Microbiology Research

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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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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

Abstract

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

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12 pages, 374 KiB

Open AccessArticle

Microbiological Profile and Resistance Patterns in Periprosthetic Joint Infections: A Regional Multicenter Study in Spain

by Lucia Henriquez, Ander Uribarri, Iñaki Beguiristain, Ignacio Sancho, Carmen Ezpeleta Baquedano and Maria Eugenia Portillo

Microbiol. Res. 2025, 16(7), 142; https://doi.org/10.3390/microbiolres16070142 - 1 Jul 2025

Abstract

Due to the significant number of microbiologically negative periprosthetic joint infections (PJIs), understanding the trend in etiology and resistance patterns is essential for the correct management of these infections. Currently, few studies have been published in Spain. In this study, we analyzed the [...] Read more.

Due to the significant number of microbiologically negative periprosthetic joint infections (PJIs), understanding the trend in etiology and resistance patterns is essential for the correct management of these infections. Currently, few studies have been published in Spain. In this study, we analyzed the incidence, clinical characteristics, etiology, and antibiotic resistance in patients with PJIs over the last 5 years in Navarra. In this multicentric and retrospective study, all patients diagnosed with PJIs in Navarra from 2019 to 2023 were included. Of the total 156 PJIs, 23% had negative cultures and 56% of these patients had been treated with antibiotics prior to sampling. Staphylococcus epidermidis with methicillin resistance was the predominant etiological agent, followed by Staphylococcus aureus and Cutibacterium acnes. Forty percent of the Gram-positive cocci (GPC) and 35% of the Gram-negative bacilli (GNB) were multidrug-resistant organisms (MDROs). Quinolone resistance was 46% for staphylococci and 18% for Gram-negatives. In addition, 9% of staphylococci were resistant to rifampicin. Antibiotic therapy administration prior to sampling is one of the main problems for microbiological diagnosis and is present more frequently in culture-negative PJIs (56%). New sequencing techniques could improve this difficulty. The high percentage of resistance in the microorganisms causing PJI leads us to reconsider the empirical treatment for suspected PJI, with the use of different therapeutic approaches depending on the time of infection and the possible use of new non-antibiotic therapies. Full article

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29 pages, 4367 KiB

Open AccessArticle

Endophytic Microbiome Is a Unique Repository of Bio-Foes Against Toxigenic Fungi Harming Peanut Productivity

by Nagwa I. M. Helal, Mona H. Badawi, Abeer M. El-Hadidy, Mohamed K. M. Agha, Ahmed Abou-Shady and Mohamed Fayez

Microbiol. Res. 2025, 16(7), 141; https://doi.org/10.3390/microbiolres16070141 - 1 Jul 2025

Abstract

The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture [...] Read more.

The major objective was to investigate the protective capabilities of endophytic bacterial strains isolated from a number of medicinal plant species towards Aspergillus spp. secured from the internal tissues of fungi-infected peanuts. Among 32 fungal isolates surveyed for mycotoxin production in various culture media (PDA, RBCA, YES, CA), 10 isolates qualitatively producing AFB₁, besides 10 OTA-producers, were assayed by HPLC for quantitative toxin production. Aspergillus spp. isolate Be 13 produced an extraordinary quantity of 1859.18 μg mL⁻¹ AFB₁, against the lowest toxin level of 280.40 μg mL⁻¹ produced by the fungus isolate IS 4. The estimated amounts of OTA were considerably lower and fell in the range 0.88–6.00 μg mL⁻¹; isolate Sa 1 was superior, while isolate Be 7 seemed inferior. Based on ITS gene sequencing, the highly toxigenic Aspergillus spp. isolates Be 13 and Sa 1 matched the description of A. novoparasiticus and A. ochraceus, respectively, ochraceus, respectively, which are present in GenBank with identity exceeding 99%. According to 16S rRNA gene sequencing, these antagonists labeled Ar6, Ma27 and So34 showed the typical characteristics of Pseudomonas aeruginosa, Bacillus subtilis and Bacillus velezensis, respectively, with similarity percentages of 99–100. The plant growth-promoting activity measurements of the identified endophytes indicated the production of 16.96–80.00 μg/100 mL culture medium of IAA. Phosphate-solubilizing capacity varied among endophytes from 2.50 to 21.38 μg/100 mL. The polysaccharide production pool of bacterial strains ranged between 2.74 and 6.57 mg mL⁻¹. P. aeruginosa Ar6 and B. velezensis successfully produced HCN, but B. subtilis failed. The in vitro mycotoxin biodegradation potential of tested bacterial endophytes indicated the superiority of B. velezensis in degrading both mycotoxins (AFB₁-OTA) with average percentage of 88.7; B. subtilis ranked thereafter (85.6%). The 30-day old peanut (cv. Giza 6) seedlings grown in gnotobiotic system severely injured due to infection with AFB₁/OTA-producing fungi, an effect expressed in significant reductions in shoot and root growth traits. Simultaneous treatment with the endophytic antagonists greatly diminished the harmful impact of the pathogens; B. velezensis was the pioneer, not P. aeruginosa Ar6. In conclusion, these findings proved that several endophytic bacterial species have the potential as alternative tools to chemical fungicides for protecting agricultural commodities against mycotoxin-producing fungi. Full article

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14 pages, 1872 KiB

Open AccessArticle

Insights into the Thriving of Bacillus megaterium and Rhodotorula mucilaginosa in Mining Areas: Their Adaptation and Tolerance Under Extreme Levels of Cu and Mn

by Alfonso Álvarez-Villa, Maribel Plascencia-Jatomea, Kadiya Calderón, Katiushka Arévalo-Niño, Guadalupe López-Avilés and Francisco Javier Almendariz-Tapia

Microbiol. Res. 2025, 16(7), 140; https://doi.org/10.3390/microbiolres16070140 - 1 Jul 2025

Abstract

Understanding microbial adaptation and tolerance based on the cellular concentration and biosorption capacity provides critical insights for evaluating microbial performance under heavy metal stress, which is essential for selecting efficient strains or consortia for bioremediation applications. In this study, the adaptation and tolerance [...] Read more.

Understanding microbial adaptation and tolerance based on the cellular concentration and biosorption capacity provides critical insights for evaluating microbial performance under heavy metal stress, which is essential for selecting efficient strains or consortia for bioremediation applications. In this study, the adaptation and tolerance of Bacillus megaterium and Rhodotorula mucilaginosa to elevated concentrations of copper (Cu) and manganese (Mn) were investigated by introducing the maximum adaptation concentration (MAC) alongside the maximum tolerable concentration (MTC) and the minimum inhibitory concentration (MIC). A Gaussian model was fitted to the relative growth responses to estimate the MACs, MTCs, and MICs. B. megaterium exhibited MACs of 4.6 ppm Cu and 393.9 ppm Mn, while R. mucilaginosa showed MACs of 59.6 ppm Cu and 64.4 ppm Mn, corresponding to concentrations that stimulated their maximum cell density. A biosorption analysis revealed average capacities of 6.3 ± 5.3 mg Cu/g biomass and 28.6 ± 17.2 mg Mn/g biomass, positively correlated with the MTCs, indicating enhanced metal uptake under sublethal stress. The co-culture assays demonstrated dynamic microbial interactions shaped by the type and concentration of metal, including coexistence, competitive substitution, and dominance by tolerance. These findings support the use of MACs as indicators of growth stimulation and MTCs as thresholds for enhanced metal uptake, providing a dual-parameter framework for selecting metallotolerant microorganisms for metal recovery strategies. Full article

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