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Microorganisms, Volume 13, Issue 6 (June 2025) – 244 articles

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12 pages, 820 KiB  
Article
Prevalence, Antimicrobial Resistance Profile, and Genetic Characteristics of Methicillin-Resistant Staphylococcus aureus Isolated from Retail Raw Fish in South Korea
by Haiseong Kang, Jonghoon Lee, Ji Min Han, Yong hoon Kim, Insun Joo and Hyochin Kim
Microorganisms 2025, 13(6), 1415; https://doi.org/10.3390/microorganisms13061415 - 17 Jun 2025
Abstract
Given the limited genetic characterization of methicillin-resistant Staphylococcus aureus (MRSA) in South Korea, we performed whole-genome sequencing (WGS) on eight MRSA strains isolated from raw fish products, including 327 sliced raw flatfish, 111 flatfish stew products, 85 sliced raw rockfish, and 11 rockfish [...] Read more.
Given the limited genetic characterization of methicillin-resistant Staphylococcus aureus (MRSA) in South Korea, we performed whole-genome sequencing (WGS) on eight MRSA strains isolated from raw fish products, including 327 sliced raw flatfish, 111 flatfish stew products, 85 sliced raw rockfish, and 11 rockfish stew products. Phylogenetic analysis revealed two distinct clusters—comprising five ST72-t324-SCCmecIVc strains and two novel sequence types—as well as a singleton strain (ST630-t4549-SCCmecV). A total of five antimicrobial resistance genes (ARGs), four plasmid replicon genes, three mobile genetic element genes, and seventy-three virulence factor genes were identified, with distinct genetic profiles observed between the clusters. Notably, several MRSA strains were isolated from samples obtained at the same retail market, indicating potential local clustering. Four ST72-t324-SCCmecIVc strains, collected from the same market, shared identical profiles in terms of four ARGs, two plasmid replicons, two mobile genetic elements, and several virulence factor genes. These findings provide valuable insights into the genomic characteristics of MRSA in raw fish products and highlight the need for ongoing surveillance and monitoring efforts in South Korea. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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15 pages, 3010 KiB  
Article
Effects of Years of Operation of Photovoltaic Panels on the Composition and Diversity of Soil Bacterial Communities in Rocky Desertification Areas
by Wenjiao Gao, Yungen Liu, Jun Hu, Zhifeng Luo, Jiaxu Zhang and Yan Wang
Microorganisms 2025, 13(6), 1414; https://doi.org/10.3390/microorganisms13061414 - 17 Jun 2025
Abstract
Soil bacterial community composition and diversity can be an important bioindicator for assessing ecosystem stability, and photovoltaic (PV) shading is a key factor influencing soil bacterial communities in rocky desertification areas; however, how the composition and diversity of soil bacterial communities change with [...] Read more.
Soil bacterial community composition and diversity can be an important bioindicator for assessing ecosystem stability, and photovoltaic (PV) shading is a key factor influencing soil bacterial communities in rocky desertification areas; however, how the composition and diversity of soil bacterial communities change with PV operation duration remains unclear. Focusing on the experimental demonstration site of Shilin ecological photovoltaic (PV) power plant in Yunnan Province, we compared soil properties under PV arrays and non-PV control areas with different operation durations (7 and 13 years). The results showed that long-term PV operation significantly increased soil TN and TK content compared to CK, while increasing Ure and ALP activities, but inhibiting CAT activity and decreasing soil moisture, pH, SOC, and TP. High-throughput sequencing revealed stable dominant bacterial phyla (e.g., Aspergillus, Acidobacteriota) and beneficial genera (e.g., RB41, Sphingomonas), with an increase in relative abundance of Bacillota-like phyla but a decrease in Acidobacterium. The α-diversity (ACE, Chao1 index) and β-diversity of soil bacteria greatly increased with years of PV operation, reaching a maximum in the 13-year PV operation area. Correlation analyses showed that differences in soil bacterial communities in regions with different years of PV operation were mainly influenced by differences in PH and enzyme activities. Full article
(This article belongs to the Section Environmental Microbiology)
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17 pages, 5545 KiB  
Article
A Comprehensive Investigation of Potential Bacterial Pathogens in Largemouth Bass (Micropterus salmoides)
by Yun-Yao Tu, Qun Lu, Na Zhang, Jie Leng, Qin Yang, Jie Yu, Cheng-Ke Zhu, Tao He, Jian-Yong Hu, Ming-Ji Lv and Song Zhu
Microorganisms 2025, 13(6), 1413; https://doi.org/10.3390/microorganisms13061413 - 17 Jun 2025
Abstract
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers [...] Read more.
In the study, a comprehensive investigation on potential bacterial pathogens affecting largemouth bass (Micropterus salmoides) was performed. Monthly surveys were conducted from April to October 2024. Diseased largemouth bass exhibited diverse clinical symptoms, such as rot of gill and fin, ulcers on body surface, and petechial hemorrhages in liver. Following isolation and identification, a total of 21 potential bacterial pathogens (numbered strain 1 to 21, respectively) were identified. The genus Aeromonas had the highest proportion (67.14%), among which the frequency of Aeromonas veronii was 24.60%. TEM analysis revealed that the bacterial strains exhibited three predominant shapes (rod-shaped, spherical, and curved) with length ranging from 0.5 to 3 μm. Flagellar structures were observed in strains 1–4, 6–8, 11–17, and 19–21, with variations in number and growth sites. Three isolates (strains 9, 10, 18) demonstrated Gram-positive characteristic, and strains 5, 11, and 18 have capsule structures. Strains 5, 9, 10, and 18 were non-motile, and strains 1–4, 6, 7, 9–11, 16–18, and 21 exhibited β-hemolysis. Physiological and biochemical characteristics of the 21 bacterial isolates were comprehensively analyzed. Antibiotic sensitivity testing revealed that florfenicol and enrofloxacin exhibited excellent antibacterial effects. These data will enrich the potential bacterial diseases information and promote the healthy development of the largemouth bass industry. Full article
(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment)
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20 pages, 3756 KiB  
Article
Reducing Cd Uptake by Wheat Through Rhizosphere Soil N-C Cycling and Bacterial Community Modulation by Urease-Producing Bacteria and Organo-Fe Hydroxide Coprecipitates
by Junqing Zhang, Shuangjiao Tang, Hao Wei, Lunguang Yao, Zhaojin Chen, Hui Han, Mingfei Ji and Jianjun Yang
Microorganisms 2025, 13(6), 1412; https://doi.org/10.3390/microorganisms13061412 - 17 Jun 2025
Abstract
The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms [...] Read more.
The bioavailability of heavy metals is profoundly influenced by their interactions with active soil components (microorganisms, organic matter, and iron minerals). However, the effects of urease-producing bacteria combined with organo-Fe hydroxide coprecipitates (OFCs) on Cd accumulation in wheat, as well as the mechanisms underlying these effects, remain unclear. In this study, pot experiments integrated with high-throughput sequencing were employed to investigate the impacts of the urease-producing bacterial strain TJ6, ferrihydrite (Fh), and OFCs on Cd enrichment in wheat grains, alongside the underlying soil–microbial mechanisms. The results demonstrate that the strain TJ6-Fh/OFC consortium significantly (p < 0.05) reduced (50.1–66.7%) the bioavailable Cd content in rhizosphere soil while increasing residual Cd fractions, thereby decreasing (77.4%) Cd accumulation in grains. The combined amendments elevated rhizosphere pH (7.35), iron oxide content, and electrical conductivity while reducing (14.5–21.1%) dissolved organic carbon levels. These changes enhanced soil-colloid-mediated Cd immobilization and reduced Cd mobility. Notably, the NH4+ content and NH4+/NO3 ratio were significantly (p < 0.05) increased, attributed to the ureolytic activity of TJ6, which concurrently alkalinized the soil and inhibited Cd uptake via competitive ion channel interactions. Furthermore, the relative abundance of functional bacterial taxa (Proteobacteria, Gemmatimonadota, Enterobacter, Rhodanobacter, Massilia, Nocardioides, and Arthrobacter) was markedly increased in the rhizosphere soil. These microbes exhibited enhanced abilities to produce extracellular polymeric substances, induce phosphate precipitation, facilitate biosorption, and promote nutrient (C/N) cycling, synergizing with the amendments to immobilize Cd. This study for the first time analyzed the effect and soil science mechanism of urease-producing bacteria combined with OFCs in blocking wheat’s absorption of Cd. Moreover, this study provides foundational insights and a practical framework for the remediation of Cd-contaminated wheat fields through microbial–organic–mineral collaborative strategies. Full article
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24 pages, 393 KiB  
Review
New Trends in Sexually Transmitted Infections Among Adolescents and Young People: Epidemiology, Clinical and Diagnostic Management
by Nunzia Zanotta, Nicole West, Carolina Cason, Stefania degli Ivanissevich, Alessia Meneghel, Francesco Righi, Laura Brunelli, Alessandra Casuccio, Silvia Gazzetta, Daniele Gianfrilli, Teresa Maria Assunta Fasciana, Maria Cristina Salfa, Franz Sesti, Barbara Suligoi, Francesca Valent, ESPRIT Study Collaboration Group and Manola Comar
Microorganisms 2025, 13(6), 1411; https://doi.org/10.3390/microorganisms13061411 - 17 Jun 2025
Abstract
Sexually transmitted infections (STIs) are a significant public health issue, especially among adolescents and young adults. Despite improvements in diagnostic tools and treatments, over 1 million new STIs occur daily worldwide, many of which are asymptomatic. These infections can severely affect quality of [...] Read more.
Sexually transmitted infections (STIs) are a significant public health issue, especially among adolescents and young adults. Despite improvements in diagnostic tools and treatments, over 1 million new STIs occur daily worldwide, many of which are asymptomatic. These infections can severely affect quality of life and reproductive health, particularly when contracted at a young age. This review provides an overview of STIs’ recent epidemiology data, clinical trends, and diagnostic challenges in Italian adolescents and young adults, focusing on the Chlamydia trachomatis, Neisseria gonorrhoeae, Treponema pallidum, Thricomonas vaginalis, and Mycoplasma/Ureaplasma species. Worrying new evidence indicates that young women are at a higher risk of contracting STIs than men and multidrug-resistant strains have increased in young heterosexuals. This evidence shows a general change in lifestyle, where a lack of awareness about the risks of STI reflects a significant educational gap. To address the rising STI rates, targeted school educational interventions and innovative multidisciplinary healthcare models, such as the hub-and-spoke approach, are needed. Full article
(This article belongs to the Section Medical Microbiology)
20 pages, 1053 KiB  
Review
The Interplay Between the Gut Microbiota and Colorectal Cancer: A Review of the Literature
by Marco Cintoni, Marta Palombaro, Eleonora Zoli, Giuseppe D’Agostino, Gabriele Pulcini, Elena Leonardi, Pauline Raoul, Emanuele Rinninella, Flavio De Maio, Esmeralda Capristo, Antonio Gasbarrini and Maria Cristina Mele
Microorganisms 2025, 13(6), 1410; https://doi.org/10.3390/microorganisms13061410 - 17 Jun 2025
Abstract
Lifestyle, diet, and genetics are established risk factors for developing colorectal cancer (CRC). In recent years, the role of the gut microbiota (GM) has been increasingly highlighted in several studies, suggesting an effect on both the disease’s pathogenesis and the efficacy and tolerability [...] Read more.
Lifestyle, diet, and genetics are established risk factors for developing colorectal cancer (CRC). In recent years, the role of the gut microbiota (GM) has been increasingly highlighted in several studies, suggesting an effect on both the disease’s pathogenesis and the efficacy and tolerability of treatments. We conducted a search on Medline, aiming to identify published studies exploring the role of the GM in the development and treatment of CRC. Dysbiosis, an imbalance in GM, is common in CRC patients and is associated with precancerous lesions, aggressive tumors, and varied therapy outcomes. Restoring GM balance can reduce treatment complications and may improve prognosis. The review details how GM influences CRC through metabolite production, inflammation modulation, and immune response alteration. Diet significantly impacts GM composition, with processed meats and high-fat diets increasing CRC risk, while fiber-rich diets are protective. The role of the GM in CRC treatments like surgery, chemotherapy, radiotherapy, and immunotherapy is also explored, noting its influence on complications, chemoresistance, and treatment efficacy. Future strategies involving GM modulation through diet, probiotics, and fecal microbiota transplantation (FMT) show promise for CRC prevention and treatment, warranting further research. Full article
(This article belongs to the Special Issue Gut Microbiota, Diet, and Gastrointestinal Cancer)
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18 pages, 2333 KiB  
Article
Molecular Structure and Biosynthesis of Pyoverdines Produced by Pseudomonas fulva
by Eri Ochiai, Takeru Kawabe, Masafumi Shionyu and Makoto Hasegawa
Microorganisms 2025, 13(6), 1409; https://doi.org/10.3390/microorganisms13061409 - 17 Jun 2025
Abstract
This study explored the biosynthetic mechanisms and structural diversity of pyoverdines (PVDs) produced by Pseudomonas fulva. Genomic analysis using antiSMASH identified the PVD biosynthetic gene cluster, although the C-terminal peptide sequence could not be predicted. Subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) [...] Read more.
This study explored the biosynthetic mechanisms and structural diversity of pyoverdines (PVDs) produced by Pseudomonas fulva. Genomic analysis using antiSMASH identified the PVD biosynthetic gene cluster, although the C-terminal peptide sequence could not be predicted. Subsequent liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis revealed the full peptide structure, including modified residues, such as N-acetylhydroxyornithine and cyclohydroxyornithine, and confirmed the presence of several PVD isoforms with different chromophore side chains. Comparative LC-MS analysis across Pseudomonas species demonstrated that P. fulva produces unique PVD molecular mass patterns. The bioinformatic and structural modeling of non-ribosomal peptide synthetase PvdL open reading frame 3 revealed that the A2 and A3 adenylation domains are lysine selective. Although their sequences differ from known lysine-specific signatures, AlphaFold3-based structural prediction revealed conserved substrate-binding configurations, suggesting that similar substrate-binding features may have arisen independently. Notably, Thr297, a unique residue in the non-ribosomal code, likely plays a key role in lysine recognition. The high degree of sequence similarity between the A2 and A3 domains may reflect domain duplication and could be involved in the diversification of the PVD structure. Further functional and ecological studies are required to assess the physiological significance of P. fulva PVDs in microbial iron acquisition. Full article
(This article belongs to the Section Environmental Microbiology)
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21 pages, 1894 KiB  
Article
Optimizing Cocoa Productivity Through Soil Health and Microbiome Enhancement: Insights from Organic Amendments and a Locally Derived Biofertilizer
by Jennifer E. Schmidt, Julia Flores, Luigy Barragan, Freddy Amores, Jr. and Sat Darshan S. Khalsa
Microorganisms 2025, 13(6), 1408; https://doi.org/10.3390/microorganisms13061408 - 17 Jun 2025
Abstract
Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer [...] Read more.
Despite growing interest in improving soil health on cocoa farms, applied research on the impacts of specific amendments on soil and plant outcomes is lacking. An integrated assessment of the impacts of two different organic amendments (compost and vermicompost) and a microbial biofertilizer on soil physical, chemical, and biological properties, as well as cocoa flowering, fruit set, and yield, was conducted in Guayaquil, Ecuador. Complementary culture-dependent and culture-independent methods were used to assess the impacts of amendments on microbial diversity, community composition, and specific taxa. Compost or vermicompost application affected soil chemical properties, including potassium, phosphorus, and sodium, and had small but significant effects on fungal beta diversity. Biofertilizer application slightly lowered soil pH and altered the total abundance of specific taxonomic groups including Azotobacter sp. and Trichoderma sp., with borderline significant effects on Azospirillum sp., Lactobacillus sp., Pseudomonas sp., calcium-solubilizing bacteria, and phosphorus-solubilizing bacteria. Amplicon sequencing (16S, ITS) identified 15 prokaryotic and 68 fungal taxa whose relative abundance was influenced by organic amendments or biofertilizer. Biofertilizer application increased cherelle formation by 19% and monthly harvestable pod counts by 11% despite no impact on flowering index or annual pod totals. This study highlights the tangible potential of microbiome optimization to simultaneously improve on-farm yield and achieve soil health goals on cocoa farms. Full article
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22 pages, 1052 KiB  
Review
Antimicrobial Photodynamic Therapy for Superficial, Skin, and Mucosal Fungal Infections: An Update
by Laura Beatriz Borim da Silva, Ivana Giovannetti Castilho, Fabiana Alves de Souza Silva, Mahmoud Ghannoum, Maíra Terra Garcia and Paulo Henrique Fonseca do Carmo
Microorganisms 2025, 13(6), 1406; https://doi.org/10.3390/microorganisms13061406 - 17 Jun 2025
Abstract
The global burden of fungal infections is rising at an alarming rate, with superficial, cutaneous, and mucosal mycoses among the most prevalent. Conventional treatments rely on oral and topical antifungal agents; however, these therapies are often limited by adverse effects, toxicity, frequent recurrence, [...] Read more.
The global burden of fungal infections is rising at an alarming rate, with superficial, cutaneous, and mucosal mycoses among the most prevalent. Conventional treatments rely on oral and topical antifungal agents; however, these therapies are often limited by adverse effects, toxicity, frequent recurrence, and poor patient adherence due to prolonged treatment regimens. Moreover, the emergence of antifungal resistance and multidrug-resistant species such as Candidozyma auris and Trichophyton indotineae highlights the urgent need for alternative therapeutic strategies, such as antimicrobial photodynamic therapy (aPDT). aPDT is based on photophysical and photochemical processes involving a photosensitizer (PS), a light source, and molecular oxygen. When combined, these elements generate reactive oxygen species that selectively destroy microbial cells. In this review, we explore various PSs and their effectiveness in aPDT against infections caused by dermatophytes, Candida spp., and other pathogenic fungi. Promisingly, aPDT has demonstrated antifungal activity against both susceptible and resistant strains. In addition, aPDT has been successfully used in cases of mycoses unresponsive to conventional therapies, showing favorable clinical outcomes and overall safety. Current evidence supports aPDT as a valuable strategy for the management of cutaneous, mucosal, and superficial fungal infections and as a potential strategy to combat antifungal resistance. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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16 pages, 2408 KiB  
Article
Bacteriome Signature in SARS-CoV-2-Infected Patients Correlates with Increased Gut Permeability and Systemic Inflammatory Cytokines
by Larissa S. Souza, Alexandre S. Ferreira-Junior, Pedro C. Estella, Ricardo K. Noda, Lhorena F. Sousa, Miguel T. Y. Murata, Lucas A. L. Carvalho, João L. Brisotti, Daniel G. Pinheiro, Josias Rodrigues, Carlos M. C. B. Fortaleza and Gislane L. V. de Oliveira
Microorganisms 2025, 13(6), 1407; https://doi.org/10.3390/microorganisms13061407 - 16 Jun 2025
Abstract
The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this [...] Read more.
The COVID-19 pandemic has highlighted the complex interplay between the gut microbiota and systemic immune responses, particularly through the gut–lung axis. Disruptions in gut microbial diversity and function—commonly referred to as dysbiosis—have been increasingly implicated in the pathogenesis of SARS-CoV-2 infection. In this study, we assessed the gut bacteriome and permeability in SARS-CoV-2-infected patients using 16S sequencing and ELISA assays, respectively. We also measured blood inflammatory cytokines and fecal secretory IgA to evaluate systemic and mucosal immune responses. Significant alterations in both alpha and beta diversity metrics were observed in patients with COVID-19 (n = 79) and those with post-COVID-19 condition (n = 141) compared to the controls (n = 97). Differential abundance and taxonomic analyses revealed distinct microbial profiles in the infected groups. Increased plasma levels of IL-2, IL-6, IL-17A, IFN-γ, and zonulin were detected in patient samples. Some genera were elevated during acute infection, which was positively correlated with C-reactive protein, while Enterobacteriaceae and Escherichia-Shigella were associated with increased zonulin levels, indicating compromised intestinal barrier function. These findings suggest that gut dysbiosis may contribute to bacterial translocation and systemic inflammation. Overall, our results highlight the importance of the gut–lung axis and suggest that modulating the gut microbiota could support immune regulation in SARS-CoV-2 infection. Full article
(This article belongs to the Special Issue Correlations Between the Gastrointestinal Microbiome and Diseases)
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15 pages, 1043 KiB  
Article
Clinical Characteristics and Outcomes in Multisystemic Inflammatory Syndrome in Children (MIS-C) Associated with COVID-19: A 12-Month Prospective Study
by Viorela Gabriela Nitescu, Diana-Andreea Usurelu, Teodora Olsavszky, Ana-Maria Mihalcea, Andra Postelnicu, Ruxandra Florea, Simona Stanca, Iolanda Cristina Vivisenco, Madalina Elena Petran, Maria-Dorina Craciun, Carmen-Daniela Chivu, Alexandru Ulici and Coriolan Emil Ulmeanu
Microorganisms 2025, 13(6), 1405; https://doi.org/10.3390/microorganisms13061405 - 16 Jun 2025
Abstract
Multisystemic inflammatory syndrome in children (MIS-C) is a rare but potentially severe condition that affects multiple organ systems. This study aimed to assess the clinical characteristics and outcomes of patients diagnosed with multisystemic inflammatory syndrome in children (MIS-C) associated with COVID-19. A 12-month [...] Read more.
Multisystemic inflammatory syndrome in children (MIS-C) is a rare but potentially severe condition that affects multiple organ systems. This study aimed to assess the clinical characteristics and outcomes of patients diagnosed with multisystemic inflammatory syndrome in children (MIS-C) associated with COVID-19. A 12-month prospective study was conducted at the “Grigore Alexandrescu” Clinical Emergency Hospital for Children, Bucharest. This study included children aged 0–18 years who were diagnosed with MIS-C, as defined by the World Health Organization (WHO), the Royal College of Paediatrics and Child Health (RCPCH), and the Centers for Disease Control and Prevention (CDC) criteria. Data on age, gender, clinical and laboratory findings, treatment, and outcomes were analyzed. Follow-up evaluations occurred at one, three, six, nine, and twelve months post-discharge. Among 36 patients (47.3% female, 52.7% male; mean age, 9.9 years), fever and inflammatory syndrome were present in all patients. Other common symptoms included mucocutaneous (63.8%), gastrointestinal (52.7%), cardiac (47.2%), pulmonary (38.8%), and neurological (11.1%) manifestations. At admission, 14/36 were IgM-positive, while 34/36 were IgG-positive. Follow-up revealed sequelae in two patients, including coronary aneurysms and ground-glass pulmonary opacities. Although MIS-C can be severe, most patients had favorable outcomes with proper treatment. Few long-term, organ-specific complications were observed, highlighting the importance of systematic monitoring to ensure full recovery. Full article
(This article belongs to the Special Issue Infectious Disease Surveillance in Romania)
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18 pages, 2791 KiB  
Article
Assessment of Biodegradation Mechanisms of Ceftiofur Sodium by Escherichia sp. CS-1 and Insights from Transcriptomic Analysis
by Meng-Yang Yan, Cai-Hong Zhao, Jie Wu, Adil Mohammad, Yi-Tao Li, Liang-Bo Liu, Yi-Bo Cao, Xing-Mei Deng, Jia Guo, Hui Zhang, Hong-Su He and Zhi-Hua Sun
Microorganisms 2025, 13(6), 1404; https://doi.org/10.3390/microorganisms13061404 - 16 Jun 2025
Abstract
Ceftiofur sodium (CFS) is a clinically significant cephalosporin widely used in the livestock and poultry industries. However, CFS that is not absorbed by animals is excreted in feces, entering the environment and contributing to the emergence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes [...] Read more.
Ceftiofur sodium (CFS) is a clinically significant cephalosporin widely used in the livestock and poultry industries. However, CFS that is not absorbed by animals is excreted in feces, entering the environment and contributing to the emergence of antibiotic-resistant bacteria (ARB) and antibiotic-resistant genes (ARGs). This situation poses substantial challenges to both environmental integrity and public health. Currently, research on the biodegradation of CFS is limited. In this study, we isolated a strain of Escherichia coli, designated E. coli CS-1, a Gram-negative, rod-shaped bacterium capable of utilizing CFS as its sole carbon source, from fecal samples collected from hog farms. We investigated the effects of initial CFS concentration, pH, temperature, and inoculum size on the degradation of CFS by E. coli CS-1 through a series of single-factor experiments conducted under aerobic conditions. The results indicated that E. coli CS-1 achieved the highest CFS degradation rate under the following optimal conditions: an initial CFS concentration of 50 mg/L, a pH of 7.0, a temperature of 37 °C, and an inoculum size of 6% (volume fraction). Under these conditions, E. coli CS-1 was able to completely degrade CFS within 60 h. Additionally, E. coli CS-1 exhibited significant capabilities for CFS degradation. In this study, six major degradation products of (CFS) were identified by UPLC–MS/MS: desfuroyl ceftiofur, 5-hydroxymethyl-2-furaldehyde, 7-aminodesacetoxycephalosporanic acid, 5-hydroxy-2-furoic acid, 2-furoic acid, and CEF-aldehyde. Based on these findings, two degradation pathways are proposed. Pathway I: CFS is hydrolyzed to break the sulfur–carbon (S–C) bond, generating two products. These products undergo subsequent hydrolysis and redox reactions for gradual transformation. Pathway II: The β-lactam bond of CFS is enzymatically cleaved, forming CEF-aldehyde as the primary degradation product, which is consistent with the biodegradation mechanism of most β-lactam antibiotics via β-lactam ring cleavage. Transcriptome sequencing revealed that 758 genes essential for degradation were upregulated in response to the hydrolysis and redox processes associated with CFS. Furthermore, the differentially expressed genes (DEGs) of E. coli CS-1 were functionally annotated using a combination of genomics and bioinformatics approaches. This study highlights the potential of E. coli CS-1 to degrade CFS in the environment and proposes hypotheses regarding the possible biodegradation mechanisms of CFS for future research. Full article
(This article belongs to the Special Issue Antibiotic and Resistance Gene Pollution in the Environment)
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14 pages, 2224 KiB  
Article
Comparative Analysis of Bacterial Tick-Borne Pathogens in Questing Ticks from Sambia Peninsula, Kaliningrad Oblast, Russia: Spring and Autumn Prevalence and Public Health Risks
by Alexey V. Rakov, Evgenii G. Volchev, Ketevan Petremgvdlishvili and Tatiana A. Chekanova
Microorganisms 2025, 13(6), 1403; https://doi.org/10.3390/microorganisms13061403 - 16 Jun 2025
Abstract
The Kaliningrad Oblast, located in the westernmost part of Russia and bordering European Union countries, is a popular tourist destination. However, limited research has been conducted on the bacteria found in ticks in this region. We, therefore, investigated the prevalence of certain bacteria, [...] Read more.
The Kaliningrad Oblast, located in the westernmost part of Russia and bordering European Union countries, is a popular tourist destination. However, limited research has been conducted on the bacteria found in ticks in this region. We, therefore, investigated the prevalence of certain bacteria, including Borrelia, Rickettsia, Anaplasma, and Ehrlichia, as well as the genospecies of the spotted fever group Rickettsia (SFGR) in Ixodes ricinus and Dermacentor reticulatus tick species. To accomplish this, we employed commercial qPCR for pathogen screening. We identified specific genospecies by sequencing the gltA and ompA gene fragments. In I. ricinus ticks, we found Borrelia burgdorferi sensu lato DNA in 35.6% of samples. We also found Rickettsia helvetica in 17.5% of ticks. Additionally, we detected Borrelia miyamotoi in 1.7% and Anaplasma phagocytophilum in 2.6%, while Ehrlichia chaffeensis/Ehrlichia muris were present in 0.6%. In D. reticulatus ticks, we detected only Rickettsia conorii subsp. raoultii DNA, with a prevalence of 6.1%. These findings demonstrate a substantial risk of Lyme disease and other tick-borne infections from early spring through late autumn, emphasizing the importance of ongoing monitoring for these pathogens in the region. Full article
(This article belongs to the Special Issue Ticks and Threats: Insights on Tick-Borne Diseases)
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21 pages, 4789 KiB  
Article
Zika Virus Infection Modulates Extracellular Vesicle Biogenesis and Morphology in Human Umbilical Cord Endothelial Cells: A Proteomic and Microscopic Analysis
by Manuel Adrián Velázquez-Cervantes, Arturo Flores-Pliego, Yazmín Rocío Benitez-Zeferino, Victor Javier Cruz-Holguín, Luis Herrera Moro-Huitron, Addy Cecilia Helguera-Repetto, David Eduardo Meza-Sánchez, José Luis Maravillas-Montero, Nicolás Cayetano-Castro, Javier Mancilla-Ramírez, Aurora Casarrubias-Betancourt, Guadalupe León-Reyes, Macario Martínez-Castillo, Isabel Wong-Baeza, Luis Adrián De Jesús-González, María Isabel Baeza-Ramírez and Moisés León-Juárez
Microorganisms 2025, 13(6), 1402; https://doi.org/10.3390/microorganisms13061402 - 16 Jun 2025
Abstract
Infection with Zika virus (ZIKV) is a perinatal health problem and a vertical infection that promotes neurological fetal damage. ZIKV infects different cellular components at the maternal–fetal interface, including umbilical cord endothelial cells (HUVECs). Extracellular vesicles (EVs) are cellular components that mediate extracellular [...] Read more.
Infection with Zika virus (ZIKV) is a perinatal health problem and a vertical infection that promotes neurological fetal damage. ZIKV infects different cellular components at the maternal–fetal interface, including umbilical cord endothelial cells (HUVECs). Extracellular vesicles (EVs) are cellular components that mediate extracellular communication. Viruses have the capacity to hijack and modify the biogenesis machinery of EVs for their own benefit. The present work provides proteomic results (2D electrophoresis) that show the regulation of the expression of proteins involved in autophagy, oxidative stress, and exosome biogenesis in HUVECs infected with ZIKV. We confirmed that Alix and CD9 proteins were downregulated following the infection. Additionally, EVs isolated from infected cells showed the expression of Alix, and CD9 was increased in contrast to the mock condition. Interestingly, nanoparticle tracking and cryo-microscopy assays revealed that these EVs showed an increase in the quantity and size of ZIKV infection to differences in mock conditions. Furthermore, EVs isolated from infected cells showed infectivity, and both RNA and viral proteins were detected. Finally, our cryo-microscopy analysis revealed that the viral infection promoted morphological changes in these extracellular vesicles to identify vesicles with double and triple vesicles and electrodense and double membranes. In conclusion, our data suggest that ZIKV infection can modulate cellular factors involved in the formation and morphology of EVs in HUVECs. Furthermore, these EVs carry viral elements that may contribute to the dissemination of infection. Future studies aimed at the proteomic and lipidomic composition analyses of these EVs are needed to understand the biological implications in vertical infection. Full article
(This article belongs to the Special Issue Genomics and Epidemiology of Clinical Microorganisms)
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15 pages, 1112 KiB  
Article
The Identification of Novel Mutations in ATP-Dependent Protease ClpC1 Assists in the Molecular Diagnosis of Obscured Pyrazinamide-Resistant Tuberculosis Clinical Isolates
by H. M. Adnan Hameed, Cuiting Fang, Zhiyong Liu, Yamin Gao, Shuai Wang, Xinwen Chen, Nanshan Zhong, Htin Lin Aung, Jinxing Hu and Tianyu Zhang
Microorganisms 2025, 13(6), 1401; https://doi.org/10.3390/microorganisms13061401 - 16 Jun 2025
Abstract
Pyrazinamide (PZA) is a key component of tuberculosis treatment, with drug resistance (PZAR) primarily related to pncA mutations. However, discordance between phenotypic resistance and conventional pncA-based molecular diagnostics challenges diagnostic accuracy. This study investigates discrepancies between phenotypic and genotypic resistance [...] Read more.
Pyrazinamide (PZA) is a key component of tuberculosis treatment, with drug resistance (PZAR) primarily related to pncA mutations. However, discordance between phenotypic resistance and conventional pncA-based molecular diagnostics challenges diagnostic accuracy. This study investigates discrepancies between phenotypic and genotypic resistance profiles among Mycobacterium tuberculosis (Mtb) clinical isolates. Fifty-three Mtb isolates from Guangzhou Chest Hospital were tested for PZA resistance using the BACTEC MGIT 960 system and PZase activity assay. Thirty-one phenotypically PZAR strains were genetically assessed by Sanger sequencing of PZAR-associated customary genes. Five pncA-wild-type PZAR strains were investigated through whole-genome sequencing. ClpC1P1P2 activity was evaluated by proteolytic degradation assay. Notably, 26/31 of the PZAR strains harbored mutations in pncA and/or its upstream region, aligning PZase activity and phenotypic profiles. However, five PZAR strains lacked pncA mutations. The WGS of five discordant strains revealed four novel mutations (Gly58Ser, Val63Ala, Ala567Val, and Pro796Leu) across ClpC1 domains. Incorporating clpC1 mutations improved molecular diagnostic sensitivity and accuracy from 48.3% and 69.8% (pncA alone) to 100%. This is the first report from southern China that identifies novel clpC1 mutations in wild-type pncA PZAR Mtb isolates. Our findings underscore the limitations of pncA-targeted diagnostics and support the integration of WGS and clpC1 analysis in molecular diagnostics to prevent false-negative diagnoses and improve clinical outcomes. Full article
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23 pages, 3320 KiB  
Article
Impact of c-di-AMP Accumulation, L-cysteine, and Oxygen on Catalase Activity and Oxidative Stress Resistance of Listeria monocytogenes 10403S
by Mahide Muge Yilmaz Topcam, Dimitrios P. Balagiannis and Kimon Andreas G. Karatzas
Microorganisms 2025, 13(6), 1400; https://doi.org/10.3390/microorganisms13061400 - 16 Jun 2025
Abstract
Listeria monocytogenes is a foodborne pathogen frequently exposed to oxidative stress in diverse environmental conditions. Cyclic di-AMP (c-di-AMP) is a second messenger that plays a key role in stress resistance. This study investigates the role of pdeA (degrades c-di-AMP) and how c-di-AMP accumulation [...] Read more.
Listeria monocytogenes is a foodborne pathogen frequently exposed to oxidative stress in diverse environmental conditions. Cyclic di-AMP (c-di-AMP) is a second messenger that plays a key role in stress resistance. This study investigates the role of pdeA (degrades c-di-AMP) and how c-di-AMP accumulation affects catalase activity and oxidative stress response and gene expression. Survival and catalase activity assays were conducted under oxidative stress, and c-di-AMP levels were quantified in L. monocytogenes 10403S under aerobic, anaerobic, and L-cysteine-supplemented conditions. ΔpdeA, which accumulates c-di-AMP, exhibited greater sensitivity to oxidative stress (4.6 log reduction for the wild type (WT) vs 7.34 log reduction for ΔpdeA at 10 h) and lower catalase activity than the WT in the early stationary phase. However, in the late stationary phase, while the catalase activity levels of ΔpdeA remained stable (~6.33 cm foam height), it became resistant to oxidative stress (5.85 log reduction). These findings indicate that pdeA contributes to catalase activity in L. monocytogenes. Transcriptomic analysis revealed differential expression of pathways mainly including pentose phosphate pathway, carbon metabolism, O-antigen nucleotide sugar biosynthesis and ABC transporters in ΔpdeA compared to WT. Our transcriptomic data provided promising insights into the molecular mechanisms underlying c-di-AMP regulation, which may enhance stress resistance. Moreover, oxidative stress led to increased intracellular c-di-AMP levels. Under L-cysteine supplementation, catalase activity levels in WT were similar to ΔpdeA (~1.86 cm foam height for both), but the latter showed enhanced oxidative stress resistance and c-di-AMP levels. Anaerobic conditions also elevated c-di-AMP levels in WT and ΔpdeA but resulted in greater oxidative stress sensitivity. Understanding these regulatory mechanisms provides valuable insights into oxidative stress resistance, with potential implications for food safety and pathogen control. Full article
(This article belongs to the Special Issue Exploring Foodborne Pathogens: From Molecular to Safety Perspectives)
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19 pages, 5381 KiB  
Article
Complementary Rhizosphere Microbial Strategies Drive Functional Specialization in Coastal Halophyte Succession: Differential Adaptation of Suaeda glauca and Phragmites communis to Saline–Alkali Stress
by Hao Dai, Mingyun Jia, Jianhui Xue, Zhuangzhuang Liu, Dongqin Zhou, Zhaoqi Hou, Jinping Yu and Shipeng Lu
Microorganisms 2025, 13(6), 1399; https://doi.org/10.3390/microorganisms13061399 - 16 Jun 2025
Abstract
While rhizosphere microbiome functions in saline soils are well documented, complementary microbial strategies between pioneer and late-successional halophytes remain unexplored. Here, we used 16S rRNA sequencing and FAPROTAX functional prediction to compare the rhizosphere bacterial communities of two key halophytes—Suaeda glauca and [...] Read more.
While rhizosphere microbiome functions in saline soils are well documented, complementary microbial strategies between pioneer and late-successional halophytes remain unexplored. Here, we used 16S rRNA sequencing and FAPROTAX functional prediction to compare the rhizosphere bacterial communities of two key halophytes—Suaeda glauca and Phragmites communis—in a reclaimed coastal wetland. The results demonstrate that both plants significantly restructured microbial communities through convergent enrichment of stress-tolerant taxa (Firmicutes, Pseudomonas, Bacillus, and Planococcus) while suppressing sulfur-oxidizing bacteria (Sulfurovum and Thiobacillus). However, they exhibited distinct microbial specialization: S. glauca uniquely enriched organic-matter-degrading taxa (Promicromonospora and Zhihengliuella) and upregulated aromatic compound degradation (2.29%) and ureolysis (0.86%) according to FAPROTAX analysis, facilitating carbon mobilization in early successional stages. Notably, P. communis selectively recruited nitrogen-cycling Serratia, with increased nitrate respiration (3.51% in P. communis vs. 0.91% in S. glauca) function, reflecting its higher nitrogen demand. Environmental factors also diverged: S. glauca’s microbiome correlated with potassium and sodium, whereas P. communis responded to phosphorus and chloride. These findings uncover distinct microbial recruitment strategies by halophytes to combat saline stress—S. glaucaP. communis synergy through microbial carbon-nitrogen coupling—offering a template for consortia design in saline soil restoration. Full article
(This article belongs to the Section Plant Microbe Interactions)
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22 pages, 782 KiB  
Review
From Infection to Autoimmunity: S. pyogenes as a Model Pathogen
by Virginia Girlando, Luisa De Angelis, Gianluca D’Egidio, Armando Di Ludovico and Luciana Breda
Microorganisms 2025, 13(6), 1398; https://doi.org/10.3390/microorganisms13061398 - 16 Jun 2025
Abstract
Group A β-hemolytic Streptococcus (GAS) is a Gram-positive, coccoid-shaped bacterium that tends to grow in chains; it is a non-spore-forming, facultatively anaerobic, catalase-negative, aerobic bacterium. It is known to cause a wide range of infections in children, ranging from mild upper respiratory tract [...] Read more.
Group A β-hemolytic Streptococcus (GAS) is a Gram-positive, coccoid-shaped bacterium that tends to grow in chains; it is a non-spore-forming, facultatively anaerobic, catalase-negative, aerobic bacterium. It is known to cause a wide range of infections in children, ranging from mild upper respiratory tract infections, such as pharyngitis, to severe invasive disease. GAS also notably triggers post-infectious immune sequelae, including acute poststreptococcal glomerulonephritis (APSGN), acute rheumatic fever (ARF), and rheumatic heart disease (RHD), which are major health burdens, especially in low-income countries. In this review, we will present the general characteristics of GAS, highlighting its structural and microbiological features. We will also discuss its pathogenetic mechanisms, especially molecular mimicry, and its ability to cause autoimmune responses. Finally, we will elucidate some of the autoimmune sequelae that mark GAS infections, such as ARF, RHD, APSGN, and guttate psoriasis. Understanding GAS as a model pathogen for infection-induced autoimmunity provides insight into host–pathogen interactions and supports the development of targeted interventions. Emphasis on early diagnosis and antibiotic treatment is essential to reduce the burden of autoimmune complications Full article
(This article belongs to the Special Issue Infections, Immune Mechanisms and Host-Pathogen Interactions)
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11 pages, 1698 KiB  
Article
Pseudorabies Virus IE180 Inhibits Virus Replication by Activating the Type I Interferon Pathway
by Feiyang Zheng, Jingjing Song, Xuan Chen, Dongyue Xing, Rulan Bai, Changyong Cheng, Jin Yuan and Rui Zhang
Microorganisms 2025, 13(6), 1397; https://doi.org/10.3390/microorganisms13061397 - 16 Jun 2025
Abstract
The immediate-early protein IE180 of pseudorabies virus (PRV) is a multifunctional regulator of viral and host gene expression. However, its role in modulating antiviral immune responses remains poorly understood. Here, we demonstrate that IE180 overexpression significantly inhibits PRV and H1N1 influenza virus replication [...] Read more.
The immediate-early protein IE180 of pseudorabies virus (PRV) is a multifunctional regulator of viral and host gene expression. However, its role in modulating antiviral immune responses remains poorly understood. Here, we demonstrate that IE180 overexpression significantly inhibits PRV and H1N1 influenza virus replication in Hep2 and A549 cells, respectively. Mechanistically, IE180 activates the type I interferon (IFN-I) pathway by enhancing IFN-β promoter activity and IFN transcription, leading to upregulated expression of interferon-stimulated genes (ISGs). Notably, IE180 failed to suppress PRV or H1N1 replication in Vero cells, which lack functional IFN-I signaling, confirming the dependence of its antiviral function on the IFN-I pathway. Domain mapping revealed that the ICP4-Like2 domain of IE180 is critical for IFN-β activation and antiviral activity. These findings establish IE180 as a novel viral immunomodulator that activates host innate immunity to restrict viral replication, providing insights into PRV-host interactions and potential therapeutic strategies. Full article
(This article belongs to the Section Virology)
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18 pages, 2736 KiB  
Article
Synergistic Effects of Different Endophytic Actinobacteria Combined with Organic Fertilizer on Soil Nutrients and Microbial Diversity in Camellia oleifera
by Yinghe Peng, Kunpeng Cui, Huimin Jian, Zhen Zhang, Longsheng Chen, Yanming Xu, Zhigang Li, Hongsheng Liu, Ting Xu and Rui Wang
Microorganisms 2025, 13(6), 1396; https://doi.org/10.3390/microorganisms13061396 - 15 Jun 2025
Viewed by 54
Abstract
Camellia oleifera, a prominent species of edible oil tree in China, depends on improved soil fertility for its sustainable growth. Although the application of bacterial manure has been demonstrated to enhance soil nutrient conditions, the specific contributions of endophytes within fertilizers and [...] Read more.
Camellia oleifera, a prominent species of edible oil tree in China, depends on improved soil fertility for its sustainable growth. Although the application of bacterial manure has been demonstrated to enhance soil nutrient conditions, the specific contributions of endophytes within fertilizers and their interactions with soil microbial ecosystems remain inadequately explored. This study investigates the impact of organic fertilizers combined with three endophytes (CoT10, CoH27, and CoH17) on the physicochemical properties, enzymatic activities, and microbial diversity of soils in C. oleifera plantations. Findings indicate that the integration of endophytes with organic fertilizers significantly improved soil nutrient levels (including total nitrogen, total phosphorus, and hydrolysable nitrogen), enzymatic activities (such as phosphatase, amylase, and nitrate reductase), and microbial diversity compared to the application of organic fertilizer alone. Notably, the endophyte CoT10, when applied alone with organic fertilizer, resulted in increased levels of total nitrogen, total phosphorus, and hydrolysable nitrogen in the soil, as well as a marked enhancement in the activities of soil phosphatase, amylase, and nitrate reductase. Furthermore, the combination of CoT10 with other endophytes in organic fertilizer improved the functionality of the other microorganisms and the efficiency of organic fertilizer utilization. This study underscores the synergistic effects of endophytes and organic fertilizers, providing scientific insights and practical strategies for the sustainable cultivation of C. oleifera. Full article
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16 pages, 2672 KiB  
Article
Molecular Characterization of a Transcriptional Regulator GntR for Gluconate Metabolism in Industrial 2-Ketogluconate Producer Pseudomonas plecoglossicida JUIM01
by Mengxin Qu, Lulu Li, Xinyi Zan, Fengjie Cui, Lei Sun and Wenjing Sun
Microorganisms 2025, 13(6), 1395; https://doi.org/10.3390/microorganisms13061395 - 15 Jun 2025
Viewed by 57
Abstract
The GntR is a transcriptional regulator generally known as a gluconate-operon repressor to specifically regulate the transportation and phosphorylation of gluconate. In the present study we report the cloning of the GntR-encoding gene of the industrial 2-ketogluconate (2KGA)-producer Pseudomonas plecoglossicida JUIM01, which is [...] Read more.
The GntR is a transcriptional regulator generally known as a gluconate-operon repressor to specifically regulate the transportation and phosphorylation of gluconate. In the present study we report the cloning of the GntR-encoding gene of the industrial 2-ketogluconate (2KGA)-producer Pseudomonas plecoglossicida JUIM01, which is involved in the regulation of gluconate metabolism, along with the identification of some of its target genes and its operator sequence. GntR is a 36.36-kDa cytoplasmic and hydrophobic DNA-binding transcriptional regulator belonging to the LacI family. The knockout of gntR resulted in the significant upregulation of the transcription of the gluconate kinase gene gntK and, to a lesser extent, the permease gene gntP, as well as downregulation of genes involved in glucose uptake (oprB-1, gltB, gltF, gltG, and gltK) and those involved in 2-ketogluconate (2KGA) transport (kguT) and catabolism (kguE, kguK, and kguD). These results indicated that GntR positively regulated glucose and 2KGA transport and catabolism, while negatively affecting GntP-mediated gluconate uptake and gluconate phosphorylation by GntK. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting analyses confirmed that GntR interacted with operator sequences in the divergent promoter regions of gntK and gntP, as well as in the gntR promoter region. A putative operator sequence (consensus 5′-AG-N2-AGCGCT-N-TCT-3′) was identified. These data suggest that GntR positively regulates genes involved in glucose uptake/transport and 2KGA transport/catabolism, while repressing its own expression as well as that of genes involved in gluconate transport/catabolism. These findings not only elucidate the regulation of GntR and its target genes in P. plecoglossicida, but also provide valuable insights for optimizing industrial 2KGA production. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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20 pages, 3249 KiB  
Article
A Study on the Changing Law of Bacterial Communities in the Milk of Bactrian Camels with Subclinical Mastitis
by Wanpeng Ma, Lin Zhang, Huaibing Yao, Yi Zhang, Wei Wang, Yifan Liu, Xueting Zhao and Zhanqiang Su
Microorganisms 2025, 13(6), 1394; https://doi.org/10.3390/microorganisms13061394 - 15 Jun 2025
Viewed by 149
Abstract
Subclinical mastitis is a critical disease affecting camel health and milk quality. However, research on shifts in milk bacterial communities following subclinical mastitis in camels is limited. We evaluated changes in bacterial communities following subclinical mastitis in Bactrian camels. Three portions of California [...] Read more.
Subclinical mastitis is a critical disease affecting camel health and milk quality. However, research on shifts in milk bacterial communities following subclinical mastitis in camels is limited. We evaluated changes in bacterial communities following subclinical mastitis in Bactrian camels. Three portions of California Mastitis Test (CMT)-negative milk and five portions of CMT-positive milk were collected from each Jimunai County and Keping County using the CMT, and the bacterial community composition of the camel milk was analyzed using amplicon sequencing of the v34 region of the 16S rRNA gene. Subclinical mastitis induced genus-level differences in the core bacterial microbiota of Bactrian camel milk. To our knowledge, Delftia was identified in camel milk for the first time, predominantly in Jimunai County. Bacterial abundance in camel milk from Keping County was increased and altered. Alpha diversity analysis revealed that subclinical mastitis induced lower and higher bacterial abundance in milk from Jimunai County and Keping County, respectively, compared to that of healthy camels. Therefore, these findings provide direction for future research on pathogenic microorganisms for the prevention and control of subclinical mastitis in Bactrian camels. Full article
(This article belongs to the Section Medical Microbiology)
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20 pages, 1816 KiB  
Article
Interactive Effects of Precipitation and Nitrogen on Soil Microbial Communities in a Desert Ecosystem
by Qianqian Dong, Zhanquan Ji, Hui Wang, Wan Duan, Wenli Cao, Wenshuo Li and Yangyang Jia
Microorganisms 2025, 13(6), 1393; https://doi.org/10.3390/microorganisms13061393 - 14 Jun 2025
Viewed by 33
Abstract
Increased precipitation and nitrogen (N) deposition critically influence ecological processes and stability in desert ecosystems. Studying how the soil microbial community responds to these climatic changes will improve our understanding of the impacts of climate changes on arid environments. Therefore, we conducted a [...] Read more.
Increased precipitation and nitrogen (N) deposition critically influence ecological processes and stability in desert ecosystems. Studying how the soil microbial community responds to these climatic changes will improve our understanding of the impacts of climate changes on arid environments. Therefore, we conducted a field experiment in the Gurbantunggut Desert, applying phospholipid fatty acid (PLFA) analysis to assess the responses of soil microbial community to climate change. We found that in years with normal precipitation, increased precipitation promoted soil bacterial growth, whereas in drought years, increased N deposition promoted soil bacterial growth more effectively. Although soil microbial diversity did not change significantly overall, it decreased with increasing N deposition. Random forest analysis and linear regression analysis indicated that soil pH and microbial biomass carbon (MBC) were the main drivers for the changes in soil microbial community. Structural equation modeling (SEM) further revealed that increased precipitation increased soil Gram-positive bacteria (G+) by raising soil MBC, while decreasing soil Actinomycetes (Act), fungi, and Dark Septate Endophyte (DSE). In contrast, increased N deposition affected soil microbial community by altering soil pH and MBC. Our results highlight the synergistic effects of increased precipitation and N deposition on soil microbial community structure. Further research should pay more attention to the effects of climate changes on soil microbial communities with long-term monitoring to confirm our findings across different ecosystems. Full article
(This article belongs to the Section Environmental Microbiology)
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15 pages, 2920 KiB  
Article
Grazing Intensities Regulated the Effects of Seasonal Dietary Pattern on Gut Bacterial Community Composition of Sheep
by Pengzhen Li, Zhenhao Zhang, Thomas A. Monaco, Yao Dong and Yuping Rong
Microorganisms 2025, 13(6), 1392; https://doi.org/10.3390/microorganisms13061392 - 14 Jun 2025
Viewed by 38
Abstract
Gut microbiota “enterotypes” are strongly associated with diet and host health. For grazing animals, plant species richness and nutrient content of vegetation may alter the food supply and diet composition of animals. Understanding this relationship is critical to clarify the adaption of gut [...] Read more.
Gut microbiota “enterotypes” are strongly associated with diet and host health. For grazing animals, plant species richness and nutrient content of vegetation may alter the food supply and diet composition of animals. Understanding this relationship is critical to clarify the adaption of gut microbiota to changes in vegetation quantity and quality in grassland ecosystems. Here, we studied the relationship between dietary and gut microbiota composition of sheep (lambs) over a growing season in a grassland ecosystem in northern China. Variation in vegetation composition among grazing intensities was greatest in September: and sheep preferred forbs and Rosaceae throughout the grazing period in all grazing treatments, yet their preference for Fabaceae was reduced in HG treatments in September. Grazing intensity and seasonal variations in food resource availability influenced dietary patterns, which in turn affected gut bacterial community composition. Enterotype 1, dominated by Christensenellaceae_R_7_group and Clostridia_UCG_014_unclassified, predominated during the warm season (July) for both LG and HG treatments. In contrast, Enterotype 2, dominated by Escherichia_Shigella, prevailed during the cool season (September) in HG. Diversity of Enterotype 1 exceeded (p < 0.001) that of Enterotype 2. For MG, Enterotype 1 and Enterotype 2 were evenly distributed over the grazing period. Our results highlight the importance of regulating grazing intensity to maintain the balance and health of gut microbiota according to temporal changes in plant nutrients and aboveground biomass of grassland ecosystems. Full article
(This article belongs to the Special Issue Advances in Diet–Host–Gut Microbiome Interactions)
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27 pages, 1689 KiB  
Review
Occupational Risk from Avian Influenza Viruses at Different Ecological Interfaces Between 1997 and 2019
by Maria Alessandra De Marco, Alessandra Binazzi, Paola Melis, Claudia Cotti, Michela Bonafede, Mauro Delogu, Paola Tomao and Nicoletta Vonesch
Microorganisms 2025, 13(6), 1391; https://doi.org/10.3390/microorganisms13061391 - 14 Jun 2025
Viewed by 40
Abstract
Unprotected exposures to infected poultry or wild birds, and/or to the related avian influenza virus (AIV)-contaminated environments, could account for AIV infection in workers. This study was aimed at highlighting the ecological interfaces related to domestic poultry and wild birds posing an occupational [...] Read more.
Unprotected exposures to infected poultry or wild birds, and/or to the related avian influenza virus (AIV)-contaminated environments, could account for AIV infection in workers. This study was aimed at highlighting the ecological interfaces related to domestic poultry and wild birds posing an occupational risk regarding AIV. A search of all the articles investigating the possible presence of AIV in workers attested through virological and serological techniques and published up to August 2019 was performed on PubMed and Scopus electronic databases. Ninety-four articles consisting of 11 virological, 67 serological, and 16 mixed (both virological and serological) studies were obtained. Both virological and serological evidences of AIV infection were mainly related to H5, H7, and H9 subtypes. In addition, one piece of virological evidence for H10 subtype was reported, whereas seropositivity to all hemagglutinin subtypes from H4 to H11 was detected by serological studies. The number of AIV subtype exposures inferred from serological results showed that workers from large-scale industrial poultry farms and markets were the most represented, whereas workers from small-scale and backyard poultry farms showed seropositivity to a greater number of AIV subtypes. Workers exposed to wild bird habitats tested seropositive to H5, H9, and H11. In the occupational settings, direct contact with infected poultry or wild birds could account for AIV infection in workers. This AIV spillover can result in severe health complications for the workers, also posing a potential pandemic risk to the general population. From a public health perspective, the surveillance and early detection of AIV in workplaces should be a priority faced by a one-health approach. Full article
(This article belongs to the Special Issue Ecology of Influenza A Viruses: 2nd Edition)
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16 pages, 371 KiB  
Review
The Intersection of SARS-CoV-2 and Diabetes
by Jacob H. Nichols, Amber M. Smith and Colleen B. Jonsson
Microorganisms 2025, 13(6), 1390; https://doi.org/10.3390/microorganisms13061390 - 14 Jun 2025
Viewed by 26
Abstract
The interplay between comorbidities and viral infections is a critical factor that influences disease severity and outcomes. Diabetes Mellitus (DM) is one such comorbidity that significantly elevates the risk of severe viral infection from coronaviruses, namely, SARS-CoV-2. DM is characterized by either a [...] Read more.
The interplay between comorbidities and viral infections is a critical factor that influences disease severity and outcomes. Diabetes Mellitus (DM) is one such comorbidity that significantly elevates the risk of severe viral infection from coronaviruses, namely, SARS-CoV-2. DM is characterized by either a lack of insulin production (type 1 diabetes) or insulin resistance (type 2 diabetes), both of which contribute to a state of hyperglycemia, or high blood sugar. Hyperglycemia significantly promotes chronic inflammation, metabolic dysfunction, and immune dysregulation, which put diabetics at an elevated risk of critical health outcomes. Additionally, diabetes is hypothesized to amplify viral titers during infection by promoting the expression of the viral entry receptor ACE2 and providing a favorable cellular energy environment for viral replication. This review focuses on explaining the mechanisms that link diabetics with more severe COVID-19 disease and exploring some of the mechanisms that contribute to the phenomenon where COVID-19 can promote new-onset diabetes. By highlighting the interconnections between diabetes and COVID-19, this review aims to emphasize the implications that the SARS-CoV-2 outbreak has had on metabolic health. Full article
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11 pages, 916 KiB  
Article
Fluoroquinolone Residues in Piglet Viscera and Their Impact on Intestinal Microbiota Resistance: A One Health Approach
by Olga Cardoso, Maria Manuel Donato, Sara Carolina Henriques and Fernando Ramos
Microorganisms 2025, 13(6), 1389; https://doi.org/10.3390/microorganisms13061389 - 14 Jun 2025
Viewed by 25
Abstract
The presence of fluoroquinolone (FQ) residues in food-producing animals has raised concerns regarding antimicrobial resistance. This study evaluated the occurrence of FQ residues in the liver and kidneys of piglets and their association with resistance patterns in Escherichia coli and Enterococcus species from [...] Read more.
The presence of fluoroquinolone (FQ) residues in food-producing animals has raised concerns regarding antimicrobial resistance. This study evaluated the occurrence of FQ residues in the liver and kidneys of piglets and their association with resistance patterns in Escherichia coli and Enterococcus species from piglets’ intestinal microbiota. FQ residues were found in 44% of livers and 23% of kidneys. Among 340 E. coli isolates from feces, resistance to ciprofloxacin (CIP) (43.2%) and multidrug resistance (MDR) (82.7%) were prominent. The presence of FQ in kidneys significantly increased the odds of CIP-resistant E. coli (OR = 2.94, p = 0.0013) and MDR (OR = 2.70, p = 0.0047). Enterococci (n = 130) were evenly distributed among the species E. faecalis, E. faecium, and Enterococcus spp. and presented resistance to CIP (34.6%). FQ in kidneys were associated with higher odds of CIP-resistant enterococci (OR = 3.78, p = 0.015). Interaction models revealed species-dependent responses, with Enterococcus spp. showing high resistance in the presence of FQ in kidneys (OR = 18, p = 0.006), while E. faecium exhibited lower resistance compared to E. faecalis. These findings emphasize the role of FQ residues in promoting bacterial resistance and underscore the need for the stricter regulation and routine surveillance of antimicrobial use in livestock to curb the spread of bacterial resistance to clinical drugs, and mitigate public health risks—One Health. Full article
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20 pages, 1338 KiB  
Article
Effects of Dietary Protein Levels on Production Performance, Meat Quality Traits, and Gut Microbiome of Fatting Dezhou Donkeys
by Yunpeng Wang, Keqiang Diao, Han Li, Chongyu Zhang, Guiguo Zhang and Cuihua Guo
Microorganisms 2025, 13(6), 1388; https://doi.org/10.3390/microorganisms13061388 - 14 Jun 2025
Viewed by 40
Abstract
This study aimed to investigate the effects of varying dietary protein levels on growth performance, meat quality traits, amino acid and fatty acid compositions, and hindgut microbiota in Dezhou donkeys. Eighteen 12-month-old male donkeys, weighing 188 ± 9 kg, were randomly allocated into [...] Read more.
This study aimed to investigate the effects of varying dietary protein levels on growth performance, meat quality traits, amino acid and fatty acid compositions, and hindgut microbiota in Dezhou donkeys. Eighteen 12-month-old male donkeys, weighing 188 ± 9 kg, were randomly allocated into three groups and fed diets containing 11.03% (LP), 12.52% (MP), and 14.06% (HP) protein. The average daily gain (ADG) was significantly higher (p < 0.05) in the HP and MP groups, while the feed conversion ratio (FCR) was lower (p < 0.05) compared to the LP group. The MP group exhibited superior performance in terms of serum albumin (ALB) and high-density lipoprotein (HDL) levels, as well as protein digestibility (p < 0.05). Improvements in meat tenderness, as well as increased levels of leucine, flavor amino acids (FAAs), and non-essential amino acids (NEAAs) (p < 0.05), were observed in the MP group compared to those in the LP and HP groups. The levels of total fatty acids (TFAs), saturated fatty acids (SFAs), unsaturated fatty acids (UFAs), and monounsaturated fatty acids (MUFAs) were higher (p < 0.05) in the LP and MP groups than in the HP group, with no significant differences (p > 0.05) observed between the LP and MP groups. The genera Prevotella, Clostridium_sensu_stricto_1, NK4A214_group, Oscillospiraceae_UCG-002, and Oscillospiraceae_UCG-005 in the rectum were identified as differential microbes associated with varying dietary protein levels. In conclusion, this study indicates that a dietary protein level of 12.52% could enhance the growth performance, dietary nutrient digestibility, slaughter performance, and meat quality of Dezhou donkeys by modulating hindgut microbial communities. Full article
(This article belongs to the Section Veterinary Microbiology)
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18 pages, 2880 KiB  
Article
ESBL-Producing Escherichia coli and Klebsiella pneumoniae Exhibit Divergent Paths During In-Human Evolution Towards Carbapenem Resistance
by Michelle Chioma Kalu, Akanksha Acharya, Peter Jorth and Annie Wong-Beringer
Microorganisms 2025, 13(6), 1387; https://doi.org/10.3390/microorganisms13061387 - 14 Jun 2025
Viewed by 30
Abstract
Treatment of infections caused by ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) with carbapenem antibiotics can lead to the development of carbapenem resistance over time through the acquisition of porin mutations and plasmids bearing blaKPC. However, the impact of genetic background [...] Read more.
Treatment of infections caused by ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) with carbapenem antibiotics can lead to the development of carbapenem resistance over time through the acquisition of porin mutations and plasmids bearing blaKPC. However, the impact of genetic background and the presence of CRISPR-Cas systems on the evolutionary path towards carbapenem resistance in EC and KP has yet to be investigated. The in-human evolution following repeated carbapenem treatment among ESBL-producing Escherichia coli (EC) and Klebsiella pneumoniae (KP) clinical pairs (n = 45 pairs) was examined to determine the relationship between strain genetic background (MLST, CRISPR-Cas) and the evolved genetic mutations related to resistance, virulence, and metabolism by whole genome sequencing. ST131 and ST258 were predominant among seven distinct STs in EC (70%, 19/27) and 11 STs in KP (33%, 6/18), respectively. Complete CRISPR-Cas systems were present in 22% EC (6/27) and 27.8% (5/18) KP pairs, but none in strains belonging to ST131 or ST258; partial loss of CRISPR-Cas was associated with increased carbapenem resistance. Porin, virulence, and metabolism-related genetic mutations were present on the chromosome in both the EC and KP evolved strains, but their presence was differentially associated with the CRISPR-Cas system. Future research on the role of antibiotic exposure in the species-specific resistance evolution of the Enterobacterales could guide antimicrobial stewardship efforts. Full article
(This article belongs to the Collection Feature Papers in Antimicrobial Agents and Resistance)
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15 pages, 2038 KiB  
Article
Comparison of Photofermentative Hydrogen Production in Cylindrical Photobioreactors Using Different Mixing Systems
by Raffaella Margherita Zampieri, Eleftherios Touloupakis, Cecilia Faraloni and Isabela Calegari Moia
Microorganisms 2025, 13(6), 1386; https://doi.org/10.3390/microorganisms13061386 - 14 Jun 2025
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Abstract
In this work, the ability of the photosynthetic purple non-sulfur bacterium Rhodopseudomonas sp. to produce H2 was investigated in two cylindrical photobioreactors (PBRs). The PBRs used in this work had different working volumes: 0.2 L of working volume (named 0.2-PBR) and 4.0 [...] Read more.
In this work, the ability of the photosynthetic purple non-sulfur bacterium Rhodopseudomonas sp. to produce H2 was investigated in two cylindrical photobioreactors (PBRs). The PBRs used in this work had different working volumes: 0.2 L of working volume (named 0.2-PBR) and 4.0 L of working volume (named 4.0-PBR). Two mixing methods were tested in the 4.0-PBR. The first used a rotor with four paddles, and the second a spiral rotor. Additionally, light conversion efficiency (LCE) was assessed for the three conditions tested. The culture in the 0.2-PBR produced 142.15 mL of H2 with an average H2 production rate of 0.74 mL/h, an average productivity of 3.70 mL/L/h and an LCE = 0.59%. The culture in the 4.0-PBR produced a total of 806.05 mL and 1642 mL of H2 with the paddle rotor and the spiral rotor, respectively. The average H2 production rate and LCE of the two rotors were 2.29 mL/h and LCE = 0.58% in the case of the paddle rotor and 2.87 mL/h and LCE = 0.72% in the case of the spiral rotor. The more uniform and thus more efficient mixing of the cells achieved with the spiral rotor played an important role compared to the paddle rotor, resulting in a higher LCE. This study presents a scale-up from 0.2 L to 4.0 L of the photofermentation process using the purple non-sulfur bacterium Rhodopseudomonas sp. S16-VOGS3. Full article
(This article belongs to the Section Microbial Biotechnology)
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