently faced abandonment and intensification, being replaced by plantations of fast-growing trees or subject to encroachment. Following a change in dehesa communities and structure, a change in soil microbial diversity and functionality in dehesas is expected, but dehesas’ microbial diversity is still a big unknown. In this work, we bring to light the soil prokaryotic taxonomic diversity in dehesa ecosystems and present a first approach to assessing their metabolic diversity through metabarcoding data. For this, we compared three dehesas dominated by different tree species: (i) one dehesa dominated by Quercus ilex; (ii) one dominated by Pinus pinea; and (iii) one dominated by a mixture of Q. ilex and Q. suber. At each dehesa, samples were taken under the canopy and in the open grassland, as well as through two seasons of peak vegetation productivity (autumn and spring). Our results show the following findings: (1) seasonality plays an important role in prokaryotic richness, showing higher values in autumn, and higher evenness in spring; (2) the effect of seasonality on the soil’s prokaryotic diversity is often modulated by the effect of tree species and canopy; (3) taxonomic diversity is driven mainly by the site effects, i.e., the opposite of the metabolic diversity that seemed to be driven by complex interactions among seasons, tree species, and canopies. Full article

► Show Figures

Figure 1

15 pages, 495 KiB

Open AccessArticle

Comprehensive Analysis of Etiological Agents and Drug Resistance Patterns in Ventilator-Associated Pneumonia

by Harendra K. Thakur, Bansidhar Tarai, Aradhana Bhargava, Pankaj Soni, Anup Kumar Ojha, Sudhakar Kancharla, Prachetha Kolli, Gowtham Mandadapu and Manoj Kumar Jena

Microbiol. Res. 2025, 16(7), 152; https://doi.org/10.3390/microbiolres16070152 - 4 Jul 2025

Ventilator-associated pneumonia (VAP) develops in patients who stay on mechanical ventilation for more than 48 h. In the presence of causative pathogens, the patient develops clinical signs such as purulent tracheal discharge, fever, and respiratory distress. A prospective observational study was carried out [...] Read more.

Ventilator-associated pneumonia (VAP) develops in patients who stay on mechanical ventilation for more than 48 h. In the presence of causative pathogens, the patient develops clinical signs such as purulent tracheal discharge, fever, and respiratory distress. A prospective observational study was carried out in the Intensive Care Unit (ICU) of Max Healthcare Centre, New Delhi, from 2020 to 2023. The study comprised 70 samples from patients diagnosed with VAP. This study thoroughly examined VAP-associated microorganisms and resistance in the hospital ICU. Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa were the most commonly reported pathogens. Significant drug resistance was seen in P. aeruginosa, K. pneumoniae, A. baumannii and Staphylococcus aureus. The heatmap also supported the antibiotic resistance data patterns obtained from conventional and automated systems of determination. Notably, Serratia marcescens, Escherichia coli, Klebsiella pneumoniae, Ralstonia insidiosa, and Ralstonia mannitolilytica, showed 60 to 100% of resistance to a number of antibiotics. Among all VAP patients, 31.42% early-onset and 68.57% late-onset VAP cases were detected. Out of 70 patients, 43 patients died (mortality rate 61.4%); majority of them suffered from late-onset VAP. The study goal was to describe the antibiotic resistance patterns and microbial ecology of the pathogens that were isolated from VAP patients. According to the heatmap analysis, a varied VAP microbiome with high prevalences of MDR in A. baumannii, P. aeruginosa, K. pneumoniae, and S. aureus was identified. To address the increasing prevalence of MDR VAP, the study highlights the critical need for improved VAP monitoring, strong infection control, and appropriate antibiotic usage. Full article

► Show Figures

Figure 1

19 pages, 5267 KiB

Open AccessArticle

Microbial Biocontrol Agents Engineer Plant Biometrics and Host Response Against Xanthomonas oryzae pv. oryzae in Rice

by Popy Bora, Sanjay Kumar Chetia, Anwesha Sharma, Shenaz Sultana Ahmed, Pranamika Sharma, Ashok Bhattacharyya, Rupam Borgohain, Mrinal Saikia, Parinda Barua, Milon Jyoti Konwar, Shabrin Sultana Ahmed, Abhisek Rath, Mehjebin Rahman, Bishal Saikia, Trishna Taye, Naseema Rahman, Parveen Khan, Mayuri Baruah, Rituraj Sakia and Arunima Bharali

Microbiol. Res. 2025, 16(7), 151; https://doi.org/10.3390/microbiolres16070151 - 4 Jul 2025

Plant-beneficial microbes are a perennial ally in an agroecosystems, providing multiple benefits to crop plants. The present study explored the potential of two microbial biocontrol agents (MBCAs), viz., Trichoderma asperellum and Pseudomonas fluorescens, against the bacterial blight pathogen of rice, Xanthomonas oryzae [...] Read more.

Plant-beneficial microbes are a perennial ally in an agroecosystems, providing multiple benefits to crop plants. The present study explored the potential of two microbial biocontrol agents (MBCAs), viz., Trichoderma asperellum and Pseudomonas fluorescens, against the bacterial blight pathogen of rice, Xanthomonas oryzae pv. oryzae. In vitro, MBCAs resulted in significant inhibition of X. oryzae pv. oryzae, as evidenced through the distortion of pathogen cell morphology and formation of a pathogen biofilm. Pot studies on the effect of MBCAs in rice showed increased germination, increased vigor index of seedlings, increased tiller numbers, a 10.29% reduction in percentage disease incidence (PDI), and low disease severity following individual inoculation. Activity of plant defense enzymes also increased with MBCA treatment (phenylalanine ammonia-lyase, 2.7-fold increase; peroxidase and polyphenol oxidase, 5-fold increase), establishing the priming effect of MBCAs on host defense. The quantitative polymerase chain reaction data revealed that pathogenesis-related genes (OsPR1a, OsPR1b, and OsPR10a) and X. oryzae pv. oryzae resistance genes (Xa1 and Xa26) were upregulated 4- to 14-fold in MBCA-treated rice plants over control plants. These results provide insights into the phenological, physiological, and molecular responses of rice crops treated with MBCAs in the presence of X. oryzae pv. oryzae and could be used to develop an effective field management strategy. Full article

► Show Figures

Figure 1

13 pages, 1208 KiB

Open AccessArticle

Acaricidal Activity of Biosurfactants Produced by Serratia ureilytica on Tetranychus urticae and Their Compatibility with the Predatory Mite Amblyseius swirskii

by Arnoldo Wong-Villareal, Esaú Ruiz-Sánchez, Marcos Cua-Basulto, Saúl Espinosa-Zaragoza, Avel A. González-Sánchez, Ernesto Ramos-Carbajal, Cristian Góngora-Gamboa, René Garruña-Hernández, Rodrigo Romero-Tirado, Guillermo Moreno-Basurto and Erika P. Pinson-Rincón

Microbiol. Res. 2025, 16(7), 150; https://doi.org/10.3390/microbiolres16070150 - 4 Jul 2025

This study evaluated the acaricidal effects of biosurfactants produced by Serratia ureilytica against the two-spotted spider mite Tetranychus urticae and their compatibility with the predatory mite Ambliseus swirski. The biosurfactants were obtained via liquid cultures of the bacterial strains. In the laboratory, [...] Read more.

This study evaluated the acaricidal effects of biosurfactants produced by Serratia ureilytica against the two-spotted spider mite Tetranychus urticae and their compatibility with the predatory mite Ambliseus swirski. The biosurfactants were obtained via liquid cultures of the bacterial strains. In the laboratory, T. urticae was exposed via acaricide-immersed leaves and A. swirskii via acaricide-coated glass vials. In the greenhouse, mite-infested plants were sprayed with the biosurfactants. In the laboratory, biosurfactants produced by S. ureilytica NOD-3 and UTS exhibited strong acaricidal activity, causing 95% mortality in adults and reducing egg viability by more than 60%. In the greenhouse trial, all biosurfactants significantly suppressed T. urticae populations at all evaluated periods (7, 14, and 21 days post-application). Gas chromatography–mass spectrometry (GC-MS) analysis of the biosurfactants identified several fatty acids, including hexadecanoic acid, pentanoic acid, octadecanoic acid, decanoic acid, and tetradecanoic acid, as well as the amino acids L-proline, L-lysine, L-valine, and glutamic acid. These fatty acids and amino acids are known structural components of lipopeptides. Furthermore, the bioinformatic analysis of the genomes of the three S. ureilytica strains revealed nonribosomal peptide synthetase (NRPS) gene clusters homologous to those involved in the biosynthesis of lipopeptides. These findings demonstrate that S. ureilytica biosurfactants are promising eco-friendly acaricides, reducing T. urticae populations by >95% while partially sparing A. swirskii. Full article

► Show Figures

Figure 1

16 pages, 2103 KiB

Open AccessArticle

Morinda citrifolia Essential Oil in the Control of Banana Anthracnose: Impacts on Phytotoxicity, Preventive and Curative Effects and Fruit Quality

by Maysa C. Santos, Luis O. Viteri, Paulo R. Fernandes, Rosilene C. Carvalho, Manuel A. Gonzalez, Osmany M. Herrera, Pedro R. Osório, Dalmarcia S. C. Mourão, Sabrina H. Araujo, Cristiano B. Moraes, Marcos V. Giongo, Wellington S. Moura, Marcos P. Camara, Alex Sander R. Cangussu, Raimundo W. S. Aguiar, Eugênio E. Oliveira and Gil R. Santos

Microbiol. Res. 2025, 16(7), 149; https://doi.org/10.3390/microbiolres16070149 - 3 Jul 2025

Bananas, one of the most widely consumed tropical fruits in the world, are susceptible to attack by the anthracnose fungus Colletotrichum musae during the post-harvest period. Currently, fungus control is generally based on the use of chemical products, often applied a few days [...] Read more.

Bananas, one of the most widely consumed tropical fruits in the world, are susceptible to attack by the anthracnose fungus Colletotrichum musae during the post-harvest period. Currently, fungus control is generally based on the use of chemical products, often applied a few days before harvest, which could lead to a risk of residues in the fruit, thus creating a high demand for fresh and organic fruits. Therefore, essential oils present an emerging alternative for the treatment of anthracnose. Here, we evaluated the chemical composition and potential of Morinda citrifolia essential oil as a preventive and curative measure to control C. musae in bananas, also considering the quality of the fruit. In addition, computational docking analysis was conducted to predict potential molecular interactions between octanoic and butanoic acids and the enzyme Tyrosine tRNA, as a potential target for the M. citrifolia essential oil fungicide actions. We also evaluated the essential oil’s safety for beneficial organisms such as the fungus Trichoderma asperellum and the ladybugs Eriopis connexa Germar and Coleomegilla maculata DeGeer. Initially, in vitro growth inhibition tests were performed with doses of 10.0, 30.0, and 50.0 µL/mL of M. citrifolia essential oil, as well as an assessment of the phytotoxic effects on the fruit. Subsequently, using non-phytotoxic doses, we evaluated the effect of the essential oil as a preventive and curative measure against anthracnose and its impact on fruit quality. Our results showed that octanoic, butanoic, and hexanoic acids were the major compounds in M. citrifolia essential oil, inhibiting the growth of C. musae by interacting with the Tyrosine tRNA enzyme of C. musae. The non-phytotoxic dose on the fruit was 10 µL/mL of noni essential oil, which reduced C. musae growth by 30% when applied preventively and by approximately 25% when applied as a curative measure. This significantly reduced the Area Under the Disease Progress Curve without affecting the fruit weight, although there was a slight reduction in °Brix. The growth of non-target organisms, such as T. asperellum and the insect predators Co. maculata and E. connexa, was not affected. Collectively, our findings suggest that M. citrifolia essential oil is a promising alternative for the prevention and control of anthracnose in banana fruit caused by C. musae, without adversely affecting its organoleptic characteristics or non-target organisms. Full article

► Show Figures

Figure 1

10 pages, 438 KiB

Open AccessArticle

Epidemiology and Molecular Identification of Dermatophytes: Focus on the Detection of the Emerging Species Trichophyton indotineae in Northern Italy

by Valentina Lepera, Gabriella Tocci, Giorgia Palladini, Marco Enrico Giovanni Arosio, Claudio Farina, Giuliana Lo Cascio and on behalf of the Medical Mycology Committee (CoSM)—Italian Association of Clinical Microbiology (AMCLI)

Microbiol. Res. 2025, 16(7), 148; https://doi.org/10.3390/microbiolres16070148 - 2 Jul 2025

Background: Trichophyton indotineae, a new emerging pathogen according to the WHO, is known to cause severe forms of tinea. Given that traditional identification methods rely on morphological characteristics, and the morphological distinctions among T. indotineae, T. mentagrophytes, and T. [...] Read more.

Background: Trichophyton indotineae, a new emerging pathogen according to the WHO, is known to cause severe forms of tinea. Given that traditional identification methods rely on morphological characteristics, and the morphological distinctions among T. indotineae, T. mentagrophytes, and T. interdigitale are minimal, the adoption of alternative diagnostic techniques, such as RT-PCR or gene sequencing, has become critically important to prevent misidentification. The purpose of this study was firstly to analyze the local epidemiology of dermatophytes isolated and secondly to investigate the presence of T. indotineae among the isolated strains. Methods: Between January 2021 and June 2024, 1096 samples of skin adnexa were analysed. The isolated strains belonging to the genus Trichophyton were submitted to molecular identification by ITS sequencing, and T. indotineae strains were subjected to squalene epoxidase (SQLE) sequencing analysis. Results: Trichophyton rubrum and Trichophyton interdigitale appear to be the most prevalent pathogenic species. Molecular identification reveals four T. indotineae strains (4/87; 4.61%) from Asian patients, which were also characterized by gene mutations associated with terbinafine resistance. Conclusions: This study has made it clear that there is a need to implement basic mycological diagnostics with molecular methods to avoid misidentifications, ensure the correct identification, and evaluate the presence of mutations associated with antifungal drug resistance. Full article

► Show Figures

Figure 1

11 pages, 4880 KiB

Open AccessCommunication

The Nosocomial Transmission of Carbapenem-Resistant Gram-Negative Bacteria in a Hospital in Baoding City, China

by Shengnan Liao, Wei Su, Tianjiao Li, Zeyang Li, Zihan Pei, Jie Zhang and Wenjuan Yin

Microbiol. Res. 2025, 16(7), 147; https://doi.org/10.3390/microbiolres16070147 - 2 Jul 2025

Background: The global rise of multidrug-resistant Gram-negative bacteria, particularly non-fermenting species and carbapenemase-producing Enterobacteriaceae, poses a significant challenge to hospital infection control. Methods: In this study, a total of 89 Acinetobacter spp. isolates, 14 Pseudomonas aeruginosa, and 14 carbapenem-resistant Enterobacteriaceae isolates were [...] Read more.

Background: The global rise of multidrug-resistant Gram-negative bacteria, particularly non-fermenting species and carbapenemase-producing Enterobacteriaceae, poses a significant challenge to hospital infection control. Methods: In this study, a total of 89 Acinetobacter spp. isolates, 14 Pseudomonas aeruginosa, and 14 carbapenem-resistant Enterobacteriaceae isolates were collected from patients in a tertiary hospital. Whole-genome sequencing and antimicrobial susceptibility testing were conducted. Resistance mechanisms and evolutionary relationships were analyzed using phylogenetic analysis and genetic context mapping. Results: Among the non-fermenting isolates, A. baumannii exhibited high resistance to carbapenems, clustering into distinct clonal groups enriched with genes associated with biofilm formation and virulence genes. P. aeruginosa isolates harbored fewer resistance genes but carried notable mutations in the efflux pump systems and the oprD gene. In Enterobacteriaceae, four bla_NDM alleles were identified within a conservative structural sequence, while bla_KPC-2 was located in a non-Tn4401 structure flanked by IS481- and IS1182-like insertion sequences. Phylogenetic analysis revealed that bla_NDM-positive E. coli strains were closely related to susceptible lineages, indicating horizontal gene transfer. Conversely, K. pneumoniae isolates harboring bla_KPC-2 formed a tight clonal cluster, suggesting clonal expansion. Conclusions: The study reveals distinct transmission patterns between resistance genes: horizontal dissemination of bla_NDM and clonal expansion of bla_KPC-2 in K. pneumoniae. These findings emphasize the need for resistance-gene-specific genomic surveillance and infection control strategies to prevent further nosocomial dissemination. Full article

► Show Figures

Figure 1

11 pages, 2141 KiB

Open AccessCommunication

Transcriptomic Analysis of Macrophages Infected with Mycobacterium smegmatis

by Hong Sun, Yue Hou, Wenzhao Xu, Wenjing Wang, Na Tian, Dingyi Liu and Zhaogang Sun

Microbiol. Res. 2025, 16(7), 146; https://doi.org/10.3390/microbiolres16070146 - 2 Jul 2025

Mycobacterium tuberculosis (MTB) can cause serious infectious diseases. MTB is retained in the macrophages of an organism, activating the immune response or evading the immune response through other mechanisms. Mycobacterium smegmatis (M. smeg) has the advantage of high safety and maneuverability [...] Read more.

Mycobacterium tuberculosis (MTB) can cause serious infectious diseases. MTB is retained in the macrophages of an organism, activating the immune response or evading the immune response through other mechanisms. Mycobacterium smegmatis (M. smeg) has the advantage of high safety and maneuverability as an alternative to MTB. M. smeg has physiological functions similar to those of MTB. It is mainly used to study the molecular mechanism of the interaction between the modified M. smeg carrying MTB-related components and cells. There are few studies on the interaction between the unmodified M. smeg and macrophages. Transcriptomics is an emerging research tool in recent years, which can deeply explore the relevant molecules inside a cell and explore the possible regulatory mechanisms more comprehensively. In this study, we first constructed an in vitro model of M. smeg-infected macrophages, collected RNA extracted from the infected cells, performed transcriptome sequencing using the Illunima platform, and verified the expression levels of the main markers related to phenotypic or functional changes in macrophages by qPCR and ELISA. In this study, through the transcriptomic analysis of M. smeg-infected macrophages, we found that M. smeg can regulate multiple cell signaling pathways in macrophages dominated by immune responses and activate the production of the cytokines IL-6 and TNF-α, which are mainly involved in the immune response in macrophages. This study suggests that M. smeg and MTB have similar physiological functions in activating the immune response of macrophages. Meanwhile, the interaction between M. smeg and macrophages also indicates the primary position and significant role of immune regulation in cellular signaling pathways. Therefore, studying the interaction mechanism between macrophages and M. smeg through transcriptomics is conducive to a comprehensive understanding of the related physiological functions of M. smeg in regulating immune responses or immune escape, providing strong evidence for its use as a model alternative bacteria for MTB in the future research on MTB immunity and related physiological functions. Full article

► Show Figures

Figure 1

20 pages, 2729 KiB

Open AccessArticle

Occurrence of Philaenus spumarius in Xylella fastidiosa Demarcated Zones of Northern Portugal

by Talita Loureiro, Luís Serra, Ângela Martins, Isabel Cortez and Patrícia Poeta

Microbiol. Res. 2025, 16(7), 145; https://doi.org/10.3390/microbiolres16070145 - 2 Jul 2025

The introduction of non-native species like Xylella fastidiosa to new environments can lead to potentially catastrophic ecological and economic repercussions. This work comprehended the prospection phase (insect sampling and submission of samples to the laboratory) from X. fastidiosa demarcated zones of Área Metropolitana [...] Read more.

The introduction of non-native species like Xylella fastidiosa to new environments can lead to potentially catastrophic ecological and economic repercussions. This work comprehended the prospection phase (insect sampling and submission of samples to the laboratory) from X. fastidiosa demarcated zones of Área Metropolitana do Porto; Sabrosa; Alijó; Baião; Mirandela; Mirandela II; and Bougado and the research phase (collecting and organizing data and statistical treatment). The results of this study showed the presence of the bacterium in some tested spittlebugs species captured in DZ of Área Metropolitana do Porto, which highlights the role of the vector in mediating the disease’s propagation. Most insects were found in public gardens and in nurseries/gardens where there is a diverse array of food sources, shelter, mating locations, and suitable substrates for egg laying that serve as ideal conditions for the population of Philaenus spumarius. We observed that most insects were found in the first trimester (36.5%), followed by the third trimester (23.2%). Finally, it was shown that, in our study, the most frequent host plants where insects were found included Lavandula dentata, Ulex minor, Ulex europaeus, Quercus suber, Plantago lanceolata. Our findings imply a robust connection between plant communities, ecological conditions, and insect populations with the occurrence of Xylella fastidiosa, particularly within the examined climatic context. Full article

► Show Figures

Figure 1

14 pages, 1774 KiB

Open AccessArticle

Microbial Changes in Hand Skin During COVID-19: A Longitudinal Study in Majorca, Spain

by Cristina Turpín and Antonio Doménech-Sánchez

Microbiol. Res. 2025, 16(7), 144; https://doi.org/10.3390/microbiolres16070144 - 2 Jul 2025

The COVID-19 pandemic prompted widespread adoption of intensified hand hygiene practices, raising concerns about their medium-term impact on the skin microbiome. This study investigates alterations in the hand microbiome of healthy adults during the pandemic compared to pre-pandemic periods in Majorca, Spain. A [...] Read more.

The COVID-19 pandemic prompted widespread adoption of intensified hand hygiene practices, raising concerns about their medium-term impact on the skin microbiome. This study investigates alterations in the hand microbiome of healthy adults during the pandemic compared to pre-pandemic periods in Majorca, Spain. A total of 30 volunteers (16 women, 14 men; mean age 44.1 ± 8.8 years) were sampled between 2014 and 2021. Palm swabs were collected following WHO guidelines, alongside measurements of skin pH, temperature, and handwashing frequency. Bacterial DNA was extracted and analyzed via 16S rRNA (V3-V4) metagenomic sequencing to assess microbial diversity and composition. Results revealed a significant decline in microbial diversity during the COVID-19 period, accompanied by a marked shift in the community structure. The Firmicutes phylum dominated, with Bacillales increasing from 30.7% to 84.1%, primarily driven by a surge in Staphylococcus species (e.g., S. pasteuri). Conversely, S. hominis and Actinomycetales nearly disappeared. No significant associations were observed with gender or handwashing frequency. The skin temperature increased during the pandemic, while the pH remained stable. The Staphylococcus/Bacillus ratio shifted significantly, favoring Staphylococcus dominance. These findings, derived from a geographically limited population in Majorca, Spain, demonstrate that stringent hygiene measures during COVID-19 reduced microbial diversity and restructured hand microbiome composition. The study underscores the necessity for balanced hygiene strategies that mitigate pathogen transmission while preserving beneficial microbial communities critical to skin health. Full article

► Show Figures

Figure 1

18 pages, 2156 KiB

Open AccessArticle

The TOR Regulatory Mechanism Controls the Metabolism of Nitrate and the Fermentation Activity in the Yeast Dekkera bruxellensis GDB 248

by Karolini Miranda, Beatriz Câmara de Melo, Gilberto Henriques Teles, Irina Charlot Peña-Moreno, Rafael Barros de Souza and Marcos Antonio de Morais, Jr.

Microbiol. Res. 2025, 16(7), 143; https://doi.org/10.3390/microbiolres16070143 - 1 Jul 2025

Dekkera bruxellensis is already known for its great biotechnological potential, part of this due to the ability to assimilate nitrate during fermentation. Despite the previous works on nitrogen metabolism in this yeast, especially regarding nitrate assimilation, the relation between this metabolism and the [...] Read more.

Dekkera bruxellensis is already known for its great biotechnological potential, part of this due to the ability to assimilate nitrate during fermentation. Despite the previous works on nitrogen metabolism in this yeast, especially regarding nitrate assimilation, the relation between this metabolism and the TOR (Target of Rapamycin) regulatory mechanism remains unexplored. This connection may reveal key regulatory mechanisms to maximize its fermentative performance and biotechnological use. Herein, we evaluated the physiological, metabolic, and gene expression profile of D. bruxellensis GDB 248 cultivated in ammonium and nitrate as nitrogen sources in the presence of TOR complex 1 (TORC1) inhibitor rapamycin. Our results showed that inhibition of the TORC1 significantly reduces cell growth and fermentative capacity, especially in nitrate media. Gene expression analysis revealed that TORC1 plays a central role in regulating genes involved in nitrate assimilation and the adaptive performance of D. bruxellensis in fermentative environments. Therefore, the regulation of nitrate assimilatory genes YNTI, YNRI, and YNI1 responds to a nitrate-dependent mechanism as well as to a TOR-dependent mechanism. These findings expand the understanding of the regulation of nitrogen metabolism in D. bruxellensis, providing valuable information that may aid in the development of future strategies for its use as an industrial yeast. Full article

► Show Figures

Graphical abstract

More Articles...

Submit to Microbiology Research Review for Microbiology Research

Journal Menu

Journal Browser

► Journal Browser

Highly Accessed Articles

View More...

Latest Books

More Books and Reprints...

E-Mail Alert

News

4 July 2025
MDPI’s Newly Launched Journals in June 2025

2 July 2025
MDPI INSIGHTS: The CEO's Letter #24 - 2024 Impact Factor & CiteScore, MDPI Summits France & USA, Tu Youyou Award

26 June 2025
Meet Us at the 12^th Congress on Trends in Medical Mycology (TIMM-12), 19–22 September 2025, Bilbao, Spain

More News & Announcements...

Topics

Propose a Topic

Topic in Antibiotics, Antioxidants, JoF, Microbiology Research, Microorganisms

Redox in Microorganisms, 2nd Edition Topic Editors: Michal Letek, Volker Behrends
Deadline: 31 July 2025

Topic in JoF, Microbiology Research, Microorganisms, Pathogens

Pathophysiology and Clinical Management of Fungal Infections Topic Editors: Allan J. Guimarães, Marcos de Abreu Almeida
Deadline: 30 November 2025

Topic in Applied Microbiology, Fermentation, Foods, Microbiology Research, Microorganisms

Fermented Food: Health and Benefit Topic Editors: Niel Van Wyk, Alice Vilela
Deadline: 31 December 2025

Topic in Applied Microbiology, Microbiology Research, Microorganisms, IJMS, IJPB, Plants

New Challenges on Plant–Microbe Interactions Topic Editors: Wenfeng Chen, Junjie Zhang
Deadline: 31 January 2026

More Topics

Conferences

Announce Your Conference

More Conferences...

Special Issues

Propose a Special Issue

Special Issue in Microbiology Research

Antileishmanial Agents Guest Editor: Edson Roberto da Silva
Deadline: 31 August 2025

Special Issue in Microbiology Research

Probiotics, Pebiotics and Pet Health Guest Editors: Bing Han, Lihong Zhao
Deadline: 30 September 2025

Special Issue in Microbiology Research

Host–Microbe Interactions in Health and Disease Guest Editors: Josué Juárez, Pablo Mendez-Pfeiffer, Manuel Ballesteros-Monrreal
Deadline: 31 October 2025

Special Issue in Microbiology Research

Zoonotic Bacteria: Infection, Pathogenesis and Drugs—Second Edition Guest Editors: Yang Wang, Shaohui Wang
Deadline: 30 December 2025

More Special Issues

Topical Collections

Topical Collection in Microbiology Research

Microbiology and Technology of Fermented Foods Collection Editor: Salam A. Ibrahim

Topical Collection in Microbiology Research

Public Health and Quality Aspects Related to Animal Productions Collection Editors: Beniamino T. Cenci-Goga, Massimo Zerani

Topical Collection in Microbiology Research

Microorganisms and Their Incredible Potential to Face Societal Challenges Collection Editor: Mireille Fouillaud

Back to TopTop