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Microorganisms
Volume 13
Issue 12
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Microorganisms, Volume 13, Issue 12 (December 2025) – 240 articles

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20 pages, 1394 KB  
Systematic Review
Comparative Effectiveness of Different Probiotic Delivery Methods in Oral Candidiasis: A Systematic Review
by Reihaneh Ashouritoustani, Cláudia Pinho, Ana Isabel Oliveira, Piedade Barros and Agostinho Cruz
Microorganisms 2025, 13(12), 2883; https://doi.org/10.3390/microorganisms13122883 - 18 Dec 2025
Viewed by 546
Abstract
Oral candidiasis, mainly from Candida albicans, affects immunocompromised individuals, the elderly, and denture wearers. Probiotics offer immunomodulatory and microbiota-balancing benefits as potential antifungal alternatives. However, the comparative impact of different probiotic delivery methods remains inadequately explored. This systematic review evaluated the effectiveness [...] Read more.
Oral candidiasis, mainly from Candida albicans, affects immunocompromised individuals, the elderly, and denture wearers. Probiotics offer immunomodulatory and microbiota-balancing benefits as potential antifungal alternatives. However, the comparative impact of different probiotic delivery methods remains inadequately explored. This systematic review evaluated the effectiveness of various probiotic delivery methods in reducing Candida colonization and clinical symptoms in oral candidiasis. Following PRISMA 2020 guidelines, a systematic review search across multiple databases included human clinical studies based (Medline, Web of Science, ScienceDirect, and ProQuest) on PICO criteria across all age groups. Outcomes assessed included Candida load, oral microbiota changes, symptom improvement, and disease recurrence. Of 297 articles screened, 10 met inclusion criteria. Delivery methods investigated included lozenges, capsules, yogurt, and cheese. Most studies reported reductions in Candida colony-forming units (CFUs) or prevalence, mainly for C. albicans and for non-albicans species, with probiotics such as Lactobacillus reuteri, L. rhamnosus, L. acidophilus, and Bifidobacterium strains. Some studies reported improved immunological markers, while symptom relief, especially when probiotics were combined with antifungals. Probiotics reduce Candida colonization and symptoms, with potential prolonged effects. They show promise as adjunctive therapies, but standardized, large-scale trials are needed for optimization. Full article
(This article belongs to the Section Medical Microbiology)
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15 pages, 1358 KB  
Article
Integrative Multi-Omics Analysis of the Rumen in Tan Sheep with Contrasting Average Daily Gain
by Hao Zheng, Xiaohong Han, Wenjuan Shen, Xinrui Zhang, An Shi, Tonggao Liu, Chong Yang and Jinzhong Tao
Microorganisms 2025, 13(12), 2882; https://doi.org/10.3390/microorganisms13122882 - 18 Dec 2025
Viewed by 310
Abstract
Understanding the drivers of average daily gain (ADG) is key to enhancing the productivity of Tan sheep. This study employed an integrated multi-omics approach to compare rumen microbial communities (16S rRNA sequencing) and metabolomic profiles between Tan sheep with high (HADG) and low [...] Read more.
Understanding the drivers of average daily gain (ADG) is key to enhancing the productivity of Tan sheep. This study employed an integrated multi-omics approach to compare rumen microbial communities (16S rRNA sequencing) and metabolomic profiles between Tan sheep with high (HADG) and low (LADG) ADG. The novelty of this work lies in the systems-level identification of functional linkages between specific rumen bacteria and metabolites that underlie divergent growth phenotypes. The results revealed no significant difference in initial body weight between the two groups (p > 0.05). However, the HADG group showed significantly higher final body weight (p < 0.05), markedly greater ADG and Average Daily Dry Matter Intake (ADFI) (p < 0.01), and a substantially lower FCR (p < 0.01). Plasma Total Antioxidant Capacity (T-AOC) and Superoxide Dismutase (SOD) levels were significantly elevated in the HADG group (p < 0.05), while Malondialdehyde (MDA) concentration was significantly reduced (p < 0.05). In contrast, plasma Globulin (GLB), Glucose (GLU), and Triglycerides (TG) concentrations were significantly lower in HADG sheep (p < 0.05). Rumen metabolomics identified 265 differentially abundant metabolites between groups, with 64 down-regulated and 201 up-regulated in LADG compared to HADG sheep. These metabolites were significantly enriched in tyrosine metabolism, β-alanine metabolism, and thiamine metabolism pathways. Receiver Operating Characteristic (ROC) curve analysis identified 15 key differential metabolites, including succinic acid, 2-hydroxyglutarate, and pyridoxal phosphate. 16S rRNA sequencing indicated significant differences in microbial genera such as UCG-002, Blautia, norank_f__Bacteroidales_UCG-001, and norank_f__norank_o__Rhodospirillales. Correlation analysis revealed that UCG-002 and norank_f__Bacteroidales_UCG-001 were highly negatively correlated with succinic acid (p < 0.01), and significantly negatively correlated with 1-aminocyclopropanecarboxylic acid, pyridoxal phosphate, and 2-hydroxyglutarate (p < 0.05). Conversely, beta-alanine, ureidoacrylic acid, L-proline, and 2′-deoxyguanosine showed a highly significant positive correlation with norank_f__Bacteroidales_UCG-001 (p < 0.01), and a significant positive correlation with UCG-002 (p < 0.05). These findings elucidate the molecular mechanisms behind growth differences in Tan sheep and provide actionable insights for developing targeted nutritional strategies. Full article
(This article belongs to the Section Microbiomes)
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14 pages, 2040 KB  
Article
Glucose-Lowering Effects and Safety of Bifidobacterium longum CKD1 in Diabetic Dogs and Cats
by Yukyung Choi, Ji-Eun Kim, Kyung Hwan Kim, Sunghee Lee and Chang Hun Shin
Microorganisms 2025, 13(12), 2881; https://doi.org/10.3390/microorganisms13122881 - 18 Dec 2025
Viewed by 290
Abstract
Diabetes mellitus is a common endocrine disorder in dogs and cats, and achieving stabilization with insulin alone can be challenging. This study evaluated the glucose-lowering efficacy and safety of Bifidobacterium longum CKD1 in diabetic companion animals. Nine dogs and 13 cats received B. [...] Read more.
Diabetes mellitus is a common endocrine disorder in dogs and cats, and achieving stabilization with insulin alone can be challenging. This study evaluated the glucose-lowering efficacy and safety of Bifidobacterium longum CKD1 in diabetic companion animals. Nine dogs and 13 cats received B. longum CKD1 daily for 12 weeks. Fasting blood glucose (FBG) levels decreased by 26.2% in dogs and 18.0% in cats. Remarkable improvement in FBG was observed in dogs and cats with baseline levels exceeding 200 mg/dL in dogs and 250 mg/dL in cats. Notably, dogs exhibited a significant 61.8% reduction (p < 0.05), while cats showed a 38.4% decrease. Insulin-treated cats required significantly lower insulin doses by Week 12 (p < 0.05). Continuous glucose monitoring in cats demonstrated a 21.6% reduction in mean glucose levels and a significant 32.3% decrease in the time spent with glucose levels above 181 mg/dL (p < 0.05). Microbiota analysis revealed an increase in beneficial commensals and short-chain fatty acid producers, along with a reduction in pathobionts. No treatment-related adverse effects were observed. These findings indicate that B. longum CKD1 improves glycemic control and safely modulates the gut microbiota, supporting its potential use in managing diabetes mellitus in companion animals. Full article
(This article belongs to the Special Issue Probiotics, Prebiotics and Pet Health)
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23 pages, 370 KB  
Review
Mechanisms and Applications of Gastrointestinal Microbiota–Metabolite Interactions in Ruminants: A Review
by Urga, Xingdong Wang, Huimin Wei and Gerelt Zhao
Microorganisms 2025, 13(12), 2880; https://doi.org/10.3390/microorganisms13122880 - 18 Dec 2025
Viewed by 557
Abstract
The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing [...] Read more.
The gastrointestinal microbiota of ruminants constitutes a complex invisible organ, which converts plant fibers into volatile fatty acids (VFAs) and microbial protein through fermentation, serving as the primary energy and protein sources for the host. While substantial progress has been made in characterizing this system, critical gaps remain in understanding causal mechanisms and translating knowledge into scalable interventions. This review systematically synthesizes current knowledge on the composition, function, and metabolite profiles of gastrointestinal microbial communities in ruminants, with emphasis on interaction mechanisms, methodological advances, and intervention strategies. We highlight persistent challenges, including the uncultured majority of microbes, causal inference limitations, and translational bottlenecks. The review further evaluates strategies for targeted microbiome modulation aimed at improving production performance and reducing environmental emissions. Finally, we propose integrated research priorities for developing efficient, low-carbon, and sustainable ruminant production systems. Full article
(This article belongs to the Special Issue Rumen Microorganisms)
23 pages, 8038 KB  
Article
Transcriptomic Profiling of mRNA and lncRNA During the Developmental Transition from Spores to Mycelia in Penicillium digitatum
by Ting Zhou, Yajie Yang, Fei Wang, Linqian Liang, Ziqi Zhang, Heru Dong, Zhaocheng Jiang, Pengcheng Zhang and Tongfei Lai
Microorganisms 2025, 13(12), 2879; https://doi.org/10.3390/microorganisms13122879 - 18 Dec 2025
Viewed by 360
Abstract
The fungus Penicillium digitatum causes citrus green mold, a major postharvest disease. Understanding the molecular mechanisms underlying its development is crucial for devising effective control strategies. In this study, we performed a comprehensive transcriptomic analysis of P. digitatum across three key developmental stages: [...] Read more.
The fungus Penicillium digitatum causes citrus green mold, a major postharvest disease. Understanding the molecular mechanisms underlying its development is crucial for devising effective control strategies. In this study, we performed a comprehensive transcriptomic analysis of P. digitatum across three key developmental stages: spores, germinated spores, and mycelia. A total of 2175 novel mRNAs, 3957 novel long non-coding RNAs (lncRNAs), and 144 circular RNAs (circRNAs) were identified in P. digitatum. Genetic variation analysis revealed 12,396 Insertion-Ddeletion and 23,264 single nucleotide polymorphisms, with their prevalence decreasing as development progressed. The expression levels, temporal expression patterns and significant differences in mRNAs and lncRNAs across different developmental stages were also observed. Functional enrichment analysis of differentially expressed mRNAs and differentially expressed lncRNA target genes highlighted key biological processes and pathways associated with macromolecular metabolism, signal transduction, DNA replication, and reactive oxygen species scavenging. Additionally, differential expression analysis explored the potential interactions between differentially expressed lncRNAs and their target genes, as well as those between lncRNAs and circRNAs. Our findings provide valuable insights into the complex regulatory networks underpinning the development and pathogenicity of P. digitatum, offering a foundation for future research aimed at controlling green mold. Full article
(This article belongs to the Special Issue Exploring Foodborne Pathogens: From Molecular to Safety Perspectives)
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13 pages, 1266 KB  
Article
Portable Lab for Shipping (POLS): A Biosensor-Based System for Rapid Onboard Detection of Escherichia coli and Enterococcus spp. in Ballast Water
by Stephanie Agioti, Emmanouil Loulakis, Lazaros Konstantinou, Eleni Varda, Antonios Inglezakis, Konstantinos Loizou, Theofylaktos Apostolou and Agni Hadjilouka
Microorganisms 2025, 13(12), 2878; https://doi.org/10.3390/microorganisms13122878 - 18 Dec 2025
Viewed by 273
Abstract
Ballast water (BW) is a major pathway for the spread of invasive microorganisms and pathogens, posing significant ecological and public health risks. The International Maritime Organization (IMO) has established strict discharge standards, yet routine monitoring remains limited, and no reliable onboard test is [...] Read more.
Ballast water (BW) is a major pathway for the spread of invasive microorganisms and pathogens, posing significant ecological and public health risks. The International Maritime Organization (IMO) has established strict discharge standards, yet routine monitoring remains limited, and no reliable onboard test is currently available to assist crews in verifying BW quality before discharge. This study presents the development of a rapid, portable method for onboard microbiological assessment of BW, based on potentiometric detection and biosensors engineered with the Bioelectric Recognition Assay (BERA). Two complementary approaches were evaluated: (i) direct potentiometric measurements of contaminated and non-contaminated samples, which confirmed the feasibility of detecting microbial presence but were restricted by high detection limits, and (ii) development of biosensors specifically engineered for Escherichia coli and Enterococcus spp. to improve specificity and lower the limit of detection (LOD). Results demonstrated successful detection of both microorganisms, with performance characteristics of 83.3% sensitivity and 81.9% accuracy for Enterococcus spp. (LOD: 102 CFU 100 mL−1), and 89.8% sensitivity and 85.1% accuracy for Escherichia coli (LOD: 250 CFU 100 mL−1). These findings underscore the potential of biosensor-based systems as practical, crew-operated tools for early warning and real-time monitoring of ballast water quality, supporting compliance with IMO standards and contributing to safer, more sustainable maritime operations. Full article
(This article belongs to the Special Issue Marine Microbiology: Pollution, Bioremediation and Resource Utilization)
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17 pages, 4105 KB  
Article
Fungal Community Responses to Natural Humus Amendment Potentially Facilitate the Enhancement of Saline–Alkali Soil Multifunctionality
by Xiaoting Sun, Jing Lei, Hang Chu, Yimin Liu, Fei Liu, Yang Li, Xuejia Zheng, Hui Zhang, Hui Pan, Congzhi Zhang and Qicong Wu
Microorganisms 2025, 13(12), 2877; https://doi.org/10.3390/microorganisms13122877 - 18 Dec 2025
Viewed by 404
Abstract
Natural humus, characterized by its high organic carbon content and high degree of humification, is widely used in soil improvement. However, the impact of natural humus on the multifunctionality of saline–alkali soils and its relationship with soil microbial diversity remain poorly understood. This [...] Read more.
Natural humus, characterized by its high organic carbon content and high degree of humification, is widely used in soil improvement. However, the impact of natural humus on the multifunctionality of saline–alkali soils and its relationship with soil microbial diversity remain poorly understood. This study conducted experiments with varying concentrations of natural humus to explore changes in soil multifunctionality and its driving factors. The results indicate that the addition of natural humus increases soil organic matter (by 23.5–45.73%) and alkali-hydrolyzable nitrogen (by 40–81.57%), while reducing electrical conductivity (by 1.8–35.9%). These changes enhance soil microbial diversity and improve soil multifunctionality. As natural humus is a high C/N material, nitrogen limitation in soil microorganisms may occur with increasing humus addition. However, the increase in K-strategy fungi (which are more efficient in resource utilization) helps maintain a relatively high level of soil multifunctionality. At the maximum application rate (30 t/ha), soil multifunctionality reached its peak value of 0.41. These findings highlight the significant role of natural humus in improving saline–alkali soils and enhancing soil functions, particularly through its effects on microbial communities, especially K-strategy fungi. Full article
(This article belongs to the Special Issue Microbial Mechanisms for Soil Improvement and Plant Growth)
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21 pages, 6874 KB  
Article
Responses of Soil Microbial Communities and Anthracnose Dynamics to Different Planting Patterns in Dalbergia odorifera
by Long Xu, Kexu Long, Yichi Zhang, Guoying Zhou and Junang Liu
Microorganisms 2025, 13(12), 2876; https://doi.org/10.3390/microorganisms13122876 - 18 Dec 2025
Viewed by 238
Abstract
Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera [...] Read more.
Anthracnose is one of the major diseases affecting Dalbergia odorifera T. Chen. However, the soil microbial mechanisms underlying D. odorifera responses to anthracnose remain largely unexplored. This study investigated three planting systems: a Dalbergia odorifera monoculture (J); a mixed plantation of D. odorifera and Pterocarpus macrocarpus (JD); and a composite mixed plantation of D. odorifera, P. macrocarpus, and Clinacanthus nutans (JDY). Using amplicon sequencing technology for soil microbial analysis and combining soil physical and chemical properties with disease severity, we comprehensively analyzed changes in soil microbial community structure and function across different planting modes. The results showed that the diverse mixed mode (JD, JDY) significantly improved soil physicochemical properties and promoted soil nutrient cycling. Redundancy analysis (RDA) indicated that soil organic matter (SOM) and disease severity, quantified by the area under the disease progress curve (AUDPC), were the primary environmental drivers of microbial community variation. Genera positively correlated with SOM and negatively correlated with AUDPC were significantly enriched in JDY and JD, whereas genera showing opposite relationships were predominantly enriched in J. Functional predictions revealed enhanced nutrient-cycling capacities in JD and JDY, with JDY uniquely harboring functional groups such as Arbuscular Mycorrhizal, Epiphyte, and Lichenized taxa. In contrast, microbial functions in the J plantation were mainly limited to environmental amelioration. Co-occurrence network analysis further showed that as planting patterns shifted from J to JDY, microbial communities evolved from competition-dominated networks to cooperative defensive networks, integrating efficient decomposition with strong pathogen suppression potential. The study demonstrates that complex mixed planting systems regulate soil properties, enhance the enrichment of key functional microbial taxa, reshape community structure and function, and ultimately enable ecological control of anthracnose disease. This study provides new perspectives and theoretical foundations for ecological disease management in plantations of rare tree species and for microbiome-based ecological immunization strategies. Full article
(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)
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15 pages, 1047 KB  
Article
Disruption of the Nitric Oxide Reductase Operon via norD Deletion Does Not Affect Brucella abortus 2308W Virulence
by Faisal Rasheed, Amaia Zúñiga-Ripa, Miriam Salvador-Bescós, Hamid Irshad, Raquel Peña-Villafruela, Pilar M. Muñoz, María Jesús de Miguel, Qurban Ali, Raquel Conde-Álvarez and Saeed-ul-Hassan Khan
Microorganisms 2025, 13(12), 2875; https://doi.org/10.3390/microorganisms13122875 - 18 Dec 2025
Viewed by 245
Abstract
Brucella are intracellular pathogens that use flexible respiratory strategies to adapt to oxygen-limited conditions. The nor operon encodes components of nitric oxide reductase (Nor), which are involved in denitrification and nitric oxide (NO) detoxification. In this study, the role of the norD gene [...] Read more.
Brucella are intracellular pathogens that use flexible respiratory strategies to adapt to oxygen-limited conditions. The nor operon encodes components of nitric oxide reductase (Nor), which are involved in denitrification and nitric oxide (NO) detoxification. In this study, the role of the norD gene in nitrate-dependent respiration, resistance to nitrosative stress, and intracellular persistence in B. abortus was evaluated. A non-polar ΔnorD mutant was generated in strain 2308W and its survival and growth under aerobic and anaerobic conditions, with and without nitrate, as well as its tolerance to NO donors, were analyzed. In addition, its behavior was evaluated in activated and non-activated murine RAW264.7 and human THP-1 macrophages and in a murine infection model. The deletion of norD did not affect viability or growth under any of the conditions tested, nor did it alter resistance to NO in vitro or within activated macrophages. Furthermore, the mutant showed virulence comparable to the wild-type strain in BALB/c mice. These results contrast with those described for other Brucella species, suggesting that norD is dispensable in B. abortus 2308W virulence and that in the Brucella genus, there are species-specific differences in the role of the nor operon during infection. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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18 pages, 18264 KB  
Article
Isolation of Monascus purpureus HC-5 and Optimization of Solid-State Fermentation for High-Yield Pigment Production
by Wenli Quan, Shuanglian Chen, Han Li, Zhen Tang, Mohammad Nur Alam and Xun Liu
Microorganisms 2025, 13(12), 2874; https://doi.org/10.3390/microorganisms13122874 - 18 Dec 2025
Viewed by 294
Abstract
Monascus pigments (MPs) are valuable natural colorants, but their industrial production is often hampered by scarce high-yield strains and inefficient processes. In this study, a novel MPs-producing strain was isolated from red yeast rice and named as Monascus purpureus HC-5. This strain exhibited [...] Read more.
Monascus pigments (MPs) are valuable natural colorants, but their industrial production is often hampered by scarce high-yield strains and inefficient processes. In this study, a novel MPs-producing strain was isolated from red yeast rice and named as Monascus purpureus HC-5. This strain exhibited notable hydrolase activities, indicating a high efficiency in substrate utilization. In addition, using rice as the optimal substrate, the key parameters of solid-state fermentation were optimized. Response surface analysis revealed that soaking time and temperature were the most critical influencing factors. The optimal combination conditions were an inoculum size of 8.91%, a soaking time of 13.59 h, and a temperature of 32 °C. Under these optimized conditions, the MPs yield reached 2185 ± 255.7 U/g, which displayed an approximately four-fold increase compared to the initial unoptimized process. Briefly, this study identified a strain of Monascus purpureus and optimized its solid-state fermentation conditions, which significantly increased the yield of MPs. This provides an important theoretical basis and scientific evidence for the large-scale industrial production of MPs. Full article
(This article belongs to the Section Microbial Biotechnology)
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3 pages, 595 KB  
Editorial
Editorial for Special Issue “Phytopathogens: Detection and Control”
by Miłosz Tkaczyk
Microorganisms 2025, 13(12), 2873; https://doi.org/10.3390/microorganisms13122873 - 18 Dec 2025
Viewed by 302
Abstract
Plant diseases caused by a wide range of pathogens—including fungi, bacteria, viruses, and fungus-like organisms (oomycetes)—represent one of the most significant threats to global food security, agricultural sustainability, and ecosystem balance [...] Full article
(This article belongs to the Special Issue Phytopathogens: Detection and Control)
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1 pages, 137 KB  
Correction
Correction: Chen et al. Purpureocillium jiangxiense sp. nov.: Entomopathogenic Effects on Ostrinia furnacalis and Galleria mellonella. Microorganisms 2024, 12, 1041
by Wei Chen, Yanhong Tang, Tongyi Liu, Hongwang Hu, Cuiyi Ou, Qiongbo Hu and Qunfang Weng
Microorganisms 2025, 13(12), 2872; https://doi.org/10.3390/microorganisms13122872 - 18 Dec 2025
Viewed by 137
Abstract
There was an error in the original publication [...] Full article
(This article belongs to the Section Environmental Microbiology)
20 pages, 3749 KB  
Article
Mining of Novkitasetaline, a New Sulfur-Containing Antimalarial β-Carboline Alkaloid, from Streptomyces sp. PRh3 by Functional Ribosome Engineering Directed Heterologous Expression
by Xingyu Chen, Xiaohui He, Yanmin Wang, Yangping Feng, Zihan Wang, Chunhui Song, Xinyu Yu and Yunchang Xie
Microorganisms 2025, 13(12), 2871; https://doi.org/10.3390/microorganisms13122871 - 18 Dec 2025
Viewed by 450
Abstract
The endophytic Streptomyces sp. PRh3 (PRh3), isolated from Dongxiang wild rice (DXWR), exhibited impaired biosynthetic capacity in the laboratory. To address this defect, rifampicin-based ribosome engineering was first applied to PRh3 to generate PRh3-r55, which acquired a characteristic H473Y rifampicin-resistant mutation in rpoB [...] Read more.
The endophytic Streptomyces sp. PRh3 (PRh3), isolated from Dongxiang wild rice (DXWR), exhibited impaired biosynthetic capacity in the laboratory. To address this defect, rifampicin-based ribosome engineering was first applied to PRh3 to generate PRh3-r55, which acquired a characteristic H473Y rifampicin-resistant mutation in rpoB to activate the production of two β-carboline alkaloids JBIR-133 and JBIR-134. Then the biosynthetic gene cluster (BGC) ksl was introduced into PRh3-r55 for heterologous expression, generating PRh3-r55K. This combined approach achieved a synergistic effect, enabling the strain to produce not only the expected JBIR-133, JBIR-134, and kitasetaline, but also a novel sulfur-containing molecule, novkitasetaline. Structural elucidation identified novkitasetaline as a unique tryptamine-substituted kitasetaline derivative at the C-3 position of its pyridine ring. Notably, this structural modification conferred significant antimalarial activity to novkitasetaline, rendering it active against drug-sensitive Plasmodium falciparum 3D7 (IC50 = 32.65 ± 2.93 μM) and three other drug-resistant P. falciparum strains: K13C580Y, Dd2, and HB3 (IC50 = 45.98 ± 4.17~59.67 ± 3.15 μM), primarily by disrupting late-stage parasite development. These efforts not only identified a promising antimalarial lead compound but also demonstrated that combining ribosome engineering with heterologous expression is an effective strategy for discovering bioactive natural products from Streptomyces. Full article
(This article belongs to the Special Issue Microbial Biotechnological Application for Metabolite Bioprocesses)
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13 pages, 1635 KB  
Article
Soil Microbial Life History Strategies Drive Microbial Carbon Use Efficiency Following Afforestation
by Hongyan Cheng, Haoyuan Chong, Minshu Yuan, Chengjie Ren, Jun Wang and Fazhu Zhao
Microorganisms 2025, 13(12), 2870; https://doi.org/10.3390/microorganisms13122870 - 17 Dec 2025
Viewed by 359
Abstract
Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation [...] Read more.
Soil microbial carbon use efficiency (CUE) is the core of the soil carbon (C) cycle that captures a dual microbial control point between soil organic C (SOC) accumulation and loss. The interpretation of these patterns and drivers of microbial CUE after long-term afforestation remains, however, a major scientific challenge. In particular, there are major uncertainties about the role of microbial traits in driving CUE. Here, we compared sites along a 45-year afforestation chronosequence and combined the novel 18O-H2O tracer method with metagenomic analysis to quantify CUE and explore the mechanisms underlying microbe-mediated C dynamics. The results showed that soil microbial CUE significantly increased following afforestation and showed a positive relationship with SOC, which suggested that microbial CUE could promote C accumulation in afforested ecosystems. We further found the critical role of microbial traits in the regulation of CUE through altering microbial life history strategies: microbial CUE was positively and significantly correlated with resource acquisition (A) genes, but showed a negative and significant correlation with stress tolerance (S) strategy genes. These results suggested that soil microbes reduce investment in S strategies and shift to A and high yield (Y) strategies, thereby increasing CUE. This knowledge is important because it advances our understanding of the microbial physiological and evolutionary tradeoffs mediating soil C cycling in the context of human-induced land use change. Full article
(This article belongs to the Special Issue Advances in Soil Microbial Ecology, 3rd Edition)
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14 pages, 3547 KB  
Article
Seasonal Shifts from Water Depth to Nitrate Reorganize Protistan Communities Following Lake Freeze–Thaw Events
by Yanying Zhou, Zhengming Luo and Jinxian Liu
Microorganisms 2025, 13(12), 2869; https://doi.org/10.3390/microorganisms13122869 - 17 Dec 2025
Viewed by 300
Abstract
The seasonal freeze–thaw cycle induces a fundamental regime shift in lake ecosystems, primarily through the restructuring of microbial communities. This study investigated the dynamics and mechanisms of species diversity maintenance in protistan communities in Gonghai Lake, a shallow subalpine lake in China, across [...] Read more.
The seasonal freeze–thaw cycle induces a fundamental regime shift in lake ecosystems, primarily through the restructuring of microbial communities. This study investigated the dynamics and mechanisms of species diversity maintenance in protistan communities in Gonghai Lake, a shallow subalpine lake in China, across both ice-covered and ice-free periods. During ice cover, the protistan community exhibited a vertically stratified structure dominated by cryotolerant diatoms such as Stephanodiscus. Following thaw, the community transitioned to a more homogeneous, resource-driven assembly. Concurrently, the key environmental controls shifted from physical stratification (proxied by depth) to resource availability (notably NO3− and TOC), a change reflected in the taxonomic succession from Ochrophyta to Chlorophyta. Nevertheless, depth retained ecological relevance mediated by benthic–pelagic coupling, which supported a distinct near-sediment community. Our findings demonstrate that freeze–thaw-mediated terrestrial nutrient inputs directly modified protistan diversity and community structure. These alterations have fundamental implications for ecosystem functions in subalpine lakes, including nutrient cycling rates and energy flow through the microbial loop. Full article
(This article belongs to the Section Environmental Microbiology)
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16 pages, 4840 KB  
Article
Generation of a Human–Mouse Chimeric Anti-Japanese Encephalitis Virus and Zika Virus Monoclonal Antibody Using CDR Grafting
by Yusha Liu, Jiayi Zhang, Jiayang Zhu, Hongxia Ni, Dong Chen, Meiqing Zhang, Yuqian Fang, Cheng Ma, Shuangwei Wang, Jie Chen, Yitian Zheng, Li Chi, Lin Cai and Jinsheng Wen
Microorganisms 2025, 13(12), 2868; https://doi.org/10.3390/microorganisms13122868 - 17 Dec 2025
Viewed by 339
Abstract
Japanese encephalitis (JE) caused by Japanese encephalitis virus (JEV) is a dominant arthropod-borne disease in Asian countries. However, effective antiviral treatment for JEV has not yet been established. 2H4 is a previously identified mouse monoclonal antibody (mAb) which exhibited neutralizing activity against JEV [...] Read more.
Japanese encephalitis (JE) caused by Japanese encephalitis virus (JEV) is a dominant arthropod-borne disease in Asian countries. However, effective antiviral treatment for JEV has not yet been established. 2H4 is a previously identified mouse monoclonal antibody (mAb) which exhibited neutralizing activity against JEV infection. Herein, we designed a novel mAb F(ab’)2 2A10-2H4-CDR by transplanting the complementarity-determining regions (CDRs) of 2H4 into the corresponding regions of a murine mAb 2A10 which has high homology with human mAb. We further expressed the recombinant human–mouse chimeric mAb 2A10-2H4-CDR-hFc by linking 2A10-2H4-CDR with CH2 and CH3 domains of one human mAb. The results of indirect immunofluorescence assay and ELISA show that 2A10-2H4-CDR-hFc can recognize the E proteins of JEV and Zika virus (ZIKV), similar to its original form 2H4. Moreover, 2A10-2H4-CDR-hFc displayed neutralizing activities against JEV and ZIKV equivalent to that of 2H4 in vitro (NT50 value against JEV = 0.079 μg/mL versus 0.022 μg/mL, respectively; NT50 value against ZIKV = 1.584 μg/mL versus 0.446 μg/mL, respectively). Both 2H4 and 2A10-2H4-CDR-hFc significantly increased the survival and reduced the serum viral burden of mice challenged by JEV or ZIKV. This study successfully validates an anti-JEV and ZIKV human–mouse chimeric mAb and establishes a basis for future application of this Ab in preventing or/and treating of both JEV and ZIKV infections. Full article
(This article belongs to the Section Virology)
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15 pages, 1816 KB  
Article
Culture-Dependent Bioprospecting of Halophilic Microorganisms from Portuguese Salterns
by Eduarda Almeida, Adrianna Jackiewicz, Maria de Fátima Carvalho and Olga Maria Lage
Microorganisms 2025, 13(12), 2867; https://doi.org/10.3390/microorganisms13122867 - 17 Dec 2025
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Abstract
Extreme hypersaline environments harbour a unique biodiversity capable of surviving in such habitats, including halophilic and halotolerant bacteria. Microbial adaptations to these environments comprehend two main strategies: the “salt-in” that involves a high intracellular concentration of salts (e.g., potassium), and the “salt-out” that [...] Read more.
Extreme hypersaline environments harbour a unique biodiversity capable of surviving in such habitats, including halophilic and halotolerant bacteria. Microbial adaptations to these environments comprehend two main strategies: the “salt-in” that involves a high intracellular concentration of salts (e.g., potassium), and the “salt-out” that relies on the accumulation of small organic compounds (e.g., glycine betaine and trehalose). These evolutionary haloadaptations, combined with natural population competitiveness, often promotes the production of distinctive antimicrobial compounds, highlighting hypersaline environments as promising rich sources of novel natural products with biotechnological potential. Aiming at enlarging the knowledge on the microbiota of two Portuguese salterns (Aveiro and Olhão), microbial isolation was performed using salt and saline sediment samples. A total of 39 microbial isolates were obtained in a saline medium, affiliated with Bacillota, Pseudomonadota, Actinomycetota, and Rhodothermaeota and the archaeal phylum Euryarchaeota. All isolates are generally common in saline habitats, with most (79%) exhibiting a halotolerant profile. Regarding the presence of biosynthetic related genes, 28% of the isolates lacked type I genes for polyketide synthases or non-ribosomal peptide synthetases, 36% contained at least one of these genes, and 36% possessed both. This study provides evidence of the biotechnological potential of the microbiota from two Portuguese salterns. Full article
(This article belongs to the Section Microbial Biotechnology)
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16 pages, 1895 KB  
Review
MecVax, an Epitope- and Structure-Based Broadly Protective Subunit Vaccine Against Enterotoxigenic Escherichia coli (ETEC)
by Weiping Zhang
Microorganisms 2025, 13(12), 2866; https://doi.org/10.3390/microorganisms13122866 - 17 Dec 2025
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Abstract
No vaccines are licensed against enterotoxigenic Escherichia coli (ETEC), a leading diarrheal cause in children and travelers. ETEC adhesins and enterotoxins are the virulence determinants and become the primary targets in ETEC vaccine development. However, ETEC strains produce > 25 adhesins and two [...] Read more.
No vaccines are licensed against enterotoxigenic Escherichia coli (ETEC), a leading diarrheal cause in children and travelers. ETEC adhesins and enterotoxins are the virulence determinants and become the primary targets in ETEC vaccine development. However, ETEC strains produce > 25 adhesins and two potent enterotoxins, particularly the poorly immunogenic heat-stable toxin (STa), greatly hindering ETEC vaccine development. To overcome these challenges, we developed a multiepitope-fusion-antigen (MEFA) platform. MEFA presented multiple adhesin epitopes on a backbone and generated a polyvalent adhesin immunogen, CFA/I/II/IV MEF. CFA/I/II/IV protected against the seven ETEC adhesins (CFA/I, CS1-CS6) associated with two-thirds of ETEC diarrheal cases. We further used toxoids as safe antigens and created a toxoid fusion, 3xSTaN12S-mnLTR192G/L211A. This antigen induced antibodies neutralizing the enterotoxicity of STa and heat-labile toxin (LT), which, alone or together, cause all ETEC diarrheal cases. By combining two polyvalent proteins, we developed a multivalent ETEC vaccine, MecVax, that protects against seven ETEC adhesins and two enterotoxins. MecVax is broadly immunogenic. MecVax prevents intestinal colonization by ETEC strains expressing any of the seven adhesins and protects against clinical diarrhea from ETEC strains producing LT or STa enterotoxin preclinically, becoming a broadly protective ETEC vaccine candidate against children’s diarrhea and travelers’ diarrhea. Full article
(This article belongs to the Special Issue Advancement in Enterotoxigenic Escherichia coli (ETEC) Vaccines)
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22 pages, 5401 KB  
Case Report
Fatal Congenital Toxoplasmosis with Progressive Liver Failure and Genomic Characterization of a Novel Isolate from the United States
by Katsuaki Kojima, Indu Varier, Rouba Sayegh, Masako Shimamura, Bimal P. Chaudhari, Anas Bernieh, Matthew J. Schulz, Peter White, James Fitch, Alexandra K. Medoro, Hernan A. Lorenzi and Rima McLeod
Microorganisms 2025, 13(12), 2865; https://doi.org/10.3390/microorganisms13122865 - 17 Dec 2025
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Abstract
Congenital toxoplasmosis presents with a wide clinical spectrum, ranging from asymptomatic infection to severe disease with multi-organ failure. We report a rare fatal case of disseminated congenital toxoplasmosis in a human neonate. The infant initially had thrombocytopenia and mild hepatitis, which rapidly progressed [...] Read more.
Congenital toxoplasmosis presents with a wide clinical spectrum, ranging from asymptomatic infection to severe disease with multi-organ failure. We report a rare fatal case of disseminated congenital toxoplasmosis in a human neonate. The infant initially had thrombocytopenia and mild hepatitis, which rapidly progressed to fulminant liver failure. Despite initiation of standard therapy with pyrimethamine, sulfadiazine, and folinic acid on postnatal day 25, the infant died two days later. Autopsy revealed widespread involvement of the liver, spleen, brain, heart, lungs, urinary bladder, and skeletal muscle. To further characterize the infection, genomic sequencing of the isolate (TgHsUS2) was performed, which placed it within clade C (Haplogroup 9) and closely related to reference strains P89 and TgCatBr3. Variant analysis showed type III-like alleles in ROP18, ROP16, and GRA15. These alleles are known to modulate host immunity and may have influenced disease severity in this case. This report highlights the need for rapid recognition and targeted therapy as well as how strain genomics can inform disease mechanisms. Prevention through prenatal screening and maternal treatment during pregnancy may reduce infant mortality. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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15 pages, 6493 KB  
Article
Modulation of Dextran Sodium Sulfate-Induced Colitis in Germ-Free Mice by Enterococcus faecalis Monocolonization
by Beate Vestad, Petra Hanzely, Indrė Karaliūtė, Oda Ramberg, Jurgita Skiecevičienė, Rokas Lukoševičius, Jørgen V. Bjørnholt, Kristian Holm, Juozas Kupčinskas, Henrik Rasmussen, Johannes R. Hov and Espen Melum
Microorganisms 2025, 13(12), 2864; https://doi.org/10.3390/microorganisms13122864 - 16 Dec 2025
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Abstract
Inflammatory bowel diseases (IBDs), including Crohn’s disease and ulcerative colitis (UC), are characterized by chronic gastrointestinal inflammation and involve complex interactions of genetic, environmental, and immune factors. Enterococcus faecalis, a gut commensal bacterium, has been implicated in IBD pathogenesis. This study investigated [...] Read more.
Inflammatory bowel diseases (IBDs), including Crohn’s disease and ulcerative colitis (UC), are characterized by chronic gastrointestinal inflammation and involve complex interactions of genetic, environmental, and immune factors. Enterococcus faecalis, a gut commensal bacterium, has been implicated in IBD pathogenesis. This study investigated the effects of monocolonization with a UC-derived E. faecalis strain on acute dextran sulfate sodium (DSS)-induced colitis in germ-free (GF) mice, focusing on epithelial injury, inflammatory markers, hematologic indices, and bacterial translocation. In DSS-treated mice, monocolonization was associated with modest and mixed effects, including a higher colitis-related disease activity score, reduced anemia, increased fecal albumin and a trend towards reduced fecal calprotectin. Despite translocation of E. faecalis to mesenteric lymph nodes, no systemic dissemination was observed. Histological analysis revealed broadly similar inflammatory patterns between DSS-treated groups, with slightly more epithelial injury observed in colonized mice. These findings suggest that E. faecalis may influence discrete aspects of DSS injury in a strain-dependent and context-specific manner, rather than broadly altering overall disease severity. This study highlights the utility of GF models for examining strain-specific host–microbe interactions and underscores that individual bacterial isolates may exert heterogeneous and selective effects on acute colitis. Further research is needed to elucidate these complex mechanisms. Full article
(This article belongs to the Section Gut Microbiota)
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15 pages, 2921 KB  
Article
Impact of Antibiotic Exposure on Growth and Biofilms Formation in Aeromonas salmonicida Subspecies Isolated from Atlantic Salmon (Salmo salar)
by Dong Hwi Kim, Min Soo Joo, Se Rin Jang, Hee Jin Kim, Joon Gyu Min and Bo Hye Nam
Microorganisms 2025, 13(12), 2863; https://doi.org/10.3390/microorganisms13122863 - 16 Dec 2025
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Abstract
Aeromonas salmonicida is a major pathogen in aquaculture, and its ability to form biofilms contributes significantly to antibiotic resistance and chronic infections. This study investigated the effects of four antibiotics—ampicillin, amoxicillin, oxytetracycline, and doxycycline—at various concentrations on bacterial growth, biofilm formation, and gene [...] Read more.
Aeromonas salmonicida is a major pathogen in aquaculture, and its ability to form biofilms contributes significantly to antibiotic resistance and chronic infections. This study investigated the effects of four antibiotics—ampicillin, amoxicillin, oxytetracycline, and doxycycline—at various concentrations on bacterial growth, biofilm formation, and gene expression related to antibiotic resistance and quorum sensing (QS) in two subspecies: A. salmonicida subsp. masoucida (ASM) and A. salmonicida subsp. salmonicida (ASS). Bacterial isolates from Atlantic salmon were identified using 16S rRNA and vapA gene sequencing. Growth inhibition was more pronounced in ASS than ASM under high antibiotic concentrations. Conversely, sub-inhibitory concentrations (sub-MICs) enhanced biofilm formation in both subspecies, particularly in ASM. PCR results showed that tetA and tetE resistance genes were present only in ASM. qRT-PCR analysis revealed that expression of QS-related genes (ahyI and ahyR) was generally downregulated under tetracycline treatment, while litR expression varied across antibiotic conditions and strains. Some isolates showed increased litR expression alongside elevated biofilm formation, suggesting involvement of additional regulatory mechanisms. These results highlight the potential for sub-MIC antibiotic exposure to promote biofilm development and modulate gene expression, emphasizing the need for careful antibiotic use in aquaculture and providing insight into alternative pathogen control strategies. Full article
(This article belongs to the Section Antimicrobial Agents and Resistance)
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13 pages, 4796 KB  
Article
Variety of Bacterial Pathogens in Ticks Removed from Humans, Northeastern China
by Xiao-Ling Su, Jin-Ling Ye, Ming-Zhu Zhang, Yi-Fei Wang, Yi Sun, Ya-Fei Wu, Cai Bian, Nan-Nan Yao, Yuan-Chun Zheng, Jia-Fu Jiang, Xiao-Min Zheng and Wu-Chun Cao
Microorganisms 2025, 13(12), 2862; https://doi.org/10.3390/microorganisms13122862 - 16 Dec 2025
Viewed by 253
Abstract
Ticks transmit diverse pathogens, posing significant public health threats in northeastern China; clarifying human-biting tick species and their carried pathogens is crucial for risk assessment and prevention. This study was designed as a pathogen detection and molecular epidemiological investigation. During the May-August period [...] Read more.
Ticks transmit diverse pathogens, posing significant public health threats in northeastern China; clarifying human-biting tick species and their carried pathogens is crucial for risk assessment and prevention. This study was designed as a pathogen detection and molecular epidemiological investigation. During the May-August period of each of 2023 and 2024, 232 ticks that had bitten humans were collected from a local sentinel hospital. Ticks were morphologically identified, followed by DNA extraction, semi-nested/nested PCR targeting specific genetic markers, and Sanger sequencing to detect bacterial pathogens. Four tick species were found, with Ixodes persulcatus dominant (87.9%), followed by Dermacentor silvarum (6.9%), Haemaphysalis concinna (3.5%), and Haemaphysalis japonica (1.7%). Seven bacterial pathogens were detected, including Candidatus Rickettsia tarasevichiae (35.3%) and Borreliella garinii (17.2%); 49.6% of ticks were pathogen-positive. The coinfection rate was 13.8%, most commonly Candidatus R. tarasevichiae plus B. garinii, and I. persulcatus carried all pathogens. These findings provide basic data on human-biting tick species and their bacterial pathogen spectrum in the region, serving as a reference for subsequent tick-borne disease research and targeted prevention. Full article
(This article belongs to the Section Public Health Microbiology)
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15 pages, 1963 KB  
Article
Comparative Mechanisms of Different Bifidobacteria in Combating Pathogen Infection and Prolonging the Lifespan in Caenorhabditis elegans
by Xueer Wang, Shixiang Wu, Wen Zhao, Zhaozhong Zeng, Jian He, Hanglian Lan, Bing Fang, Haina Gao, Yue Liu, Jingyu Li, Weilian Hung and Ming Zhang
Microorganisms 2025, 13(12), 2861; https://doi.org/10.3390/microorganisms13122861 - 16 Dec 2025
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Abstract
The research employed Caenorhabditis elegans to compare the anti-infection and lifespan-extending properties of Bifidobacterium. The results demonstrated that BL-99 and YLGB-1496 intervention improved the nematodes’ resistance to Staphylococcus aureus infection, resulting in lifespan extensions of 5.90% and 14.38%, respectively, accompanied by the [...] Read more.
The research employed Caenorhabditis elegans to compare the anti-infection and lifespan-extending properties of Bifidobacterium. The results demonstrated that BL-99 and YLGB-1496 intervention improved the nematodes’ resistance to Staphylococcus aureus infection, resulting in lifespan extensions of 5.90% and 14.38%, respectively, accompanied by the alleviation in the decline of pharyngeal pumping rate and locomotor capacity. Furthermore, both probiotic strains significantly extended the mean lifespan of nematodes by 10.96% and 12.14%, and significantly alleviated pharyngeal pumping and locomotion. Importantly, BL-99 and YLGB-1496 have different underlying mechanisms of action. Transcriptomic analyses indicated that the BL-99 strain enhanced nematode resistance to Gram-positive pathogens through the upregulation of lysozyme, saposin-like antimicrobial peptides, and c-type lectin family genes. Conversely, YLGB-1496 improved the epidermal permeability barrier by upregulating genes involved in collagen synthesis and assembly. Overall, this study provides novel insights into the species-specific effects of Bifidobacteria on pathogen resistance and lifespan extension. Full article
(This article belongs to the Section Molecular Microbiology and Immunology)
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25 pages, 6146 KB  
Article
Evaluation of Soil Amelioration Effects of Different Afforestation Measures in Alpine Sandy Land: A Case Study of the Gonghe Basin
by Shaobo Du, Huichun Xie, Gaosen Zhang, Feng Qiao, Tianyue Zhao, Guigong Geng and Chongyi E
Microorganisms 2025, 13(12), 2860; https://doi.org/10.3390/microorganisms13122860 - 16 Dec 2025
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Abstract
Desertification poses a severe challenge in China. Although long-term sand control measures have proven effective, the extensive and challenging nature of sandy land necessitates systematic research to identify optimal sand control measures for soil amelioration, thereby promoting ecological restoration in sandy areas. This [...] Read more.
Desertification poses a severe challenge in China. Although long-term sand control measures have proven effective, the extensive and challenging nature of sandy land necessitates systematic research to identify optimal sand control measures for soil amelioration, thereby promoting ecological restoration in sandy areas. This study focused on the Gonghe Basin to assess the effectiveness of four 24-year afforestation treatments—Salix cheilophila + Populus simonii, S. cheilophila, P. simonii (YY), and Caragana korshinskii—compared to untreated mobile dunes. Surface soils (0–10 cm and 10–20 cm) were analyzed for physicochemical properties, enzyme activities, and bacterial community structure using Illumina high-throughput sequencing and PICRUSt2 functional prediction. All afforestation treatments significantly improved soil quality, increasing fine particle content, moisture, nutrients, enzyme activity, and microbial richness and diversity, especially in the topsoil. Bulk density and pH were notably reduced. Among the treatments, YY demonstrated the most substantial improvements. pH emerged as the primary factor influencing bacterial community structure, with enzyme activities also playing a significant role. Metabolism was the dominant functional category across all sites, while YY enhanced environmental information processing functions in the topsoil. Secondary functions showed high redundancy across treatments. These findings confirm that afforestation can effectively rehabilitate degraded alpine sandy soils, with the YY treatment offering the greatest benefits. The study provides a scientific basis for optimizing sand control measures and supports broader ecological restoration efforts in similar environments worldwide. Full article
(This article belongs to the Special Issue Diversity, Function, and Ecology of Soil Microbial Communities)
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2 pages, 145 KB  
Correction
Correction: Schalli et al. Cefsulodin and Vancomycin: A Supplement for Chromogenic Coliform Agar for Detection of Escherichia coli and Coliform Bacteria from Different Water Sources. Microorganisms 2022, 10, 2499
by Michael Schalli, Sarah Maria Inwinkl, Sabine Platzer, Rita Baumert, Franz F. Reinthaler, Petra Ofner-Kopeinig and Doris Haas
Microorganisms 2025, 13(12), 2859; https://doi.org/10.3390/microorganisms13122859 - 16 Dec 2025
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Abstract
In the original publication [...] Full article
(This article belongs to the Topic Food Hygiene and Food Safety)
12 pages, 645 KB  
Article
Clinical Manifestations, Antifungal Susceptibilities, and Outcome of Ocular Infections Caused by Purpureocillium lilacinum
by Xinlei Zhao, Jinliang Jiang, Huijing Huang, Jiayi Zheng, Liuxueying Zhong and Fang Duan
Microorganisms 2025, 13(12), 2858; https://doi.org/10.3390/microorganisms13122858 - 16 Dec 2025
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Abstract
Purpureocillium lilacinum is an emerging pathogen that can cause severe ocular infections. This study aimed to investigate the risk factors, clinical manifestations, antifungal susceptibilities, and outcomes of ocular infections caused by P. lilacinum at a large ophthalmic center in Southern China. This retrospective [...] Read more.
Purpureocillium lilacinum is an emerging pathogen that can cause severe ocular infections. This study aimed to investigate the risk factors, clinical manifestations, antifungal susceptibilities, and outcomes of ocular infections caused by P. lilacinum at a large ophthalmic center in Southern China. This retrospective study reviewed the medical records of 34 patients with culture-proven P. lilacinum oculomycosis treated at the Zhongshan Ophthalmic Center from January 2020 to December 2024. The study included 34 patients (17 males, 17 females). The most common risk factor was ocular trauma (38.2%). In vitro susceptibility testing revealed high resistance to fluconazole and caspofungin, but general susceptibility to voriconazole (median MIC 0.25 mg/L). Despite 97.1% of patients receiving voriconazole therapy, outcomes were generally poor, with 54.5% of patients experiencing a poor outcome (vision worse than counting fingers). A significantly shorter time to microbiological diagnosis was associated with a favorable outcome (median 26 days vs. 65 days, p = 0.007). In conclusion, the visual outcomes of this infection remain generally poor, with the major clinical challenge being the delay in diagnosis. Therefore, prompt microbiological investigation is recommended for patients with suspected intraocular infection. Voriconazole remains the first-line therapeutic choice, the therapeutic potential of newer triazoles warrants further investigation. Full article
(This article belongs to the Special Issue Fungal Infections and Antifungal Agents)
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30 pages, 3234 KB  
Article
Isolation and Genome Analysis of Serratia ureilytica T6, a Heavy Metal(loid)-Resistant and Plant Growth-Promoting Bacterium, from Rice Soil
by Syed Muhammad Azam, Ziting Lin, Yanqing Bai, Yijia Fu, Hend Alwathnani, Guo-Hong Liu and Christopher Rensing
Microorganisms 2025, 13(12), 2857; https://doi.org/10.3390/microorganisms13122857 - 16 Dec 2025
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Abstract
Lead and zinc pollution is a prevalent issue in agricultural soils surrounding lead and zinc mines, posing a serious risk to crop growth and soil health. Heavy metal-resistant, plant growth-promoting bacteria (PGPB) capable of supporting plant development under high metal exposure have significant [...] Read more.
Lead and zinc pollution is a prevalent issue in agricultural soils surrounding lead and zinc mines, posing a serious risk to crop growth and soil health. Heavy metal-resistant, plant growth-promoting bacteria (PGPB) capable of supporting plant development under high metal exposure have significant potential for mitigating these deleterious effects. Here we isolated and identified the Pb- and Zn-resistant and plant growth-promoting bacterial strain Serratia ureilytica T6 based on 16S rRNA and average nucleotide identity (ANI) analysis. Furthermore, 14 strains (T1–T14) from a rice paddy soil irrigated by Pb-Zn mine effluent were isolated and identified, and their phytopromoting characteristics were determined. Genome analysis of S. ureilytica T6 showed a genome size of 5,102,941 bp, with G + C content of 59.74%. A total of 4822 genes were annotated by RAST, among which 15 genes were putatively associated with Pb-Zn resistance. The genome of S. ureilytica T6 was found to possess multiple genes associated with probiotic properties by a comparative analysis of KEGG, GO, and COG databases. Several taxonomic identifications of S. ureilytica T6 revealed that strain T6 is Gram-negative, facultative anaerobic and motile. The pH growth range of S. ureilytica T6 was between 4.00 and 9.50; temperature growth range was 4–37 °C; NaCl tolerance was 0–9%. S. ureilytica T6 displayed a high tolerance to a variety of heavy metals, with minimum inhibitory concentrations of 1.5 and 9 mmol·L−1 for Pb and Zn. S. ureilytica T6 can utilize a variety of carbon sources and nitrogen sources. T6 has the ability to produce indole-3-acetic acid (IAA), siderophore, and phosphorus and potassium solubilization, and it was initially judged that strain T6 has the potential for plant growth-promoting ability. Different plant growth-promoting effects of T6 inoculations were observed in improving rice biomass, plant height, etc. We observed that with increasing Pb and Zn stress, SOD activity first increased and then decreased, while POD and CAT activities gradually decreased. The addition of S. ureilytica T6 significantly enhanced the activities of SOD, POD, and CAT in rice seedlings under low to moderate Pb and Zn stress but had no significant effect under high concentrations (150 mg·L−1) of Pb or Zn. In addition, S. ureilytica T6 has the potential to be used as a phytoremediation tool. Full article
(This article belongs to the Special Issue Plant Growth—Promoting Bacteria and Plant—Soil Interactions in Harsh Environments, 2nd Edition)
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14 pages, 1427 KB  
Article
Fungal Aerosol Exposure and Stage-Specific Variations in Taihang Chicken Houses During Winter
by Yejin Yang, Zitong Yang, Zhibin Ren, Wenhao Feng, Zhenyue Li, Yi Lu, Mengxi Yan, Zhuhua Liu, Ran Zhu, Mingli Liu, Xiaolong Chen, Cheng Zhang, Shishan Dong, Huan Cui and Huage Liu
Microorganisms 2025, 13(12), 2856; https://doi.org/10.3390/microorganisms13122856 - 16 Dec 2025
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Abstract
Fungal aerosols are critical yet understudied bioaerosol components in enclosed poultry environments, particularly during winter when ventilation is restricted. This study investigated stage-specific variations in fungal aerosol concentration, size distribution, and community composition in Taihang chicken houses across three growth stages (15, 60, [...] Read more.
Fungal aerosols are critical yet understudied bioaerosol components in enclosed poultry environments, particularly during winter when ventilation is restricted. This study investigated stage-specific variations in fungal aerosol concentration, size distribution, and community composition in Taihang chicken houses across three growth stages (15, 60, and 150 days). Culturable fungal concentrations significantly increased from 3.16 × 103 CFU/m3 to 1.24 × 104 CFU/m3 with bird age (p < 0.001, ANOVA). Respirable particles (<4.7 μm) consistently dominated the fungal size distribution. ITS sequencing revealed progressive increases in fungal richness and distinct community shifts among stages. Several fungi with zoonotic potential, including Aspergillus, Cladosporium, Cryptococcus, and Fusarium, were detected across all stages. These findings demonstrate that wintertime enclosed ventilation, while thermally beneficial, promotes the accumulation of respirable fungal aerosols and elevates occupational and environmental health risks. From a One Health perspective, stage-specific mitigation strategies—such as ventilation optimization, reduction in organic dust sources, and routine monitoring of respirable fungal fractions—are essential for reducing exposure risks in cold-season poultry production. Full article
(This article belongs to the Section Veterinary Microbiology)
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17 pages, 3419 KB  
Article
Synergistic Effects of Fertilization and Reclamation Age on Inorganic Phosphorus Fractions and the pqqC-Harboring Bacterial Community in Reclaimed Coal Mining Soils
by Zhiwen Fang, Kunli Liu, Yunlong Jiang, Jianfang Wang, Zhuomin Song, Huisheng Meng, Xianjun Hao, Jie Zhang and Xiangying Wang
Microorganisms 2025, 13(12), 2855; https://doi.org/10.3390/microorganisms13122855 - 16 Dec 2025
Viewed by 246
Abstract
Fertilization is an effective measure to rapidly improve soil quality in reclaimed mining areas. However, the combined effects of fertilization regimes and reclamation age on phosphorus (P) fraction transformation and the pqqC-harboring microbial community in reclaimed soils remain unclear. In this study, [...] Read more.
Fertilization is an effective measure to rapidly improve soil quality in reclaimed mining areas. However, the combined effects of fertilization regimes and reclamation age on phosphorus (P) fraction transformation and the pqqC-harboring microbial community in reclaimed soils remain unclear. In this study, we investigated the dynamics of inorganic P fractions and the pqqC-harboring bacterial community under different fertilization treatments (no fertilizer: CK; chemical fertilizer: CF; organic manure: M) and reclamation ages (1, 5, and 10 years) in a coal mining reclamation area of Shanxi Province, using long-term field experiments combined with high-throughput sequencing. Results showed that compared with the CF and CK treatments, the M treatment significantly increased soil organic matter (SOM), available P (AP), and total nitrogen (TN) content, and promoted the conversion of moderately labile P (NaOH-Pi) to labile P fractions (H2O-Pi, NaHCO3-Pi). Meanwhile, the pqqC gene abundance increased with reclamation age, with the M treatment maintaining the highest levels in all fertilization regimes. Co-occurrence network analysis of core species revealed that the number of connections gradually decreased and the network structure simplified with increasing reclamation age. Correspondingly, the microbial community transitioned from an initial stage characterized by rapid response and intense competition to a stable phase. Specifically, Pseudomonas spp. played a key role in P mobilization. Structural equation modeling (SEM) further demonstrated that reclamation age directly promoted the pqqC gene abundance and AP content, whereas fertilization indirectly influenced P transformation by regulating microbial diversity. Our findings reveal that reclamation age and fertilization synergistically shape the inorganic P profile and the associated bacterial community, providing insights for developing targeted P management strategies in reclaimed lands. Full article
(This article belongs to the Section Environmental Microbiology)
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24 pages, 5291 KB  
Article
teamNGS Balances Sensitivity for Viruses with Comprehensive Microbial Detection in Clinical Specimens
by Julie Yamaguchi, Gregory S. Orf, Jenna Malinauskas, Maximillian Mata, Sonja L. Weiss, Kenn Forberg, Todd V. Meyer, Peter O. Wiebe, Illya Mowerman, Stanley J. Piotrowski, Daniel Glownia, Mary A. Rodgers, John Hackett, Jr., Yupin Suputtamongkol, Pakpoom Phoompoung, Selvamurthi Gomathi, Amrose Pradeep, Sunil S. Solomon, Nicholas Bbosa, Pontiano Kaleebu, Ambroise D. Ahouidi, Souleymane Mboup, Austin F. Sequeira, Arinobu Tojo, Gavin A. Cloherty and Michael G. Bergadd Show full author list remove Hide full author list
Microorganisms 2025, 13(12), 2854; https://doi.org/10.3390/microorganisms13122854 - 16 Dec 2025
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Abstract
Probe-based capture represents a highly sensitive and cost-effective approach for overcoming host background and enriching viruses in metagenomic NGS (mNGS) libraries. Using clinical specimens collected globally from patients with fever or respiratory illness, we generated mNGS libraries by random priming and Nextera XT [...] Read more.
Probe-based capture represents a highly sensitive and cost-effective approach for overcoming host background and enriching viruses in metagenomic NGS (mNGS) libraries. Using clinical specimens collected globally from patients with fever or respiratory illness, we generated mNGS libraries by random priming and Nextera XT tagmentation, followed by target enrichment (teNGS) with Comprehensive Viral Research Panel (CVRP) probes. Capture pool sizes and total reads were optimized, and libraries were initially sequenced separately. Using only 3–4% of reads required for standard mNGS, teNGS achieved increased sensitivity, 100–10,000× increases in depth, and >50% genome coverage for pathogens with titers ≥ 1000 cp/mL. Application to >2000 clinical specimens from various matrices and to contrived samples containing viruses absent from the CVRP probe set enabled detection of diverse viral families and established a minimum 65% nucleotide identity for hybridization, respectively. To save time and resources, teNGS and mNGS libraries were then combined into one sequencing run: teamNGS. In addition to streamlining the workflow, teamNGS also improved genome recovery. Coupling methods maintain the sensitivity and coverage for viruses achieved by enrichment alone while also ensuring comprehensive recovery of non-viral microbes. teamNGS has the potential to improve patient management and lower the rates of unnecessary testing and antibiotic use. Full article
(This article belongs to the Special Issue Detection and Identification of Emerging and Re-Emerging Pathogens)
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