Microorganisms

16 pages, 2825 KB

Open AccessArticle

From Surfaces to Spillover: Environmental Persistence and Indirect Transmission of Influenza A(H3N8) Virus

by Yifei Jin, Huan Cui, Lina Jiang, Li Li, Jing Zheng, Yidun Zhang, Heng Wang, Yanrui Li, Yan Wang, Yixin Zhao, Cheng Zhang, Zhixin Yang, Yan Zhang and Zhongyi Wang

Microorganisms 2025, 13(12), 2782; https://doi.org/10.3390/microorganisms13122782 (registering DOI) - 6 Dec 2025

Abstract

Avian influenza viruses (AIVs) pose a significant zoonotic threat, with the emerging H3N8 subtype raising increasing concern due to sporadic human infections. Current strategies for risk assessment of novel AIVs primarily rely on genetic surveillance and isolated case reports, which provide limited insight [...] Read more.

Avian influenza viruses (AIVs) pose a significant zoonotic threat, with the emerging H3N8 subtype raising increasing concern due to sporadic human infections. Current strategies for risk assessment of novel AIVs primarily rely on genetic surveillance and isolated case reports, which provide limited insight into their cross-species transmission potential. However, these approaches may overlook critical phenotypic determinants, such as pathogenicity, transmissibility, and environmental persistence, that directly influence zoonotic risk. This study investigates the evolutionary relationships, receptor-binding properties, replication dynamics, pathogenicity in mice, transmission efficiency in guinea pigs, and environmental persistence of three H3N8 strains isolated from a live poultry market. All three H3N8 strains bound exclusively to α-2,3 sialic acid receptor and achieved 100% transmissibility among guinea pigs through direct contact. Notably, the environment-origin strain A09 exhibited an indirect contact transmission efficiency of 33.3%. The findings reveal strain-specific differences, with A09 displaying enhanced pathogenicity, broader transmission routes, and greater environmental persistence compared with A05 and A01. This perspective underscores the value of integrated profiling from genotype to phenotype combined with multi-route transmission and environmental persistence analyses to delineate the adaptive roadmap of H3N8 from avian to mammalian hosts and to assess its emerging infection risk. Future directions for surveillance and intervention were also discussed, highlighting their potential to strengthen preparedness against zoonotic influenza threats. Full article

(This article belongs to the Section Environmental Microbiology)

12 pages, 323 KB

Open AccessArticle

An ICU Outbreak Due to Two Populations of Carbapenem-Resistant Klebsiella pneumoniae Isolates Belonging to ST11 and ST39 Types, Harbouring Double Carbapenemase Genes

by Olga Koutsopetra, Sophia Vourli, Georgios Stravopodis, Sophia Hatzianastasiou, Stavros Dimopoulos, Themistocles Chamogeorgakis, Despina Tassi-Papatheou, Spyros Pournaras and Joseph Papaparaskevas

Microorganisms 2025, 13(12), 2781; https://doi.org/10.3390/microorganisms13122781 (registering DOI) - 6 Dec 2025

Abstract

Carbapenem-resistant Klebsiella pneumoniae isolates harbouring double carbapenemases, from patients in a surgical and transplantation ICU, were investigated to better understand the dispersion of the pathogen. Twenty-three carbapenem-resistant K. pneumoniae isolates harbouring at least two different carbapenemases (by immunochromatography screening), were consecutively collected during [...] Read more.

Carbapenem-resistant Klebsiella pneumoniae isolates harbouring double carbapenemases, from patients in a surgical and transplantation ICU, were investigated to better understand the dispersion of the pathogen. Twenty-three carbapenem-resistant K. pneumoniae isolates harbouring at least two different carbapenemases (by immunochromatography screening), were consecutively collected during a seven-month period from patients in a surgical and transplantation ICU. Identification and susceptibility testing were performed using the MALDI-TOF Vitek MS and the Vitek2 system (BioMerieux), respectively. Whole genome sequencing (WGS) was performed in an Illumina NextSeq2000 platform and MLST and resistome analysis of assembled genomes were performed by ResFinder, through the Center for Genomic Epidemiology platform. All isolates were resistant to ertapenem, imipenem, meropenem, and most to meropenem–varbobactam. Seventeen isolates belonged to the ST11 type and were positive for the OXA-48/NDM combination (by immunochromatography and NGS). Four isolates belonged to the ST39 type and were positive for the KPC/NDM combination (by immunochromatography and NGS). Finally, two isolates belonged to the ST258 type. One of them was positive for the OXA-48/KPC/NDM combination (by immunochromatography), but only bla_KPC was detected by WGS, and the second was positive for the OXA-48/KPC combination (by immunochromatography) and confirmed by WGS. This is the first report of an outbreak in Greece due to two simultaneous carbapenem-resistant populations harbouring double carbapenemases: a larger one comprising ST11 isolates harbouring the combination bla_NDM-1/bla_OXA-48, coupled by a smaller one comprising ST39 isolates harbouring the combination bla_KPC-2/bla_NDM-1. The implications of this particular situation regarding public health as well as intra-nosocomial infection prevention and control should be further monitored and studied. Full article

(This article belongs to the Special Issue New Advancements in Clinical Microbiology: Surveillance, Diagnosis, and Treatment)

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19 pages, 5915 KB

Open AccessArticle

LuxR-Type Regulator RRP₆ Positively Regulates the Biosynthesis of Plantaricin EF and Improves Its Production in Lactiplantibacillus plantarum 163

by Yaxuan Liu, Siqi Liu, Zixian Li, Chuangen Huo, Guangli Wang, Xin Zeng, Bingyue Xin and Deyin Zhao

Microorganisms 2025, 13(12), 2780; https://doi.org/10.3390/microorganisms13122780 (registering DOI) - 6 Dec 2025

Abstract

The two-component system HPK₆/RRP₆ related to the pln locus of plantaricin biosynthesis was screened out. The overexpression of LuxR-type regulator RRP₆ promoted the transcription of ABC transporter-related genes, thereby increasing plantaricin EF yield. Its yield in 163(rrp₆ [...] Read more.

The two-component system HPK₆/RRP₆ related to the pln locus of plantaricin biosynthesis was screened out. The overexpression of LuxR-type regulator RRP₆ promoted the transcription of ABC transporter-related genes, thereby increasing plantaricin EF yield. Its yield in 163(rrp₆) reached 16.01 mg/L, which was 1.20-fold that of the original strain. The regulatory mechanism indicated that RRP₆ could bind to two sites of the plnG1 promoter, promoting its transcription and translation, accelerating the secretion of plantaricin and auto-inducing peptide, and enhancing the extracellular plantaricin yield. Amino acids Q73, R144, T171, and Y175 play a crucial role in the binding of RRP₆. Furthermore, potential regulatory compensation within the Lactiplantibacillus plantarum 163 genome may compensate for the negative effects after the deletion of rrp₆. These results provide a novel strategy for increasing plantaricin EF yield, which facilitates its large-scale application as a natural and safe food preservative in agriculture and the food industry. Full article

(This article belongs to the Special Issue Advances in Food Microbial Biotechnology)

13 pages, 3723 KB

Open AccessArticle

Chromatin Remodeler TaSWI3D Controls Wheat Susceptibility to Pathogenic Fungus Blumeria graminis forma specialis tritici

by Yixian Fu, Wanzhen Chen, Mengdi Zhang, Xiaoyu Wang and Cheng Chang

Microorganisms 2025, 13(12), 2779; https://doi.org/10.3390/microorganisms13122779 (registering DOI) - 6 Dec 2025

Abstract

Pathogenic fungus Blumeria graminisforma specialistritici (B.g. tritici) is the causal agent of the devastating wheat powdery mildew disease. Identifying the key regulators governing wheat susceptibility to the B.g. tritici pathogen is essential for developing wheat varieties with improved powdery [...] Read more.

Pathogenic fungus Blumeria graminisforma specialistritici (B.g. tritici) is the causal agent of the devastating wheat powdery mildew disease. Identifying the key regulators governing wheat susceptibility to the B.g. tritici pathogen is essential for developing wheat varieties with improved powdery mildew resistance. In this study, we demonstrated that the wheat chromatin remodeler TaSWI3D positively regulates wheat susceptibility to B.g. tritici. Overexpression of TaSWI3D gene attenuates wheat resistance against B.g. tritici, while silencing of TaSWI3D gene potentiates wheat powdery mildew resistance. TaSWI3D protein was found to be enriched at the promoter regions of the TaSARD1 gene encoding the salicylic acid (SA) biosynthesis activator, and silencing of TaSWI3D resulted in decreased nucleosome occupancy at the TaSARD1 promoter regions. Activated TaSARD1 transcription and increased SA accumulation were observed in the TaSWI3D-silenced wheat plants. Silencing of TaSARD1 and the SA biosynthesis gene TaICS1 resulted in attenuated SA biosynthesis and decreased powdery mildew resistance in the TaSWI3D-silenced wheat plants. These findings support that the chromatin remodeler TaSWI3D maintains epigenetic suppression of the SA biosynthesis activator gene TaSARD1 and negatively regulates SA biosynthesis, thereby positively contributing to wheat powdery mildew susceptibility. Full article

(This article belongs to the Special Issue Biological Control of Microbial Pathogens in Plants)

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18 pages, 1333 KB

Open AccessReview

Bacterial Adaptation to Stress Induced by Glyoxal/Methylglyoxal and Advanced Glycation End Products

by Dorota Kuczyńska-Wiśnik, Karolina Stojowska-Swędrzyńska and Ewa Laskowska

Microorganisms 2025, 13(12), 2778; https://doi.org/10.3390/microorganisms13122778 (registering DOI) - 6 Dec 2025

Abstract

Glyoxal (GO) and methylglyoxal (MGO) are highly toxic metabolic byproducts that induce carbonyl stress in bacteria and eukaryotes. Their accumulation in cells is linked to non-enzymatic glycosylation (glycation) of proteins, nucleic acids, and lipids, leading to the formation of advanced glycation end products [...] Read more.

Glyoxal (GO) and methylglyoxal (MGO) are highly toxic metabolic byproducts that induce carbonyl stress in bacteria and eukaryotes. Their accumulation in cells is linked to non-enzymatic glycosylation (glycation) of proteins, nucleic acids, and lipids, leading to the formation of advanced glycation end products (AGEs). In humans, AGEs are associated with several health problems, such as diabetes, Alzheimer’s disease, cancer, and aging. Recent studies indicate that, despite their short lifespan, bacteria are also affected by AGEs formation. In this review, we summarize the pathways and mechanisms that help bacteria cope with GO, MGO, and AGEs. We also discuss the impact of dietary AGEs on gut microbiota and the antibacterial activity of host-derived GO/MGO. Recent studies highlight three main areas for future research: the role of AGEs in dysbiosis, the regulation of protein activities by MGO/GO-dependent modifications, and the potential use of glyoxalase pathway inhibitors to combat pathogens. This last point is especially important due to the rising prevalence of multidrug-resistant strains and the failure of antibiotic therapies. Full article

(This article belongs to the Special Issue The Molecular Mechanisms Regulating Stress-Adaptive Responses in Bacteria)

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34 pages, 11345 KB

Open AccessArticle

Estradiol Modulates the Sensitivity to Vancomycin of Lactobacillus paracasei and Staphylococcus aureus Biofilms—Constituents of Human Skin and Vaginal Microbiota

by Anna M. Mosolova, Nadezhda A. Loginova, Ecaterina V. Diuvenji, Artem G. Chebotarevskii, Marina V. Sukhacheva, Sergey V. Tsibulnikov, Polina Y. Bikmulina, Vera M. Tereshina, Elena A. Ianutsevich, Olga A. Danilova, Aleksandra S. Novikova, Vladimir K. Plakunov, Sergey V. Martyanov, Alexander I. Netrusov and Andrei V. Gannesen

Microorganisms 2025, 13(12), 2777; https://doi.org/10.3390/microorganisms13122777 - 5 Dec 2025

Abstract

We investigated the effects of vancomycin, estradiol, ethanol, and their combinations on the growth of mono- and binary-species biofilms of Lactobacillus paracasei and Staphylococcus aureus. It was found that vancomycin at a subinhibitory concentration of 0.001 µg/mL, estradiol, and ethanol acted antagonistically in [...] Read more.

We investigated the effects of vancomycin, estradiol, ethanol, and their combinations on the growth of mono- and binary-species biofilms of Lactobacillus paracasei and Staphylococcus aureus. It was found that vancomycin at a subinhibitory concentration of 0.001 µg/mL, estradiol, and ethanol acted antagonistically in all cases. This effect was observed across all strains studied. Furthermore, the effects of the active compounds were evident at population, cellular and molecular levels, and were reflected in changes to the count of colony-forming units (CFUs), gene expression, and the physiological and biochemical characteristics of cells (e.g., lipid composition of membranes and the extracellular matrix). Therefore, at subinhibitory concentrations of vancomycin in the medium, estradiol can modulate the antibiotic’s effect on biofilms, thereby regulating deeply microbial communities. Full article

(This article belongs to the Special Issue Biofilm: Formation, Control, and Applications)

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16 pages, 1139 KB

Open AccessArticle

Effects of Long-Term Elevated CO₂ on Soil Aggregate Structure and Microbial Communities in a Deyeuxia angustifolia Wetland of the Sanjiang Plain

by Lanying Shi, Hongjie Cao, Rongtao Zhang, Haixiu Zhong, Yingnan Liu, Jifeng Wang, Donglai Zhang, Lin Li and Hongwei Ni

Microorganisms 2025, 13(12), 2776; https://doi.org/10.3390/microorganisms13122776 - 5 Dec 2025

Abstract

To investigate the effects of long-term elevated atmospheric CO₂ (eCO₂) on the distribution and stability of soil aggregates and microbial characteristics in wetland soils and to reveal the mechanisms by which eCO₂ influences soil organic carbon (SOC) sequestration, a [...] Read more.

To investigate the effects of long-term elevated atmospheric CO₂ (eCO₂) on the distribution and stability of soil aggregates and microbial characteristics in wetland soils and to reveal the mechanisms by which eCO₂ influences soil organic carbon (SOC) sequestration, a multi-temporal-scale eCO₂ control experiment was conducted in the Sanjiang Plain wetland with treatments at ambient CO₂ concentration (AC), 550 ppm, and 700 ppm CO₂. Soil aggregate fractionation, phospholipid fatty acid (PLFA) analysis, and redundancy analysis (RDA) were used to analyze changes in aggregate size distribution, stability indices (MWD, GMD), microbial biomass, and community structure. The results showed that eCO₂ significantly affected aggregate size distribution. Both short- and long-term exposure to low-concentration eCO₂ reduced the proportion of large aggregates. Over time, the proportion of silt and clay particles increased, while microaggregates decreased. Although CO₂ concentration did not directly affect MWD and GMD, long-term eCO₂ significantly reduced soil aggregate stability. Microbial biomass and diversity were not sensitive to CO₂ concentration but decreased significantly with prolonged exposure. In contrast, microbial community structure was significantly affected by both CO₂ level and exposure duration. RDA indicated that, under short-term eCO₂, aggregate fractions were positively correlated with microbial biomass, whereas, under medium- and long-term treatments, they were positively correlated with soil physicochemical properties. Macroaggregates were positively correlated with aggregate stability, while microaggregates and silt–clay fractions were negatively correlated—a relationship that strengthened with longer eCO₂ exposure. Thus, long-term eCO₂ altered soil aggregate structure and microbial communities, ultimately influencing SOC stability. These findings provide data and theoretical support for predicting soil carbon stability and ecosystem functioning in wetlands under climate change. Full article

(This article belongs to the Section Environmental Microbiology)

20 pages, 2171 KB

Open AccessArticle

by Lan Wang, Ciren Quzong, Sang-Gyal Skal, Chengwei Mu, Yaqin Zhao, Bo Fang, Yuan Zhang, Zhiyong Yang, Erping Hei, Xin Yuan and Tsechoe Dorji

Microorganisms 2025, 13(12), 2775; https://doi.org/10.3390/microorganisms13122775 - 5 Dec 2025

Abstract

The Beishan region near Shiquanhe Town in Ngari, western Xizang (Tibet), represents a typical alpine desert ecosystem on the Qinghai–Xizang Plateau. However, depth-related patterns of soil microbial communities and their physicochemical controls remain insufficiently understood. Here, microbial community composition and functional attributes were [...] Read more.

The Beishan region near Shiquanhe Town in Ngari, western Xizang (Tibet), represents a typical alpine desert ecosystem on the Qinghai–Xizang Plateau. However, depth-related patterns of soil microbial communities and their physicochemical controls remain insufficiently understood. Here, microbial community composition and functional attributes were examined across three soil horizons—topsoil (0–20 cm), subsoil (20–40 cm), and deep subsoil (40–60 cm)—sampled in May 2024 prior to artificial greening. High-throughput 16S rRNA and ITS sequencing combined with physicochemical analyses revealed clear vertical stratification: bacteria were dominated by Proteobacteria and Actinobacteriota, and fungi by Ascomycota. Bacterial diversity was higher in the topsoil, whereas fungal diversity exhibited a gradual increase with soil depth; however, these trends did not reach statistical significance (p > 0.05). Functional predictions indicated predominantly aerobic heterotrophic bacteria and a shift from pathogenic to saprotrophic fungi with depth. Multivariate analyses (RDA, CCA, BRT) consistently identified soil pH and moisture as fundamental habitat constraints, and organic carbon, available phosphorus, and available potassium as physicochemical drivers with nonlinear threshold responses. These results highlight soil pH, moisture, and nutrient status (N, P, K) as primary determinants of microbial community assembly and provide guidance for microbially informed ecological restoration in alpine desert ecosystems. Full article

(This article belongs to the Special Issue State-of-the-Art Environmental Microbiology in China 2025)

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14 pages, 535 KB

Open AccessArticle

Evaluation of Total Volatile Basic Nitrogen, Formaldehyde, and Formic Acid as Markers to Define the Acceptability of Farmed Sea Bass and Sea Bream Stored Under Vacuum (VP) or in Modified-Atmosphere Packaging (MAP) at 4 ± 2 °C

by Michela Pellegrini, Debbie Andyanto, Lucilla Iacumin and Giuseppe Comi

Microorganisms 2025, 13(12), 2774; https://doi.org/10.3390/microorganisms13122774 - 5 Dec 2025

Abstract

The aim of this work was to propose an objective parameter to define the acceptability of fresh sea bass and sea bream among concentrations of formaldehyde, formic acid, and TVB-N. As indicated, TVB-N appeared to be the most appropriate index. The formaldehyde value [...] Read more.

The aim of this work was to propose an objective parameter to define the acceptability of fresh sea bass and sea bream among concentrations of formaldehyde, formic acid, and TVB-N. As indicated, TVB-N appeared to be the most appropriate index. The formaldehyde value cannot be used because it increased until day 6 and then decreased because it was transformed into formic acid. The decrease was observed at all of the times tested. Nevertheless, formic acid also cannot be considered as a valid parameter because in both of the tested fish, it reached values of less than 7.2 mg/kg at 15 days of storage, even though the sensorial analysis indicated the loss of acceptability. In addition, this value is 4–7 times lower than the concentration present in other fresh fish. Consequently, TVB-N represents the only parameter of interest for defining acceptability for both fish species and it can be accepted as the freshness index. Considering the results of the microbial, physico-chemical, and sensory analysis, a level of TVB-N less or equal to 35 mg N/100 g of product was observed up to 12 days of storage. Then, at 15 days, TVB-N reached values over 40 mg N/100 g and both the fish were no longer acceptable, as demonstrated by sensory analysis. For this reason, this value can also be proposed as the limit of freshness for sea bass and sea bream, stored either in VP or in MAP at 4 ± 2 °C. Considering the microbial, physico-chemical, and sensorial analysis of both fish species, a shelf-life limit of 12 days was proposed. Full article

(This article belongs to the Section Food Microbiology)

22 pages, 3715 KB

Open AccessArticle

Integrating Statistical and Machine-Learning Approaches for Salmonella enterica Surveillance in Northwestern Italy: A One Health Data-Driven Framework

by Aitor Garcia-Vozmediano, Angelo Romano, Mattia Begovoeva, Monica Pitti, Elisabetta Crescio, Aldo Brenda, Michela Di Roberto, Anna Gioia, Adriana Giraldo, Eva Massone, Michela Nobile Lanzarini, Alessia Raggio, Erica De Vita, Giuseppe Ru and Cristiana Maurella

Microorganisms 2025, 13(12), 2773; https://doi.org/10.3390/microorganisms13122773 - 5 Dec 2025

Abstract

Salmonella enterica is a major cause of foodborne illness globally. We analysed 41,945 food samples collected under official surveillance in Piedmont (north-western Italy) between 2013 and 2023 to characterise contamination patterns and evaluate an integrated analytical framework combining classical statistical modelling with machine-learning [...] Read more.

Salmonella enterica is a major cause of foodborne illness globally. We analysed 41,945 food samples collected under official surveillance in Piedmont (north-western Italy) between 2013 and 2023 to characterise contamination patterns and evaluate an integrated analytical framework combining classical statistical modelling with machine-learning prediction. Overall prevalence was low (2.20%; 95% CI: 2.06–2.35) but heterogeneous across matrices, with poultry and pork displaying the highest contamination levels (11.8% and 7.14%). Risk increased at distribution/retail stages, and contamination declined markedly from 2013 to 2018, with lower levels in late autumn. Meteorological factors had minimal influence. Mixed-effects models identified food category and production stage as the main determinants of contamination, while the XGBoost algorithm showed stable predictive performance (median absolute error ≈ 0.02) and spatially coherent estimates. SHAP analyses confirmed food composition variables as the dominant predictors. These findings highlight persistent vulnerabilities within poultry and swine supply chains, particularly at post-production stages, and illustrate the complementary value of combining explanatory and predictive approaches to strengthen risk-based, One Health-aligned food-safety surveillance. Full article

(This article belongs to the Special Issue One Health Perspectives on the Detection and Control of Foodborne Pathogens)

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22 pages, 2670 KB

Open AccessArticle

Biochar–Urea Peroxide Composite Particles Alleviate Phenolic Acid Stress in Pogostemon cablin Through Soil Microenvironment Modification

by Yuting Tu, Baozhu Chen, Qiufang Wei, Yanggui Xu, Yiping Peng, Zhuxian Li, Jianyi Liang, Lifang Zhuo, Wenliang Zhong and Jichuan Huang

Microorganisms 2025, 13(12), 2772; https://doi.org/10.3390/microorganisms13122772 - 5 Dec 2025

Abstract

The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological [...] Read more.

The continuous-cropping obstacles of Pogostemon cablin (patchouli) is severely constrained by autotoxic phenolic acids accumulated in the rhizosphere soil. Biochar adsorption and chemical oxidation are common remediation strategies; they often fail to simultaneously and efficiently remove phenolic allelochemicals while improving the soil micro-ecological environment. To address this issue, this study developed a novel biochar–urea peroxide composite particle (BC-UP). Batch degradation experiments and electron paramagnetic resonance (EPR) analysis confirmed the synergistic adsorption-oxidation function of BC-UP. A pot experiment demonstrated that application of BC-UP (5.0 g/kg) significantly alleviated phenolic acid stress. Specifically, BC-UP application significantly enhanced shoot biomass by 28.8% and root surface area by 49.3% compared to the phenolic acid-stressed treatment and concurrently reduced the total phenolic acid content in the rhizosphere soil by 37.3%. This growth promotion was accompanied by the enhanced accumulation of key bioactive compounds (volatile oils, pogostone, and patchouli alcohol). BC-UP amendment also improved key soil physicochemical properties (e.g., pH, and organic matter) and enhanced the activities of critical enzymes. Furthermore, BC-UP reshaped the microbial community, notably reducing the fungi-to-bacteria OTU ratio by 49.7% and enriching the relative abundance of Firmicutes and Nitrospirota but suppressing the Ascomycota phylum abundance. Redundancy analysis identified soil sucrase and catalase activity, total phenolic acid content, and Ascomycota abundance as key factors influencing patchouli biomass. In conclusion, BC-UP effectively mitigates phenolic acid stress through combined adsorption and radical oxidation, subsequently improving soil properties and restructuring the rhizosphere microbiome, offering a promising soil remediation strategy for patchouli and other medicinal crops. Full article

(This article belongs to the Topic Recent Advances in Soil Health Management)

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15 pages, 634 KB

Open AccessArticle

Evaluation of Antimicrobial and Antibiofilm Activity of Eucalyptus urograndis (Clone I144) Pyroligneous Extract on Bovine Mastitis Isolate of Multiple-Drug-Resistant Staphylococcus aureus Strains

by Isadora Karoline de Melo, Caio Sergio Santos, Nilza Dutra Alves, Gustavo Lopes Araujo, Aline Maciel Clarindo, Alexandre Santos Pimenta, Denny Parente de Sá Barreto Maia Leite, Rinaldo Aparecido Mota and Francisco Marlon Carneiro Feijó

Microorganisms 2025, 13(12), 2771; https://doi.org/10.3390/microorganisms13122771 - 5 Dec 2025

Abstract

Milk is an important agricultural product and is consumed worldwide. However, the dairy sector faces a significant challenge due to bovine mastitis, a common disease that has a substantial impact on the dairy industry. In more severe cases, it leads to the culling [...] Read more.

Milk is an important agricultural product and is consumed worldwide. However, the dairy sector faces a significant challenge due to bovine mastitis, a common disease that has a substantial impact on the dairy industry. In more severe cases, it leads to the culling of chronically infected cows. Mastitis poses a risk due to the frequent use of antibiotics in treatment, which contributes to the spread of bacteria with antimicrobial resistance. The present study aimed to evaluate the antimicrobial and antibiofilm potential of a pyroligneous extract of Eucalyptus urograndis (clone I144) against multidrug-resistant Staphylococcus aureus, the causative agent of mastitis. Sensitivity profiles to various conventional antibiotics were assessed, including the minimum inhibitory concentration (MIC), the minimum bactericidal concentration (MBC), and biofilm inhibition, in ten Staphylococcus aureus strains using the crystal violet method. The results showed that the multidrug-resistant strains were sensitive to the pyroligneous extract of Eucalyptus urograndis (clone I144) at a concentration of 12.5% and exhibited antibiofilm activity starting at a concentration of 3.13%. In conclusion, our findings show that the pyroligneous extract of Eucalyptus urograndis (clone I144), at 12.5%, inhibited different multidrug-resistant S. aureus and MRSA strains isolated from bovine mastitis. These results indicate that the extract represents an effective preventive strategy against mastitis-causing pathogens that are difficult to treat, making it a promising alternative to reduce the dependence on synthetic antibiotics. In vivo studies are needed to confirm these findings and provide a basis for evidence-based clinical guidelines. Full article

(This article belongs to the Special Issue Advances in Veterinary Microbiology)

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18 pages, 2284 KB

Open AccessArticle

Inter-Row Grassing Reshapes Nitrogen Cycling in Peach Orchards by Influencing Microbial Pathways in the Rhizosphere

by Zhuo Pang, Jiale Guo, Hengkang Xu, Yufeng Li, Chao Chen, Guofang Zhang, Anxiang Lu, Xinqing Shao and Haiming Kan

Microorganisms 2025, 13(12), 2770; https://doi.org/10.3390/microorganisms13122770 - 5 Dec 2025

Abstract

Traditional clean tillage in peach orchards leads to soil degradation and nitrogen (N) loss. While inter-row grassing can optimize N cycling, the specific rhizosphere microbial mechanisms involved have not been fully understood. This study investigated how different inter-row grassing modes influence N availability [...] Read more.

Traditional clean tillage in peach orchards leads to soil degradation and nitrogen (N) loss. While inter-row grassing can optimize N cycling, the specific rhizosphere microbial mechanisms involved have not been fully understood. This study investigated how different inter-row grassing modes influence N availability through microbial communities in a peach orchard. The experiment included a monoculture of Trifolium repens L. (Tr), a monoculture of Lolium perenne L. (Pr), their mixture (TPr), and clean tillage (CK). By combining soil physicochemical analyses, metagenomic sequencing, functional gene quantification, and multivariate statistics, the study systematically examined the impacts of inter-row grassing modes on soil N cycling. The results showed that inter-row grassing modes played a significant role in reshaping N processes. Pr enhanced mineralization and nitrification, increasing inorganic N through specific genes (amoA, hao). Tr, on the other hand, promoted diazotrophs (Bradyrhizobium) and dissimilatory nitrate-reducing bacteria, enhancing biological N fixation and retention. TPr combined these benefits, leading to enhanced nitrification, increased labile carbon, and elevated enzyme activities, creating a complex microbe–gene network that mediated nitrification and denitrification. Overall, inter-row grassing modulates rhizosphere functions by enhancing N cycling through a “carbon input–microbial regulation” mechanism, offering an effective strategy for improving N use efficiency and promoting sustainable orchard management. Full article

(This article belongs to the Special Issue Advances in Agro-Microbiology)

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2 pages, 308 KB

Open AccessCorrection

Correction: Kozusnik et al. Aberrant Bodies: An Alternative Metabolic Homeostasis Allowing Survivability? Microorganisms 2024, 12, 495

by Thomas Kozusnik, Simone E. Adams and Gilbert Greub

Microorganisms 2025, 13(12), 2769; https://doi.org/10.3390/microorganisms13122769 - 5 Dec 2025

Abstract

In the original publication [...] Full article

(This article belongs to the Special Issue Intracellular Bacteria: From Basic Research to Clinics 2.0)

18 pages, 2482 KB

Open AccessArticle

An rpoB Sequence Type Network as a Framework for the Evolutionary Investigation of Clostridium perfringens

by Sun-Min Ahn, Seungeun Son, Yongwoo Son, So-Jeong Lim, Danil Kim, Kang-Seuk Choi and Hyuk-Joon Kwon

Microorganisms 2025, 13(12), 2768; https://doi.org/10.3390/microorganisms13122768 - 4 Dec 2025

Abstract

Clostridium perfringens is an opportunistic Gram-positive bacterium that causes necrotic enteritis and other severe infections in animals, as well as food poisoning in humans. In this study, we introduce a framework consisting of rpoB sequence typing (RSTing) and network analysis to investigate the [...] Read more.

Clostridium perfringens is an opportunistic Gram-positive bacterium that causes necrotic enteritis and other severe infections in animals, as well as food poisoning in humans. In this study, we introduce a framework consisting of rpoB sequence typing (RSTing) and network analysis to investigate the evolutionary trajectories of C. perfringens. By analyzing 319 rpoB sequences—300 from public databases and 19 newly sequenced isolates from chicken and cattle sources—we identified 84 rpoB sequence types (RSTs). Among them, the early emerging RST 1-1 was the most prevalent (21.3%), while the putative ancestral type, RST 0, was the fifth most common (4.7%). The high RST diversity and the predominance of RST 1-1, mainly from chickens, suggest that chickens may serve as an important reservoir. By integrating virulence gene profiling, MLST, and comparative genomics, we separated identical RSTs into distinct genotypes and uncovered genomic evidence of possible interspecies transmission between chickens and cattle, two major food-producing species. These findings indicate that RSTing provides a useful complementary approach to investigating the evolutionary and epidemiological dynamics of C. perfringens. Full article

(This article belongs to the Special Issue Epidemiology of Zoonotic Pathogens)

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19 pages, 18071 KB

Open AccessArticle

Controlled Carbon Loss: Threshold-Dependent Overflow Metabolism in Synechocystis sp. PCC 6803

by Janette T. Alford, Nathalie S. Becker, Johanna Rapp, Andreas Kulik, Janine Kaewbai-ngam, Tanakarn Monshupanee, Hannes Link and Karl Forchhammer

Microorganisms 2025, 13(12), 2767; https://doi.org/10.3390/microorganisms13122767 - 4 Dec 2025

Abstract

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as [...] Read more.

Cyanobacteria such as Synechocystis sp. PCC 6803 are promising chassis for sustainable bioproduction. During nitrogen starvation, Synechocystis redirects fixed carbon from biomass growth toward glycogen accumulation as a carbon and energy reserve. Inhibiting glycogen synthesis results in the excretion of excess carbon as organic acids, predominantly pyruvate and 2-oxoglutarate. Efficiently rerouting this carbon toward the formation of value-added products such as the plastic alternative polyhydroxybutyrate requires a deeper understanding of carbon partitioning and overflow metabolism. To investigate this, we quantified intra- and extracellular metabolites in Synechocystis wild-type and mutant strains with altered glycogen metabolism (Δpgm, ΔglgC, ΔglgA1, ΔglgA2), nitrogen signaling (ΔglnB), and carbon allocation (ΔpirC), including the double mutant ΔglgCΔpirC. Metabolites were analyzed after two days of nitrogen-replete or -depleted growth using enzymatic glycogen quantification and liquid chromatography-mass spectrometry. Excretion was primarily triggered by inhibition of glycogen synthesis but modulated by other changes in carbon flow, such as pirC deletion. Besides pyruvate and 2-oxoglutarate, small amounts of glutamate, succinate, and malate were excreted. Our findings suggest that, rather than a passive consequence of metabolite accumulation, excretion is a selective, threshold-dependent process that limits intracellular metabolite buildup, revealing an additional layer of metabolic control relevant to cyanobacterial bioengineering. Full article

(This article belongs to the Special Issue Bioproducts from Cyanobacteria and Microalgae: Current Trends and Future Perspectives)

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19 pages, 1093 KB

Open AccessReview

Cell-to-Cell and Patient-to-Patient Variability in Antimicrobial Resistance

by Xiaoyun Huang, Junjie Huang, Claire Chenwen Zhong and Martin C. S. Wong

Microorganisms 2025, 13(12), 2766; https://doi.org/10.3390/microorganisms13122766 - 4 Dec 2025

Abstract

Antimicrobial resistance (AMR) remains a global health crisis, yet treatment outcomes cannot be explained by resistance genes alone. Increasing evidence highlights the importance of variability at two levels: within bacterial populations and across patients. At the microbial level, cell-to-cell variability including genetic mutations, [...] Read more.

Antimicrobial resistance (AMR) remains a global health crisis, yet treatment outcomes cannot be explained by resistance genes alone. Increasing evidence highlights the importance of variability at two levels: within bacterial populations and across patients. At the microbial level, cell-to-cell variability including genetic mutations, stochastic gene expression, persister cell formation, heteroresistance, and spatial heterogeneity within biofilms creates phenotypic diversity that allows subsets of bacteria to survive antimicrobial stress. At the host level, patient-to-patient variability including differences in genetic background, immune competence, comorbidities, gut microbiome composition, and pharmacokinetics shapes both susceptibility to resistant infections and the likelihood of treatment success. Together, these dimensions explain why infections with the same pathogen can lead to divergent clinical outcomes. Understanding and integrating both microbial and host variability offers a path toward more precise diagnostics, personalized therapy, and novel strategies to counter AMR. Full article

(This article belongs to the Special Issue Challenges in Combating Antimicrobial Resistance in the Vulnerable Population)

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21 pages, 3213 KB

Open AccessArticle

Study on the Influence Mechanism of the Rhizosphere Soil Microbial Community and Physicochemical Factors on the Occurrence of Pepper Phytophthora Blight

by Xin Wang, Fan Yang, Ying Zhang, Miaomiao Liu, Yuting Hong, Xiaoke Chang, Hongxun Jiang, Wenrui Yang, Qiuju Yao and Baoming Tian

Microorganisms 2025, 13(12), 2765; https://doi.org/10.3390/microorganisms13122765 - 4 Dec 2025

Abstract

In order to clarify the changes and correlations among microbial community structure and soil environmental factors in the rhizosphere soil of peppers under healthy and diseased conditions, Illumina MiSeq technology was used to perform high-throughput sequencing of the V3-V4 region of the bacterial [...] Read more.

In order to clarify the changes and correlations among microbial community structure and soil environmental factors in the rhizosphere soil of peppers under healthy and diseased conditions, Illumina MiSeq technology was used to perform high-throughput sequencing of the V3-V4 region of the bacterial 16S rRNA gene and the ITS hypervariable region of fungi in the rhizosphere soil of peppers. The dominant species and key environmental factors affecting the occurrence of pepper Phytophthora blight were analyzed and screened, and the functions of bacteria and fungi in the samples were predicted by PICRUSt2 and FUNGuild. The results showed that except for soil pH, the contents of microbial biomass carbon, magnesium, zinc, and iron in the rhizosphere soil of healthy peppers were significantly higher than those in the diseased soil. Alpha diversity analysis showed that the diversity index of the bacterial community in healthy soil was higher than that in diseased soil, while the diversity index of the fungal community was significantly lower than that in diseased soil. The relative abundance of beneficial bacteria such as Proteobacteria, Actinobacteriota, Burkholderiales, and Rhodanobacteraceae in the rhizosphere soil of healthy peppers was higher. Pathogens such as Penicillium and Fusarium were significantly enriched in the rhizosphere soil of diseased pepper plants. The functional prediction results showed that soil bacteria were mainly metabolized, including the biosynthesis of ansamycin, the biosynthesis of vancomycin antibiotics, the biosynthesis of valine, leucine, and isoleucine, the metabolism of C5-branched dicarboxylic acid, and the biosynthesis of fatty acids. The main nutritional strategies of the fungal community are disease prototype and saprophytic. Combined with the key environmental factors, microbial composition, and correlation analysis of pepper rhizosphere soil, it is speculated that the occurrence of pepper Phytophthora blight may be related to the synergistic effect of soil nutrients and microbial flora, which provides a theoretical basis for the biological control of pepper Phytophthora blight in the future. Full article

(This article belongs to the Special Issue Molecular Studies of Microorganisms in Plant Growth and Utilization)

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16 pages, 661 KB

Open AccessArticle

Emergence of Multidrug-Resistant and Biofilm-Producing Staphylococcus aureus from Raw Poultry in Algeria: Implications for Public Health

by Feryal Belfihadj, Meriem Elkolli, Naouel Boussoualim, Amira Bourouba, Charefeddine Mouffok, Maryem Kraouia, Vesna Milanovic, Andrea Osimani, Lucia Aquilanti, Mohammad Raish, Byong-Hun Jeon, Hyun-Jo Ahn and Yacine Benguerba

Microorganisms 2025, 13(12), 2764; https://doi.org/10.3390/microorganisms13122764 - 4 Dec 2025

Abstract

Staphylococcus aureus is a common foodborne pathogen, posing significant concern due to the emergence of its multidrug-resistant (MDR) strains. The aim of this study was to assess the antibiotic resistance profiles in S. aureus isolated from raw poultry, the associated resistance genes, and [...] Read more.

Staphylococcus aureus is a common foodborne pathogen, posing significant concern due to the emergence of its multidrug-resistant (MDR) strains. The aim of this study was to assess the antibiotic resistance profiles in S. aureus isolated from raw poultry, the associated resistance genes, and their ability to form biofilms. S. aureus was isolated and identified using conventional microbiological methods. Antimicrobial susceptibility profiles were assessed using the disk diffusion method, and biofilm-forming ability was evaluated using the microtiter plate assay. The presence of antimicrobial resistance genes was determined by PCR. A total of 45 isolates were isolated. High resistance rates were observed against penicillin (88.9%), tetracycline (86.7%) and doxycycline (66.7%). Of the isolates, 71.1% were classified as multidrug-resistant (MDR) organisms, and 60% exhibited a multiple antibiotic resistance index greater than 0.2. PCR analysis revealed the presence of the resistance genes blaZ (86.7%), mecA (27.3%), tet(M) (46.2%), tet(K) (35.9%), tet(S) (59%), erm(B) (51.9%), and erm(C) (59.3%). A total of 44 isolates were biofilm producers: 46.7% were weak producers, 46.7% were moderate producers, and 4.4% were strong producers. These findings highlight a significant public health concern, emphasizing the need for stringent hygiene practices and continuous monitoring to limit the spread of resistant pathogens through the food chain. Full article

(This article belongs to the Section Antimicrobial Agents and Resistance)

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