Microbiology Research

19 pages, 1037 KiB

Open AccessReview

Evolution and Functional Diversity of GATA Transcription Factors in Filamentous Fungi: Structural Characteristics, Metabolic Regulation and Environmental Response

by Danni Hu, Ruoyu Zhao, Yingxu Lin and Chunmiao Jiang

Microbiol. Res. 2025, 16(6), 120; https://doi.org/10.3390/microbiolres16060120 - 6 Jun 2025

Abstract

Filamentous fungi hold critical industrial value for their ability to produce enzymes, antibiotics, organic acids, and food fermentation. GATA transcription factors (TFs) serve as central regulators of nitrogen metabolism, synthesis of secondary metabolites, stress adaptation, and directly influence fungal development and pathogenicity in [...] Read more.

Filamentous fungi hold critical industrial value for their ability to produce enzymes, antibiotics, organic acids, and food fermentation. GATA transcription factors (TFs) serve as central regulators of nitrogen metabolism, synthesis of secondary metabolites, stress adaptation, and directly influence fungal development and pathogenicity in filamentous fungi. In this review, we primarily discuss the structural characterization, different types, and phylogenetic analysis of filamentous fungi GATA TFs in filamentous fungi. Subsequently, we systematically summarize the multifunctions of GATA TFs in the mycelial growth, morphological differentiation, and conidial development of filamentous fungi. In addition, we explore their functions in the synthesis of secondary metabolites such as antibiotics (e.g., cephalosporins, penicillins) and organic acids (e.g., ganoderic acid, fumaric acid) in filamentous fungi. Furthermore, we focus on the key roles of GATA TFs AreA and AreB in nitrogen and carbon metabolism in filamentous fungi and their potential synergistic regulatory relationships. Finally, we review the important roles of GATA TFs in the adaptation of filamentous fungi to environmental changes. This review provides research ideas for the development of genetically engineered strains with optimized growth characteristics, increased target metabolites in the fermentation production process, and enhanced environmental adaptability. Full article

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13 pages, 495 KiB

Open AccessArticle

Distribution of Treponema Species in Active Digital Dermatitis Lesions and Non-Lesional Skin of Dairy Cattle

by Simona Mekková, Miriam Sondorová, Natália Šurín Hudáková, Viera Karaffová, Marián Maďar, Pavel Gomulec and Pavol Mudroň

Microbiol. Res. 2025, 16(6), 119; https://doi.org/10.3390/microbiolres16060119 - 5 Jun 2025

Abstract

This study examined the prevalence, distribution, and detection methods linked to Treponema species associated with active bovine digital dermatitis (BDD) in dairy cattle. Tissue, surface swabs, interdigital space swabs, and faecal samples were collected from 20 Holstein-Friesian cows from a farm in Eastern [...] Read more.

This study examined the prevalence, distribution, and detection methods linked to Treponema species associated with active bovine digital dermatitis (BDD) in dairy cattle. Tissue, surface swabs, interdigital space swabs, and faecal samples were collected from 20 Holstein-Friesian cows from a farm in Eastern Slovakia. Molecular analysis revealed that all cows tested positive for at least one Treponema species. The most prevalent species were Treponema medium (100%), Treponema pedis (95%), and Treponema brennaborense (75%). Distribution analysis demonstrated significant differences in the occurrence of these species across sampling methods, with T. pedis being more prevalent in tissue biopsies and surface swabs (p < 0.001), and T. brennaborense in surface swabs (p < 0.001). A comparison of qualitative real-time PCR and standard PCR revealed that real-time PCR detected T. pedis and T. brennaborense in 70% and 75% of tissue samples, respectively, while standard PCR failed to detect T. brennaborense. Furthermore, real-time PCR showed a significantly higher prevalence of T. brennaborense (p < 0.001). These findings underscore the enhanced sensitivity of real-time PCR in detecting T. brennaborense and highlight the complex distribution of Treponema species in BDD lesions, which may inform the development of more effective control strategies for BDD. Full article

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19 pages, 4087 KiB

Open AccessArticle

The Global Antimicrobial Resistance Trends of Staphylococcus aureus and Influencing Factors

by Haitao Yuan, Jie Xu, Ying Wang, Yuan Li, Yuqing Hao, Jinzhao Long, Fang Liu, Jingyuan Zhu and Haiyan Yang

Microbiol. Res. 2025, 16(6), 118; https://doi.org/10.3390/microbiolres16060118 - 4 Jun 2025

Abstract

The increase in the antimicrobial resistance (AMR) of Staphylococcus aureus (S. aureus) has become a global public health concern. This study globally monitored the large-scale longitudinal trend of AMR in S. aureus and examined the various human and environmental climate factors [...] Read more.

The increase in the antimicrobial resistance (AMR) of Staphylococcus aureus (S. aureus) has become a global public health concern. This study globally monitored the large-scale longitudinal trend of AMR in S. aureus and examined the various human and environmental climate factors that influence the occurrence and spread of AMR in S. aureus, which might provide valuable data to support the development of a global surveillance system for S. aureus AMR and provide a theoretical basis for coordinated actions to control the emergence and development of AMR from multiple perspectives. There was a significantly positive correlation between the number of antibiotic resistance genes (ARGs) in S. aureus and the collection year, with a sharp increase in ARGs over time. The number of ARGs in S. aureus genomes significantly increased each decade, with the average number of ARGs per genome rising from 10.37 ± 3.55 before 1990 to 12.75 ± 4.04 after 2010, suggesting a growing problem of S. aureus AMR. The Spearman correlation results indicated that the human development index (HDI), antibiotic consumption, and mobile genetic elements (MGEs) were significantly associated with the AMR of S. aureus, and these factors played a crucial role in the emergence and development of S. aureus AMR. The results of structural equation modeling showed that the HDI significantly promoted an increase in antibiotic consumption, thereby indirectly enhancing the AMR of S. aureus. Antibiotic consumption also indirectly facilitated the progression of AMR in S. aureus through its impact on MGEs. The results of restricted cubic spline and generalized linear models showed that climate change also played a significant role in the progression of S. aureus AMR. In summary, this study provides a theoretical framework for monitoring the longitudinal trend of ARGs in S. aureus isolates and examining the possible influencing variables of ARGs in these isolates. Full article

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16 pages, 2028 KiB

Open AccessArticle

Succession Characteristics of Soil Microbial Communities Along Elevational Gradients in the Lhasa River Basin and Analysis of Environmental Driving Factors

by Xiaoyu Li, Xiangyang Sun, Baosheng An, Suyan Li, Jiule Li and Chuanfei Wang

Microbiol. Res. 2025, 16(6), 117; https://doi.org/10.3390/microbiolres16060117 - 4 Jun 2025

Abstract

The Qinghai-Xizang Plateau is among the most ecologically vulnerable and responsive areas worldwide. Studying the characteristics of soil microbial communities along altitudinal gradients on plateaus and revealing the response mechanisms and vertical distribution patterns of microbial communities in alpine ecosystems is of significant [...] Read more.

The Qinghai-Xizang Plateau is among the most ecologically vulnerable and responsive areas worldwide. Studying the characteristics of soil microbial communities along altitudinal gradients on plateaus and revealing the response mechanisms and vertical distribution patterns of microbial communities in alpine ecosystems is of significant academic value for assessing the ecological stability of the Qinghai-Xizang Plateau. This research examines the Lhasa River Basin by employing Illumina NovaSeq high-throughput sequencing to investigate how soil bacterial and fungal communities shift across elevation gradients in the Duilong Qu subbasin. This study also explored the key environmental drivers behind these microbial distribution patterns. The results indicate the following: (1) Key bacterial groups in the Duilong Qu Basin soil include Proteobacteria, Acidobacteria, and Actinobacteria, with Ascomycota, Mortierellomycota, and Basidiomycota as the prevalent fungal phyla. (2) Soil bacterial richness fluctuates with increasing elevation, and diversity exhibits a V-shaped distribution; fungal richness increases monotonically with elevation, whereas diversity shows no altitudinal dependence. (3) Principal coordinate analysis (PCoA) revealed that bacterial community structures exhibit separation trends across different elevations, with high intragroup consistency; fungal community structures at mid-elevations (4000–5000 m) show clustering similarity, whereas those at 3650–5000 m and 5500 m remain highly distinct from those at other elevations. (4) RDA reveals that factors such as accessible phosphorus, potassium, and organic content have a major effect on how bacterial communities are arranged. On the other hand, soil conductivity, along with available and total phosphorus levels, as well as pH, plays a key role in shaping fungal communities. (5) Functional prediction analysis suggests that soil bacteria shift from aerobic and biofilm-forming to facultatively anaerobic, stress-tolerant, and pathogenic traits with increasing elevation. Fungi are predominantly undefined saprotrophs, transitioning from ectomycorrhizal and pathogenic functions to saprotrophic functions at relatively high elevations. Full article

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13 pages, 893 KiB

Open AccessArticle

HIV-1 and Antiretroviral Therapy Modulate HERV Pol and Syncytin Gene Expression in Mothers and Newborns

by Anna Pau, Ilaria Galliano, Stefano Gambarino, Anna Clemente, Paola Montanari, Cristina Calvi, Pier-Angelo Tovo and Massimiliano Bergallo

Microbiol. Res. 2025, 16(6), 116; https://doi.org/10.3390/microbiolres16060116 - 3 Jun 2025

Abstract

Background: Human endogenous retroviruses (HERVs) are remnants of ancestral retroviral infections integrated into the human genome, some of which maintain a residual active expression and retain physiological relevance. HIV-1 infection and antiretroviral therapy (ART) are known to modulate HERV expression, yet their specific [...] Read more.

Background: Human endogenous retroviruses (HERVs) are remnants of ancestral retroviral infections integrated into the human genome, some of which maintain a residual active expression and retain physiological relevance. HIV-1 infection and antiretroviral therapy (ART) are known to modulate HERV expression, yet their specific effects during pregnancy remain poorly understood. This study aimed to investigate the peripartum transcriptional activity of selected HERV sequences in HIV-1-positive women receiving ART and their newborns exposed to the therapy and HIV-1-negative healthy controls. Methods: We quantified the expression of pol regions of HERV-H, -K, and -W and of Syncytin 1 and Syncytin 2 in peripheral blood samples collected at delivery using real-time PCR. Results: In HIV-1-positive mothers on ART therapy, we observed a significant downregulation in the pol gene expression of HERV-H, HERV-K, and HERV-W, as well as of Syncytin 1 and Syncytin 2, compared to healthy mothers. In contrast, no differences in the expression of the different targets were found in the two groups of newborns. All the HERV genes analyzed were also found to be expressed at significantly higher levels in the newborns compared to their mothers. Discussion: The results obtained suggest that antiretroviral therapy may influence and modulate HERV expression during pregnancy in both the mother and the fetus. Full article

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13 pages, 2095 KiB

Open AccessArticle

Microbial Inoculants and Fertilizer Reduction in Sorghum Cultivation: Implications for Sustainable Agriculture

by Luana Beatriz Gonçalves, Carlos Henrique Barbosa Santos, Dalilla Berlanda de Lima Gonilha, Edvan Teciano Frezarin, Matheus Toller Pires da Costa and Everlon Cid Rigobelo

Microbiol. Res. 2025, 16(6), 115; https://doi.org/10.3390/microbiolres16060115 - 3 Jun 2025

Abstract

Sorghum (Sorghum bicolor L. Moench) is a versatile cereal crop with diverse applications in human food, animal feed, and other industries. This study investigated the effects of microbial inoculation on sorghum growth and nutrient uptake at two fertilizer levels (100% and 80% [...] Read more.

Sorghum (Sorghum bicolor L. Moench) is a versatile cereal crop with diverse applications in human food, animal feed, and other industries. This study investigated the effects of microbial inoculation on sorghum growth and nutrient uptake at two fertilizer levels (100% and 80% of the recommended dose). Bacillus subtilis, B. pumilus, B. licheniformis, Purpureocillium lilacinum, and Trichoderma harzianum were applied to the soil and plants in a greenhouse experiment using a completely randomized design with six replicates per treatment. Plant growth parameters, including height, shoot and root dry matter, nitrogen and phosphorus content in the shoots and roots and chlorophyll, were assessed. The results showed no statistically significant differences among the treatments for most parameters, except for plant height and shoot dry matter, where the B. subtilis treatment exhibited the lowest values. Notably, treatments that received 80% of the recommended fertilizer dose performed similarly to those that received 100%, suggesting the potential for reduced fertilizer usage with microbial inoculants. Although the microbial treatments did not significantly enhance sorghum growth in this study, evaluating their effects remains crucial for developing eco-friendly alternatives to reduce chemical fertilizers. Further research is needed to optimize the application of microbial inoculants and to understand their impact on soil health and agricultural productivity under various environmental conditions. Full article

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12 pages, 1573 KiB

Open AccessArticle

Therapeutic Effects of Lycopene Alone or in Combination with Cephalexin on Chronic Prostatitis Caused by Staphylococcus aureus in a Rat Model

by Soumia Keddari, Djahira Hamed, Abla Bouhend, Mokhtaria Yasmina Boufadi, Meriem Mokhtar, Bouasria Benbouziane, Nabil Touzout, Sabrina Lekmine, Jie Zhang, Abdeltif Amrane and Hichem Tahraoui

Microbiol. Res. 2025, 16(6), 114; https://doi.org/10.3390/microbiolres16060114 - 2 Jun 2025

Abstract

Chronic bacterial prostatitis (CBP) is caused by bacterial infection, commonly treated with fluoroquinolones. Due to rising antibiotic resistance, alternative therapies such as phytotherapy are being explored. Lycopene, a potential antioxidant with anti-inflammatory properties, is a candidate for such therapy. This study aims to [...] Read more.

Chronic bacterial prostatitis (CBP) is caused by bacterial infection, commonly treated with fluoroquinolones. Due to rising antibiotic resistance, alternative therapies such as phytotherapy are being explored. Lycopene, a potential antioxidant with anti-inflammatory properties, is a candidate for such therapy. This study aims to evaluate lycopene’s therapeutic effects alone or with cephalexin against chronic prostate infections induced by Staphylococcus aureus using the Wistar rat model. The CBP model was established by introducing S. aureus through the urethra into the prostatic duct in 25 rats, confirming infection via uriculture and spermoculture analysis. Infected rats (n = 21) were grouped randomly: G1 (control), G2 (lycopene), G3 (cephalexin), and G4 (lycopene/cephalexin), in addition to negative control (G5) with healthy rats. Treatments were administered intragastrically, two times per day for 2 weeks: lycopene (10 mg/kg), cephalexin (2.5 mg/kg), or both. Biological samples (blood, urine, and prostate specimens) were collected for microbiological and histological analysis. The results showed a significant reduction in bacterial counts in urine and prostate (p < 0.01), especially in the group treated with both lycopene and cephalexin. This group also exhibited notable anti-inflammatory effects compared to single-treatment and control groups. In conclusion, lycopene combined with cephalexin demonstrated a beneficial synergistic effect, indicating its potential as an effective treatment for CBP caused by S. aureus. Full article

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25 pages, 2854 KiB

Open AccessReview

Ellagitannins and Their Derivatives: A Review on the Metabolization, Absorption, and Some Benefits Related to Intestinal Health

by Erick M. Raya-Morquecho, Pedro Aguilar-Zarate, Leonardo Sepúlveda, Mariela R. Michel, Anna Iliná, Cristóbal N. Aguilar and Juan A. Ascacio-Valdés

Microbiol. Res. 2025, 16(6), 113; https://doi.org/10.3390/microbiolres16060113 - 2 Jun 2025

Abstract

Ellagitannins are bioactive phenolic acids found in various fruits, plants, and beverages such as wine and spirits. This review aims to discuss the metabolism, absorption, and some health benefits related to the intestinal activity of these molecules, as well as some supplements developed [...] Read more.

Ellagitannins are bioactive phenolic acids found in various fruits, plants, and beverages such as wine and spirits. This review aims to discuss the metabolism, absorption, and some health benefits related to the intestinal activity of these molecules, as well as some supplements developed from them. Ellagitannins are first biodegraded to ellagic acid and then to urolithins, which are more easily absorbed. This process is mediated by specific enzymes and intestinal microbiota. Not all individuals can metabolize ellagitannins into urolithins due to differences in the composition of the intestinal microbiota, resulting in three phenotypes: metabotypes A, B, and 0. In recent decades, ellagitannins and their derivatives (ellagic acid and urolithins) have gained significant attention for their potential benefits against various digestive diseases, including irritable bowel syndrome, peptic ulcers, gastritis, colon cancer, esophageal cancer, and pancreatic cancer. As a result, nutraceutical supplements have been developed to treat these conditions, representing significant and promising applications of these compounds in digestive health. Full article

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26 pages, 649 KiB

Open AccessArticle

Biothermodynamic Analysis of Norovirus: Mechanistic Model of Virus–Host Interactions and Virus–Virus Competition Based on Gibbs Energy

by Marko E. Popović, Vojin Tadić and Marijana Pantović Pavlović

Microbiol. Res. 2025, 16(6), 112; https://doi.org/10.3390/microbiolres16060112 - 1 Jun 2025

Abstract

Norovirus is a leading cause of viral gastroenteritis worldwide and has been studied extensively from the perspective of life and biomedical sciences. However, no biothermodynamic analysis of Norovirus has been reported in the literature. Such an analysis would provide insights into the role [...] Read more.

Norovirus is a leading cause of viral gastroenteritis worldwide and has been studied extensively from the perspective of life and biomedical sciences. However, no biothermodynamic analysis of Norovirus has been reported in the literature. Such an analysis would provide insights into the role of energetic constraints in the interactions between Norovirus and its host cells and other viruses. In this research, Norovirus was characterized from the aspect of chemistry and chemical thermodynamics, with the determination of its molecular formula, empirical formula, molar mass and thermodynamic properties (enthalpy, entropy, Gibbs energy) of formation. Based on these properties, biosynthesis reactions were formulated that show how Norovirus particles are synthetized inside host cells, and the thermodynamic properties of biosynthesis were determined. Moreover, the thermodynamic properties of the binding of Norovirus to its host cell receptor were determined. These were then used to develop a model of virus–host interactions at the cell membrane (antigen-receptor binding) and inside the cytoplasm (virus multiplication), with the phenomenological equations of nonequilibrium thermodynamics. Based on the model, an analysis of the virus–virus competition between Norovirus and Rotavirus was conducted. Full article

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11 pages, 11390 KiB

Open AccessArticle

Evaluation of Anti-Aspergillus flavus Activity of Lactic Acid Bacteria Isolated from Vietnamese Fermented Cocoa Beans

by Tien Cuong Nguyen, Thi Thao Hoang and Hoang Hiep Nguyen

Microbiol. Res. 2025, 16(6), 111; https://doi.org/10.3390/microbiolres16060111 - 29 May 2025

Abstract

The use of biological agents in food preservation is considered a sustainable, modern, and promising approach, in which the use of lactic acid bacteria (LAB) is a potential solution. Additionally, Vietnamese fermented cocoa beans, a naturally diverse microflora, have not yet been assessed [...] Read more.

The use of biological agents in food preservation is considered a sustainable, modern, and promising approach, in which the use of lactic acid bacteria (LAB) is a potential solution. Additionally, Vietnamese fermented cocoa beans, a naturally diverse microflora, have not yet been assessed for the selection of antifungal LAB. Therefore, this study focused on evaluating the antifungal activities against Aspergillus flavus UBOCC-A-10866 of 19 LAB strains isolated from Vietnamese fermented cocoa beans from the Dak Lak and Dong Nai provinces. The results showed that lactic strains were all capable of inhibiting fungi growth (from 18–99% of the fungal colony diameter after 7 days), of which five LAB strains (L13E48, L7E96, L22E96, L41E96, and L2DN120) were selected due to their great fungi inhibition activities (inhibition rate > 75%). The strain L41E96 (Lactiplantibacillus plantarum) was chosen as the best antifungal species with the minimum inhibitory concentration (MIC) and the minimum fungicidal concentration (MFC) of 0.36 mg/mL. Full article

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37 pages, 3412 KiB

Open AccessReview

Silver Nanoparticle-Based Antimicrobial Coatings: Sustainable Strategies for Microbial Contamination Control

by Edith Dube and Grace Emily Okuthe

Microbiol. Res. 2025, 16(6), 110; https://doi.org/10.3390/microbiolres16060110 - 28 May 2025

Abstract

Silver nanoparticles have gained significant attention due to their remarkable antimicrobial properties, making them ideal candidates for incorporation into various coatings. These coatings exhibit antimicrobial activity through multiple mechanisms, including the release of silver ions, the generation of reactive oxygen species, and the [...] Read more.

Silver nanoparticles have gained significant attention due to their remarkable antimicrobial properties, making them ideal candidates for incorporation into various coatings. These coatings exhibit antimicrobial activity through multiple mechanisms, including the release of silver ions, the generation of reactive oxygen species, and the disruption of microbial cell membranes and intracellular metabolic pathways. The integration of silver nanoparticles into coating matrices through physical embedding, chemical bonding, or surface grafting not only influences the controlled release of antimicrobial agents but also affects the mechanical stability and longevity of the coatings. Several factors, including nanoparticle size, shape, surface chemistry, and functionalization, influence the antimicrobial efficiency of these nanoparticle-based coatings. As a result, silver nanoparticle coatings have been widely applied in medical devices, textiles, antifouling surfaces, and food packaging. This review discusses the advances in using silver nanoparticles in antimicrobial coatings, focusing on the mechanisms of action, fabrication methods, and diverse applications. The review also highlights the influence of nanoparticle characteristics on antimicrobial performance, providing insights into the future directions for smart coatings. Future research is expected to focus on optimizing the fabrication techniques, enhancing the stability of silver nanoparticle coatings, and exploring innovative applications in emerging fields. Full article

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14 pages, 1406 KiB

Open AccessArticle

Zika Virus in Malaria-Endemic Populations: A Climate Change-Driven Syndemic in the Sudan Savannah, Nigeria

by Rebecca B. Atai, Maryam Aminu, Elijah E. Ella, Grace S. N. Kia, Emmanuel T. Obishakin, Helen G. Luka, Ganih S. Joel and Anyebe B. Onoja

Microbiol. Res. 2025, 16(6), 109; https://doi.org/10.3390/microbiolres16060109 - 27 May 2025

Abstract

Zika and malaria are important vector-borne febrile illnesses in humans. In this study, we determined the circulation of Zika virus and malaria infections, their hotspots, and their predominant clinical features. A cross-sectional study was carried out in six Local Government Areas (LGAs) in [...] Read more.

Zika and malaria are important vector-borne febrile illnesses in humans. In this study, we determined the circulation of Zika virus and malaria infections, their hotspots, and their predominant clinical features. A cross-sectional study was carried out in six Local Government Areas (LGAs) in Kaduna State, Nigeria, from September 2018 to May 2019. Four hundred and twenty sera were screened for Zika virus (ZV) IgM and IgG, and Plasmodium falciparum antigen using ELISA and immunochromatographic test, respectively. Overall, a seroprevalence of 14.5% was found for Zika, and 9.3% for malaria. Nineteen (4.5%) and thirty-five (8.3%) patients were seropositive for ZV IgM and IgG, respectively. Co-infection rates for Zika (ZV IgM) and malaria (0.5%: 2/420), and for ZV IgG and malaria (0.7%: 3/420) were observed. Lere (10%: 7/70 for ZV IgM), Kachia (14.3%: 10/70 for ZV IgG) and Zaria (18.6%: 13/70 for malaria) LGAs were identified as hotspots for Zika and malaria. Age was significantly associated with malaria (p = 0.008) and ZV IgG (p = 0.004). Patients aged 1–10 years had the highest malaria seroprevalence (18.4%), while those aged 21–30 years had the highest ZV IgM prevalence (6.1%: 7/114). Out of the pregnant patients (56/420) tested, 5.37% (3/56) had antibodies to both recent and past ZV infection. A significant association was found between maculopapular rash (p = 0.021) and Zika, as well as between duration of the fever and recent Zika infection (p = 0.041). We highlight that malaria is endemic in Kaduna and that ZV is silently circulating, providing baseline data for further molecular epidemiological studies. Full article

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14 pages, 1706 KiB

Open AccessArticle

Comparison of Antioxidant and Antibacterial Properties of Five Plants with Anti-Diabetes and Anti-Cancer Potential

by Nassiba Mimi, Leila Madani, Djamila Kerrouche, Nabila Boucherit, Nabil Touzout, Jie Zhang, Abdeltif Amrane and Hichem Tahraoui

Microbiol. Res. 2025, 16(6), 108; https://doi.org/10.3390/microbiolres16060108 - 26 May 2025

Abstract

Polyphenols and flavonoids are bioactive organic compounds extracted from medicinal plants. They exhibit significant antioxidant and antibacterial properties, which help fight several chronic diseases, such as diabetes and cancer. Numerous therapeutic effects and a broad spectrum of biological activities are exhibited by the [...] Read more.

Polyphenols and flavonoids are bioactive organic compounds extracted from medicinal plants. They exhibit significant antioxidant and antibacterial properties, which help fight several chronic diseases, such as diabetes and cancer. Numerous therapeutic effects and a broad spectrum of biological activities are exhibited by the following five medicinal plants traditionally utilized in medicine for the treatment of diabetes and cancer: Ginger, ephedra alata, ajuga iva, nettle, and graviola (annona muricata). The objective of the present study is to examine ethanolic and aqueous extracts exhaustively obtained from these plants through decoction and maceration using ethanol, with particular emphasis on the content of total polyphenols and flavonoids, and to evaluate their in vitro antioxidant and antibacterial potential. The antibacterial effect was assessed on the strains Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Streptococcus pneumoniae. The study was complemented by an FTIR analysis of the different extracts. The results indicate that for ginger, graviola, and ajuga iva, as opposed to ephedra alata, maceration appears to be the more efficacious technique compared to decoction. The highest yield (27.465%) was observed in the case of the ethanolic extract of ginger. Ethanolic extracts contain higher concentrations of polyphenols and flavonoids than aqueous extracts. The aqueous extracts of ajuga iva and nettle demonstrate the highest inhibition of Staphylococcus aureus bacteria. Full article

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15 pages, 355 KiB

Open AccessArticle

Carriage of Rifampicin- and Multidrug-Resistant Pseudomonas aeruginosa in Apparently Healthy Camels: A View Through a Zoonosis Lens

by Dalia Hamza and Hala M. Zaher

Microbiol. Res. 2025, 16(6), 107; https://doi.org/10.3390/microbiolres16060107 - 25 May 2025

Abstract

Pseudomonas aeruginosa poses a significant global concern in human and veterinary medicine due to its resistance to multiple antimicrobials. Limited research has been carried out on rifampicin-resistant P. aeruginosa, particularly in food-producing animals such as camels. Therefore, the purpose of this study [...] Read more.

Pseudomonas aeruginosa poses a significant global concern in human and veterinary medicine due to its resistance to multiple antimicrobials. Limited research has been carried out on rifampicin-resistant P. aeruginosa, particularly in food-producing animals such as camels. Therefore, the purpose of this study was to investigate the occurrence of rifampicin- and multidrug-resistant P. aeruginosa in apparently healthy camels. Nasal swabs and tissue samples were collected from one hundred apparently healthy slaughtered camels, and they were subjected to bacteriological isolation and identification of P. aeruginosa. Antimicrobial susceptibility testing was performed, followed by phenotypic and genotypic detection of ESBL-producing P. aeruginosa isolates. Twenty-two P. aeruginosa strains were investigated for the rpoB gene, including rifampicin-resistant isolates. P. aeruginosa was found in 16% (16/100) of the investigated apparently healthy slaughtered camels. P. aeruginosa was confirmed in sixteen and six isolates from nasal swabs and tissue samples, respectively, by pigment production on cetrimide agar. The most predominant beta-lactamase-encoding gene in twenty-two ESBL-producing isolates was bla_PER (40.9%), followed by bla_CTX-M (36.4%), bla_TEM (31.8%), and bla_SHV (27.3%). Multidrug resistance was identified in 54.5% (12/22) of P. aeruginosa isolates. The rpoB gene was detected in 11 (50%) out of 22 P. aeruginosa strains, with eleven positive isolates being regarded as rifampicin-resistant. Furthermore, phylogenetic analysis of a rifampicin- and multidrug-resistant P. aeruginosa rpoB gene sequence revealed a genetic relatedness to P. aeruginosa strains retrieved from human clinical cases. In conclusion, this study provides a snapshot on the occurrence of rifampicin- and multidrug-resistant P. aeruginosa among apparently healthy camels. In line with a possible risk of animal-to-human transfer, further molecular studies on rifampicin-resistant P. aeruginosa in animals are required to better understand and combat this serious zoonotic pathogen. Full article

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20 pages, 3633 KiB

Open AccessArticle

Identification and Evaluation of the Salt and Acid—Alkaline Resistance of Rhizobium Species of Desmodium

by Yunchi Zhu, An Hu, Xinyong Li, Lijuan Luo and Rongshu Dong

Microbiol. Res. 2025, 16(5), 106; https://doi.org/10.3390/microbiolres16050106 - 21 May 2025

Abstract

Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus [...] Read more.

Inoculation with Rhizobium can improve not only host yield and quality but also host adaptability to stress. The match between inoculated strains and hosts and resistance to stress are the key factors determining the inoculation effect. Four types of Desmodium, Pleurolobus gangeticus, Puhuaea sequax, Grona heterocarpos, and Polhillides velutina, were used to capture Rhizobium strains in soil, and the phylogenetic classification and salt and acid—alkaline resistances of the strains were determined through isolation, identification, and different salt and pH treatments. The phylogenetic classification of the 62 rhizobial strains was determined by 16S rDNA analysis. After comparison, the strains were grouped into 10 groups with known strains of rhizobia, including 14 strains of fast-growing rhizobia grouped with Rhizobium tropici and Rhizobium oryzicola and 48 strains of slow-growing rhizobia. The salt tolerance and acid—base adaptability of 52 strains were qualitatively and quantitatively determined in this study, and salt stress was found to have varying effects on the growth of different strains. Some strains grew normally on media with NaCl concentrations of 0.4 and 0.35 mol/L and had strong salt tolerance. The plants grew normally on media with pH 5–9. This study provides theoretical support for the classification of Desmodium and provides efficient Rhizobium strains for the cultivation and application of Desmodium. Full article

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24 pages, 767 KiB

Open AccessReview

The Potential of Beneficial Microbes for Sustainable Alternative Approaches to Control Phytopathogenic Diseases

by Ramadan Bakr, Ali Abdelmoteleb, Vianey Mendez-Trujillo, Daniel Gonzalez-Mendoza and Omar Hewedy

Microbiol. Res. 2025, 16(5), 105; https://doi.org/10.3390/microbiolres16050105 - 20 May 2025

Abstract

Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the [...] Read more.

Sustainable agricultural practices are essential for eradicating global hunger, especially in light of the growing world population. Utilizing natural antagonists, such as fungi and bacteria, to combat plant diseases, rather than relying solely on synthetic chemical pesticides, which pose significant risks to the environment and human health, is known as biocontrol. Microbial biological control agents (MBCAs) have proven effective against phytopathogens and are increasingly embraced in agricultural practices. MBCAs possess several beneficial traits, including antagonistic potential, rhizosphere competence, and the ability to produce lytic enzymes, antibiotics, and toxins. These biocontrol mechanisms directly target soil-borne pathogens or indirectly stimulate a plant-mediated resistance response. The effectiveness of MBCAs in managing plant diseases depends on various mechanisms, such as hyperparasitism, antibiosis, competition for nutrients or space, disruption of quorum-sensing signals, production of siderophores, generation of cell wall-degrading enzymes, and the induction and priming of plant resistance. Formulating effective biopesticides requires optimal conditions, including selecting effective strains, considering biosafety, appropriate storage methods, and ensuring a prolonged shelf life. Therefore, formulation is crucial in developing pesticide products, particularly concerning efficacy and production costs. However, several challenges must be addressed to ensure the successful application of biological control, including the shelf life of biopesticides, slower efficacy in pest management, inadequate awareness and understanding of biocontrol methods, regulatory registration for commercialization, and suitable agricultural applications. This review clarifies the principles of plant disease biocontrol, highlighting the mechanisms of action and functionality of MBCAs in biocontrol activities, the formulation of biopesticides derived from microorganisms, and the challenges and barriers associated with the development, registration, commercialization, and application of biopesticides. Full article

(This article belongs to the Collection Microorganisms and Their Incredible Potential to Face Societal Challenges)

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18 pages, 1935 KiB

Open AccessReview

Progress in CRISPR Technology for Antiviral Treatments: Genome Editing as a Potential Cure for Chronic Viral Infections

by Fatemeh Nouri, Farnaz Alibabaei, Behina Forouzanmehr, Hamed Tahmasebi, Valentyn Oksenych and Majid Eslami

Microbiol. Res. 2025, 16(5), 104; https://doi.org/10.3390/microbiolres16050104 - 20 May 2025

Abstract

The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks [...] Read more.

The CRISPR–Cas system has transformed molecular biology by providing precise tools for genome editing and pathogen detection. Originating from bacterial adaptive immunity, CRISPR technology identifies and cleaves genetic material from pathogens, thereby preventing infections. CRISPR–Cas9, the most widely utilized variant, creates double-stranded breaks in the target DNA, enabling genetic disruptions or edits. This approach has shown significant potential in antiviral therapies, addressing chronic infections, such as HIV, SARS-CoV-2, and hepatitis viruses. In HIV, CRISPR–Cas9 edits the essential viral genes and disrupts latent reservoirs, while CCR5 gene modifications render the T cells resistant to viral entry. Similarly, SARS-CoV-2 is targeted using CRISPR–Cas13d to inhibit the conserved viral genes, significantly reducing viral loads. Hepatitis B and C treatments leverage CRISPR technologies to target conserved genomic regions, limiting replication and expression. Emerging innovations, such as the PAC-MAN approach for influenza and base-editing systems to reduce off-target effects, further highlight the therapeutic versatility of CRISPR. Additionally, advances in Cas12a and Cas13 have driven the development of diagnostic platforms like DETECTR and SHERLOCK, which provide rapid and cost-effective viral detection. Innovative tools like AIOD-CRISPR enable accessible point-of-care diagnostics for early viral detection. Experimental approaches, such as targeting latent HSV-1 reservoirs, highlight the transformative potential of CRISPR in combating persistent infections. Full article

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11 pages, 1233 KiB

Open AccessCase Report

Atopobium vaginae: An Overview of the Bacteria Through Clinical Cases

by Anna Vaseruk, Stepan Nedzelskyi, Roksolana Konechna, Halyna Lavryk, Alicja Sękowska and Yulian Konechnyi

Microbiol. Res. 2025, 16(5), 103; https://doi.org/10.3390/microbiolres16050103 - 20 May 2025

Abstract

Atopobium vaginae (nowadays Fannyhessea vaginae) is an anaerobic bacterium increasingly implicated not only in bacterial vaginosis (BV) but also in a broader range of infections. Despite growing recognition of its clinical relevance, comprehensive data on the characteristics of A. vaginae remain limited. [...] Read more.

Atopobium vaginae (nowadays Fannyhessea vaginae) is an anaerobic bacterium increasingly implicated not only in bacterial vaginosis (BV) but also in a broader range of infections. Despite growing recognition of its clinical relevance, comprehensive data on the characteristics of A. vaginae remain limited. This study aimed to isolate and thoroughly characterize the clinical strains of A. vaginae from both vaginal and oral cavity samples. A multifaceted methodological approach was employed, including antibiotic susceptibility testing to assess resistance and sensitivity profiles, PCR for genetic identification, and biochemical profiling using the VITEK-2 Compact system. Additionally, the morphological traits and growth dynamics of the isolates were examined. Given the established role of A. vaginae as a significant contributor to BV, the results of this study aim to support the development of evidence-based antimicrobial strategies for effective management of A. vaginae-associated infections. Full article

(This article belongs to the Topic Microbiota Diversity and Its Broader Biological Implications Across Human and Animal Health)

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10 pages, 610 KiB

Open AccessArticle

Polysaccharides from Marine Bacteria and Their Anti-SARS-CoV-2 Activity

by Tatyana A. Kuznetsova, Natalia V. Krylova, Maksim S. Kokoulin, Elena V. Persiyanova, Olga S. Maistrovskaya, Pavel. G. Milovankin, Yurii A. Belov and Mikhail Yu. Shchelkanov

Microbiol. Res. 2025, 16(5), 102; https://doi.org/10.3390/microbiolres16050102 - 19 May 2025

Abstract

This study investigated the anti-SARS-CoV-2 activity of Polysaccharides (PSs) from three species of marine bacteria (Alteromonas nigrifaciens KMM 156, Cobetia amphilecti KMM 3890, and Idiomarina abyssalis KMM 227^T). The chemical structure of PSs from marine bacteria is characterized using ¹ [...] Read more.

This study investigated the anti-SARS-CoV-2 activity of Polysaccharides (PSs) from three species of marine bacteria (Alteromonas nigrifaciens KMM 156, Cobetia amphilecti KMM 3890, and Idiomarina abyssalis KMM 227^T). The chemical structure of PSs from marine bacteria is characterized using ¹H and ¹³C NMR spectroscopy, including 2D NMR experiments. PS from A. nigrifaciens KMM 156 consists of tetrasaccharide repeating units containing two L-rhamnose residues and one residue each of 2-acetamido-2-deoxy-D-glucose and an ether of D-glucose with (R)-lactic acid, 3-O-[(R)-1-carboxyethyl]-D-glucose. PS from C. amphilecti KMM 3890 is constructed from branched trisaccharide repeating units consisting of D-glucose, D-mannose, and sulfated 3-deoxy-D-manno-oct-2-ulosonic acid. A unique PS from deep-sea marine bacterium I. abyssalis KMM 227^T consists of branched pentasaccharide repeating units and is characterized by the presence of a rare bacterial polysaccharide component 2-O-sulfate-3-N-(4-hydroxybutanoyl)-3,6-dideoxy-D-glucose. The activity of PSs against SARS-CoV-2 was assessed by inhibition of the virus cytopathogenic effect (CI) in the methylthiazolyl tetrazolium (MTT) test and using a real-time reverse transcription polymerase chain reaction (RT-PCR-RV). Results of the study demonstrate that PSs, which differ in chemical structure, exhibited anti-SARS-CoV-2 activity differences. This is confirmed both in the test of inhibition of the virus CI and in the reduction in the SARS-CoV-2 virus RNA level. PSs from A. nigrifaciens KMM 156 exhibited the strongest anti-SARS-CoV-2 effect, effectively inhibiting the stages of attachment and penetration of SARS-CoV-2 into the cells. Full article

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