Microorganisms

19 pages, 390 KB

Open AccessReview

Virulence Regulation in Borrelia burgdorferi

by Sierra George and Zhiming Ouyang

Microorganisms 2025, 13(9), 2183; https://doi.org/10.3390/microorganisms13092183 - 18 Sep 2025

Borrelia burgdorferi, the causative agent of Lyme disease, is the most common vector-borne disease in the United States. Compared with other bacterial pathogens, B. burgdorferi has many unique features. For instance, its highly segmented genome was predicted to encode very few proteins directly [...] Read more.

Borrelia burgdorferi, the causative agent of Lyme disease, is the most common vector-borne disease in the United States. Compared with other bacterial pathogens, B. burgdorferi has many unique features. For instance, its highly segmented genome was predicted to encode very few proteins directly dedicated to gene expression regulation. Yet, the spirochete continuously reprograms its transcriptome and proteome to promote survival and pathogenesis as spirochetes traverse the enzootic lifecycle between ticks and mammals. Signal sensing systems, a unique alternative sigma factor cascade, and multi-functional regulators work in concert to coordinate virulence gene expression under different tick and mammal environments. In this review, we have summarized recent advances in gene regulation in B. burgdorferi. Full article

(This article belongs to the Special Issue Ticks, Tick Microbiome and Tick-Borne Diseases)

15 pages, 4506 KB

Open AccessArticle

Transmissibility of Clade IIb Monkeypox Virus in Young Rabbits

by Zhaoliang Chen, Lei Zhang, Linzhi Li, Mingjie Shao, Mingda Zhang, Zongzheng Zhao, Chao Shang, Zirui Liu, Juxiang Liu and Zhendong Guo

Microorganisms 2025, 13(9), 2182; https://doi.org/10.3390/microorganisms13092182 (registering DOI) - 18 Sep 2025

Abstract

The monkeypox virus (MPXV) has spread globally, posing a severe challenge to global public health. This study systematically evaluated the aerosol shedding dynamics of the epidemic Clade IIb MPXV strain in infected young rabbits, along with its direct contact and airborne transmission potential [...] Read more.

The monkeypox virus (MPXV) has spread globally, posing a severe challenge to global public health. This study systematically evaluated the aerosol shedding dynamics of the epidemic Clade IIb MPXV strain in infected young rabbits, along with its direct contact and airborne transmission potential among them. We found that young rabbits could be experimentally infected with MPXV, exhibiting distinct pathogenic features and viral shedding patterns. Young rabbits infected with MPXV shed the virus through nasal secretions and exhaled aerosols, peaking at 7 dpi. In total, 89–95.8% of virus-laden respiratory particles had a diameter ≥4.7 μm. Notably, MPXV can be efficiently shed and transferred among young rabbits through direct contact and airborne routes. The nasal secretions and exhaled virus particles from donor rabbits can be contacted or inhaled by recipient rabbits. Large amounts of viral DNA were detected in the nasal wash of rabbits exposed to contact or airborne exposure. Furthermore, virus particles invade the lungs, causing pathological changes and disseminating them to multiple organs. However, no infectious virus was successfully recovered from these recipient rabbits, as their exposed or inhaled MPXV dose might have been below the MPXV’s minimum infectious dose for young rabbits. These findings indicate that although the airborne transmissibility of the current MPXV strain is relatively limited, inhalation of viral particles following airborne exposure can still result in bodily damage. Continuous monitoring of MPXV transmissibility and mutation evolution is imperative to prevent efficient respiratory aerosol transmission, which guides global monkeypox prevention and control strategies. Full article

(This article belongs to the Special Issue The Microbial Pathogenesis)

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18 pages, 1138 KB

Open AccessArticle

Sorption–Biological Treatment of Coastal Substrates of the Barents Sea in Low Temperature Using the Rhodococcus erythropolis Strain HO-KS22

by Vladimir Myazin, Maria Korneykova, Nadezhda Fokina, Ekaterina Semenova, Tamara Babich and Milana Murzaeva

Microorganisms 2025, 13(9), 2181; https://doi.org/10.3390/microorganisms13092181 - 18 Sep 2025

Abstract

The efficiency of the sorption–biological method for treatment of oil-polluted coastal substrates (soil and sand) of the Barents Sea under low temperature (10 °C) using the active hydrocarbon-oxidizing bacterial strain Rhodococcus erythropolis HO-KS22 was assessed in the laboratory. The highest rate of hydrocarbon [...] Read more.

The efficiency of the sorption–biological method for treatment of oil-polluted coastal substrates (soil and sand) of the Barents Sea under low temperature (10 °C) using the active hydrocarbon-oxidizing bacterial strain Rhodococcus erythropolis HO-KS22 was assessed in the laboratory. The highest rate of hydrocarbon degradation was in sand polluted with a low-density oil emulsion and in soil polluted with a medium-density oil emulsion. Sorption–biological treatment increased the rate of hydrocarbon degradation in sand by 3–4 times during the first month and enhanced the overall efficiency by 20% over a three-month period. The use of sorbents (granular activated carbon, thermally activated vermiculite and peat) both in sand and soil prevents secondary pollution of coastal ecosystems, since it significantly reduces the hydrocarbons’ desorption and their leaching by water. Rhodococcus erythropolis HO-KS22, in combination with sorbents, can be applied during the biological remediation of coastal sandy substrates following the initial removal of emergency oil spills. However, for biological treatment of oil-polluted soils of the Barents Sea coast, further selection of active strains of hydrocarbon-oxidizing bacteria resistant to low pH values and temperatures typical for this region is necessary. The use of microbiological preparations without taking into account the soil and climatic factors of the region may be ineffective, which will increase the cost of remediation of the territory without significantly improving its condition. Full article

(This article belongs to the Section Environmental Microbiology)

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20 pages, 4396 KB

Open AccessArticle

Unveiling Species Diversity of Plectosphaerellaceae (Sordariomycetes) Fungi Involved in Rhizome and Root Rots of Ginger in Shandong Province, China

by Qian Zhao, Ao Jia, Hongjuan Yang, Jinming Hu, Xuli Gao, Weiqin Zhao, Lifeng Zhou, Miao Zhang, Zhaoxia Li and Weihua Zhang

Microorganisms 2025, 13(9), 2180; https://doi.org/10.3390/microorganisms13092180 - 18 Sep 2025

Abstract

Ginger holds significant economic importance in both China and worldwide agriculture. Fungi from the family Plectosphaerellaceae are globally recognized as aggressive plant pathogens. However, the effects of Plectosphaerellaceae species on ginger have been poorly understood. In this research, we identified two novel Musidium [...] Read more.

Ginger holds significant economic importance in both China and worldwide agriculture. Fungi from the family Plectosphaerellaceae are globally recognized as aggressive plant pathogens. However, the effects of Plectosphaerellaceae species on ginger have been poorly understood. In this research, we identified two novel Musidium species (M. shandongensis sp. nov. and M. zingiberis sp. nov.), one newly recorded species (Gibellulopsis serrae) and one new host record (Plectosphaerella cucumerina) from the rotten rhizomes and roots of ginger in Shandong Province, China, utilizing morphological observations combined with multilocus phylogenetic analysis of the 28S large subunit (LSU), internal transcribed spacer (ITS) region, and translation elongation factor 1-alpha (TEF1-α) gene, along with pathogenicity analyses. Key diagnostic features include M. shandongensis exhibiting abundant mycelium ropes and coils, M. zingiberis showing dark olivaceous colonies, G. serrae producing brown chlamydospores, and P. cucumerina displaying conspicuous guttulae conidia. Comparative analyses with closely related taxa were based on detailed morphological descriptions, illustrations, and phylogenetic analyses. Artificial inoculation of healthy ginger in vitro and in vivo assays caused characteristic symptoms, such as wilt, leaf yellowing, and rhizome necrosis, identical to those observed on naturally infected plants. Our findings broaden current knowledge on the diversity of Plectosphaerellaceae associated with ginger, revealing them as serious threats to ginger cultivation in China. Full article

(This article belongs to the Special Issue Advances in Fungal Plant Pathogens: Diagnosis, Resistance and Control)

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22 pages, 3210 KB

Open AccessArticle

Amino Acid Balanced Compound Low-Protein Diets Improve Resource Efficiency in Sanhua Goose Production: Impacts on Metabolism, Gut Health, and Microbial Diversity

by Xianze Wang, Huiying Wang, Yi Liu, Guangquan Li, Daqian He, Shufang Chen, Huiyan Jia, Jiuli Dai and Xiao Zhou

Microorganisms 2025, 13(9), 2179; https://doi.org/10.3390/microorganisms13092179 - 18 Sep 2025

Abstract

This study investigated a compound low-protein diet (CLPD) strategy to reduce soybean meal (SBM) dependency in meat geese. Diets were formulated with crude protein (CP) levels decreasing from 16.5% (corn-soybean meal diet, CSD) to 9.8%, incorporating alternative ingredients such as rapeseed meal, corn [...] Read more.

This study investigated a compound low-protein diet (CLPD) strategy to reduce soybean meal (SBM) dependency in meat geese. Diets were formulated with crude protein (CP) levels decreasing from 16.5% (corn-soybean meal diet, CSD) to 9.8%, incorporating alternative ingredients such as rapeseed meal, corn distillers dried grains with solubles (DDGS), broken rice, and rice bran. All diets were balanced for limiting amino acids (lysine, methionine, threonine, and valine) through supplemental synthetic amino acids. A total of 192 four-week-old Sanhua geese were randomly assigned according to a single-factor completely randomized design to four dietary treatment groups: the 16.5% (CSD) group and three CLPD treatment groups (14.0% CP, 11.5% CP, and 9.8% CP). Each treatment consisted of six replicate pens with eight geese per pen. During the six-week trial, evaluations included growth performance, organ weights, nutrient digestibility, serum biochemistry, amino acid profiles, intestinal morphology, and cecal microbiota composition. Results demonstrated that compared to the 16.5% (CSD) group, the 11.5% CP (CLPD) group significantly improved final body weight (p < 0.05), average daily gain (P_Linear < 0.01, p < 0.05), and feed conversion efficiency (P_Linear < 0.01, p < 0.05), alongside enhanced apparent digestibility of crude protein and amino acids (P_Linear < 0.01, p < 0.05). Organ weights were generally stable, though the 9.8% CP (CLPD) group showed reduced liver weight (p < 0.05) and increased abdominal fat (P_Linear < 0.01, p < 0.05). Serum levels of low-density lipoprotein cholesterol increased (P_Linear < 0.05, p < 0.05). Intestinal morphology improved in the duodenum and jejunum: in the duodenum, villus height and villus-to-crypt ratio were significantly increased, and crypt depth was significantly decreased (P_Linear < 0.01, p < 0.05); in the jejunum, villus height was significantly increased (p < 0.05) and crypt depth was significantly decreased (p < 0.05). Cecal microbiota alpha diversity remained consistent. The dominant genera in the 9.8% CP (CLPD) group were unclassified_Oscillospiraceae and unclassified_Ruminococcaceae (p < 0.05), among which, Megamonas, Prevotellaceae_Ga6A1_group, and Rikenellaceae_RC9_gut_group dominated in the 16.5% (CSD) group (p < 0.05). These findings indicate that a compound low-protein diet (CLPD) with 11.5% CP, precisely balanced for limiting amino acids, supports optimal growth performance, improves nutrient utilization, and maintains intestinal health in meat geese. Overall, this offers a viable approach to easing SBM reliance in poultry nutrition while enhancing resource efficiency. Full article

(This article belongs to the Section Veterinary Microbiology)

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18 pages, 5085 KB

Open AccessArticle

Developments in Microbial Communities and Interaction Networks in Sludge Treatment Ecosystems During the Transition from Anaerobic to Aerobic Conditions

by Xiaoli Pan, Lijun Luo, Hui Wang, Xinyu Chen, Yongjiang Zhang, Yan Dai and Feng Luo

Microorganisms 2025, 13(9), 2178; https://doi.org/10.3390/microorganisms13092178 - 18 Sep 2025

Abstract

The transition between anaerobic and aerobic conditions represents a fundamental ecological process occurring ubiquitously in both natural ecosystems and engineered wastewater treatment systems. This study investigated the microbial community succession and co-occurrence network dynamics during the transition from anaerobic sludge to aerobic cultivation. [...] Read more.

The transition between anaerobic and aerobic conditions represents a fundamental ecological process occurring ubiquitously in both natural ecosystems and engineered wastewater treatment systems. This study investigated the microbial community succession and co-occurrence network dynamics during the transition from anaerobic sludge to aerobic cultivation. High-throughput 16S and 18S rDNA sequencing revealed two distinct succession phases: an initial “aerobic adaptation period” (Day 1) and a subsequent “aerobic stable period” (Day 15). Eukaryotic communities shifted from Cryptomycota to the unassigned eukaryotes dominance, while prokaryotic communities maintained Firmicutes and Proteobacteria as core phyla, with persistent low-abundance archaea indicating functional adaptation. Network analysis highlighted predominant co-occurrence patterns between eukaryotic and prokaryotic communities, suggesting synergistic interactions. These findings provide insights into microbial ecological dynamics during anaerobic-to-aerobic transitions, offering potential applications for optimizing wastewater treatment processes. Full article

(This article belongs to the Special Issue Advances in Genomics and Ecology of Environmental Microorganisms)

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20 pages, 4894 KB

Open AccessArticle

Transcriptome Analysis of Chenopodium album in Response to Infection by Botrytis Strain HZ-011

by Haixia Zhu, Le Zhang, Yongqiang Ma and Lu Hou

Microorganisms 2025, 13(9), 2177; https://doi.org/10.3390/microorganisms13092177 - 18 Sep 2025

Abstract

This study conducted a transcriptome sequencing analysis of the interaction between Chenopodium album and Botrytis strain HZ-011 to identify genes involved in the response to fungal infections and elucidate the molecular mechanisms underlying the interaction. High-throughput RNA-seq technology was employed to analyze the [...] Read more.

This study conducted a transcriptome sequencing analysis of the interaction between Chenopodium album and Botrytis strain HZ-011 to identify genes involved in the response to fungal infections and elucidate the molecular mechanisms underlying the interaction. High-throughput RNA-seq technology was employed to analyze the transcriptomes of C. album leaves at 1, 4, and 5 days post-inoculation (dpi) with Botrytis strain HZ-011. The results revealed 11,645 differentially expressed genes (DEGs) at 1 dpi, including 7399 upregulated and 4246 downregulated genes; 11,285 DEGs at 4 dpi (7801 upregulated and 3484 downregulated); and 9976 DEGs at 5 dpi (7723 upregulated and 2253 downregulated). GO functional analysis indicated that downregulated DEGs were significantly enriched in chloroplast and plastid functional expression at 1, 4, and 5 dpi. Following infection by Botrytis strain HZ-011, downregulated genes were significantly enriched in pathways related to photosynthesis, including photosynthetic pathways, light-harvesting antenna proteins, and carotenoid biosynthesis. This suggests that the photosynthetic process in C. album was markedly inhibited, disrupting nutrient supply and leading to herbicidal effects. Notably, genes such as PSB28, PSBP, CAP10A, and CRTL-E-1 were significantly enriched in these pathways, indicating their potential roles in the herbicidal mechanism. These findings provide a foundation for understanding the herbicidal activity of strain HZ-011 and identifying potential targets for developing novel microbial herbicides. Full article

(This article belongs to the Special Issue Signaling Molecules and Their Roles in Plant–Microbe Interactions for Environmental Stress Resilience)

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36 pages, 1750 KB

Open AccessReview

Pattern Recognition Receptors (PRRs) Expression and Activation in COVID-19 and Long COVID: From SARS-CoV-2 Escape Mechanisms to Emerging PRR-Targeted Immunotherapies

by Luca Maddaloni, Ginevra Bugani, Matteo Fracella, Camilla Bitossi, Alessandra D’Auria, Francesca Aloisi, Abir Azri, Letizia Santinelli, Manel Ben M’Hadheb, Alessandra Pierangeli, Federica Frasca and Carolina Scagnolari

Microorganisms 2025, 13(9), 2176; https://doi.org/10.3390/microorganisms13092176 - 17 Sep 2025

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recognized by pattern recognition receptors (PRRs), which play a vital role in triggering innate immune responses such as the production of type I and III interferons (IFNs). While modest PRR activation helps to defend against [...] Read more.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is recognized by pattern recognition receptors (PRRs), which play a vital role in triggering innate immune responses such as the production of type I and III interferons (IFNs). While modest PRR activation helps to defend against SARS-CoV-2, excessive or sustained activation can cause harmful inflammation and contribute to severe Coronavirus Disease 2019 (COVID-19). Altered expression of Toll-like receptors (TLRs), which are among the most important members of the PRR family members, particularly TLRs 2, 3, 4, 7, 8 and 9, has been strongly linked to COVID-19 severity. Furthermore, retinoic acid-inducible gene I (RIG-I) and melanoma differentiation-associated protein 5 (MDA5), collectively known as RLRs (RIG-I-like receptors), act as sensors that detect SARS-CoV-2 RNA. The expression of these receptors, as well as that of different DNA sensors, varies in patients infected with SARS-CoV-2. Changes in PRR expression, particularly that of TLRs, cyclic GMP-AMP synthase (cGAS), and the stimulator of interferon genes (STING), have also been shown to play a role in the development and persistence of long COVID (LC). However, SARS-CoV-2 has evolved strategies to evade PRR recognition and subsequent signaling pathway activation, contributing to the IFN response dysregulation observed in SARS-CoV-2-infected patients. Nevertheless, PRR agonists and antagonists remain promising therapeutic targets for SARS-CoV-2 infection. This review aims to describe the PRRs involved in recognizing SARS-CoV-2, explore their expression during SARS-CoV-2 infection, and examine their role in determining the severity of both COVID-19 and long-term manifestations of the disease. It also describes the strategies developed by SARS-CoV-2 to evade PRR recognition and activation. Moreover, given the considerable interest in modulating PRR activity as a novel immunotherapy approach, this review will provide a description of PRR agonists and antagonists that have been investigated as antiviral strategies against SARS-CoV-2. This review aims to explore the complex interplay between PRRs and SARS-CoV-2 in depth, considering its implications for prognostic biomarkers, targeted therapeutic strategies and the mechanistic understanding of long LC. Additionally, it outlines future perspectives that could help to address knowledge gaps in PRR-mediated responses during SARS-CoV-2 infection. Full article

(This article belongs to the Special Issue Immunity and Viral Immune Evasion Strategies: Recent Insights)

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21 pages, 6074 KB

Open AccessArticle

Therapeutic Potential of Probiotic-Derived P8 Protein as an Anti-Metastatic Agent in Colorectal Cancer

by Byung Chull An, Seungwoo Kim, Jaewon Ha, Sang-Hyuk Seok, Jun Won Park, Yongku Ryu and Myung Jun Chung

Microorganisms 2025, 13(9), 2175; https://doi.org/10.3390/microorganisms13092175 - 17 Sep 2025

Abstract

We previously described the use of probiotics to deliver a Lactobacillus rhamnosus-derived therapeutic protein, P8, which has been identified as a candidate colorectal cancer (CRC) suppressor protein with anti-proliferation and anti-migration activities. P8 was found to penetrate cell membranes by endocytosis, suppressing [...] Read more.

We previously described the use of probiotics to deliver a Lactobacillus rhamnosus-derived therapeutic protein, P8, which has been identified as a candidate colorectal cancer (CRC) suppressor protein with anti-proliferation and anti-migration activities. P8 was found to penetrate cell membranes by endocytosis, suppressing cell proliferation through G₂ cell cycle arrest. Despite the ability of P8 to suppress cell migration in vitro, its mechanism of action in CRC is unclear. We profiled the P8-interacting partner proteins using the pull-down method with His-tagged bait P8 and then identified them by LC-MS/MS. Among the interacting targets, we focused on the mothers against decapentaplegic homolog 1 (Smad1), which is well known as one of the important modulators of the bone morphogenetic protein (BMP)-derived migration pathway in CRC. The present study discovers that P8 prevents the phosphorylation of Smad1 or heterologous complexes within the Smad family, interfering with the importation of Smad1 or its complexes into the nucleus. Thus, P8 significantly inhibits the up-regulation of epithelial–mesenchymal transition (EMT)-related genes mediated by Smad1. P8 also inhibits the morphological changes required for cell migration or adhesion. P8 induces morphologic changes in DLD-1 cells, and their spheroid surfaces, resulting in a significant reduction of the number and length of filopodia, as well as the down-regulation of the expression of myosin X and its accumulation in filopodia tips. This phenomenon seems to be a major negative regulator of cell motility that could be of key importance in metastasis. Use of a mouse model of human CRC metastasis confirmed that P8 significantly suppresses the liver metastatic rate. Probiotic-derived protein P8 significantly suppresses CRC metastasis through inhibition of the Smad1-EMT signal pathway and cell–cell adhesion. Full article

(This article belongs to the Topic News and Updates on Probiotics)

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15 pages, 1350 KB

Open AccessArticle

A Comparative Study of Extended Gentamicin and Tobramycin Release and Antibacterial Efficacy from Palacos and Simplex Acrylic Cements

by Débora Coraça-Huber, Martina Humez and Klaus-Dieter Kühn

Microorganisms 2025, 13(9), 2174; https://doi.org/10.3390/microorganisms13092174 - 17 Sep 2025

Abstract

Antibiotic-loaded bone cements (ALBCs) are used to prevent and treat periprosthetic joint infections (PJI). This study compares the in vitro release and antibacterial effectiveness of gentamicin from Palacos^® R+G and tobramycin from Simplex^® T. Standardized cylindrical specimens of Palacos^® R+G [...] Read more.

Antibiotic-loaded bone cements (ALBCs) are used to prevent and treat periprosthetic joint infections (PJI). This study compares the in vitro release and antibacterial effectiveness of gentamicin from Palacos^® R+G and tobramycin from Simplex^® T. Standardized cylindrical specimens of Palacos^® R+G and Simplex^® T were incubated in phosphate-buffered saline. Antibiotic release was quantified using high-performance liquid chromatography (HPLC) over 14 and 42 days. Antibacterial efficacy was assessed using inhibition zone tests (IZT) against Staphylococcus aureus, Staphylococcus epidermidis, and Escherichia coli over 42 days. Palacos^® R+G exhibited a significantly higher and more sustained antibiotic release of gentamicin compared to tobramycin from Simplex^® T. The cumulative release of gentamicin from Palacos^® R+G was 1.148 µg/cm², while Simplex^® T released 198.87 µg/cm² tobramycin over 14 days. Inhibition zone tests showed that Palacos^® R+G maintained antibacterial activity for 42 days, while Simplex^® T’s activity diminished after 14 days. Statistical analysis confirmed significant differences in antibacterial efficacy between the two cements. Palacos^® R+G demonstrated superior gentamicin release and sustained antibacterial activity compared to tobramycin from Simplex^® T. These findings suggest that Palacos^® R+G may offer better clinical outcomes in preventing and treating PJIs. Full article

(This article belongs to the Special Issue Challenges of Biofilm-Associated Bone and Joint Infections)

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19 pages, 2244 KB

Open AccessArticle

Analysis of Microbial Community Structure and Diversity in Different Soil Use Types in the Luo River Basin

by Li Dai, Xiaolong Hao, Tong Niu, Zhen Liu, Yanmei Wang, Xiaodong Geng, Qifei Cai, Juan Wang, Yongyu Ren, Fangming Liu, Hongen Liu and Zhi Li

Microorganisms 2025, 13(9), 2173; https://doi.org/10.3390/microorganisms13092173 - 17 Sep 2025

Abstract

The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, [...] Read more.

The Luohe River boasts a profound historical heritage. Due to long-term impacts of human activities along its banks, significant variations in soil environmental conditions may exist across different land use types within the region. This study focused on four land use types (farmland, bamboo forest, grassland, and abandoned land) in Luoning County of the Luohe River Basin and employed high-throughput sequencing technology to analyze the characteristics of soil microbial communities and differences in soil nutrients. The results showed the following: There were significant differences in soil nutrients and microbial diversity among different land use types. Specifically, the organic matter content in farmland was significantly higher than that in bamboo forests (p < 0.05), and the available phosphorus content in farmland was significantly higher than that in abandoned land (p < 0.05); the abandoned land had a significant advantage in alkali-hydrolyzable nitrogen and available potassium contents (p < 0.05) but the lowest soil water content (p < 0.05). Microbial diversity indices indicated that Pielou’s evenness index (Pieloue) in farmland was significantly higher than that in grassland. The bacterial community was dominated by Acidobacteria, Proteobacteria, and Actinobacteria. At the genus level, available potassium was the key factor affecting the top 20 dominant bacterial genera. Redundancy Analysis (RDA) showed that pH was the core environmental variable driving the variation of bacterial community structure. Metabolic pathway analysis revealed that biosynthetic metabolism was the main pathway, and grassland exhibited outstanding performance in the secondary metabolite synthesis pathway. The results of this study fill the gap in soil microbial ecology research in this region and provide a theoretical basis for the sustainable utilization of land resources and agricultural ecological management in the Luohe River Basin. Full article

(This article belongs to the Special Issue Restoring the Integrated Behaviour of the Soil-Plant-Microbe System, 2nd Edition)

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24 pages, 6096 KB

Open AccessArticle

Impacts of Lead and Nanoplastic Co-Exposure on Decomposition, Microbial Diversity, and Community Assembly Mechanisms in Karst Riverine Miscanthus Litter

by Peijian Chen, Tianjiao Mei, Xingbing He, Yonghui Lin, Zaihua He and Xiangshi Kong

Microorganisms 2025, 13(9), 2172; https://doi.org/10.3390/microorganisms13092172 - 17 Sep 2025

Abstract

Karst rivers are increasingly contaminated by both heavy metals and nanoplastics, yet their combined impact on riparian litter decomposition remains unresolved. We conducted a 90-day microcosm experiment using Miscanthus floridulus leaf litter collected from the Donghe River, Jishou, China, and exposed it to [...] Read more.

Karst rivers are increasingly contaminated by both heavy metals and nanoplastics, yet their combined impact on riparian litter decomposition remains unresolved. We conducted a 90-day microcosm experiment using Miscanthus floridulus leaf litter collected from the Donghe River, Jishou, China, and exposed it to Pb (1 mg L⁻¹), polystyrene nanoplastics (10 and 100 µg L⁻¹), and their combinations. Pb alone modestly inhibited mass loss (61.0%) and respiration, while NP10 significantly accelerated decomposition (67.0%), and NP100 suppressed it (60.4%); co-exposure produced non-monotonic, concentration-dependent effects. Enzyme stoichiometry revealed that all treatments intensified nitrogen limitation but alleviated carbon limitation through reduced microbial activity. Bacterial communities, dominated by Pseudomonadota, exhibited remarkably stable phylum-level composition, high network complexity, and identical keystone taxa across all treatments, indicating strong functional redundancy and resilience. In contrast, fungal communities suffered severe declines in Basidiomycota abundance, collapsed network stability, and a single keystone taxon, underscoring their vulnerability. βNTI–RC_bray analyses demonstrated that stochastic processes (>50%) overwhelmingly governed both bacterial and fungal assembly, with only marginal deterministic shifts. Collectively, our findings highlight that bacteria—not fungi—serve as the primary decomposers under Pb–NP co-stress and that stochastic assembly, coupled with bacterial redundancy, buffers ecosystem function against emerging mixed pollutants in subtropical riverine systems. Full article

(This article belongs to the Collection Biodegradation and Environmental Microbiomes)

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15 pages, 1808 KB

Open AccessArticle

Strain-Dependent Thermoadaptation in the Fish Pathogen Aeromonas salmonicida subsp. salmonicida

by Kim C. Fournier, Pierre-Étienne Marcoux, Antony T. Vincent and Steve J. Charette

Microorganisms 2025, 13(9), 2171; https://doi.org/10.3390/microorganisms13092171 - 17 Sep 2025

Abstract

Strains of Aeromonas salmonicida subsp. salmonicida, a major pathogen of salmonids, typically do not grow at temperatures above 30 °C. The effects of thermal stress on this bacterium have been extensively studied. Recently, we demonstrated that repeated exposure to cyclical thermal stress, [...] Read more.

Strains of Aeromonas salmonicida subsp. salmonicida, a major pathogen of salmonids, typically do not grow at temperatures above 30 °C. The effects of thermal stress on this bacterium have been extensively studied. Recently, we demonstrated that repeated exposure to cyclical thermal stress, reaching up to 37 °C, can induce permanent thermoadaptation in certain strains of this bacterium. Many aspects of this adaptation process remain poorly understood. We generated 88 thermoadapted strains of A. salmonicida subsp. salmonicida capable of sustained growth at 33 °C or higher demonstrating that prolonged heat exposure can shift a substantial proportion of psychrophilic strains toward a more mesophilic-like behavior. Although growth at 35 °C was still weaker than in naturally mesophilic A. salmonicida strains, some thermoadapted strains were able to grow up to 37 °C. North American strains harboring the genomic island AsaGEI1a, a known biomarker, exhibited a significantly reduced capacity for thermoadaptation, suggesting a possible genetic constraint, although genomic analyses indicate that AsaGEI1a itself is not directly responsible for this limitation. Genotyping and phenotypic analyses revealed that thermoadaptation is frequently associated with the loss of Type III secretion system and the A-layer, two key virulence factors. Only 7% of the thermoadapted strains retained both features. Overall, our findings suggest that thermoadaptation may represent a potential mechanism influencing the persistence of some psychrophilic A. salmonicida subsp. salmonicida strains in warming aquatic environments under climate change. Full article

(This article belongs to the Section Veterinary Microbiology)

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23 pages, 1594 KB

Open AccessArticle

Bioprospecting of Goat Rumen Microbiota for Optimum Cellulase Enzyme Production to Support Sustainable Bioenergy Systems

by Kgodiso J. Rabapane and Tonderayi S. Matambo

Microorganisms 2025, 13(9), 2170; https://doi.org/10.3390/microorganisms13092170 - 17 Sep 2025

Abstract

This study reports the isolation and optimization of cellulase-producing bacteria from the gastrointestinal tract of South African goats for the pretreatment of lignocellulosic biomass in bioenergy applications. Among the isolates, three strains, Bacillus KC50, Bacillus KC70, and Proteus mirabilis KC94, were identified by [...] Read more.

This study reports the isolation and optimization of cellulase-producing bacteria from the gastrointestinal tract of South African goats for the pretreatment of lignocellulosic biomass in bioenergy applications. Among the isolates, three strains, Bacillus KC50, Bacillus KC70, and Proteus mirabilis KC94, were identified by 16S rDNA sequencing. To our knowledge, this is the first report of cellulolytic optimization in P. mirabilis derived from goat rumen. Enzyme production was optimized under varying pH, temperature, and incubation conditions. P. mirabilis KC94 exhibited robust enzyme activity at pH 7 and 35 °C, with stability across a broader range than the Bacillus strains. Peak activity occurred at 84 h of incubation, reflecting strain-specific metabolic adaptation. The presence of organic solvents and surfactants inhibited enzyme activity, whereas mild oxidative stress induced by H₂O₂ stimulated cellulase production. Amplification of GH39, GH45, and GH48 genes revealed KC94’s strong genetic potential for efficient lignocellulose degradation. These findings highlight the biotechnological potential of rumen-derived cellulolytic bacteria, particularly P. mirabilis KC94, for advancing sustainable bioenergy systems. Full article

(This article belongs to the Special Issue Advances in Microbial Cell Factories, 3rd Edition)

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9 pages, 723 KB

Open AccessArticle

Real-Time PCR Test (Flora Select™) for Assessing the Effectiveness of Bacterial Vaginosis Treatment During Pregnancy

by Hajime Ota, Shigeki Shimada, Yuta Kobayashi, Tatsuya Yoshiwara, Osamu Yoshino, Yoshiyuki Fukushi, Shinichiro Wada, Soromon Kataoka and Hideto Yamada

Microorganisms 2025, 13(9), 2169; https://doi.org/10.3390/microorganisms13092169 - 17 Sep 2025

Abstract

Preterm birth is a major cause of perinatal mortality and morbidity in newborns, and its risk is increased by bacterial vaginosis (BV) during pregnancy. This multicenter prospective cohort study aimed to evaluate whether Flora select™ (FS), a newly developed real-time polymerase chain reaction [...] Read more.

Preterm birth is a major cause of perinatal mortality and morbidity in newborns, and its risk is increased by bacterial vaginosis (BV) during pregnancy. This multicenter prospective cohort study aimed to evaluate whether Flora select™ (FS), a newly developed real-time polymerase chain reaction test, is clinically useful for assessing the effectiveness of BV treatment during pregnancy. The vaginal microbiome characterized by relative dominance rates of Lactobacillus ≤ low (<50%), together with a positive test for Gardnerella, Prevotella, or Atopobium species, was defined as BV-FS A criterion. The vaginal microbiome characterized by Lactobacillus medium (50%≤, <80%), together with positive tests for Gardnerella plus either Prevotella species or Atopobium species, was defined as BV-FS B criterion. This study enrolled 25 pregnant women with classical BV (Nugent score ≥ 7) at initial examinations, and they met the BV-FS A (n = 23) and BV-FS B (n = 2) criteria. No woman with classical BV had a missed diagnosis of molecular BV. Treatments with metronidazole vaginal tablets resulted in the improvement of 88.0% (22/25) of classical BV, 65.2% (15/23) of BV-FS A, and 50.0% (1/2) of BV-FS B cases, whereas positive rates of Ureaplasma species in women with classical BV increased by 42.9%. Although most classical BV cases were cured following metronidazole treatments, a considerable proportion still harbored molecular BV detected by FS. Although the Nugent scoring system revealed that 80.0% (20/25) of women with classical BV (Nugent score ≥ 7) were sufficiently cured as BV-negative (Nugent scores 0–3), 5 (25%) of the 20 cured cases still met the BV-FS A/B criteria. FS particularly detected Ureaplasma species in 9 (45%) of the 20 cured cases. It could identify pregnant women who require additional treatments for residual molecular BV and Ureaplasma species. Therefore, the FS test may be clinically useful for assessing the vaginal microbiome and evaluating the effectiveness of BV treatments. Full article

(This article belongs to the Special Issue Editorial Board Members’ Collection Series: Bacterial Infection)

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21 pages, 9517 KB

Open AccessArticle

Genomic and Transcriptomic Profiling of a Highly Virulent Plesiomonas shigelloides Strain: Insights into Pathogenicity and Host Immune Response

by Zhixiu Wang, Shaoxuan Gu, Wen Lv, Jiayi Chen, Min Xue, Suli Liu, Jiaming Mao and Guohong Chen

Microorganisms 2025, 13(9), 2168; https://doi.org/10.3390/microorganisms13092168 - 17 Sep 2025

Abstract

Plesiomonas shigelloides, a Gram-negative bacterium prevalent in aquatic environments and also frequently isolated from livestock and poultry, was investigated through integrated whole-genome sequencing and functional analyses. We deciphered the pathogenic mechanisms of P. shigelloides CA-HZ1, a highly virulent strain isolated from a [...] Read more.

Plesiomonas shigelloides, a Gram-negative bacterium prevalent in aquatic environments and also frequently isolated from livestock and poultry, was investigated through integrated whole-genome sequencing and functional analyses. We deciphered the pathogenic mechanisms of P. shigelloides CA-HZ1, a highly virulent strain isolated from a novel piscine host, revealing a complete genome assembly with a 3.49 Mb circular chromosome and 311 kb plasmid housing 3247 predicted protein-encoding genes. Critical genomic features included 496 virulence factors and 225 antibiotic resistance genes. Pathogenicity analysis indicated that P. shigelloides was responsible for disease outbreaks. Antimicrobial susceptibility tests showed resistance to various drugs, such as kanamycin, erythromycin, and penicillin. Histopathological examination showed significant alterations in the infected hosts. Quantitative real-time PCR (qRT-PCR) was carried out to analyze immune-related gene (IL-6, IL-1β, IL-21, STAT1, and HSP70) levels in liver and intestinal tissues, demonstrating the potent immunity triggered by P. shigelloides infection. An analysis of the liver transcriptome revealed that P. shigelloides has the potential to influence the cellular composition, molecular functions, and biological processes. Collectively, this study describes the genomic basis underlying both the pathogenic potential and hypervirulence of P. shigelloides CA-HZ1, establishing a foundational framework for investigating its broad host tropism and immune response. Full article

(This article belongs to the Section Veterinary Microbiology)

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22 pages, 1743 KB

Open AccessArticle

Water Parameters Predicting the Seasonal and Spatial Dynamics of the Vibrio Harveyi- and Splendidus-Clade Pathogens

by Karagan Royer and Andrei L. Barkovskii

Microorganisms 2025, 13(9), 2167; https://doi.org/10.3390/microorganisms13092167 - 17 Sep 2025

Abstract

Vibrio species of the Harveyi and Splendidus clades are the causative agents of vibriosis, resulting in mortality rates of up to 100% in common aquaculture species. They are primarily responsible for seafood-related illnesses in humans, causing gastroenteritis. Except for V. parahaemolyticus, the [...] Read more.

Vibrio species of the Harveyi and Splendidus clades are the causative agents of vibriosis, resulting in mortality rates of up to 100% in common aquaculture species. They are primarily responsible for seafood-related illnesses in humans, causing gastroenteritis. Except for V. parahaemolyticus, the ecological behaviour of these pathogens is poorly understood. We investigated the spatial and temporal distribution of V. parahaemolyticus, V. alginolyticus, V. harveyi/V. campbellii, and V. splendidus in three Georgia (USA) grounds for Crassostrea virginica and Mercenaria mercenaria. DNA from oysters, clams, water, and sediment was collected over a year-long study and analyzed using quantitative PCR (qPCR) to assess the prevalence and concentrations of the above Vibrio species. The study targeted the tlh, VA1198230, rpoA, and recA genes using species-specific primers. Species abundance was estimated based on the concentrations of the corresponding genes. The species abundance was profiled for water parameters and concentrations of the clade-specific virulence genes toxR, luxR, srp, vhhA, vhh, and vhp that were previously detected in the study area. V. parahaemolyticus was the most common species, detected year-round in 61% and 44% of the water and sediment samples, respectively, followed by V. splendidus (67% and 17%) and V. harveyi/V. campbellii (19% and 33%). V. alginolyticus was rarely detected in water and never in sediment. In bivalves, the highest frequency was observed for V. parahaemolyticus. This species was detected in 89% of clam and 100% of oyster samples, followed by V. alginolyticus (22% and 17%) and V. splendidus at 17% in both species. No V. harveyi/V. campbellii has been detected in clams and oysters. Seasonal dynamics and concentrations varied between the species. Water temperature (r = 0.58–0.63, p ≤ 0.05), pH (r = −0.46), and dissolved oxygen (r = −0.42 to −0.56, p ≤ 0.05) were reliable predictors for the abundance of the Harveyi and Splendidus clade pathogens in bivalves and the water column, but not in sediments. In water and sediments, the abundances of V. harveyi/V. campbellii and V. parahaemolyticus were highly correlated (r = 0.80–0.99, p ≤ 0.001) to concentrations of most of the virulence genes, with some heterogeneities between the sites. The study revealed the species-specific dynamic of the Harveyi and Splendidus clade pathogens, provided the first evidence for the presence of V. harveyi/V. campbellii in the Atlantic USA waters, and identified environmental predictors for monitoring the Harveyi and Splendidus clade pathogens in mollusks and the water column. Full article

(This article belongs to the Section Environmental Microbiology)

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14 pages, 1044 KB

Open AccessReview

Aquatic Chlamydiae: A Review of Their Roles in Fish Health

by Basma Mahmoud-Elkamouny, Carole Kebbi-Beghdadi and Gilbert Greub

Microorganisms 2025, 13(9), 2166; https://doi.org/10.3390/microorganisms13092166 - 17 Sep 2025

Abstract

Aquaculture plays a vital role in meeting the global demand for high-quality protein. However, the fish industry is challenged by infectious diseases, including gill conditions such as epitheliocystis. Epitheliocystis is characterized by cyst-like epithelial lesions, which occur in the gills of fish, and [...] Read more.

Aquaculture plays a vital role in meeting the global demand for high-quality protein. However, the fish industry is challenged by infectious diseases, including gill conditions such as epitheliocystis. Epitheliocystis is characterized by cyst-like epithelial lesions, which occur in the gills of fish, and is associated with intracellular bacteria including Chlamydia-related bacteria. Although epitheliocystis was initially regarded as of low significance, attention is increasing due to its impact on commercially important fish species in intense farming conditions. This review evaluates the roles of aquatic chlamydiae as pathogens contributing to fish morbidity and mortality, and as members of fish microbiota. Additionally, Chlamydia-related bacteria are thought to be involved in complex gill disease (CGD), characterized by lamellar fusion, epithelial hyperplasia, and inflammation. Recent discoveries have expanded the diversity of Chlamydiota isolated from fish, with novel species such as Candidatus (Ca.) Panilichlamydia rohitae, Ca. Piscichlamydia trichopodus, and Chlamydia vaughanii identified in different fish hosts. Most causative agents of epitheliocystis have not yet been cultured in vitro, although C. vaughanii, the first Chlamydiaceae member isolated from fish, was successfully cultured. As C. vaughanii was recently shown to be able to propagate in mammalian cells, it raises concerns about its zoonotic potential, although a pathogenic role has yet to be described. Full article

(This article belongs to the Section Veterinary Microbiology)

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19 pages, 2506 KB

Open AccessArticle

Evaluation of the Impact of Coinfection and Superinfection on Chikungunya and Mayaro Viruses’ Replication in Aedes aegypti

by Maria Eduarda dos Santos Pereira de Oliveira, Larissa Krokovsky, Maria Júlia Brito Couto, Duschinka Ribeiro Duarte Guedes, George Tadeu Nunes Diniz, Constância Flávia Junqueira Ayres and Marcelo Henrique Santos Paiva

Microorganisms 2025, 13(9), 2165; https://doi.org/10.3390/microorganisms13092165 - 17 Sep 2025

Abstract

The simultaneous circulation of multiple arboviruses, often driven by (re)emergence events, poses challenges to public health systems. In Brazil, the co-circulation of Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHIKV), and Oropouche virus (OROV), together with the potential urban emergence of Mayaro [...] Read more.

The simultaneous circulation of multiple arboviruses, often driven by (re)emergence events, poses challenges to public health systems. In Brazil, the co-circulation of Dengue virus (DENV), Zika virus (ZIKV), Chikungunya virus (CHIKV), and Oropouche virus (OROV), together with the potential urban emergence of Mayaro virus (MAYV), underscores the importance of understanding interactions among these pathogens within their vectors. This study investigated the effects of CHIKV and MAYV coinfection and superinfection on replication dynamics in Aedes aegypti. Mosquitoes were experimentally exposed to CHIKV and MAYV through artificial blood meals under coinfection and superinfection conditions. Infection (IR), dissemination (DR), and transmission (TR) rates, as well as viral loads, were quantified by quantitative reverse transcription PCR (qRT-PCR). To confirm viral replication and assess cytopathic effects, positive saliva samples were inoculated in Vero cells, followed by serial passages and plaque assays for viral titration. The results showed that Ae. aegypti is capable of transmitting both CHIKV and MAYV concurrently during coinfection. However, in superinfection scenarios, prior infection with either virus significantly reduced the transmission efficiency of the subsequently acquired virus, indicating viral interference at the replication level. These findings underscore the complexity of arboviral interactions within vectors and highlight their potential implications for transmission dynamics. Continuous entomo-virological surveillance and targeted research are essential for anticipating and mitigating the impact of arboviral co-circulation in endemic regions. Full article

(This article belongs to the Special Issue Emerging Trends in Arboviral Research: Surveillance, Diagnostics, Virus–Host Interactions, and Therapeutic Strategies)

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