Microorganisms doi: 10.3390/microorganisms14051098

Authors: Darshana Kadekar Deepak Velayudhan Ester Vinyeta Jianqiang Zhang Ethan Aljets Veeraya Bamrung Panchan Sitthicharoenchai Alyona Michael Keith Frogue Meng Heng Amy Liu Cristina Bongiorni Manasi Bhate David A. Estell Chong Shen Charlotte Poulsen

Porcine reproductive and respiratory syndrome virus (PRRSV) remains a major challenge to swine production worldwide. Current vaccines have limited efficacy against genetically diverse PRRSV strains. Therefore, strategies with alternative modes of action—such as antiviral approaches that target conserved virus–host interactions, including viral attachment and entry, rather than relying solely on adaptive immune responses—are needed. We first evaluated the in vitro effect of griffithsin (GRFT), a high-mannose-binding lectin, in the monkey kidney cell line MARC-145. Cells were pre-treated with GRFT (50–200 µg/mL) prior to PRRSV infection, after which cell morphology and viral RNA replication (measured by RT-qPCR) were assessed. Pre-treatment with 100–200 µg/mL GRFT, followed by PRRSV inoculation at a multiplicity of infection of 1 or 10, reduced viral replication in MARC145 cells in a dose-dependent manner, achieving almost 100% inhibition of ORF5 and ORF7 RNA compared with untreated controls (p < 0.0001). We next investigated the in vivo effects of intranasal GRFT administration (7.5 or 15 mg/day) in pigs (n = 56). Pigs treated with 15 mg/day GRFT exhibited significantly reduced (p < 0.05) viremia 2, 4 and 7 days post-challenge, compared with untreated, challenged, and controls (log10 8.1 ± 0.2 vs. 9.0 ± 0.25, 8.2 ± 0.1 vs. 9.1 ± 0.2, and 8.9 ± 0.2 vs. 9.3 ± 0.2, respectively), along with earlier resolution of fever and a trend toward increased average daily gain over 42 days (p < 0.1). These findings are the first report of GRFT efficacy in pigs and support its potential as an antiviral strategy against PRRSV, alongside existing interventions.

Microorganisms doi: 10.3390/microorganisms14051096

Authors: András P. Bózsik Dömötör M. László Borisz Egri

Research increasingly identifies wild birds, particularly long-distance migratory species, as epidemiologically relevant hosts and vectors for tick-borne Borrelia species that pose risks to both avian and human health. This review contextualizes avian-associated Borrelia research historically and microbiologically, showing the role of avian hosts in the ecology of agents causing relapsing fever and Lyme borreliosis. We identify key publications that trace the evolution of Borrelia research—from early microscopic observations of spirochetes to the modern molecular and serological evidence. The review collects literature on the process by which Borrelia gained early scientific attention due to its characteristic morphology and elevated bloodstream concentrations during septicemic phases, which enabled early etiological links between the microbe and disease. It follows the recognition of avian spirochetosis caused by Borrelia anserina and charts the shift in focus after the discovery of Borrelia burgdorferi sensu lato (Subgen. novum recomm. Borreliella, Lyme-group Borrelia). Publications listed show that birds can transport infected human-parasitic ticks over long distances and, in certain bird species, selectively amplify Lyme-group Borrelia species, especially Borrelia garinii, which has the highest temperature tolerance and is thus potentially viable in avian hosts. The literature supports the role of birds in maintaining and disseminating Borrelia infections and infected ticks across continents.

Microorganisms doi: 10.3390/microorganisms14051097

Authors: Antonia Mataragka Marios Mataragas Nikolaos Tzimotoudis Ioannis Galiatsatos Panagiota Stathopoulou Spiros Paramithiotis John Ikonomopoulos Nikolaos D. Andritsos

Listeria monocytogenes is already a well-known foodborne bacterial pathogen, ubiquitously dispersed not only in the food production environment but also in the primary animal production environment as well. The present study performed whole-genome characterization of the multidrug-resistant (MDR) L. monocytogenes strain BF11, previously isolated from raw pet food and phenotypically described for antimicrobial resistance. To this end, the genomic analysis performed on the isolate confirmed the pathogen’s designation as a serotype 1/2b strain belonging to ST5 and CC5 (Lineage I), carrying multiple MDR genes, stress-related genes, and mobile genetic elements, despite the absence of plasmids. The strain is phylogenetically closely related to Lineage I epidemic strains (e.g., F2365), as it has a full-length inlA and a functional prfA, rendering it capable of invading human cells and marking its high virulence. Overall, this strain may represent a potentially novel genomic profile when core genome multilocus sequence typing (cgMLST) is used, although further data from additional isolates would be required to confirm its classification within a new Complex Type, while displaying a hybrid unique profile. It is an evolved ST5 L. monocytogenes strain that has acquired genetic material conferring a “clinical signature” (Lineage I-like) and an extensive resistance network. Therefore, presence of L. monocytogenes strain BF11 in pet food is alarming, since such hybrid strains often evade surveillance monitoring as they do not fit strictly into classical categories, posing a serious food safety and public health threat in the concept of One Health.

Microorganisms doi: 10.3390/microorganisms14051095

Authors: Edisson Ronaldo Duran Yunga María de Lourdes Rodriguez Coyago

While a conserved core microbiome is shared across healthy individuals, significant interindividual taxonomic variation exists; however, the specific influence of genetic ancestry on supragingival plaque structure in eubiosis remains unclear. This systematic review analyzed evidence regarding taxonomic variations in supragingival plaque associated with ethnicity in systemically healthy populations. A search was conducted in PubMed, Scopus, ScienceDirect, and Scielo following PRISMA 2020 guidelines, covering literature up to October 2025. Cross-sectional studies using genomic sequencing or metagenomics were included, with quality assessed via the GRADE system. Six studies met eligibility criteria. Results identified a universal core microbiome structurally dominated by Corynebacterium spp. and Streptococcus spp. However, distinct ethnic-specific taxonomic signatures emerged, such as the enrichment of Fusobacterium spp. in African Americans and Corynebacterium spp. in Caucasians, alongside the exclusive presence of Sneathia spp. in Burmese individuals. Although a basal microbial architecture necessary for homeostasis exists, ethnicity acts as a biological filter defining distinctive bacterial profiles and differential susceptibilities. These findings suggest that while the core microbiome is conserved, the composition of peripheral species in the dental plaque hedgehog structure varies according to ancestry. This supports a transition from standardized dental care to personalized medicine oriented towards the patient’s biological heritage.

Microorganisms doi: 10.3390/microorganisms14051094

Authors: Dingxiang Lu Lin Liu Zhongwei Yang Tianjiao Chen Dong Yang Danyang Shi Shuqing Zhou Junwen Li Haibei Li Min Jin

Carbapenem-resistant Pseudomonas aeruginosa is increasingly becoming a global health threat. However, although aquatic environments are key resistance reservoirs, data obtained from high-altitude ecosystems are scarce. Whole-genome sequencing of eight carbapenem-resistant P. aeruginosa isolates collected from aquatic environments in the Tibetan Plateau identified three sequence types (STs), with ST1420 predominating (62.5%, 5/8). Phylogenetic analysis revealed a close clustering of isolates with those from distant clinical settings, suggesting potential cross-habitat transmission. All studied strains were multidrug-resistant, exhibiting 100% resistance to imipenem, ceftriaxone, and trimethoprim–sulfamethoxazole. This included the PA6 strain, which showed multiple-antibiotic resistance. Eight strains harbored the intrinsic carbapenemase gene blaOXA-50. The diverse virulence-gene profiles of strains PA2, PA4, and PA6 aligned with their high pathogenicity observed both in vitro and in vivo. However, virulence genotypes sometimes did not correlate with phenotypes, revealing the limitations of relying on static genetic information alone. This study highlights the aquatic environments of the Tibetan Plateau as reservoirs of carbapenem-resistant P. aeruginosa with substantial genetic diversity and divergent pathogenic potential, underscoring their public-health relevance.

Microorganisms doi: 10.3390/microorganisms14051093

Authors: Zhihua Li Ying Liu Zhenyi Liu Zhaoling Jiang Yawen Wang Baozhu Xing Chen Mei Hongjun Wang

Avibacterium paragallinarum (A. paragallinarum) is the primary causative agent of infectious coryza in chickens. Infection often leads to growth retardation in broilers and a 10% reduction in egg production, reaching over 40% in laying hens. The problem is particularly severe under intensive farming conditions, significantly jeopardizing global poultry health and farming profitability. From a ‘One Health’ perspective, this not only disrupts the stability of the food supply chain, but also increases antibiotic usage due to disease prevention and control needs, thereby aggravating antimicrobial resistance (AMR) and posing a global public health challenge. This review systematically summarizes advances in the pathogenesis of A. paragallinarum and the protective immunity induced by subunit vaccines. It focuses on the infection mechanisms of A. paragallinarum, emphasizing its colonization strategies in the infraorbital sinus and nasal epithelium of chickens, and analyzes the roles of key virulence factors such as hemagglutinin and capsule in adhesion, colonization, and immune evasion. We integrate the tissue-specific pathogenesis of A. paragallinarum with the role of respiratory commensal microbiota in facilitating infection, providing an in-depth analysis of the bacterium’s key immune evasion strategies, thus offering novel insights into host–pathogen-microbiome interactions. Concurrently, to the best of our knowledge, this review provides the first comprehensive overview of current developments in subunit vaccines and their immunoprotective properties, with special attention to limitations in eliciting mucosal immune responses. By delving into the pathogen-host interaction mechanisms, this review aims to inform the optimization of subunit vaccine design and immunization strategies. Ultimately, it seeks to establish a theoretical basis and practical framework for precise control of A. paragallinarum.

Microorganisms doi: 10.3390/microorganisms14051092

Authors: Haogeng Zhao Meijuan Cheng Shuli Wei Gongfu Shi Jing Fang Huimin Shi Qingze Liu Yan Qu Weijing Zhang Fang Luo Yu Wang Zhanyuan Lu Dejian Zhang Xiaoqing Zhao

Conservation tillage has an influence on the cultivation and sustainable utilization of farmland. However, the microbial mechanism driving soil nutrient cycling in conservation tillage and its regulation pathway remain unclear. Based on a positioning experiment in black soil areas, this study systematically compared the effects of no-tillage (NT) and moldboard tillage (MT) combined with different straw returning amounts (straw non-returning, NS; straw half-returning, HS; straw full-returning, TS) on the composition of soil carbon (C), nitrogen (N) and phosphorus (P) and focused on the role of microbial community structure succession and functional changes in soil nutrient cycling. Microbial community remodeling driven by tillage measures was mainly regulated by C and N components. Bacterial modules 2 and 4 and fungal modules 1 and 2 were key for regulating the C, N and P cycle, of which 87 bacteria and 45 fungi taxa represented the core driving microorganisms. The total amount of no-tillage straw return reduced the formation and accumulation of labile organic carbon fractions by enriching yeast-like fungi and inhibiting the expression of complex organic matter decomposition genes. Tillage mainly promoted the accumulation of labile organic carbon fractions and nutrient release by regulating the bacterial community, while no-tillage straw returning promoted the accumulation of total organic carbon and organic nitrogen fixation by promoting the fungal community. This study revealed the biological pathway of conservation tillage that drives soil nutrient cycling by regulating key microbial communities. It also provides a microbiological basis for sustainable soil management in black soil areas.

Microorganisms doi: 10.3390/microorganisms14051091

Authors: Eun Jin Yang Hee Ra Park

Post-traumatic stress disorder (PTSD) is a debilitating psychiatric condition that impairs psychological functioning and increases susceptibility to various chronic illnesses, including inflammatory, metabolic, and cognitive disorders. Recent advances in neuroscience and microbiology have identified the brain–gut–microbiota axis as a key mediator of neuroimmune and neuroendocrine regulations, providing new insight into the pathophysiology of PTSD. This review synthesizes current findings from preclinical and clinical studies on gut microbiome alterations in PTSD, highlighting the underlying mechanistic pathways. Dysbiosis in PTSD is associated with immune dysregulation, altered neuroendocrine signaling, and neurotransmitter imbalances. Animal models, particularly those using the single prolonged stress paradigm, have demonstrated behavioral and microbial changes that mirror the characteristics of human PTSD. Human studies have revealed reduced abundance of beneficial bacterial taxa and increased inflammation-associated genera in patients with PTSD. Although emerging evidence supports the role of gut microbiota in PTSD, further research is needed to establish causal relationships and optimize microbiome-targeted therapies. Overall, the gut microbiome offers a novel and potentially modifiable target for the prevention and treatment of PTSD.

Microorganisms doi: 10.3390/microorganisms14051090

Authors: Xintong Chen Qiushi Wang Xiaoya Guo Dan Li Xinyu Wu Xiaoya Li Xiaoyu Zheng Yangyang Li Shuangshuang Han Lu Feng Bin Liu Lei Wang

Inflammatory bowel disease (IBD) is a chronic intestinal disorder with recurrent inflammation for which effective therapeutic options remain limited. Probiotics from the Bifidobacterium genus have potential beneficial effects on the prevention of IBD by improving intestinal barrier integrity and modulating immune responses. However, whether these effects are mediated by the regulation of gut metabolism remains largely unclear. This study was designed to explore the protective effect of an infant-derived Bifidobacterium animalis subsp. lactis 832 (B. lactis 832) on dextran sulfate sodium (DSS)-induced colitis in mice and its underlying mechanism. B. lactis 832 treatment significantly alleviated colitis severity (p < 0.05), as evidenced by reduced weight loss, disease activity index (DAI), and colonic injury, accompanied by significantly decreased pro-inflammatory cytokine expression and increased Il10 expression (p < 0.05). It also improved intestinal barrier integrity and modulated gut microbiota composition by reducing potentially pathogenic bacteria while enriching beneficial taxa. Surprisingly, metabolomic analysis revealed that B. lactis 832 intervention enhanced intestinal phospholipid metabolism, particularly increasing phosphatidylethanolamine (PE) and phosphatidylcholine (PC) levels. Notably, PE or PC supplementation recapitulated the protective effects against DSS-induced colitis (p < 0.05). These findings suggest that B. lactis 832 alleviates colitis through microbiota-associated metabolic regulation, highlighting a key role for phospholipid metabolism in mediating probiotic effects.

Microorganisms doi: 10.3390/microorganisms14051089

Authors: Baiyun Li Qing Zhao Hongna Li Zehua Xu Tao Zhou Xinnian Guo Lina Zhou

Irrigation-silted soil in Ningxia represents a unique, anthropogenically modified agroecosystem, beneficial for regional food security. Yet, how different agricultural management techniques influence soil microbiome diversity remains poorly explored. Full-length amplicon sequencing (16S rRNA and ITS) was applied to assess the effects of vegetable and maize cultivation, relative to an uncultivated wasteland control, on soil bacterial and fungal community. Cropping patterns significantly influenced microbial alpha diversity, with contrasting effects on bacterial and fungal communities. Specifically, bacterial diversity peaked in vegetable fields, while fungal diversity was highest in maize fields. Both the bacterial and fungal community structures differed markedly among the three land-use types (p < 0.01). Although Pseudomonadota (among bacteria) and Ascomycota (among fungi) were the dominant phyla across all soils, each land-use type harbored distinct biomarkers. For example, vegetable fields facilitated the enrichment of the genus Fusarium, whereas maize fields were characterized by both Pseudomonadota and diverse saprotrophic fungi. Based on functional prediction, sulfur oxidation and cellulose decomposition were enhanced in soil with vegetable cultivation, while maize cultivation promoted relatively broader metabolic activity and enriched arbuscular mycorrhizal fungi compared with the control. Agricultural practices act as selective filters shaping soil microbial assembly and function, which provide a theoretical foundation for sustainable management strategies aimed at preserving soil health.

Microorganisms doi: 10.3390/microorganisms14051088

Authors: Yuyang Liu Yaxin Wen Ruizheng Hu Ruyue Han Dong Liu Hailing Zhang

Ergothioneine (EGT), a naturally occurring amino acid derivative with potent antioxidant and cytoprotective properties, is widely applied in the food, cosmetic, and medical industries. Traditional production methods are limited by high costs, low efficiency, and environmental concerns, so microbial fermentation serves as a sustainable alternative for EGT production. In this study, Escherichia coli BL21 (DE3) was employed as the chassis strain. First, a basic EGT-producing engineered strain was constructed by heterologously expressing the egtB gene from Methylobacterium pseudosasicola along with the egtD and egtE genes from Mycobacterium smegmatis. This initial strain achieved a yield of 84.84 ± 1.64 mg/L of EGT in shake-flask cultures. To enhance production, solubility-enhancing tags were introduced to improve the soluble expression of the key enzymes, and metabolic pathways were rationally engineered to strengthen the supply of essential precursor amino acids. These modifications led to the development of a high-yield EGT strain. After optimizing the fermentation process, the best results were achieved using a medium with glycerol as the carbon source, 0.5 g/L of histidine, 1.5 g/L of methionine, and 1.0 g/L of cysteine, along with induction at 25 °C using 0.2 mM IPTG for 120 h. Under these conditions, the final EGT yield reached 385.70 ± 4.86 mg/L. The engineered strain for EGT synthesis and optimized fermentation strategy developed in this study offer a useful basis for further process development.

Microorganisms doi: 10.3390/microorganisms14051087

Authors: Zhen Zhao Weikang Dong Zhibin Zhou Jinglong Fan

Haloxylon ammodendron is a keystone shrub widely used for ecological restoration in arid regions of Northwest China. However, how rhizosphere bacterial communities reorganize across stand ages remains poorly understood. Rhizosphere soils were collected from one-, three-, and six-year-old stands using full-length 16S rRNA sequencing. Although alpha diversity remained relatively stable, beta diversity revealed pronounced community turnover. The dominant phyla were conserved across stands, whereas genus- and species-level composition shifted systematically along the age gradient. Younger stands were enriched in stress-tolerant and early colonizing taxa, intermediate stands showed increased representation of plant-associated and nitrogen-cycling bacteria, and older stands harbored taxa associated with complex carbon turnover and stress adaptation. Network analysis suggested modular co-occurrence patterns across stand ages and PICRUSt2-based functional inference indicated a conserved core metabolic repertoire accompanied by gradual ecological differentiation in pathways related to resource utilization and environmental response. Together, these findings suggest a stand age–associated pattern of rhizosphere bacterial succession and provide insight into microbial community differentiation in a desert shrub system.

Microorganisms doi: 10.3390/microorganisms14051086

Authors: Malihe Mehdizadeh Allaf Tianxing Yi Junhui Zhang Shouyu Zhang Kevin J. Erratt Parham Dehnavi Hassan Peerhossaini

Aquaculture is the fastest-growing food production sector, supplying more than half of the world’s seafood and projected to expand further to meet rising global protein demands. Among the various pressures confronting this industry, harmful algal blooms (HABs) rank among the most alarming. Ichthyotoxic flagellates are microalgae known for producing toxins or inducing gill damage that leads to widespread fish mortality. Their increasing frequency poses a critical threat to aquaculture, emphasizing the urgent need for effective and environmentally sustainable strategies to regulate and mitigate these harmful episodes. This study investigated the responses of three ichthyotoxic flagellates renowned for impacting aquaculture operations (Prymnesium parvum, Heterosigma akashiwo, and Fibrocapsa japonica) and tested their susceptibility to two routinely applied chemical agents, hydrogen peroxide (H2O2) and copper sulfate (CuSO4). Mortality, viability, and motility were assessed alongside trajectory-based metrics, including mean squared displacement (MSD) and probability density function (PDF). The results revealed species-specific sensitivities: P. parvum was highly susceptible to H2O2, while H. akashiwo and F. japonica were more susceptible to copper toxicity. Ichthyotoxic flagellates exhibited differential sensitivities to chemical treatments, with copper sulfate generally achieving lower EC50 thresholds and greater inhibition of motility than hydrogen peroxide, except in P. parvum. The rapid attenuation of motility at sublethal concentrations highlights swimming behavior as a functional vulnerability, reinforcing the potential for behavior-based mitigation strategies that minimize chemical loading and reduce unintended impacts on cultured fish and surrounding ecosystems.

Microorganisms doi: 10.3390/microorganisms14051084

Authors: Yuhan Zheng Ruichen Wu Huawei Feng Xunheng Wu Yi Yang

In the context of global warming, the resulting persistent thermal stress has become a critical environmental factor influencing the structural and functional homeostasis of gut microbiota in reptiles. In this study, Eremias roborowskii, a desert lizard endemic to the extreme heat conditions of the Turpan Basin, was selected as an ideal model for evaluating the ecological impacts of global warming. Meanwhile, a 60-day controlled laboratory experiment was conducted, exposing the lizards to normal (30 °C ± 1 °C), elevated (37 °C ± 1 °C), and high (42 °C ± 1 °C) temperatures to reflect future climate scenarios. Using shotgun metagenomic sequencing, the gut microbiota was characterized to investigate the dynamics of the antibiotic resistance genes (ARGs) and carbohydrate-active enzymes (CAZymes) under heat stress. The results reveal that elevated temperature selectively promotes heat-tolerant gut microbiota, such as Tetragenococcus and Faecalicatena, by altering host energy metabolism and modulating heat stress adaptation to maintain intestinal homeostasis. Moreover, the observed increase in resistome diversity and richness under elevated temperature may be attributed to temperature-induced shifts in gut microbial composition, particularly the enrichment of heat-tolerant ARG-carrying bacterial taxa. Metabolic changes in CAZymes were caused by gut microbiota remodeling, which optimized carbon utilization and preferentially allocated cell wall synthesis and repair. Furthermore, the pentose phosphate pathway and amino acid biosynthesis pathways were upregulated, providing NADPH for antioxidant defense and precursors for protein synthesis, respectively, thereby contributing to the maintenance of microbial cellular homeostasis. Our study provides a theoretical basis for understanding functional gene adaptation strategies in wildlife microbiomes due to climate change.

Microorganisms doi: 10.3390/microorganisms14051085

Authors: Lijuan Wang Shengnan Zhang Yingying Han Rixin Zhang Weigao Zhao

Algal blooms in water sources, exacerbated by global climate change and water eutrophication, pose a significant threat to water quality, ecological safety, and human health. Seasonal algae blooms in drinking water sources, particularly those in colloidal form, present substantial challenges to the safe and stable operation of drinking water treatment plants. To address these challenges and gain a better understanding, this study reviews current issues and perspectives on algae in the drinking water supply system (DWSS). Algal contaminations are more frequent and severe in the tropics and subtropics spatially, while temporally, they pose greater concern during summer and autumn. Moreover, various detection methods, including conventional and advanced techniques, are discussed based on the advantages and disadvantages in species identification, cell quantity, and morphology observation. Additionally, treatment processes in DWSS, particularly pre-oxidation and coagulation, are effective in removing most algae. Furthermore, judging from the characteristics, microalgae and Microcystis aeruginosa exist as colloidal algae among the whole process of DWSS, yet the physical states of algae have been largely overlooked in previous research. This study fills this gap by introducing colloidal algae as a distinct form and analyzing its detection and removal from a colloid science perspective. This review thus provides a new reference for targeted algae control in DWSS.

Microorganisms doi: 10.3390/microorganisms14051083

Authors: Ming Fan Yaming Yang Hui Chu Ping Chu Qiang Li

This study aimed to investigate differences and patterns in fungal communities within the root-zone soil of Lamiophlomis rotata across varying altitudes. Specifically, it analyzed the characteristics of soil fungal communities at altitudes of 3600, 3800, 4000, and 4200 m and examined their relationships with key bioactive medicinal constituents and soil nutrients. The results indicated that Ascomycota, Mortierellomycota, and Basidiomycota were the dominant fungal phyla in the L. rotata root-zone soil, with Pseudosperma and Clavaria as the predominant genera. The Shannon and Chao1 diversity indices of soil fungi initially decreased and subsequently increased with increasing altitude. At the same altitude, these indices were higher in the root-zone soil than in the non-root-zone soil. Redundancy analysis revealed that available phosphorus was the primary factor influencing fungal communities in the non-root-zone soil. In conclusion, altitude significantly affected the characteristics of fungal communities in root-zone soil, which differed significantly from those in the non-root-zone soils. These findings provide valuable data to support the conservation of L. rotata resources on the Qinghai–Tibet Plateau.

Microorganisms doi: 10.3390/microorganisms14051082

Authors: Bianca Bartocci Angelo Del Gaudio Marco Murgiano Alfredo Papa Giovanni Cammarota Antonio Gasbarrini Franco Scaldaferri Loris Riccardo Lopetuso

The gut microbiota is increasingly recognized as a key contributor in the pathogenesis and progression of inflammatory bowel disease (IBD). Compared with healthy individuals, patients with IBD show marked dysbiosis, characterized by reduced microbial diversity, an expansion of facultative anaerobes such as Proteobacteria, and a depletion of obligate anaerobes within the Firmicutes phylum. These changes have been implicated in the perpetuation of intestinal inflammation, disruption of mucosal immune homeostasis, and altered metabolic functions, further underscoring the microbiota’s relevance in IBD pathophysiology. However, microbiota-driven insights have not yet been consistently translated into therapeutic stratification or clinical decision-making. A major challenge lies in the complex and dynamic interplay between the gut microbiota and various treatment modalities, including conventional immunosuppressants, biologics, and small-molecule inhibitors. While accumulating evidence suggests that IBD treatments may modulate microbial composition and function, it remains unclear whether these changes represent a direct pharmacological effect or are secondary to inflammation control. Additionally, there is a lack of comparative data on microbiota profiles associated with differential responses to various therapeutic classes, limiting the implementation of microbiota-informed precision medicine. In this review, we synthesize current evidence on the association between gut microbiota composition and treatment outcomes, focusing on biologic agents and small-molecule therapies. Furthermore, we discuss the potential of microbiota-targeted strategies, such as fecal microbiota transplantation (FMT) and precision probiotics, in enhancing therapeutic response. A deeper understanding of host–microbe interactions could enable a more personalized and effective approach to IBD management.

Microorganisms doi: 10.3390/microorganisms14051081

Authors: Akzhigit Mashzhan Izat Smekenov Serik Bakiyev Kalamkas Utegenova Diana Samatkyzy Asset Daniyarov Ulykbek Kairov Dos Sarbassov Amangeldy Bissenbaev

We thank the authors of the Comment [...]

Microorganisms doi: 10.3390/microorganisms14051080

Authors: Antonio Martínez-Murcia Aaron Navarro Caridad Miró-Pina

In this comment, we re-evaluate the proposal of Aeromonas oralensis as a novel species by Mashzhan et al. (2025) [...]

Microorganisms doi: 10.3390/microorganisms14051079

Authors: Paige Ramkissoon Anthony DuCasse Isaac Berman Jonathan Sadanaga Ian O’Neill David C. Gondek

Antibiotic-induced dysbiosis disrupts gut microbiome diversity and functionality, often leading to negative health outcomes, including reduced short-chain fatty acid production, increased susceptibility to opportunistic pathogens, and an increased number of bacterial colonies exhibiting antibiotic resistance. This study investigates the effects of prebiotics (inulin-type fructans) and probiotic supplementation on microbiome recovery in a murine model. Broad spectrum antibiotics induced near-total microbiome depletion, significantly reducing microbial diversity and metabolite production. Prebiotic supplementation demonstrated superior efficacy during recovery in restoring microbiome diversity (~180 species), improving microbiome diversity metrics, and promoting metabolites, particularly butyrate and valerate, compared to probiotics or unmanipulated recovery. While effective in suppressing opportunistic bacterial growth, probiotics significantly delayed total microbial diversity recovery and resulted in lower diversity metrics (~50 species). However, prebiotic-treated microbiomes exhibited a wider antibiotic resistance profile in culturable bacteria, highlighting prebiotics’ unique impact on the resistome. These findings underscore the potential of prebiotics for recovery from gut dysbiosis while emphasizing the need for further research to address safety considerations regarding their impacts on antibiotic resistance. Importance: This study explores the impact of prebiotic vs. probiotic manipulation of the microbiome in an antibiotic-induced dysbiosis mouse model. Our data demonstrate that prebiotics are more efficacious at enhancing total diversity and limiting the expansion of potentially harmful opportunist bacteria. This is the first study to indicate that prebiotics increase the number of culturable bacterial colonies resistant to antibiotics. These results contribute to our understanding of microbiome manipulation to promote health and limit disease.

Microorganisms doi: 10.3390/microorganisms14051078

Authors: Silvia Arossa Shannon Grace Klein Jacqueline Victoria Alva Garcia Alexandra Steckbauer Naira Pluma Luca Genchi Sergey P. Laptenok Shiou-Han Hung Octavio R. Salazar Manuel Aranda Carlo Liberale Carlos Manuel Duarte

In the original publication [...]

Microorganisms doi: 10.3390/microorganisms14051077

Authors: Mengke He Doudou Jin Yaowei Chi Xianzhong Ma Shunping Zhang Ruiren Zhou Shaohua Chu Pei Zhou Dan Zhang

Low ambient temperatures severely restrict the start-up efficiency and microbial bioconversion of livestock manure during aerobic composting. To overcome this “cold-start” barrier, this study investigated the coupled effects of an easily accessible carbon source (molasses) and functional microbial inoculants (Streptomyces griseorubens JSD-1 and Paenarthrobacter nitroguajacolicus LDT1-8) on cattle manure composting. Results demonstrated that the combined strategy significantly expedited thermogenesis, achieving a peak temperature of 62.1 °C and extending the thermophilic phase (>50 °C) by 2 days. This enhanced microbial activity accelerated organic matter stabilization, increasing cellulose and hemicellulose degradation by 44.0% and 49.3%, respectively, and boosting humic acid content by 33.4% in treatment T7 (molasses + JSD-1 + LDT1-8). Amplicon sequencing revealed that the amendments reshaped microbial community structure, selectively enriching lignocellulose degradation and humification-driving taxa (e.g., Actinobacteriota and Mycothermus), leading to a more robust and modular metabolic network. Redundancy analysis confirmed that this directed succession was primarily driven by organic matter degradation and humic fraction accumulation. Overall, the combined application of molasses and microbial inoculants promoted temperature rise, lignocellulose degradation, and humification by reshaping microbial community structure, providing an effective strategy for improving cattle manure composting efficiency under low-temperature conditions.

Microorganisms doi: 10.3390/microorganisms14051076

Authors: Jianing Yan Li Jiang Yating Li Hui Lv Wenrui Wu Liya Yang Jianing Chen Ding Shi

Biliary atresia (BA) is a progressive fibroinflammatory cholangiopathy of infancy that rapidly advances to cholestasis, fibrosis, cirrhosis, and liver failure if bile drainage is not restored early. Although Kasai hepatoportoenterostomy (KPE) remains the standard first–line operation, many children still develop recurrent cholangitis, persistent cholestasis, and progressive native liver injury. Increasing evidence indicates that the gut microbiota participates in this clinical course through the gut–liver axis. In BA, dysbiosis may weaken the intestinal barrier, increase translocation of microbe–associated molecular patterns (MAMPs), amplify innate and adaptive immune activation, disturb bile acid signaling, and promote fibrogenic and ferroptosis–related injury. In contrast, beneficial taxa and their metabolites may preserve epithelial integrity, support immune tolerance, maintain bile acid homeostasis, and constrain oxidative stress. This review summarizes current evidence on these contrasting harmful and protective effects, stage–specific microbiome signatures reported before and after KPE, and critically evaluates the present status of microbiota–based biomarkers and interventions. We emphasize that although several microbial signatures and therapeutic approaches are promising, they are not yet ready for routine clinical implementation and require prospective validation with standardized endpoints.

Microorganisms doi: 10.3390/microorganisms14051075

Authors: Susmita Das Nishu M. Nazrul Islam

Regenerative agriculture (RA) is expanding across the Western Canadian Prairies, but its microbial foundations under climatic constraint remain insufficiently integrated. This review synthesizes evidence from long-term Prairie field experiments, regional and global datasets to evaluate how regenerative management reshapes soil biological processes and agronomic performance across systems. RA practices including no-till, diversified rotations, cover cropping, and organic amendments consistently enhance microbial biomass (up to 40–86%), arbuscular mycorrhizal fungal abundance (32–60%), and microbial diversity (≈50%), alongside increases in soil organic carbon (up to 15.6 kg C ha−1 yr−1), aggregate stability (up to 38%), and water retention (up to 30–34%). These biologically mediated improvements are linked to enhanced nutrient cycling and crop nitrogen uptake (13–47%), as well as increased microbial enzymatic activity and functional gene abundance. Agronomically, these changes translate into yield gains ranging from 10% to 147% under long-term no-till and 14–38% under diversified rotations, with additional system-level benefits including reductions in synthetic nitrogen inputs (up to 73%) and herbicide use (up to 42%). While agronomic benefits vary across temporal scales and environmental conditions, this synthesis identifies microbial communities as key mediators of interactions among climate, plant, and soil systems, underpinning improvements in soil health, pest suppression, and yield stability in semi-arid, climate-variable Prairie agroecosystems. Continued long-term, system-level research is needed to refine regionally adapted regenerative transitions and to clarify how microbial processes mediate resilience under future climate uncertainty.

Microorganisms doi: 10.3390/microorganisms14051073

Authors: Dandan Ding Hui Sun Jing Yang

Salmonella persistence contributes to infection relapse, chronic carriage, and reduced antibiotic efficacy. Traditionally viewed as dormant subpopulations that passively survive antibiotic exposure, persister cells are now increasingly recognized as dynamic, heterogeneous, and context-dependent physiological states shaped by bacterial regulatory programs and host microenvironmental pressures. This review examines Salmonella persistence from a multiscale perspective. We first clarify key antibiotic survival phenotypes, including resistance, heteroresistance, tolerance, persistence, and viable but non-culturable states. We then discuss how host-derived stressors, such as phagosomal acidification, nutritional restriction, metal perturbation, and reactive oxygen and nitrogen species, promote growth-restricted, persistence-associated bacterial states. At the bacterial level, we summarize stress-response networks involving the stringent response, SOS response, toxin–antitoxin systems, and auxiliary regulators that coordinate metabolic remodeling, growth restriction, and antibiotic survival. At the host level, we highlight how organ reservoirs, immune cell subsets, metabolic cues, and Salmonella-mediated immune niche remodeling shape persistence-associated phenotypes in vivo. Finally, we discuss clinical and translational implications, including endogenous relapse, resistance evolution, and emerging anti-persistence strategies. Together, this review provides a framework for understanding Salmonella persistence as a multiscale, niche-dependent process relevant to recurrent and chronic infection.

Microorganisms doi: 10.3390/microorganisms14051074

Authors: Jiayuan Cheng Zhenhua Zhao Binglu Teng Wenqing Zhang Yuanchi Wang

Microorganisms construct complex social communities through the exchange and interaction of chemical substances. Traditional research has typically drawn a strict distinction between quorum-sensing (QS) signaling molecules and cytotoxic secondary metabolites; however, this simplistic classification limits our in-depth understanding of microbial chemical ecology and complex collective behavior. Recent studies have shown that many secondary metabolites exhibit dual functions, acting as signaling molecules that facilitate information exchange at low concentrations. This paper proposes an integrated signaling network framework that views secondary metabolites as key nodes linking microbial collective behavior and environmental adaptation. We explore how this network mechanism overcomes the limitations of linear signaling models, thereby elucidating how microorganisms balance cell growth and metabolite synthesis in dynamic environments. We also introduce emerging spatial omics and synthetic biology tools, which hold great potential for precisely deciphering complex chemical signaling networks at the microscopic scale. Translating these mechanisms into technological applications could enable dynamic, autonomous control of bacterial metabolism in industrial biotechnology, significantly enhancing the yield of target products. Finally, we emphasize the critical importance of reframing chemical ecology as a dynamic signaling network. This shift in ecological and evolutionary perspective not only provides novel intervention pathways based on network decoupling to address the increasingly severe crisis of antibiotic resistance (AMR) but also establishes a theoretical foundation for host microbiome regulation, environmental bioremediation, and industrial multi-strain collaborative engineering.

Microorganisms doi: 10.3390/microorganisms14051072

Authors: Claudia Jessica Castillo-Villanueva Jhony Anacleto-Santos Teresa de Jesús López-Pérez Brenda Casarrubias-Tabarez Teresa I. Fortoul Marcela Rojas-Lemus Nelly López-Valdez Elisa Vega-Ávila Fernando Calzada Perla Yolanda López-Camacho Norma Rivera-Fernández

Toxoplasma gondii is an obligate intracellular parasite of the phylum Apicomplexa and the causative agent of toxoplasmosis, a disease with a worldwide distribution that causes serious consequences in immunocompromised patients and during pregnancy. Current pharmacological treatments have significant limitations, including their toxicity, lack of efficacy against the chronic phase of the parasite, and low selectivity, highlighting the need to develop new therapeutic targets. One of the most promising targets is the fatty acid synthesis pathway II (FASII), a metabolic pathway located in the parasite’s apicoplast and absent in mammalian hosts. This review synthesizes the available evidence on FASII pathway inhibitors described to date, as well as their potential impact on the viability and development of T. gondii. Overall, the reviewed studies support the FASII pathway as an attractive therapeutic target for the development of more selective and effective treatments against toxoplasmosis.

Microorganisms doi: 10.3390/microorganisms14051070

Authors: Jinghua Li Rui Geng Junfeng Chen Wei Wang Shengbo Shi Longyu Fang Yuanyuan Wang Mingchun Lin Yanru Si Lujiang Hao

dTDP-L-rhamnose (Deoxythymidine diphospho-L-rhamnose) is a crucial active sugar nucleotide that serves as the key glycosyl donor for the synthesis of rhamnose-containing polysaccharides in bacteria, holding broad application potential in pathogen-associated molecular mimicry and vaccine development. In this study, the rhamnose synthase gene cluster (Pa-RmlABCD) was successfully cloned for the first time from the marine bacterium Pseudoalteromonas agarivorans Hao 2018. Four key enzymes—Glc-1-P thymidylyltransferase (Pa-RmlA), dTDP-glucose-4,6-dehydratase (Pa-RmlB), dTDP-4-keto-6-deoxyglucose 3,5-epimerase (Pa-RmlC), and dTDP-4-keto-rhamnose reductase (Pa-RmlD)—were heterologously expressed in Escherichia coli. A one-pot four-enzyme synthesis system was constructed, and the successful synthesis of dTDP-L-rhamnose was verified by Q Exactive Focus. After correction for recovery (92% ± 2%), the actual yield reached 3.47 mg/L with a conversion rate of 53.4% ± 1.1%. Combined with bioinformatics analysis, tertiary structure modeling, and molecular docking simulations, the sequence characteristics, substrate binding modes, and catalytic mechanisms of Pa-RmlABCD were systematically elucidated. By characterizing the marine-derived Pa-RmlABCD system and achieving efficient one-pot synthesis, this work opens up a new avenue for the sustainable production of dTDP-L-rhamnose, with the potential to alleviate the current industrial supply constraints.

Microorganisms doi: 10.3390/microorganisms14051071

Authors: Claudio Tana Livia Moffa Marco Tana Samanta Moffa Claudio Ucciferri

Gram-positive infections are associated with significant morbidity and healthcare burden, often requiring prolonged intravenous therapy. Dalbavancin, a long-acting lipoglycopeptide, has emerged as a promising option beyond its approved indication for acute bacterial skin and skin structure infections (ABSSSI). A systematic review was conducted according to the PRISMA guidelines (PROSPERO: CRD420261296328). MEDLINE, Embase, CENTRAL, and Web of Science were searched from inception. Randomized controlled trials (RCTs) and observational studies evaluating dalbavancin in adult patients with Gram-positive infections were included. Outcomes of interest were clinical effectiveness, safety, and healthcare resource utilization. Risk of Bias was assessed using RoB 2 and the Newcastle–Ottawa Scale. Twenty-one studies were included. Randomized trials confirmed non-inferior efficacy of dalbavancin compared with standard therapy in ABSSSI. Observational studies demonstrated high clinical success rates across a range of infections, including osteo-articular infections, bloodstream infections, and infective endocarditis (IE), particularly in acute settings. Lower effectiveness was observed in biofilm-related infections without adequate source control. Dalbavancin was frequently used as sequential or consolidation therapy in complex patients. Its use was consistently associated with reduced length of hospital stay, facilitation of outpatient management, and potential cost savings. The safety profile was favorable, including in prolonged or multi-dose regimens. In conclusion, dalbavancin represents an effective and well-tolerated option for Gram-positive infections, with expanding evidence supporting its use in complex and off-label settings. Its pharmacokinetic profile enables simplified treatment strategies and improved healthcare resource utilization, although appropriate patient selection and source control remain essential.

Microorganisms doi: 10.3390/microorganisms14051069

Authors: Murat Güler

Endophytic bacteria are beneficial microbes that live within plant tissues and promote growth through nitrogen fixation, phosphate solubilization, and phytohormone production. Two endophytic isolates from bell pepper (Capsicum annuum L.) root were identified based on their morphology and biochemical properties using 16S rRNA gene sequencing. Winter barley seeds were inoculated with two PGP (plant growth-promoting) bacterial strains (C-14 and C-27), previously characterized for indole-derived compound (IDC) production, and evaluated in a pot experiment with four treatments: Treatment A1 (C-14), Treatment A2 (C-27), Treatment A3 Consortium (C-14 + C-27), and Treatment A4 (non-inoculated control). The results indicated that root and stem lengths increased in plants inoculated with bacteria compared to the uninoculated control. Among treatments, A2 produced the greatest root and shoot lengths (17.23 and 26.2 cm), while A3 showed the lowest (15.8 and 21.5 cm). SPAD values also increased by 6%, 10%, and 3.2% in Treatments A1, A2, and A3, respectively. This study clearly demonstrated that the endophytic isolates (C-14 and C-27) obtained from bell pepper roots significantly enhanced the growth of barley due to their ability of IDC production, thereby offering a promising alternate to chemical fertilizers.

Microorganisms doi: 10.3390/microorganisms14051068

Authors: Taozhen Chen Keyang Tao Yanguang Zhou Hao Qian Binchao Yu Mingjiang Mao Chendao Ruan Xiaofeng Yuan

Trichoderma harzianum is an important biocontrol fungus widely used to manage vascular wilt caused by Fusarium oxysporum. However, the molecular regulation and metabolic responses underlying different confrontation modes remain unclear. In this study, we integrated non-targeted and targeted metabolomics, transcriptomics, mycotoxin detoxification assays, and RNA interference (RNAi) to systematically investigate antagonistic mechanisms under direct and indirect confrontation conditions. Direct confrontation strongly inhibited F. oxysporum via physical mycoparasitism and was accompanied by enhanced mycotoxin biosynthesis. In contrast, indirect confrontation induced metabolic reprogramming, characterized by increased amino acid and energy metabolism, and promoted biomass accumulation in T. harzianum. Targeted metabolomics identified 38 core mycotoxins, several of which were significantly enriched during direct confrontation. Detoxification assays further showed that T. harzianum reduced multiple mycotoxins in a concentration-dependent manner, likely through a combination of physical adsorption and potential biochemical transformation, although the exact mechanisms remain unclear. Transcriptomic analysis revealed extensive differential gene expression in both fungi, particularly in pathways related to redox homeostasis and metabolic regulation. In addition, exogenous dsRNA effectively reduced the expression of selected pathogenicity-related genes in F. oxysporum at the transcriptional level. Overall, these findings highlight mode-specific antagonistic responses and provide a descriptive framework for understanding fungal interactions. The potential integration of microbial biocontrol with RNAi-based approaches is discussed as a conceptual perspective that requires further experimental validation.

Microorganisms doi: 10.3390/microorganisms14051067

Authors: Wenjing Cui Zhi Yang Xuhui Meng Xiaoyan Wang Wenhao Chen

Aiming to reduce synthetic fertilizer dependence and enhance soil fertility, this study isolated and characterized nitrogen-fixing bacteria from the maize rhizosphere. Nitrogen-free selective media were used for bacterial isolation, followed by detection of the nifH gene and nitrogenase activity. Phylogenetic identification was conducted via 16S rRNA sequencing. Growth-promoting traits, stress tolerance, and pot-based plant inoculation effects were assessed. Genetic modification of strain GN8811 was performed to improve nitrogen fixation and growth promotion. Seven isolates that carried the nifH gene and exhibited nitrogenase activity were closely related to four genera. Several isolates showed phosphate solubilization, iron chelation, IAA production, or potassium solubilization, with GN2003 and GN8811 tolerating high salinity and variable pH. Inoculation with GN8811 promoted maize growth comparable to nitrogen fertilization, and its genetically modified derivative (ΔnifL:PrpoD) showed further improvement even under high nitrogen conditions. These findings highlight the potential of combining microbial screening with genetic engineering to develop efficient bioinoculants for sustainable maize cultivation.

Microorganisms doi: 10.3390/microorganisms14051066

Authors: Wanling Qiu Yen-Chi Wu Fuying Li Yin Li Jingjing Zhao Shu-Jung Lai Wangchuan Xiao Chih-Hung Wu Guowen Dong Wei-Ling Zhang Chao-Jen Shih Sheng-Chung Chen Hangying Zhang Song Wang Lintao Wu

A microbial community study using a culture-dependent method was conducted on dehydrated sludge collected from a steel factory’s wastewater treatment plant. One isolate, designated QWL-01T, was a strictly anaerobic, Gram-stain-negative, non-motile, non-spore-forming bacterium with coccoid cells measuring 0.6–0.9 μm in diameter. The growth of strain QWL-01T was observed at 4–40 °C (optimum at 28–35 °C), pH 5.5–8.0 (optimum at pH 7.1), and a range of 0–3% NaCl (optimum at 0.5%). An analysis of the Biolog AN plate revealed positive carbon source utilization only for palatinose, α-ketovaleric acid, and pyruvic acid. The predominant fatty acids were iso-C13:0 (17.0%), C16:0 dimethyl acetal (12.0%), and anteiso-C13:0 (9.2%). A 16S rRNA gene sequence analysis through BLASTN demonstrated that the nearest phylogenetic neighbors of the novel strain were Youngiibacter multivorans DSM 6139T (93.82%) and Proteiniclasticum ruminis JCM 14817T (93.75%). The genome size of strain QWL-01T was 3.69 Mbp, with a G+C content of 50.8 mol%. Comparing strain QWL-01T with closely related species of genera Proteiniclasticum and Youngiibacter, the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) values ranged from 26.60% to 36.80%, 65.89% to 68.30%, and 49.27% to 51.58%, respectively. Based on phenotypic, physiological, phylogenetic, and genomic relatedness evidence, strain QWL-01T represents a novel genus in the family Clostridiaceae, for which the name Anaerococcoides asporogena gen. nov. sp. nov. is proposed. Strain QWL-01T (=BCRC 81396T = CICC 25258T = NBRC 117088T) is the type strain of the proposed novel species.

Microorganisms doi: 10.3390/microorganisms14051065

Authors: Peizhuo Zou Qian Yang Tom Defoirdt

The emergence of antibiotic resistance in aquaculture not only makes antibiotic treatments ineffective in aquaculture but also poses a threat to public health. In order to overcome this, novel strategies to control bacterial diseases are needed. Antivirulence therapy, which disrupts virulence without affecting bacterial viability, represents a promising alternative approach. This study evaluated the antivirulence activity of Qstatin against pathogenic vibrios belonging to the Harveyi clade. Qstatin specifically inhibited the three-channel quorum sensing system in Vibrio campbellii, significantly downregulated the expression of quorum sensing-regulated virulence genes (flaA, flaK, vpsR, vpsT, and vhp) and attenuated the corresponding phenotypes: swimming motility was reduced by up to 57% and biofilm formation by up to 76%. Protease activity, in contrast, was slightly increased rather than decreased. Finally, treatment with 100 μM Qstatin significantly increased the survival of gnotobiotic brine shrimp larvae upon challenge with each of 13 tested pathogenic Harveyi clade strains (belonging to the species V. campbellii, V. harveyi, or V. parahaemolyticus), without an impact on Vibrio densities in the rearing water. These findings indicate that Qstatin has a broad-spectrum antivirulence activity against Harveyi clade vibrios by inhibiting quorum sensing, thus supporting its potential as a sustainable disease control agent.

Microorganisms doi: 10.3390/microorganisms14051064

Authors: Zixi Ming Shihong Chen Jun Gu Ran Yu

Conventional aerobic composting is limited by incomplete organic matter degradation, long composting times, and low product quality. Hyperthermophiles have been applied in composting, but systematic studies on their storage conditions and inoculation strategies are lacking. In this study, the hyperthermophilic microbial consortium, designated as NJ, maintained higher post-storage regrowth capacity after 6-month storage at 25 °C and 4 °C than at −80 °C. Furthermore, inoculated at the medium-temperature stage, NJ enhanced organic matter decomposition and shortened the composting time by 50% compared with high-temperature stage inoculation (>55 °C). Compared with a commercial inoculant, NJ shortened composting time by 67%, increased the germination index from 70% to 85%,raised DTN by 40%, and led to humic substance accumulation by the end of composting, indicating improved product quality. Consequently, medium-temperature stage inoculation of NJ enhances composting efficiency and product quality by enabling earlier functional expression and effective ecological niche occupation.

Microorganisms doi: 10.3390/microorganisms14051063

Authors: Annalisa Lombardi Patrizia Riccio Maria Ragosta Mariagrazia D’Emilio Dario Bruzzese Vito Imbrenda Tonia Borriello Giuseppina La Rosa Elisabetta Suffredini Ida Torre Francesca Pennino

Wastewater monitoring has been recognized as a valid tool for monitoring coronavirus disease 2019 (COVID-19) diffusion. In this paper we analyse a dataset composed by the measurements of SARS-CoV-2 RNA load in 605 raw wastewater samples collected from nine wastewater treatment plants (WWTPs) in the Campania region from October 2021 to May 2025. We analyse the correlation structure of the dataset using multivariate statistical techniques with the aim of identifying the most representative sentinel WWTPs and thus optimizing the number of samples. Results of spatial analysis showed that there are two isolated elements, SA3 and NA1, with the highest and lowest SARS-CoV-2 load values, respectively, and other two clusters (Cl1 and Cl2) from the other WWTPs. Temporal analysis showed that NA3 WWTP had a statistically significant difference in SARS-CoV-2 load from 2022 to 2023. Our method suggests limiting samplings to three sites, as follows: SA3 (which can act as a sentinel site because it is the first site that records variation in viral load) and two with the higher variation coefficients (CV%) belonging to the two clusters, as follows: CE1 for Cl1 and NA4 for Cl2. This data analysis procedure could allow to focus only on certain WWTPs for SARS-CoV-2 monitoring, to promptly identify outbreaks.

Microorganisms doi: 10.3390/microorganisms14051062

Authors: Simona Ioana Adriana Mlendea (Gălbineanu) Alin Kraft Cristian Falup-Pecurariu Tatiana Gianina Melicianu Laurențiu Dănuț Nedelcu

Healthcare-associated infections (HAIs) are clinically relevant complications in critically ill stroke patients, particularly in neurological intensive care settings, where severe neurological injury, dysphagia, immobilization, invasive device exposure, and prolonged hospitalization increase infection susceptibility. Romanian data focused on deceased stroke patients admitted to neurological intensive care units remain limited. This retrospective descriptive single-center hospital-based study, supported by focused literature contextualization, was conducted in the Neurological Intensive Care Unit of the Brașov County Emergency Clinical Hospital, Romania. Adult stroke patients who died during hospitalization over a six-year observation period were included. Clinical data were extracted from a working hospital database and analyzed descriptively after data cleaning and harmonization. The final cohort comprised 190 deceased stroke patients; ischemic stroke was documented in 69.5% and hemorrhagic stroke in 28.9%. Hypertension (73.7%) and ischemic heart disease and/or previous myocardial infarction (60.0%) were the most frequently recorded comorbidities. Pneumonia was the dominant documented infectious complication, recorded in 52.6% of patients, followed by urinary tract infection (11.6%), pressure sore-related infection (4.7%), and sepsis-related coding (6.8%). The median in-hospital survival interval was 6 days (IQR 3.0–10.75). Because year-by-year stratification was not sufficiently robust, the temporal component was interpreted only in aggregate form. These findings provide a descriptive hospital-based profile of documented infectious complications in a fatal stroke ICU cohort and support the need for more standardized infection documentation and better linkage between clinical and microbiological data in neurocritical care settings.

Microorganisms doi: 10.3390/microorganisms14051061

Authors: Joel Ríos-Alvarado Perla Guadalupe Vázquez-Ortega Norma Urtiz-Estrada Javier López-Miranda Jesús Bernardo Páez-Lerma María Adriana Martínez-Prado Marcelo Barraza-Salas David Enrique Zazueta-Álvarez Damián Reyes-Jáquez Alma Karina Tamez-Castrellón Juan Antonio Rojas-Contreras

Yeast surface display is a powerful strategy for enzyme immobilization and whole-cell biocatalysis; however, the intracellular processing of heterologous enzymes during secretion and anchoring remains poorly understood. In this study, a GH5 endoglucanase gene (eglS, 1.4 kb) from Bacillus subtilis, originally isolated from a paper mill effluent, was cloned into the pYD1 vector and expressed in Saccharomyces cerevisiae EBY100 using the Aga1–Aga2 surface display system. The recombinant strain produced clear degradation halos on carboxymethyl cellulose (CMC) plates, confirming cellulolytic activity at the whole-cell level. Zymographic analysis revealed multiple active enzyme forms depending on the cellular fraction analyzed. Intracellular extracts displayed active bands ranging from 70 to 57 kDa, consistent with immature or partially processed Aga2 fusion proteins, whereas cell wall-associated fractions showed active bands between 55 and 35 kDa, suggesting proteolytic processing during secretion and surface anchoring. The apparent specific activity of the cytoplasmic fraction was 5.33 ± 0.31 U mg−1, while the cell wall-associated fraction exhibited a higher apparent specific activity (58.4 ± 10.1 U mg−1). Although these values were obtained from non-purified fractions and therefore do not represent intrinsic enzymatic constants, they indicate a relative enrichment of catalytically active enzyme in the cell wall-associated fraction, consistent with functional surface display. The presence of multiple active enzyme forms and the enhanced catalytic efficiency observed in the cell wall-associated fraction suggest that the engineered yeast strain may serve as a promising whole-cell biocatalyst, with potential applications in consolidated bioprocessing (CBP) strategies for lignocellulosic biomass conversion.

Microorganisms doi: 10.3390/microorganisms14051057

Authors: Mingze Chen Xin Yan Jialu Zhao Jingjing Xu Mingjun Sun Weixing Shao Shufang Sun Qiuming Du Peipei Zhang Shixiong Sun Haobo Zhang Mengda Liu Xiangxiang Sun Xiaoxu Fan Wenlong Nan

Brucellosis, a zoonotic disease caused by Brucella, requires rapid, accurate, and sensitive diagnostic methods for effective prevention and control. This study presents the development of a fluorescence microsphere immunochromatographic assay (QDMs-ICA) for detecting anti-Brucella antibodies in bovine serum and milk. Lipopolysaccharide (LPS) from the Brucella abortus strain A19 was immobilized on the nitrocellulose membrane (NC membrane) as the test line (T-line), while rabbit anti-SPG polyclonal antibody was applied as the control line (C-line). Recombinant streptococcal protein G conjugated with quantum dot microspheres (QDMs-SPG) served as the detection conjugate. After optimizing the preparation parameters of QDMs-ICA, the method demonstrated sensitivities of approximately 0.98 IU/mL for bovine serum and 1.56 IU/mL for milk. No cross-reactions were observed with antibody-positive sera from Coxiella burnetii, Mycobacterium avium paratuberculosis, Mycobacterium tuberculosis, Chlamydia abortus, Bacillus anthracis, Escherichia coli O157:H7, Vibrio cholerae or Salmonella, indicating excellent specificity. In intra- and inter-batch repeatability tests, the coefficient of variation (CV) remained below 15%, confirming good reproducibility. The detection limit remained stable after storage at 37 °C for 7 days. Parallel testing of 150 bovine serum samples and 80 milk samples showed a high degree of concordance with the ID-VET commercial kit, with coincidence rates of 97.3% and 96.3%, respectively. These results demonstrate that QDMs-ICA offers high specificity, sensitivity, repeatability, and reliability, making it an effective tool for the rapid detection and epidemiological monitoring of brucellosis.

Microorganisms doi: 10.3390/microorganisms14051060

Authors: Mehdi Serrari Lorenza Bianchi Marie Tré-Hardy Sara Törnblom-Paulander Manon Alexandre Arnaud Nevraumont Ingrid Beukinga Frédéric Buxant Hamza Bensaoud Laurent Blairon

Antenatal screening for Group B Streptococcus (GBS) does not always reflect intrapartum colonisation status, and rapid molecular point-of-care tests (POCT) have been developed to enable real-time detection during labour. This prospective single-centre study evaluated the performance of six molecular assays (easyNat, FlashDetect, GenDx, GenPad, iPonatic, Revogene) and one antigen-based test (TZcheck) for intrapartum GBS detection under real-world conditions. Vaginal–rectal swabs were collected at admission from 104 women at ≥ 37 weeks of gestation and tested directly without prior enrichment, using conventional intrapartum culture as the reference standard. Diagnostic performance varied substantially across platforms, with positive percent agreement ranging from 0.0% to 80.6%, while negative percent agreement was generally high, except for GenDx. Seven culture-positive samples yielded negative results across all molecular assays, while one sample was consistently positive across multiple molecular platforms despite negative culture. Exploratory observations suggest that differences in lysis procedures may contribute to variability in assay performance, although this could not be formally assessed. These findings highlight the variability of intrapartum molecular POCT under routine conditions and underscore the need for cautious clinical interpretation and local validation prior to implementation.

Microorganisms doi: 10.3390/microorganisms14051059

Authors: Anabel Franco-Moreno Cristina Lucía de Ancos-Aracil Ana Martínez-Casa-Muñoz Juan Torres-Macho Eva Ruiz-Navío Ana Bustamante-Fermosel María Hornero-Vázquez Miguel Ángel Casado-Suela

Background: Gut microbiota dysbiosis has been proposed as a potential contributor to venous thromboembolism (VTE), although its clinical relevance remains uncertain. Methods: This review was conducted following the PRISMA 2020 guidelines. We conducted a systematic review of studies evaluating the association between gut microbiota dysbiosis and VTE. MEDLINE/PubMed, Web of Science, EMBASE, and Scopus were searched from the inception to February 2026. Observational studies and Mendelian randomization (MR) analyses assessing microbiota composition, dysbiosis, or related metabolites in relation to VTE were included. Risk of bias was assessed using established tools. Results: Thirteen studies were included (five observational and eight MR). Observational evidence showed heterogeneous findings. Microbial metabolites such as trimethylamine N-oxide and lipopolysaccharides were associated with prothrombotic profiles in some studies, but no consistent association with VTE risk or recurrence was observed. The differences in microbiota composition were reported, although based on small populations. MR analyses identified microbial taxa with potential protective or risk associations, but most findings were modest and not robust after multiple testing correction. Conclusions: Gut microbiota dysbiosis may contribute to VTE through inflammatory and metabolic pathways; however, current clinical evidence is limited and inconsistent. Further prospective studies are needed to clarify causality and clinical implications.

Microorganisms doi: 10.3390/microorganisms14051058

Authors: Inkar Castellanos-Huerta Jacob Lum Guillermo Romero Aaron Forga Billy M. Hargis Danielle Graham

Salmonella enterica is a significant Gram-negative bacterium possessing over 2500 serovars capable of affecting both animals and humans and disseminating widely due to its adaptability, genetic diversity, and ability to form biofilms. Different serovars, such as S. enterica Typhimurium (ST), Enteritidis (SE), and Infantis (SI), display varying traits and survival strategies in harsh environments. Biofilms, composed of proteins, lipids, and DNA, enable bacteria to survive stresses such as pH changes, nutrient shortages, temperature fluctuations, and disinfectants. Evaluating disinfectants on inert surfaces is crucial for understanding their effectiveness and impact on poultry. This study assessed the efficacy of chlorine dioxide (ClO2) disinfectant against ST, SE, and SI growth, biofilm formation, and biofilm removal at varying concentrations in vitro. Results showed serotype-dependent and condition-specific responses, with SE and SI being more affected than ST, which may be associated with differences in oxidative stress response mechanisms, highlighting the need for tailored disinfection protocols.

Microorganisms doi: 10.3390/microorganisms14051056

Authors: Zhiqian Guan Yu Wang Yibo Geng Yuanyuan Wang Lilong Hou Xingling Tian Jiao Pan

The Jinshanling Great Wall is an important part of the Ming Great Wall, the most important material cultural heritage of China, and is currently facing a significant threat of microbial degradation due to the widespread biological weathering of open-air masonry buildings. This study focuses on the Qilin Screen Wall and Text Brick Wall of the Jinshanling Great Wall, utilizing scanning electron microscopy (SEM) and metabarcoding analyses to reveal the diverse microbial communities coexisting on the masonry surfaces, including various lichens, molds, and bacteria. Twelve fungal strains were successfully isolated. The antimicrobial experiment results indicated that 0.6% isothiazolinone-based antimicrobial BC01, 50 mg/mL carvacrol and 50 mg/mL thymol exhibited a certain degree of antimicrobial activity against these strains. Overall, this study has laid a solid foundation for microbial control of the masonry Great Wall through in-depth analysis of microbial community structure and screening of highly effective antimicrobials.

Microorganisms doi: 10.3390/microorganisms14051055

Authors: Yunchen Zhou Rong Xi Siran Wang Ban Li Yue Wu Chengbo Wen Dexian Zhang

Antimicrobial resistance (AMR) in Escherichia coli (E. coli) from food-producing animals constitutes a substantial public health concern. This study characterized antimicrobial resistance profiles, phylogenetic diversity, virulence-gene distribution, and plasmid-borne extended-spectrum β-lactamase (ESBL) determinants of E. coli isolates recovered from water buffaloes with subclinical mastitis. Among the 54 ESBL-producing E. coli isolates, all were resistant to ampicillin and cefotaxime. High resistance rates were also observed for cephalothin (75.9%), trimethoprim–sulfamethoxazole (74.0%), ceftiofur (70.4%), florfenicol (68.5%), and cefazolin (63.0%). Lower resistance was recorded for colistin sulfate (40.7%), enrofloxacin (33.3%), and gentamicin (25.9%). Phylogenetic analysis of ESBL producers identified phylogroup B1 (42.6%) as predominant, followed by groups A (29.6%) and D (25.9%). Multilocus sequence typing (MLST) revealed that ST50 (20.4%) was the most common sequence type, and serogroup O150 was dominant (70.4%). Virulence genes, such as iss (81.5%), astA (59.3%), and espP (38.9%), were frequently detected among ESBL isolates. ESBL genes were predominantly blaCTX-M-1 (27.8%) in all isolates, while the narrow-spectrum β-lactamase genes blaTEM-1 (55.6%) and blaOXA-10 (14.8%) were also commonly co-detected. Bioinformatic analysis predicted that all ESBL genes were associated with plasmid-derived contigs, with the predicted plasmid size ranging from approximately 32 to 187 kb and belonging to IncFIB, IncFIA, IncI1, IncFIA + I1, and IncFII replicon types. Conjugation frequencies ranged from 4.8 × 10−7 to 4.1 × 10−2, and plasmids were predicted to carry additional resistance genes mediating resistance to chloramphenicol (floR), sulfonamides (sul1, sul3), tetracyclines (tet(A) and tet(B)), and trimethoprim (dfrA1, dfrA12). The co-carriage of ESBL genes with additional antimicrobial resistance and virulence determinants suggests the potential role of water buffaloes as reservoirs of clinically relevant resistance traits that may disseminate through horizontal gene transfer.

Microorganisms doi: 10.3390/microorganisms14051054

Authors: Peng Xie Jing Sun Xiangzheng Wu Chenxi Liu Luqi Li Tong Wu Yihan Luo Caiyuan Zhou Fang Wang Yibin Hu Leilei Sun Chengbao Wang

The prevalence of blaKPC-carrying Klebsiella pneumoniae poses a significant clinical challenge, yet its systematic metabolic adaptations remain poorly understood. We employed an engineered K. pneumoniae (pACYC184/KPC-2) model and UHPLC-QE-Orbitrap-MS-based untargeted metabolomics to characterize metabolic shifts under steady-state and antibiotic-stressed conditions. OPLS-DA revealed profound metabolic divergence induced by KPC-2. At steady state, the 96 differential metabolites (30 up-regulated, 66 down-regulated) indicated enhanced cell membrane and nucleotide metabolism but suppressed carbohydrate and amino acid pathways. Under antibiotic challenge, the 90 differential metabolites (49 up-regulated, 41 down-regulated) indicated activated porphyrin, purine, and aromatic amino acid metabolism, alongside inhibited respiratory chain and lipid oxidative processes. NADH, FAD, and UDP were identified as core regulatory nodes. Our findings suggest that KPC-2 is associated with systematic metabolic rewiring that may facilitate bacterial survival and adaptation. These metabolic signatures provide novel insights into the putative physiological cost of resistance and potential therapeutic targets.

Microorganisms doi: 10.3390/microorganisms14051053

Authors: Alexander Martens Markus Schauer Mohamad Motevalli Brigitte König

Despite its clinical importance, Staphylococcus aureus colonization in community populations remains insufficiently understood. This study aimed to determine the prevalence, anatomical distribution (nasal versus throat), and antimicrobial resistance patterns of Staphylococcus aureus colonization in healthy community-dwelling adults and to identify demographic and clinical factors associated with carriage. A cross-sectional study was conducted among 100 community-dwelling adults in Germany, yielding 200 nasal/throat samples. Staphylococcal isolates were identified using MALDI-TOF MS, and antimicrobial susceptibility was determined according to EUCAST guidelines. MRSA and PVL genes were assessed using molecular assays, and genetic relatedness was evaluated by rep-PCR. Associations with demographic and clinical variables were analyzed using multivariable logistic regression in R. Staphylococcus aureus carriage prevalence was 39%, higher in the nose (33%) than the throat (19%), with rare MRSA (3%) and no PVL detection. Significant nasal–throat discordance was observed (p < 0.01), with a fair agreement between sites (κ = 0.34). Resistance patterns among Staphylococcus aureus isolates were dominated by penicillin G resistance (47%), while 35% remained fully susceptible, and multidrug resistance was rare (6%). Multivariable analyses indicated no strong associations between overall, nasal, or throat carriage and age, sex, recent antibiotic use, or other clinical exposures (p > 0.05), with wide confidence intervals, potentially reflecting limited statistical power and only modest model discrimination (AUC 0.65–0.68). These findings indicate that community Staphylococcus aureus colonization is potentially marked by modest prevalence, substantial anatomical discordance, and a low-risk resistance profile, while common demographic and clinical factors contributed little to explaining carriage patterns.

Microorganisms doi: 10.3390/microorganisms14051052

Authors: Jiayu Zhao Yuqi Zou Jian Bao Pengbo Sun Mingjian Liu Baochao Bai Xiangdong Liu Yuxuan Wang Shuai Du Muqier Zhao

Fermented total mixed ration (FTMR) is an effective approach to preserve low-quality crop residues. This study investigated the effects of ensiling duration (0, 3, 5, 7, 15 and 30 days) on nutritional dynamics, fermentation quality, in vitro digestibility, and bacterial communities of FTMR containing corn stalk and broom sorghum straw at 50% moisture. After 30 d of ensiling, FTMR had the highest crude protein content, lowest neutral detergent fiber content, peak lactic acid concentration, stable low pH, undetectable butyric acid, and maximum in vitro NDF digestibility. Bacterial alpha diversity declined significantly during ensiling, and the community was dominated by Leuconostoc, Lactiplantibacillus, and Levilactobacillus. These results clarify the microbial regulatory mechanism of mixed-straw FTMR fermentation and support the efficient utilization of crop residues in ruminant production.

Microorganisms doi: 10.3390/microorganisms14051050

Authors: Caixiang Wei Xin Gao Ruizhanghui Wang Qi Yan Qichao Gu Yuyang Liang Dongwen Qiu Yongqi Tan Huadong Luo Qingfeng Tang Zhilin Yan Jianwei Chen Caixia Zou

Based on previous findings that fiber digestibility and rumen fermentation in weaned buffalo calves were improved by a roughage combination of dried sugarcane leaves (SDL) and peanut vine (PV), this study reveals that the mechanism for improving fiber digestibility and growth performance involves increasing Succiniclasticum abundance and 3-methoxytyramine-betaxanthin level, which consequently increases ruminal acetate and propionate. Twenty-one calves were fed pelleted diets with roughage combinations the 15% SDL combined with PV (S15PV, 15% SDL + 15% PV), the 22.5% SDL combined with PV (S22.5PV, 22.5% SDL + 7.5% PV), or the 30% SDL combined with PV (S30PV, 30% SDL) for 63 days. The results showed no significant differences in α-diversity and β-diversity among the three groups (p > 0.05). A significantly higher relative abundance of Succiniclasticum was observed in the S22.5PV group than in the other two groups, by 241.57% and 136.25%, respectively (p < 0.05), and its effects were primarily exerted through carbohydrate and amino acid metabolism pathways. Differential metabolites were mainly enriched in cofactor/vitamin metabolism (vitamin B6, riboflavin) and amino acid pathways (arginine, tryptophan). By PLS-DA analysis, significantly higher levels of Bentyl and 3-Methoxytyramine-betaxanthin were observed in the S22.5PV group compared to the S15PV and S30PV groups, respectively. Positive correlations were observed between Succiniclasticum and NDFD, ADFD, acetic acid, propionic acid, isovaleric acid, as well as 3-Methoxytyramine-betaxanthin (p < 0.05). In conclusion, the rumen microbial diversity was not altered by the roughage combinations of dried sugarcane leaves and peanut vine, but the abundance of Succiniclasticum and the level of 3-Methoxytyramine-betaxanthin were significantly correlated with NDFD and ADFD, which enriched ruminal AA and PA, and may thus be associated with improved growth performance.

Microorganisms doi: 10.3390/microorganisms14051051

Authors: Lubna Shakoor Shumaila Naz Anas Rashid Muhammad Idrees

Biofilms on meat-contact surfaces pose critical food safety risks. This study investigates the interplay between biofilm architecture, metabolic vigor, and antimicrobial resistance on retail surfaces in Pakistan. Screening 300 isolates from 120 surfaces identified 42 high-risk biofilm formers. Comprehensive phenotypic screening revealed that standard visual assays severely underestimate the viability of environmental strains. Biofilm biomass and metabolic activity correlated positively (Spearman’s ρ = 0.656, p < 0.001). Crucially, Ordinary Least Squares regression established that metabolic vigor, rather than physical biomass, independently predicts resistance severity. Phenotypic profiling revealed a high-risk landscape with 81.8% multidrug-resistant and 18.2% extensively drug-resistant isolates, including resistance to colistin and Linezolid. Alarmingly, 79.5% of critical resistance phenotypes compromised WHO Reserve category antibiotics, escalating to 100% on mincer machines. Ecological analysis demonstrated surface-driven partitioning; porous wood boards fostered diverse Enterobacteriaceae, while mincers selected for uniformly resistant clades. These findings highlight processing machinery as resilient reservoirs for untreatable pathogens, necessitating targeted anti-biofilm measures, such as matrix-degrading enzymes. Bridging a critical knowledge gap, this study is among the earliest integrated ecological analyses combining phylogenetic, metabolic, and resistance profiling in Pakistan’s non-poultry meat sector.

Microorganisms doi: 10.3390/microorganisms14051048

Authors: Shahjahon Begmatov Andrey L. Rakitin Yulia Y. Berestovskaya Alexey V. Beletsky Andrey V. Mardanov Nikolai V. Ravin

Wastewater treatment plants represent a primary source of environmental dissemination of multidrug-resistant (MDR) bacteria, underscoring the urgent need for in-depth investigation of these organisms. While the resistome of MDR bacteria has been extensively studied, there remains a critical gap in understanding the role of plasmid-borne genes encoding adaptive metabolic functions. We isolated two MDR strains from municipal wastewater, Klebsiella sp. KOS9 and Pseudomonas veronii Yu15, both exhibiting resistance to antibiotics, including ampicillin, cefazolin, kanamycin, streptomycin, erythromycin, chloramphenicol, tetracycline, and ciprofloxacin. The plasmids of these strains harbored genes encoding aliphatic amidases, as well as antibiotic resistance genes (ARGs) and enzymes involved in glycogen and dTDP-L-rhamnose biosynthesis, which may contribute to virulence. In Klebsiella sp. KOS9 a single acetamidase operon, was found on the megaplasmid, along with copper and silver resistance genes. P. veronii Yu15 harbored an operon containing the acetamidase and formamidase genes on the chromosome, as well as a phylogenetically distant acetamidase operon on the conjugative megaplasmid. Both strains exhibit acetamidase activity and P. veronii Yu15 was able to utilize acetamide and formamide as sole nitrogen sources. The occurrence of ARGs and adaptive accessory genes on plasmids likely enhances the competitiveness and environmental flexibility of these MDR bacteria.

Microorganisms doi: 10.3390/microorganisms14051049

Authors: Rungting Tu Cheryl Lin G. Natasha Santoso Wendy E. Braund Ann M. Reed Pikuei Tu

The effectiveness of infection prevention depends on not only uptake but also the timing of adoption. Vaccination studies typically treat uptake as binary, overlooking when while investigating why individuals get vaccinated. Using the novel mRNA COVID-19 vaccines as a case study, the influences of risk perceptions and social norms on vaccination timing were examined through an Innovation Diffusion framework. An online survey was conducted in November 2021 to assess vaccination behaviors, attitudes, and peer expectations of 1710 U.S. residents (51.64% females, 31.23% minorities, with a relatively balanced distribution across age and income brackets). Participants were classified by vaccination timing and intentions as early adopters, early majority, late majority, or laggards for comparative analyses. One year after vaccine rollout, 64.3% had received at least one dose; 20.1% reported no intention to vaccinate, and this resistance persisted through May 2023 when the pandemic ended. Vaccine confidence and prior behavior (e.g., influenza vaccination) demonstrated strong gradients across adoption timing. Earlier uptake was associated with higher perceived vaccine importance, infection risk, and peer uptake, whereas age and education effects diminished over time. Perceived illness severity and disease knowledge showed inconsistent influences. Later adopters anticipated higher post-vaccination infection risk and greater peer non-vaccination, reinforcing hesitancy. Social norms (but not risk perception) mediated the relationship between confidence and timing; earlier adoption further predicted booster acceptance. These findings highlight the importance of trust, correcting efficacy misperceptions, and leveraging positive peer norms to promote timely vaccination and inform strategies for other infectious diseases.

Microorganisms doi: 10.3390/microorganisms14051047

Authors: Andreia La Selva Ellen Sayuri Ando-Suguimoto Ana Paula Mariano Santos Ginez Tania Oppido Schalch Renata Matalon Negreiros Dione Kawamoto Giuliana Giovinazzo Anselmo Ramos Priscila Larcher Longo Rodrigo Athanazio Marcia Pinto Alves Mayer Anna Carolina Ratto Tempestini Horliana

Periodontal status has been associated with infection in lung diseases such as chronic obstructive lung disease (COPD). However, evidence regarding its association with bronchiectasis remains limited, despite the shared clinical and pathophysiological characteristics between the two conditions. Therefore, the aim of the present study was to investigate whether periodontal treatment affects not only the microbiota of saliva but also that of sputum and nasal secretions in individuals with bronchiectasis. This single-center, parallel-group randomized controlled clinical trial included forty-nine individuals with bronchiectasis, who were randomly allocated using a predefined randomization sequence with allocation concealment to a conventional group (n = 26) submitted to mechanical periodontal treatment plus oral hygiene and a control group (n = 23) submitted to oral hygiene alone. Due to the nature of the intervention, participants and operators were not blinded. At the end of the study, all participants received periodontal treatment. The primary outcome was the quantitative assessment of Pseudomonas aeruginosa (P. aeruginosa), Staphylococcus aureus (S. aureus), and Porphyromonas gingivalis (P. gingivalis) in sputum. Secondary outcomes included the quantification of these microorganisms in saliva and nasal secretions, as well as clinical periodontal parameters and quality-of-life assessment. All variables were evaluated at baseline and three months after treatment. Results: Periodontal treatment improved gingival and plaque indices in the conventional group compared with the control group. However, no significant differences were observed in sputum samples for any of the microorganisms analyzed, suggesting no measurable effect on bacterial levels in the lower airways within the study period. At the end of the experimental period, levels of P. aeruginosa and P. gingivalis decreased in nasal secretions, and levels of P. aeruginosa decreased in saliva in the conventional group but not the control group. No significant differences were found in S. aureus levels between groups or overtime. Also, no significant differences in total OHIP-14 scores were observed between groups. In conclusion, periodontal treatment was associated with reductions in P. aeruginosa in nasal secretions and saliva, and P. gingivalis in nasal secretions, in individuals with bronchiectasis and periodontitis. Periodontal treatment improved gingival and plaque indices in the conventional group compared with the control group. However, no significant differences were observed in sputum samples for any of the microorganisms analyzed, suggesting no measurable effect on bacterial levels in the lower airways within the study period. At the end of the experimental period, levels of P. aeruginosa and P. gingivalis decreased in nasal secretions, and levels of P. aeruginosa decreased in saliva in the conventional group but not the control group. No significant differences were found in S. aureus levels between groups or overtime. Also, no significant differences in total OHIP-14 scores were observed between groups.

Microorganisms doi: 10.3390/microorganisms14051045

Authors: Julie Andreina Beltrán Yoneira Fabiola Sulbarán Lily Soto Carlos Pérez Mario Comegna María Graciela López Nahir Martínez-Urbina Moraima Hernández Marjorie Bastardo-Méndez Alejandra Zamora-Figueroa Mariana Hidalgo Flor Helene Pujol Rossana Celeste Jaspe

Hepatitis E virus (HEV) is an emerging zoonotic pathogen of increasing concern in developed regions and represents a major cause of acute viral hepatitis worldwide, primarily transmitted via the fecal–oral route. Although most infections are self-limiting, immunocompromised individuals, such as people living with human immunodeficiency virus (PLWH) and pregnant women, are at risk of severe outcomes, including chronic infection and fatal liver failure, respectively. This study was aimed at evaluating the prevalence and genetic diversity of HEV in PLWH and relevant ecological niches (swine and wastewater) in Venezuela. A total of 417 serum samples from PLWH, 85 wastewater samples, and 67 swine fecal samples were tested for serological or molecular HEV markers. The seroprevalence of anti-HEV antibodies among PLWH was 0.2% for IgM and 5.5% for IgG. HEV RNA was not detected in samples from PLWH or wastewater; however, a 1.5% prevalence of active infection was identified in swine. Phylogenetic analysis of a complete HEV genome revealed an unassignable subtype within genotype 3, tentatively designated as 3p. To the best of our knowledge, this study provides the first molecular characterization and report on HEV frequency in PLWH, wastewater, and swine in Venezuela.

Microorganisms doi: 10.3390/microorganisms14051046

Authors: Mpisana Zuko Nyangiwe Nkululeko Yawa Mandla Slayi Mhlangabezi Jaja Ishmael

Generally, ixodid ticks are important ectoparasites of cattle, including those in smallholder production systems in the Eastern Cape Province, where varying environmental conditions influence their distribution and feeding behaviour. This study investigated ecological variation in tick species composition and attachment site preferences in Bos taurus cattle across coastal and inland areas of the Eastern Cape Province, South Africa. Ticks were collected from cattle of different ages, sexes, breeds, and body condition scores. Sampling was conducted prior to acaricide treatment, and ticks were manually removed from standard predilection sites on each animal. Specimens were preserved in 70% ethanol and later identified morphologically at the Döhne Agricultural Development Institute Laboratory. Data were analysed using generalized linear mixed models with a negative binomial distribution to assess the effects of host and environmental factors on tick burden. Descriptive statistics were used to summarise species composition, while inferential statistics were applied to evaluate differences in infestation levels across host-related and spatial variables. A total of 3250 adult ixodid ticks were collected from cattle. The most prevalent species was Rhipicephalus (Boophilus) decoloratus (39.7%), followed by Rhipicephalus evertsi evertsi (21.0%), Amblyomma hebraeum (17.7%), Hyalomma rufipes (5.8%), Ixodes pilosus (5.8%), Rhipicephalus (Boophilus) microplus (4.5%), R. appendiculatus (3.0%), and R. simus (2.5%). Tick burdens were significantly higher in the coastal zone (85 ± 7.5) than in semi-arid inland areas (62 ± 5.9). Attachment site analysis showed significantly higher infestation levels (p < 0.05) on the udder/scrotum compared to other body regions. This study provides baseline information on tick species composition and attachment site ecology in cattle, contributing to improved understanding of host–parasite interactions and supporting the development of targeted, region-specific tick control strategies.

Microorganisms doi: 10.3390/microorganisms14051044

Authors: Haoyu Wu Congguo Ran Supattra Kitikhun Nan Zhou Xingyu Liu Chengying Jiang

A newly discovered facultative anaerobic strain, designated as LXY-3T, was obtained from a soil sample collected at an industrial site in Guangxi, China, known for heavy metal processing. An investigation including phenotypic, chemotaxonomic, and genomic traits was conducted. Phylogenetic analysis based on 16S rRNA showed that LXY-3T belonged to the genus Paenibacillus. The closest phylogenetic relative of this strain was Paenibacillus anaericanus MH21T with the similarity of 97.03%. Iso-C15:0, antéiso-C15:0, and C16:1 ω7c alcohol were the major cellular fatty acids. The predominant polar lipids comprised diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), unidentified phospholipids (PL1-PL8), unidentified resistant material (RM1–RM4), and lipids (L1–L3). For genome sequencing, the genomic DNA G+C content of the strain is 51.2 mol%. Comparative genomic analysis revealed that the average nucleotide identity (ANI) values between strain LXY-3T and its closest phylogenetic relatives within the genus Paenibacillus (represented by type strains) were consistently below the 95% species demarcation threshold. Nitrogen fixation gene cluster (nifB, nifE, nifK, nifN, nifV, nifX, nifD, and nifH) was conserved in the strain. Correspondingly, digital DNA–DNA hybridization (dDDH) values remained below the 70% cutoff for species delineation. These genomic metrics provide compelling evidence that strain LXY-3T represents a novel species within the genus Paenibacillus. The type strain LXY-3T (=CGMCC 1.64949T = JCM 37600T) is proposed.

Microorganisms doi: 10.3390/microorganisms14051043

Authors: Ana Margarida Silva Konstantina Sarioglou Susana Silva Carla Viegas Edna Ribeiro Maria Teresa Rebelo João Brandão

There is growing concern about the quality of sand on beaches, as users tend to spend most of their time on the sand rather than in the water. Numerous pathogenic agents have reportedly been isolated from sand, including bacteria, nematodes and opportunistic fungi. The ability of sand to retain pollutants and facilitate the transmission of pathogens raises public health concerns. We analysed sand-monitoring data from the 2024 and 2025 bathing seasons on Blue Flag beaches to find trends and patterns in total fungal counts, enterococci, and E. coli. The values recorded for microorganisms showed considerable variability, which may reflect the possible combined influence of multiple climatic, environmental, and anthropogenic factors contributing to their presence in beach sand. Our findings suggest that the total fungal count on coastal beaches may be influenced by periods of rainfall, which increases the fungal load in the sand. Values recorded from inland beaches vary considerably between beaches which may reflect the influence of local environmental characteristics, particularly vegetation and beach morphology, although the smaller number of inland samples also makes it difficult to define clear patterns and consistent reference values for this parameter. Bacterial indicators may be particularly influenced by occasional anthropogenic disturbances and contamination events. This study adds significantly to the understanding of the microbiological quality of beach sand, encouraging the integration of sand monitoring into environmental surveillance and management programmes.

Microorganisms doi: 10.3390/microorganisms14051042

Authors: Zhaohui Cai Raj Kalkeri Benjamin Haner Mi Wang Paul Skonieczny Bahar Osman Dominic Dent David Silva Kevin Auerbach Emmanuel Faust Sheau-Line Feng Miranda R. Cai Mingzhu Zhu Shane Cloney-Clark Joyce S. Plested

The pseudovirus neutralization (PNT) assay is an established high-throughput, robust, and efficient BSL-2 method for detecting neutralizing antibodies (NAbs) against SARS-CoV-2 with the correlates of protection previously established for the ancestral (Wuhan) strain. The PNT assay was validated using nonmatched ancestral sera with anti-JN.1 cross-NAbs, clinically matched JN.1 sera with anti-JN.1 NAbs, or nonmatched JN.1 sera with anti-LP.8.1, KP.2, or KP.3 cross-reacting NAbs. In line with predefined validation acceptance criteria, the PNT assay was precise, with %GCV ≤ 50 in ~90–100%/200 results (40 samples/strain). The acceptance criteria were met for linearity (slope ranged from 1.041 for ancestral sera with anti-JN.1 NAbs to 1.213 for JN.1 sera with anti-KP.2 NAbs), R2 (0.9619–0.9944 for ancestral sera with anti–JN.1 NAbs), % relative bias, and total %GCV < 50 for almost all of the 15 serum samples tested for four virus strains. Human sera collected pre–COVID-19 had no detectable titer for tested Omicron JN.1 subvariants (<LLOQ) and all influenza and RSV clinical samples tested negative (<LLOQ) for SARS-CoV-2 and highly immunogenic for seasonal influenza or RSV post-vaccination, demonstrating the PNT assay specificity. Our data suggest this assay is suitable for assessing immune responses to ancestral and current SARS-CoV-2 strains and has potential for evaluating cross-reacting NAbs against emerging Omicron JN.1 subvariants.

Microorganisms doi: 10.3390/microorganisms14051041

Authors: Tshedza Mashamba Johannes N. T. Mthembu Vhukhudo Makhomu Damien Jacobs Mpumelelo Rikhotso Leonard Kachienga Natasha Potgieter Afsatou N. Traore

Wastewater treatment plants (WWTPs) are identified as contributors to faecal pollution and the spread of antimicrobial resistance (AMR) in water ecosystems. This research examined the prevalence, profiles of antimicrobial resistance, and pathogenic types of Escherichia coli in effluent from WWTPs and nearby river systems in the Vhembe District. Between May and June 2025, 28 water samples were collected from two WWTP discharge points as well as upstream and downstream locations along the Mvudi, Luvuvhu, and Madadzhe Rivers. The enumeration of E. coli was conducted using Colilert Quanti-Tray method, with isolates obtained via membrane filtration and confirmed using API 20E and VITEK®2 systems. Antimicrobial susceptibility was assessed using VITEK®2, while pathotypes were detected through multiplex PCR. E. coli was found at all sampling locations; however, differences in concentrations across sampling sites and sampling periods were not statistically significant (p > 0.05). Out of 26 confirmed isolates, a significant resistance to β-lactam antibiotics was noted, especially ampicillin (100%). Pathotype analysis revealed strains such as ETEC, EAEC, and EPEC. These results underline extensive contamination by antimicrobial-resistant E. coli in rivers affected by WWTP discharge, which poses potential public health concerns and underscores the necessity for enhanced monitoring efforts. Additional research is needed to validate these findings.

Microorganisms doi: 10.3390/microorganisms14051040

Authors: Naim Che-Kamaruddin Jefree Johari Hasmawati Yahaya Nurhafiza Zainal Sazaly AbuBakar

Understanding how clinical symptoms relate to immune responses during major variant transitions remains important for informing post-pandemic surveillance and vaccination strategies. This study compared symptom patterns and SARS-CoV-2-specific anti-RBD IgM and anti-S1 IgG antibody responses among vaccinated individuals infected during the pre-Omicron and Omicron-dominant periods, representing a key phase in the evolution of SARS-CoV-2 population immunity. A retrospective analysis of 216 confirmed COVID-19 cases was performed by evaluating 11 predefined symptoms together with anti-RBD IgM and anti-S1 IgG levels measured at Day-14 after symptom onset, corresponding to the period when humoral antibody responses are detectable following SARS-CoV-2 infection. Participants with breakthrough infection during the Omicron-dominant period reported fewer symptoms overall compared to the pre-Omicron period, with a median of three versus four symptoms, respectively. Cough was the most common symptom during the Omicron period (82.1%), followed by sore throat (81.4%) and fever (78.6%). In contrast, loss of taste or smell was significantly more frequent in the pre-Omicron period (64.8% versus 22.9%, p < 0.05). IgG levels were significantly higher during the Omicron period than during the pre-Omicron period, increasing by 42.3%, reflecting enhanced antibody responses likely driven by repeated exposure. A consistent association between cough and elevated IgG levels was observed in both periods (p < 0.05), suggesting an association between symptom presentation and the magnitude of the early humoral response. These findings suggest that while clinical symptom profiles evolved across a major SARS-CoV-2 variant transition, certain symptom–antibody relationships remained consistent. Such associations may provide insight into how clinical manifestations relate to immune responses in populations with pre-existing immunity and may support interpretation of symptomatic infection during ongoing SARS-CoV-2 circulation.

Microorganisms doi: 10.3390/microorganisms14051039

Authors: Siqi Yang Ying Yang Shihan Feng Jianfeng Liu Yunqing Cheng

Fusarium head blight (FHB), caused by Fusarium graminearum, is a devastating wheat disease leading to significant yield loss and mycotoxin contamination. This study elucidated the biocontrol mechanism of Bacillus velezensis 20507 fermentation broth against FHB during wheat infection. The broth exhibited strong, time-dependent antifungal activity in vitro, with optimal growth suppression (inhibition rates up to 75%) achieved using broth fermented for 3–7 days. In planta experiments confirmed its efficacy in alleviating disease symptoms. Employing a dual RNA-seq strategy, we analyzed the tripartite interaction between the biocontrol agent, pathogen, and wheat host. Transcriptomic analysis revealed that the broth directly suppressed the pathogen, causing 1510 differentially expressed genes (DEGs, predominantly down-regulated) and disrupting pathways related to carbohydrate metabolism and cell wall integrity. In wheat, the fermentation broth of B. velezensis 20507 counteracted F. graminearum infection by reprogramming the host transcriptome. KEGG analysis during co-inoculation showed that the broth up-regulated defense-related pathways involved in energy, hormone signaling, and cellular maintenance, while down-regulating primary metabolic pathways, indicating a resource reallocation strategy. Furthermore, transcriptomic analysis revealed that the broth alone primed the wheat defense system, and this primed state significantly enhanced the defense response upon pathogen challenge. Untargeted metabolomics identified key antimicrobial compounds, including lipopeptides and the macrolide Macrolactin A. Bioassay-guided fractionation isolated two active fractions (Fr A and Fr B) with potent antifungal activity. This integrated multi-omics study demonstrates that B. velezensis 20507 combats FHB through a coordinated dual mechanism: direct inhibition of the fungus via specific metabolites like Macrolactin A, and simultaneous reprogramming of the host defense and metabolic landscape. These findings provide a scientific foundation for developing this strain as an effective biocontrol agent.

Microorganisms doi: 10.3390/microorganisms14051038

Authors: Jiahui Liang Mi Li Shengxia Chen

Melanoma is an aggressive skin cancer with rapid progression and high metastatic potential, and resistance to current therapies remains a major clinical challenge. In this study, Listeria monocytogenes-derived membrane vesicles (LM MVs) were isolated, characterized, and evaluated for their immunomodulatory and antitumor activities. LM MVs showed an average diameter of approximately 160 nm and contained multiple bacterial proteins, including listeriolysin O. In vitro, LM MVs promoted pro-inflammatory activation of RAW264.7 macrophages, as indicated by increased CD80/CD86 expression and enhanced transcription of inflammatory mediators. LM MV treatment was accompanied by IκB-α degradation and NF-κB p65 nuclear translocation, whereas pharmacological inhibition of NF-κB attenuated macrophage activation. In a macrophage–melanoma co-culture system, LM MVs-activated macrophages reduced the viability, migration, and invasion of B16 melanoma cells and increased tumor cell apoptosis. Additional inhibition and immunofluorescence analyses suggested that iNOS and TNF-α-associated mechanisms contributed to these tumor-suppressive effects. In a murine melanoma model, LM MVs significantly inhibited tumor growth without overt systemic toxicity, whereas macrophage depletion markedly weakened this effect. These findings indicate that LM MVs exert antitumor activity against melanoma, at least in part through macrophage activation involving NF-κB signaling.

Microorganisms doi: 10.3390/microorganisms14051037

Authors: Jiafeng Wu Nansong Jiang Qizhang Liang Hongmei Chen Rongchang Liu Qiuling Fu Guanghua Fu Chunhe Wan Ping Wei Longfei Cheng Yu Huang Tianchao Wei Weiwei Wang

Riemerella anatipestifer (RA) is the primary causative agent of infectious serositis in ducks, causing significant economic losses. In this study, a rapid and visual loop-mediated isothermal amplification (LAMP) assay targeting the conserved region of the ompA gene was developed. Specific primers and a FAM-labeled probe were designed, and amplification products were visualized using phenol red-based colorimetric detection and a lateral flow dipstick (LFD) system. Among the five candidate primer sets, primer set 2 was selected because it showed the highest amplification efficiency and specificity, with no cross-reactivity detected against 12 common waterfowl pathogens. Under optimal conditions, the phenol red-based LAMP assay yielded visible results after incubation at 65 °C for 30 min, while the LAMP-LFD assay required an additional 3~5 min probe hybridization step, with detection limits of 7.76 × 102 copies/μL for the phenol red-based method and 7.76 × 100 copies/μL for the LAMP-LFD method. Thirty clinical samples suspected of RA infection were analyzed using conventional PCR and the developed visual LAMP assays. The positive detection rates obtained with the LAMP-LFD and phenol red-based LAMP methods were 63.3% and 60%, respectively, showing high concordance with conventional PCR (56.7%). In conclusion, the LAMP assay integrating phenol red visualization and lateral flow dipstick detection is rapid, sensitive, and easy to perform, and both detection formats show potential for point-of-care or on-site applications, and can be used for the early diagnosis and detection of RA.

Microorganisms doi: 10.3390/microorganisms14051036

Authors: Shabana M. Shaik Gabriele Schiro Daniel Laubitz Juliette C. Madan Connor P. Kelley Michael Daines Sydney A. Rice Fayez K. Ghishan Pawel R. Kiela

Background: Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infections (PANDAS) are characterized by neuropsychiatric symptoms linked to immune dysregulation. Emerging evidence highlights the role of host–microbiome interactions in modulating neuro-immune functions via gut–brain axis signaling; however, its contribution to PANDAS pathophysiology remains poorly understood. Methods: We conducted microbiome analysis from samples collected across multiple sites of PANDAS patients including nasal, throat and stool. We performed an integrated multi-omics analysis of stool samples from pediatric PANDAS cases and healthy controls, including discordant twin pairs. Microbial composition and function were assessed using 16S rRNA gene sequencing, shotgun metagenomics, while untargeted metabolomic profiling was performed using ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS). Results: PANDAS cases exhibited reduced alpha diversity and significantly altered beta diversity compared to controls, indicating shifts in gut microbial composition. Shotgun metagenomic analysis revealed differential enrichment of functional pathways, including diminished quorum sensing, altered gamma-aminobutyric acid (GABA) biosynthesis, and microbial degradation processes. Multiple gut–brain modules (GBMs) and gut metabolic modules (GMMs) associated with neurotransmission, transport activities and metabolism were significantly perturbed in PANDAS. Metabolomic profiling showed reduced functional diversity and distinct clustering of metabolic profiles, with differential abundance of amino acids, bile acids, and neuroactive compounds. Integrative analysis further identified disrupted microbe–metabolite networks allied to gut–brain signaling. Conclusions: Our findings reveal significant functional shifts in gut microbiota composition, functional capacity and metabolite profile in PANDAS, suggesting dysregulation of the gut–brain axis signaling. This study provides a foundation for development of microbiome-based biomarkers and therapeutic strategies for pediatric neuropsychiatric disorders.

Microorganisms doi: 10.3390/microorganisms14051035

Authors: Han Lee Gaeun Kim Jungeun Kim OneZoong Kim Sung-Hee Jung Sunghee Hyun Chang Seok Oh

Standard 16S rRNA V3–V4 sequencing encounters primer mismatch issues and insufficient taxonomic resolution, hindering the accurate quantification of specific, low-abundance taxa, such as administered probiotic strains. Therefore, we empirically compared outcomes between the standard V3–V4 method and high-resolution targeted species sequencing (TSS) to assess bias and establish reliability metrics for probiotic efficacy assessments. A longitudinal pilot study was conducted over nine weeks in older participants receiving synbiotic supplementation; their fecal samples were collected and analyzed. V3–V4 analysis successfully captured a significant transient reduction in alpha-diversity with multidirectional genus-level fluctuations. However, taxonomic overlap between these two methods was high at the phylum level and sharply declined to 6.7% at the species level. Notably, compared with V3–V4 sequencing, TSS could successfully quantify the abundance of administered Bifidobacterium animalis. This study empirically demonstrated that 16S rRNA V3–V4 sequencing introduces substantial quantitative bias, limiting its suitability for monitoring specific probiotic strains and compromising the reliability of clinical efficacy assessments. Therefore, we recommend a dual-sequencing framework that integrates the broad ecological screening capabilities of V3–V4 with the precise species-level quantification of TSS to establish the necessary scientific rigor for assessing probiotic efficacy.

Microorganisms doi: 10.3390/microorganisms14051034

Authors: Qiyue Zhao Jiatong Guo Menghan Liu Bojie Yin Bailin Li Yumeng Song Xuming Pan

This study describes two new species of ciliates, Colpoda heilongjiangensis n. sp. and Bryometopus shii n. sp., discovered in northeastern China. Colpoda heilongjiangensis n. sp. was collected from a sewage outlet in Harbin, characterized by its large size, broadly to slenderly reniform body shape, and unique ciliary patterns. Bryometopus shii n. sp. was found in a puddle near a waste disposal station, featuring a droplet-shaped or oval and distinct oral apparatus. The morphology of both species was investigated through live observation, protargol staining, and silver carbonate and dry silver nitrate impregnation. DNA extraction and SSU-rRNA gene sequencing were performed to determine their evolutionary relationships. Phylogenetic analyses based on SSU-rRNA gene data revealed that Colpoda heilongjiangensis n. sp. clusters with C. minima, while Bryometopus shii n. sp. has a close relationship with B. atypicus. This study also discussed the non-monophyletic status of the genus Bryometopus and proposed a revision to the family Tillinidae based on morphological and molecular evidence. These findings highlight the remarkable diversity of Colpodea and contribute to the understanding of their evolutionary relationships.

Microorganisms doi: 10.3390/microorganisms14051032

Authors: Theodoros Varzakas

The role of microorganisms in food was first acknowledged a long time ago [...]

Microorganisms doi: 10.3390/microorganisms14051033

Authors: Seungjun Hur Youngki Yoo Jeong Min Chung

Magnesium is an essential divalent cation required for adenosine triphosphate (ATP)-dependent reactions, nucleic acid metabolism, and ribosomal stability. Bacteria depend on specialized transport systems to maintain intracellular Mg2+ homeostasis as it cannot freely cross the phospholipid bilayer. During infection, host nutritional immunity restricts metal availability, and magnesium limitation within the phagosome compromises bacterial metabolism and stability. This review summarizes the major bacterial magnesium transport systems and their roles in survival and pathogenicity, with an emphasis on Salmonella and extension to clinically relevant ESKAPE pathogens. We focus on the PhoPQ-regulated MgtA, MgtB, and MgtC system, in which low magnesium, acidic pH, and other host-derived signals activate PhoPQ to induce mgt gene expression. MgtA and MgtB act as high-affinity P-type ATPases, whereas MgtC promotes bacterial survival within the intramacrophage environment by inhibiting bacterial F-type ATP synthase through specific interactions with subunit a. We also discuss CorA as a conserved channel for basal Mg2+ uptake and MgtE as a Mg2+-selective channel whose gating responds to intracellular Mg2+ and ATP. Finally, we consider the conservation and variation in these systems across pathogenic bacteria and their potential as therapeutic targets for antimicrobial development.

Microorganisms doi: 10.3390/microorganisms14051031

Authors: Shurong Chen Zhengfei Qi Lina Wang Lian Wu Jiayi Xie Rui Ma Kexin Zhang Tong Ji Min Zhou Lingli Zheng Qingshan Bill Fu

Escherichia coli, a facultative anaerobic Gram-negative member of the Enterobacteriaceae, is an increasingly important opportunistic pathogen driven in part by rising resistance to clinically important antibiotics. Regulation of multidrug efflux systems by two-component signal transduction pathways, particularly the BaeSR system, plays a central role in this process. However, the functional residues governing signal transduction through the sensor kinase BaeS remain incompletely defined. In this study, we integrated domain prediction, homology-guided site-directed mutagenesis, in vitro protein purification, autophosphorylation assays, and reverse-transcription quantitative polymerase chain reaction (RT-qPCR)-based transcriptional analysis of selected BaeSR-regulated genes to delineate key residues required for BaeS function. Sequence analysis identified His250 as a candidate autophosphorylation site and Asn364 as a conserved residue within the catalytic domain. Biochemical characterization of purified wild-type BaeS and an H250A mutant demonstrated that His250 is indispensable for autophosphorylation. Consistently, RT-qPCR analysis showed that BaeS activation markedly induced the transcription of BaeSR-regulated efflux-associated genes, whereas genetic deletion of baeS or selective disruption of kinase activity by the N364A mutation abolished this response. Together, these findings establish His250 as a key residue for BaeS autophosphorylation and identify Asn364 as essential for inducible BaeSR signaling and activation of resistance-associated target genes, thereby establishing an experimental framework for elucidating BaeSR-mediated efflux regulation and informing future studies of resistance regulatory networks and potential intervention strategies centered on key signaling nodes.

Microorganisms doi: 10.3390/microorganisms14051030

Authors: Fatma A. Ameen Mahmoud E. Soliman Amira M. Hamdan Sherif F. Hammad

We evaluated the antimicrobial and antioxidant capabilities of a bacteriocin purified from a recently identified marine Lactococcus lactis (L. lactis) NAN6399 strain, a lactic acid bacterium recovered from Mediterranean coastal waters near Alexandria, Egypt, and identified by combined API 50 CHL phenotypic profiling and 16S rRNA gene sequencing. Bacteriocin purification was achieved by sequential ammonium sulfate precipitation and reverse-phase high-performance liquid chromatography (RP-HPLC). The purified bioactive fraction had an approximate molecular weight of 20 kDa by SDS-PAGE and a 106-amino-acid N-terminal sequence that, upon BLAST alignment, returned 98.1% overall identity to the Lactococcin 972 family bacteriocin AAK06118.1 from L. lactis IL1403, with divergence confined exclusively to the terminal two C-terminal residues. This sequence is structurally and functionally distinct from canonical Lcn972 (L. lactis IPLA 972): the two peptides share an identical 25-residue signal peptide but diverge entirely in their mature bioactive domains, which exhibit only 9.1% sequence identity. Canonical Lcn972 operates through Lipid II-mediated septum disruption and inhibits only Lactococcus species; the NAN6399 peptide, correctly designated as a novel member of the Lcn972-like peptide family, demonstrated broad-spectrum antimicrobial efficacy against multiple indicator organisms (Staphylococcus aureus, Salmonella typhimurium, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterococcus faecalis), producing inhibition zones of up to 30 mm and minimum inhibitory concentration (MIC) values as low as 1.25 μg/mL against S. aureus. Antioxidant capacity was assessed using the DPPH radical scavenging assay, with the purified preparation achieving 73.14 ± 0.34% inhibition. Collectively, these data establish L. lactis NAN6399 as the producer of a bifunctional Lcn972-family bacteriocin with both antimicrobial and antioxidant potential, provide the first experimental characterization of the antimicrobial activity of this Lcn972-family branch, and highlight marine LAB as a productive reservoir for novel bioactive peptide discovery.

Microorganisms doi: 10.3390/microorganisms14051029

Authors: Haotian Wang Guoyu Liu Jia Liu Yifei Zhu Jingmei Huang Shiwei Liu Huaping Pan Yafang Li Yan Zou Xueying Zeng Guankai Hao Haizhi Li Shufan Yang Shenglin Duan Juxiu Li Peng Yuan

Soybean molasses, a by-product of alcohol-based soy protein concentrate production, is rich in stachyose and other functional oligosaccharides, but its high sucrose content and other fermentable non-target sugars hinder the efficient purification of stachyose. In this study, the sugar-utilization patterns of four commonly used microbial chassis or production strains, Escherichia coli W, E. coli BL21, Saccharomyces pastorianus Weihenstephan 34/70, and Komagataella phaffii (formerly Pichia pastoris) GS115, were systematically compared to identify a suitable host for selective stachyose enrichment. Among them, E. coli W showed the best performance in rapidly consuming non-target sugars while retaining stachyose. Based on this strain, a CRISPR–Cas9 engineering strategy was applied by deleting the endogenous α-galactosidase gene melA and overexpressing the sucrose permease gene cscB. The resulting strain selectively and nearly completely removed sucrose and other non-target sugars from soybean molasses, increasing the proportion of stachyose from <30% to >90% of total soluble solids. Further optimization of nitrogen source level, inoculum size, and initial °Brix improved fermentation performance. These results demonstrate an effective biological pre-purification strategy for selective stachyose enrichment from soybean molasses.

Microorganisms doi: 10.3390/microorganisms14051027

Authors: Yunhan Zhang Chenwei Deng Yanni Liu Weiqing Lan Yong Zhao Xiaohong Sun

To address the emerging multidrug-resistance crisis caused by Klebsiella pneumoniae, we expressed the endolysin Lys59 derived from phage VB_KpP_HS106 and performed a comprehensive analysis of its antibacterial activity and structural features. Molecular modeling revealed that Lys59 carries a highly positively charged N-terminus and an amphipathic helix at the C-terminus. In vitro antibacterial assays showed that Lys59 exhibited significant bactericidal activity against K. pneumoniae with an approximately 4 log reduction at 50 µg/mL in 2 h. Meanwhile, Lys59 exhibited potent, broad-spectrum activity against both Gram-negative and Gram-positive bacteria. Stability analysis indicated that Lys59 retained high activity over a pH range of 3–9 and a temperature range of 4–55 °C. Notably, the antibacterial activity of Lys59 was found to be regulated by metal ions. Molecular docking indicated that K+ can enhance binding stability by interacting with ASN35 and VAL57. In contrast, Mg2+ and Ca2+ suppressed catalytic function by binding to the essential GLU17 residue. Furthermore, treatment with 200 µg/mL of Lys59 resulted in a 44.6% reduction in K. pneumoniae biofilm biomass. Overall, this study identified a phage-derived endolysin with broad-spectrum antimicrobial activity and demonstrated its potential as an antibacterial agent against multidrug-resistant K. pneumoniae.

Microorganisms doi: 10.3390/microorganisms14051028

Authors: Domenico Franco Salvatore Papasergi Francesco Mediati Salvatore P. P. Guglielmino Laura Maria De Plano

Pseudomonas aeruginosa is an opportunistic Gram-negative pathogen frequently associated with chronic and biofilm-related infections, largely driven by quorum sensing (QS)-related genes/phenotypes. In this study, we investigated the antivirulence activity of an engineered M13-derived phage-display particle (P9b), selected for specific binding to P. aeruginosa, which acts as a non-lytic modulator of QS through specific binding to a bacterial surface target. P9b induced a transient delay in early planktonic growth, without affecting long-term proliferation. In contrast, P9b significantly reduced biofilm-associated metabolic activity and pyocyanin production, consistent with an effect on QS-regulated pathways. Transcriptional analysis revealed significant downregulation of key QS regulators (lasI, lasR, rhlI, and rhlR) and modulation of phenazine biosynthesis genes (phzM downregulation and phzS upregulation), suggesting interference with QS-dependent regulatory circuits. Notably, P9b retained binding capacity and antibiofilm activity across clinically relevant P. aeruginosa isolates. Overall, these findings indicate that P9b acts as a selective, non-lytic modulator of virulence-associated traits, attenuating QS-regulated phenotypes without bactericidal effects. This study supports the potential of engineered filamentous phages as targeted antivirulence platforms for the development of innovative strategies against persistent and biofilm-associated infections.

Microorganisms doi: 10.3390/microorganisms14051025

Authors: Wenbo Lei Yewei Yang Yating Wen Hongrong Wu Zhongyu Li

Chlamydia trachomatis has evolved sophisticated mechanisms to manipulate key host cell signaling pathways to facilitate its intracellular reproduction. N6-methyladenosine (m6A) in RNA is known to regulate various physiological and disease processes, and is also involved in the regulation of pathogenic and developmental processes in many pathogens. However, the specific impact of m6A modification on the intracellular growth of C. trachomatis remains poorly understood. In this study, our analysis of the m6A methylation profiles of host cell mRNAs following C. trachomatis infection revealed significant alterations in the distribution of m6A modifications, methylation motifs, and m6A-modified host target genes. We further demonstrate that chlamydial intracellular reproduction is mediated by the host methyltransferase-like (METTL) enzyme METTL14. Silencing METTL14 significantly reduced the reproduction efficiency of C. trachomatis. Mechanistically, C. trachomatis activates the Mitogen-Activated Protein Kinase (MAPK) and Phosphatidylinositol 3-kinase/Protein Kinase B (PI3K/AKT) signaling pathways through METTL14, thereby inhibiting host cell apoptosis and promoting intracellular bacterial reproduction. Collectively, these findings identify METTL14 as a key host factor for chlamydial intracellular reproduction, providing new mechanistic insights and potential targets for therapeutic intervention.

Microorganisms doi: 10.3390/microorganisms14051026

Authors: Ryosuke Kadoya Ayano Kondo Ayaka Matsukawa Aoi Kuribayashi Emi Uemura Haruna Tanaka

The skin microbiota plays a key role in maintaining cutaneous homeostasis; however, microbial differences among physiological skin types within healthy individuals remain unclear. In this study, we investigated the association between skin microbiota diversity and four skin types (normal, oily, dry, and combination) in healthy young women (n = 43), with samples collected from the nasal region. Skin moisture and sebum levels were quantitatively measured, and microbiota profiles were analyzed using 16S rRNA gene amplicon sequencing targeting the V3–V4 regions. Normal skin exhibited higher alpha diversity, including Chao1 richness and Faith’s phylogenetic diversity, compared with other skin types (median Chao1 values were higher in normal skin than in other groups). Correlation analyses showed that skin moisture was positively associated with microbial richness (ρ = 0.397, p = 0.008), whereas sebum levels were negatively associated with phylogenetic diversity (ρ = −0.455, p = 0.002). Beta diversity analysis revealed that normal skin harbored a distinct microbial community structure. In addition, several bacterial genera were enriched in normal skin, whereas Enterobacterales were observed to be more abundant in non-normal skin types. These findings suggest that skin biophysical properties are associated with microbial community structure and diversity within healthy individuals, although the functional implications of these differences remain to be elucidated.

Microorganisms doi: 10.3390/microorganisms14051023

Authors: Rui Pan Hao Hu Kaixun Yang Dan Xiao Cong Wang Hanqing Wu Qiumei Ling Mingming Sun Wei Zhang Kelin Wang

Arbuscular mycorrhizal fungi (AMF) are vital for nutrient cycling, but how lithology across bulk soil and the rock–soil interface influence AMF communities remains poorly understood. We investigated the effects of karst (dolomite, limestone) and non-karst (clastic rock) lithologies across bulk soil and the rock–soil interface on AMF diversity, community composition, and co-occurrence networks in southwest China. AMF diversity did not differ among lithologies or between bulk soil and rock–soil interface, whereas community composition showed significant differences across lithology. The relative abundance of Glomus was lower in karst than in non-karst, whereas Paraglomus showed the opposite pattern. Co-occurrence network analysis revealed that karst soils exhibited higher numbers of nodes and edges but lower network density, transitivity, betweenness centrality, and average path length compared to non-karst soils. Within the same dolomite and limestone, network properties were similar between the rock–soil interface and bulk soil. Soil pH, exchangeable Ca2+ and Mg2+, total nitrogen, and nitrate nitrogen were negatively correlated with Glomus and network properties (e.g., number of nodes and edges), while ammonium nitrogen showed positive correlations. Our results indicate that lithology exerts a stronger influence than soil compartment on AMF community composition and interspecific interactions, emphasizing the key role of lithological substrates in regulating AMF communities.

Microorganisms doi: 10.3390/microorganisms14051024

Authors: Renxu Wang Yansong Wang Yongchen Zong Xiangyu Chen

To address the bottleneck of poor biological nitrogen removal efficiency caused by the extremely low carbon-to-nitrogen (C/N) ratio of domestic sewage in alpine plateau regions, this study used Hordeum vulgare var. coeleste L., a characteristic crop endemic to the Qinghai–Tibet Plateau, as raw material and adopted pretreated highland barley straw as an external carbon source. Three parallel experiments were carried out using the anaerobic–aerobic–anoxic sequencing batch reactor (AOA-SBR) process to investigate the nitrogen removal performance and functional succession of the microbial community in the AOA-SBR system under three C/N ratio ranges: 5~7, 7~9, and 9~11. The results showed that the addition of an external carbon source significantly improved nitrogen removal efficiency. The optimal C/N ratio range for nitrogen removal in this study was determined to be 7~9. A weakly alkaline environment was conducive to denitrification. The fermentation broth prepared by alkali pretreatment contained a large amount of readily biodegradable organic matter with low toxicity, and achieved excellent nitrogen removal performance, helping to realize cost reduction and efficiency improvement in wastewater treatment. At the optimal C/N ratio of 7~9, the average removal efficiencies of ammonia nitrogen (NH4+-N) and total nitrogen (TN) reached 94.46% and 61.32%, respectively, which were significantly improved compared with the blank control group without external carbon addition. During the experimental period, no obvious changes were observed in microbial abundance at the phylum level, whereas the community structure at the genus level responded significantly to the addition of a straw carbon source. Among them, genera with specific degradation capabilities for straw hydrolysates, such as norank_f__Chitinophagaceae and unclassified_f__Comamonadaceae, were highly sensitive to variations in the C/N ratio. These genera could partially replace the nitrification and denitrification functions of other microorganisms and played a key role in the nitrogen removal process. In contrast, Thauera, a typical conventional heterotrophic denitrifier, showed no significant response to changes in the C/N ratio, indicating that the straw-based external carbon source mainly affected microbial genera with specific hydrolysate-degrading functions.

Microorganisms doi: 10.3390/microorganisms14051022

Authors: Tianyu Qie Dong Lin Qingshan Fan Guangxu Sun Hongmei Wang Zhiyi Liu Xuepeng Liu

Although grazing is a key driver of nitrogen cycling in alpine meadow soils, a systematic understanding of how different grazing intensities shape the structure and functional potential of soil nitrogen-cycling microbial communities remains lacking. In this study, soil samples were collected under five grazing intensities (no grazing, light grazing, moderate grazing, heavy grazing, and extreme grazing) and metagenomic sequencing was employed to analyze variations in nitrogen-cycling microbial communities and functional genes. The results showed that bacteria were the dominant group in nitrogen-cycling communities (relative abundance: 93.99–98.98%), with significant community differentiation across grazing intensities. Light grazing maintained relatively high microbial diversity, whereas moderate and heavy grazing led to more pronounced differences in community composition. Functional gene analysis identified 41 nitrogen-cycling-related genes, primarily involved in denitrification, nitrate reduction, and ammonia assimilation. Light grazing enhanced nitrate reduction and glutamate synthesis; moderate grazing exhibited the strongest ammonia assimilation potential; heavy grazing significantly increased denitrification activity, indicating an elevated risk of nitrogen loss; and under extreme grazing, both the number and abundance of nitrogen-cycling functional genes declined markedly, with functional composition becoming simplified. Collectively, light grazing is more conducive to maintaining the balance between soil microbial diversity and nitrogen-cycling function in alpine meadows, whereas overgrazing disrupts the equilibrium between microbial communities and nitrogen metabolism. This study provides a microbiological basis for the restoration of degraded alpine meadows and sustainable grazing management.

Microorganisms doi: 10.3390/microorganisms14051021

Authors: Jie Dong Tianyue Guan Yuzheng Xue Jinsong Shi Zhenghong Xu Yan Geng Yilin Ren

Hyaluronic acid (HA) is a glycosaminoglycan commonly administered orally, and its molecular weight (MW) influences its physicochemical behavior and potential interactions with the gut microbiota. However, MW-dependent effects on community assembly and fermentation-derived metabolites within the low-molecular-weight (LMW) range remain insufficiently resolved. In this study, five HA samples (6.9–35 kDa) were evaluated using an in vitro human fecal fermentation model. Microbial composition was profiled by 16S rRNA gene sequencing, and SCFAs were quantified by UPLC. Compared with the control under the same basal medium, HA supplementation was associated with shifts in community structure and higher alpha diversity. The 6.9 and 9.5 kDa groups were associated with significantly higher total SCFA concentrations, particularly butyrate, than the 13, 17, and 35 kDa groups under the same basal medium. Because soluble starch was present in the fermentation medium, these differences should be interpreted as modulation effects rather than direct evidence of HA-specific fermentation. 16S-based functional prediction suggested MW-dependent differences in predicted central carbohydrate metabolism potential, which were consistent with the observed SCFA patterns but should be interpreted as inferred functional potential rather than direct evidence of pathway activity. These findings indicate that HA molecular weight is associated with differential microbial and SCFA response patterns under the present in vitro conditions. Lower-MW HA within the tested range was associated with higher SCFA output, particularly butyrate, under a shared starch-containing basal medium, highlighting molecular weight as a potential formulation parameter in HA microbiota-centered applications.

Microorganisms doi: 10.3390/microorganisms14051020

Authors: Lorina Badger-Emeka

Wound infections result from contamination of compromised skin following either intentional or accidental trauma. The failure of infected wounds to heal has a huge impact on global healthcare finances. For surveillance purposes, this investigation looks at wound infections and their susceptibility to antibiotics. Data obtained from the microbiology laboratory for the years 2014 and 2019 included wound characteristics, patient demographics, and causative bacteria pathogen. Also retrieved from an −80° C freezer were 270 Gram-negative bacteria isolates from wounds that formed part of patient care. Vitek Compact 2 was used for bacteria IDs and AST testing. Wound swabs were the majority (74.07%), followed by bedsore samples (12.22%). Others were tissue cultures (6.3%), skin swabs (3.7%), necrotizing fasciitis (1.48%), foot swabs (1.10%), and cervical wounds (1.11%). Isolated pathogens included Pseudomonas aeruginosa (33.6%), Escherichia coli (24.78%), Acinetobacter baumannii (21.85%), Klebsiella pneumoniae (17.65%), Proteus mirabilis (1.7%), and Morganelli morganii (0.41%). Most isolates had become MDR after 5 years, with extensive (100%) resistance to β-lactam and fluoroquinolone. Only tigecycline and amikacin maintained their antimicrobial activity for the period with some bacteria species. Suitable therapeutic options were few, irrespective of the year of isolation, particularly among the ESKAPE isolates. Overall results demonstrate that after a 5-year period, about 75% of the isolates of the bacteria pathogens had become resistant to most of the antibiotics used for their management.

Microorganisms doi: 10.3390/microorganisms14051018

Authors: Ana B. Neves Tiago M. Gonçalves Artur Alves Micael F. M. Gonçalves

Crop losses driven by fungal pathogens remain a major constraint to global food production, reinforcing agriculture’s dependence on fungicide-based disease control. Soil acts as a long-term reservoir and key hotspot for the evolution and persistence of antifungal-resistant Fusarium. The intensive, prolonged use of overlapping single-site fungicides in agriculture strongly selects for both intrinsic and acquired resistance in soilborne Fusarium populations, contributing to major crop losses, food insecurity, and One Health concerns. This review synthesizes current knowledge on (i) target-site (CYP51, β-tubulin, cytochrome b, SDH, myosin-5) and non-target-site (ABC/MFS efflux, multidrug resistance, epigenetic regulation) resistance mechanisms across the genus Fusarium; (ii) the influence of management practices and fungicide characteristics and behaviour in soil in reshaping microbial communities and selecting for resistant Fusarium; (iii) the consequences for plant disease management and the limitations of practices like cultural and biological control; and (iv) innovative strategies for plant disease management, as well as the monitoring and detection of antifungal resistance in soils. These aspects show that soil reservoirs of antifungal-resistant Fusarium are compromising fungicide-based control and increasing risks across sectors, highlighting the urgent need for sustainable, multi-layered, integrated pest management strategies combined with robust, molecularly informed resistance monitoring.

Microorganisms doi: 10.3390/microorganisms14051019

Authors: Khadija Ait Si Mhand Salma Mouhib Juan Carlos Fernández-Cadena Mohamed Hijri

Endophytic bacteria from plants adapted to arid and semi-arid environments represent an underexplored reservoir of microbial diversity with potential agricultural applications. Here, we report a polyphasic taxonomic and genome-based characterization of Achromobacter sp. isolates recovered from root and foliar tissues of Citrullus colocynthis and Peganum harmala, two medicinal plants thriving under harsh environmental conditions. Whole-genome sequencing, phylogenomic analyses, average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), multilocus sequence typing, and detailed phenotypic profiling revealed three previously undescribed species, for which we propose the names Achromobacter colocynthi sp. nov., Achromobacter maghribensis sp. nov., and Achromobacter semiaridum sp. nov. Genome assemblies were highly complete (98.7–99.2%) with minimal contamination (<1%), supporting robust taxonomic inference. All three species displayed ANI and dDDH values below accepted thresholds relative to their closest phylogenetic neighbors, despite partial inconsistencies in 16S rRNA similarity for one isolate, highlighting the value of genome-wide metrics for species delineation. Phylogenomic analyses placed the novel taxa within Achromobacter sp. as distinct evolutionary lineages. Phenotypic characterization indicated broad metabolic versatility, including utilization of carbohydrates, organic acids, and amino acids, tolerance to moderate salinity and acidic pH, and resistance to multiple antimicrobial compounds, traits likely linked to adaptation to endophytic lifestyles under semi-arid conditions. Beyond their taxonomic novelty, the isolates exhibited in vitro traits associated with plant adaptation and stress tolerance, including IAA production, ACC deaminase activity, and tolerance to Zn, Cu, and Cd. Genomic analyses further indicated functions related to phosphate acquisition and stress response. These findings expand the taxonomic framework of Achromobacter sp., establish C. colocynthis and P. harmala as reservoirs of novel endophytic bacteria, and highlight their potential relevance for agricultural biotechnology in stress-prone environments.

Microorganisms doi: 10.3390/microorganisms14051017

Authors: Yimeng Wang Nuozhou Zhang Rui Han Aozheng Lu Nan Nan Dayong Li Wenxian Sun

Rice fungal blast, one of the most devastating diseases caused by Magnaporthe oryzae, poses a severe threat to global rice production. For the breeding and deployment of rice varieties with blast resistance, it is critical to elucidate the frequencies and genetic variations in avirulence genes among M. oryzae populations. In this study, a total of 294 M. oryzae isolates were collected in 2022 from central Jilin Province, China. Pathogenicity assays on 24 monogenic rice lines revealed extensive virulence variations among the 294 isolates, with highly pathogenic strains being dominant and clear geographic differences in pathogenicity profiles. Resistance frequencies differed markedly among 24 monogenic lines, with Pi3, Pit, Pi7, Pikh, Pik, and Pia showing resistance rates over 50% and Pish exhibiting the lowest efficacy. Moreover, resistance profiles varied significantly across four sampling regions in central Jilin Province, with Pit being the most effective in Changchun and Jilin, Pi3 in Tonghua, and Pikm in Liaoyuan. In addition, the Avr genotypes of the isolates were postulated based on phenotypic data from the monogenic rice lines. Among the postulated Avr genotypes, the frequencies of Avr-Pi11 and Avr-Pish were the lowest at 29.25%. Furthermore, molecular characterization of three Avr genes (Avr-Pi9, Avr-Pita2, and Avr-Pizt) was performed by sequencing a subsample of 50 randomly selected isolates. Natural mutation sites were identified in Avr-Pita2 and Avr-Pizt, which were located within the coding sequence regions, leading to non-synonymous mutations and nonsense mutations that cause premature termination. Notably, no mutation was detected within the coding sequences of Avr-Pi9. Collectively, the findings provide a theoretical basis for breeding blast-resistant rice varieties that can be deployed in central Jilin Province, China.

Microorganisms doi: 10.3390/microorganisms14051016

Authors: Qinglian Wu Xiandong Xu Jianqin Li Han Qiu Huanhuan Huo Mo Peng Chungen Wen Gang Yang

A pathogenic bacterium strain, LBK2, was isolated from giant spiny frog (Quasipaa spinosa) tadpoles infected with perforation disease in this study. Pathogenic strain LBK2, a Gram-negative bacterium with a certain degree of infectivity, was demonstrated to cause anorexia, lethargy, epidermal necrosis, and abdominal perforation in tadpoles in artificial infection experiments. The identification results of 16S rDNA gene sequencing showed that pathogenic strain LBK2 was identified as Pseudomonas sp. Virulence gene identification displayed that strain LBK2 carried three virulence genes: aer, epr, and fla. Finally, the antibiotic susceptibility testing of 11 antibiotics suggested that strain LBK2 was highly sensitive to nine antibiotics, including chloramphenicol, enrofloxacin, and rifampicin, but was resistant to erythromycin, sulfamethoxazole/trimethoprim, and low-concentration trichloroisocyanuric acid. This study determined the pathogenicity of Pseudomonas sp. to giant spiny frog tadpoles based on histopathological analysis and virulence factor carriage, and the drug susceptibility testing further provided a scientific basis for the selection of drugs in the prevention and treatment of abdominal perforation disease in giant spiny frog tadpoles.

Microorganisms doi: 10.3390/microorganisms14051015

Authors: Marcos Abdo Arbex

Tuberculosis (TB) remains a critical global public health challenge, requiring therapeutic strategies that ensure high cure rates while minimizing bacillary transmission. The 2022 World Health Organization (WHO) update for drug-resistant TB treatment prioritized a novel, 6-month, all-oral regimen composed of bedaquiline, pretomanid, linezolid, and moxifloxacin (BPaLM) as the preferred treatment for rifampicin- and multidrug-resistant tuberculosis (RR-/MDR-TB). However, the clinical success of this shortened therapy is intrinsically linked to managing complex drug–drug interactions and treatment-emergent adverse effects which may necessitate regimen modifications. This article provides a comprehensive pharmacological review of the BPaLM components, detailing their mechanisms of action, pharmacokinetics (absorption, metabolism, and excretion), and safety profiles. Furthermore, we analyze critical drug interactions—including those involving food and antacids—and provide evidence-based guidance for special clinical populations, such as pregnant and breastfeeding women, and patients with hepatic or renal impairment. Mastery of these pharmacological nuances is essential for clinicians to optimize treatment adherence and ensure improved treatment completion rates and reduced resistance emergence.

Microorganisms doi: 10.3390/microorganisms14051013

Authors: Fanjin Ye Shuai Lu Yanfang Tian Pengsong Li Ziqing Deng Peng Gao Hongjie Gao Xiaoling Liu

Global climate change has altered temperature regimes, hydrological stability, and redox dynamics in inland waters, yet the continental-scale impact of these alterations on sediment microbiomes remains poorly understood. Here, we compiled 562 publicly available 16S rRNA gene datasets from lake sediments across five major climatic zones in China to examine how climatic gradients influence microbial diversity, community assembly, and interaction networks, as well as their associated taxonomic composition and environmental responses. Sediment microbiomes showed clear spatial differentiation in both α- and β-diversity, accompanied by climatic zone-specific taxonomic signatures and biomarker taxa. Community assembly also varied markedly across climatic zones, with stochasticity and dispersal limitation dominating in colder regions, transitional assembly in the south temperate zone, and stronger selective or high-turnover dynamics in the warm subtropics. Importantly, random forest models revealed a clear transition from climate-dominated to anthropogenic-dominated control in sediment microbiome organization: microbial variation in the plateau and temperate regions was primarily associated with climatic and geographic constraints, whereas anthropogenic factors played a more important role in shaping community differentiation in the central subtropical zone. By integrating diversity patterns, taxonomic composition, assembly processes, and network topology, we further propose a three-stage conceptual pattern of sediment microbial community organization along climatic gradients, shifting from a persistence-dominated regime in the cold plateau regions, to an efficiency-dominated regime in the temperate zones, and finally to a plasticity-dominated regime in the warm subtropical regions. These findings would provide a continental-scale framework for understanding sediment microbiome responses to coupled climatic and anthropogenic forcing in inland waters, with implications for future water quality management and ecosystem conservation.

Microorganisms doi: 10.3390/microorganisms14051014

Authors: Mark Cannon John Peldyak Paul Reynolds

Micro- and nanoplastics (MNPs) have now been detected in human blood, placenta, and arterial tissue, yet the oral cavity has received strikingly little mechanistic attention despite serving as a primary portal of environmental exposure and a local site of polymer generation from dental and oral-care materials. This narrative review addresses that gap from an environmental microbiology perspective, synthesizing recent literature on periodontal disease, chronic low-grade inflammation, oral biofilms, dental materials, microbial–plastic interactions, and systemic chronic disease risk. Unlike prior reviews, we apply an explicit three-tier evidentiary framework (established, plausible, unproven) that distinguishes what is directly demonstrated from what is biologically plausible but unproven, and we situate the periodontal environment specifically as a particle-retention and inflammatory-amplification niche. The strongest direct oral evidence shows that human dental calculus harbors at least 26 microplastic types, dominated by polyamide (41.4%), polyethylene (32.7%), and polyurethane (7.0%). Polyethylene isolated from calculus induces cytotoxicity, apoptosis, impaired migration, NF-κB activation, and upregulation of IL-1β and IL-6 in human gingival fibroblasts. From a microbiological standpoint, oral organisms actively degrade methacrylate dental polymers, and the degradation products of these polymers reciprocally modulate oral bacterial virulence gene expression. Across experimental systems, MNPs activate oxidative stress, inflammasome signaling, macrophage polarization, and barrier dysfunction, pathways that overlap extensively with periodontal pathobiology. Adjacent environmental microbiology demonstrates that plastic-associated biofilms enhance extracellular polymeric substance production, quorum sensing, pathogen persistence, and antibiotic resistance gene transfer, supporting a plausible but not yet validated oral plastisphere within plaque and calculus. We argue that periodontitis should be reconceptualized as a chronically inflamed particle-processing interface that may increase local MNP retention, cellular reactivity, and systemic inflammatory spillover, with implications for cardiovascular, metabolic, and other chronic disease risk pathways. Current evidence does not yet prove that environmental MNP exposure causes human periodontitis, and that evidentiary boundary is maintained throughout. A priority research agenda is proposed, centered on contamination-controlled subgingival biomonitoring stratified by periodontal status, spatially resolved multi-species biofilm models, polymer source attribution, and longitudinal clinical studies linking oral plastic burden to inflammatory and systemic outcomes.

Microorganisms doi: 10.3390/microorganisms14051012

Authors: Sofoklis Stavros Angeliki Gerede Nektaria Zagorianakou Efthalia Moustakli Anastasios Potiris Ismini Anagnostaki Alexios Kozonis Maria Tzeli Aikaterini Lydia Vogiatzoglou Pavlos Machairoudias Konstantinos Zacharis Athanasios Zikopoulos Dimitrios Loutradis Ekaterini Domali

Endocrine-disrupting chemicals (EDCs) are a diverse group of environmental pollutants capable of interfering with hormonal and immune system regulation. In recent years, increasing concern has been raised about the effects of chemicals, including bisphenols, phthalates, per- and polyfluoroalkyl substances (PFAS), insecticides, and parabens, on maternal and fetal health, primarily due to their widespread exposure in human populations. Pregnancy represents a critical window characterized by tightly regulated hormonal and immunological adaptations. Emerging evidence suggests that EDC exposure during this period may alter maternal microbiota, disrupt immune responses, and interfere with endocrine signaling. These changes may increase susceptibility to bacterial and viral infections, including bacterial vaginosis, urinary tract infections, and intrauterine infections, all of which are associated with adverse pregnancy outcomes. This review summarizes the current evidence on the sources and mechanisms of exposure to endocrine disruptors during pregnancy and examines the potential biological pathways linking endocrine disruption to the development of infections. Particular emphasis is placed on the interactions between immune regulation, hormonal signaling, and changes in the microbiome, which may contribute to increased susceptibility to infections. A deeper understanding of these complex mechanisms is critical to improve risk assessment, develop effective public health strategies, and ultimately protect maternal and fetal health in an environment of increasing chemical exposure. A literature search was conducted using PubMed/MEDLINE, Scopus, and Web of Science, including studies published up to January 2026.

Microorganisms doi: 10.3390/microorganisms14051011

Authors: Asta Aleksandravičienė Giedrė Jarienė Jolita Kirvaitienė Rasa Volskienė Kristina Dambrauskienė Žaneta Maželienė

Eye cosmetic products are widely used and applied in close proximity to the ocular surface, making their microbiological safety particularly important. The aim of this study was to assess bacterial contamination in used eye cosmetic products, characterize the antimicrobial resistance profiles of the isolated bacteria, and perform molecular genotypic analysis. A total of 71 samples, including mascara, eyeliner, and eyeshadow, were analyzed. Microbiological analysis revealed that Bacillus spp. and coagulase-negative staphylococci (CoNS) were the predominant microorganisms, while no major pathogens such as Staphylococcus aureus, Escherichia coli, or Pseudomonas aeruginosa were detected. Antimicrobial susceptibility testing demonstrated high susceptibility of isolates to gentamicin, vancomycin, and linezolid, whereas resistance to benzylpenicillin and clindamycin was observed among Staphylococcus spp. Molecular identification based on 16S rRNA gene sequencing confirmed the presence of Bacillus licheniformis, Bacillus subtilis, Staphylococcus epidermidis, and Staphylococcus warneri, with sequences showing high similarity to globally distributed strains. Although the detected microorganisms were predominantly opportunistic, their presence in products applied near the eyes suggests a potential risk of microbial transfer to the ocular surface. These findings highlight the importance of proper hygiene practices, regular product replacement, and effective quality control measures to minimize microbial contamination and associated health risks.

Microorganisms doi: 10.3390/microorganisms14051010

Authors: Guiliang Wang Yao Liu Chen Zhao Haitao Zhao Xiaoqing Qian Juanjuan Wang

Micronutrient limitation and rhizosphere imbalance often constrain the productivity and quality of leafy vegetables in intensively managed greenhouse soils. This study evaluated the effects of conventional fertilization (CK), micronutrient supplementation (Mi), and micronutrient supplementation combined with a compound microbial inoculant (MM) on bur clover (Medicago polymorpha L.) yield, quality, rhizosphere chemical properties, and soil microbial communities. Compared with CK, Mi increased yield by 26.53%, whereas MM increased yield by 40.77%. MM also significantly increased SPAD, soluble protein, and soluble sugar, while reducing plant nitrate content by 22.86%; Mi had no significant effect on nitrate reduction. MM decreased soil pH from 8.62 to 8.34 and increased EC, available P and K, water-soluble Ca, Mg, and K, and available Zn and B, indicating improved rhizosphere chemical conditions. Mantel analysis showed that yield and plant nitrate were significantly associated with several soil variables. MM also markedly reshaped rhizosphere microbial communities, with clear treatment separation for both bacteria and fungi. The bacterial community was significantly explained by selected soil variables, whereas the fungal model was not significant. Overall, micronutrient supplementation mainly promoted yield, while its combination with microbial inoculation further improved rhizosphere conditions, crop quality, and nitrate control.

Microorganisms doi: 10.3390/microorganisms14051008

Authors: Chunqiao Xiao

In response to the triple crises of global resource depletion, escalating waste generation, and environmental pollution, microorganisms are increasingly transitioning from basic research to engineering applications, driven by their metabolic diversity, robust environmental adaptability, and modifiable engineering characteristics [...]

Microorganisms doi: 10.3390/microorganisms14051009

Authors: Zaineb Hamzaoui Sana Ferjani Ameni Sallemi Salma Abid Amal Miraoui Ichrak Landolsi Latifa Charaa Khaled Menif Lamia Kanzari Ilhem Boutiba-Ben Boubaker

Highly mutated Omicron sub-lineages JN.1 and NB.1.8.1 harbor extensive spike changes, but their impact in preterm infants is poorly documented. We report a preterm male infant with three hospitalizations in seven weeks: severe SARS-CoV-2 ARDS at 40 days of life (DOL 40) requiring ventilation caused by JN.1.16, HCoV-OC43 infection at DOL 65, and a mild SARS-CoV-2 reinfection at DOL 87 due to NB.1.8.1, the first detection of this variant in Tunisia. Spike analysis showed a shared JN.1 backbone but distinct N-terminal and receptor-binding domain changes, supporting intra-Omicron reinfection driven by antigenic divergence and immature immunity and underscoring the value of pediatric genomic surveillance, including phylogenetic placement of case genomes within local Omicron diversity.

Microorganisms doi: 10.3390/microorganisms14051005

Authors: Shuning Zhang Xiaomin Wang Guifeng Zhang Lei Kong Yuemeng Fu Guohui Zhou Qingsong Fan Zhenhui Liu Shuzhen Jiang Yang Li

Glucose oxidase (GOD) is a natural enzyme with antioxidant and antimicrobial properties but its effects on sows remain insufficient. This study investigated the effects of dietary GOD supplementation during gestation on inflammatory response, antioxidant capacity, immune function, and gut microbiota of farrowing sows. Twenty-four primiparous sows were randomly assigned to two groups and fed a basal diet or a basal diet supplemented with GOD (300 mg/kg diet) from gestation day 30 to farrowing. GOD supplementation significantly increased triglyceride, superoxide dismutase, and immunoglobulin M levels (p < 0.05), and significantly decreased alanine aminotransferase and interleukin-6 levels in serum (p < 0.05); significantly reduced placental interleukin-1β, malondialdehyde and tumor necrosis factor-α concentrations and NF-κB gene expression (p < 0.05), and elevated glutathione peroxidase activity and relative mRNA expressions of Nrf2, HO-1, GPX1 and SOD2 (p < 0.05). Moreover, GOD supplementation altered the fecal microbial community structure (p < 0.05), significantly reducing Clostridium, dgaA-11_gut_group, Bacteroides, and Prevotellaceae_NK3B31_group abundance (p < 0.05), while enriching Lachnospira, unclassified_f_Erysipelotrichiaceae, and Anaerostipes (p < 0.05). Collectively, 300 mg/kg glucose oxidase supplementation during mid-to-late gestation improved the health status of farrowing sows by improving nutrient utilization, immune function and antioxidant capacity, and altering fecal microbial structure and relative abundances.

Microorganisms doi: 10.3390/microorganisms14051007

Authors: Ri-Han Jiang Zi-Kui Liu Bing Han Dan-Ni Liao Ji-Yun Li Yong Wu

This study investigated the epidemiology, antimicrobial resistance, and transmission risks of β-lactamase, cefotaxime-hydrolyzing, Munich (blaCTX-M)-positive Escherichia coli (CTX-M-EC) in large-scale pig farms in Jiangxi Province (China). In total, 278 samples (manure, wastewater, drinking water, and flies) were collected. CTX-M-EC strains were isolated and analyzed using antimicrobial susceptibility testing, resistance gene profiling, multilocus sequence typing, and genetic environment analysis with gene transfer assessed by transduction experiments. Twenty-seven CTX-M-EC strains (9.71%) were isolated, all exhibiting multi-drug resistance with 100% resistance to cefotaxime, ciprofloxacin, and tetracycline, and >90% resistance to ceftazidime, florfenicol, and trimethoprim-sulfamethoxazole. Four blaCTX-M subtypes were identified. blaCTX-M-55 was the predominant subtype (70.37%) and was distributed across diverse sequence types and serotypes. Each strain harbored multiple antibiotic resistance genes, plasmids, and virulence genes. Mobile elements such as ISEcp1 and IS26 were detected surrounding the blaCTX-M gene, and 96.29% of strains successfully transferred the blaCTX-M gene via transduction. Clones highly homologous to pig manure strains were detected in flies and sewage, suggesting that this resistance gene can spread between animals, the environment, and vectors. These findings highlight the high transmission risk of blaCTX-M and underscore the need for rational antibiotic use, waste management, and vector control within a One Health framework.

Microorganisms doi: 10.3390/microorganisms14051006

Authors: Lihua Guo Jiaxin Ge Min Miao Guimei Hu Jinfeng Wen Kefeng Hu Guoliang Ye

Vonoprazan–amoxicillin (VA) dual therapy offers a simplified alternative; however, its efficacy and cost-effectiveness relative to bismuth-containing quadruple therapy (BQT) in treatment-naïve patients remain unclear. This study aimed to compare the eradication rate and cost-effectiveness between the two groups using a propensity score-matched analysis. This retrospective, single-center study used outpatient electronic medical records from January 2024 to November 2025. After propensity score matching (1:1), 212 patients received vonoprazan–amoxicillin dual therapy (VA), and 212 matched patients received esomeprazole–bismuth quadruple therapy (EBAC) for two weeks. Eradication rates and cost-effectiveness were compared. According to the intention-to-treat (ITT) analysis, eradication rates were 90.56% (95% CI 85.88–93.81%) in the VA group and 90.09% (95% CI 85.33–93.43%) in the EBAC group (p = 0.869). The per-protocol (PP) analysis showed eradication rates of 93.03% (95% CI 88.64–95.80%) and 91.58% (95% CI 86.93–94.68%), respectively (p = 0.585). Multivariate logistic regression identified non-compliance as a significant risk factor for eradication failure (OR = 5.346, 95% CI 1.847–15.473, p = 0.002). Probabilistic sensitivity analysis showed that EBAC was more cost-effective than VA in stage 1. However, the eradication rate of EBAC dramatically declined, and VA became the more cost-effective option at higher WTP thresholds in stage 2. In conclusion, the 14-day VA dual therapy is as effective as BQT therapy but is safer and easier to use, offering a more streamlined eradication option. Nonetheless, EBAC remains a cost-effective option.

Microorganisms doi: 10.3390/microorganisms14051004

Authors: Heytor Lemos Martins Natália Sarmanho Monteiro Lima Luís Angel Chicoma Rojas João Francisco Bronhara Pereira João Francisco Damião Zanqueta Cristina Veloso de Castro Jhansley Ferreira da Mata Eduardo da Silva Martins Camila Cesário Fernandes Sartini Eliana Gertrudes de Macedo Lemos Pedro Luís da Costa Aguiar Alves

Peanut (Arachis hypogaea L.) forms root nodules that host microbial communities influencing plant nutrition and stress tolerance, and herbicide use may act as an environmental filter altering the cultivable nodule microbiota. This study isolated and characterized bacteria from peanut nodules collected in fields with and without imazapic application in Jaboticabal, São Paulo, Brazil. Eight isolates were obtained, and one hemolytic strain was excluded after pathogenicity screening. Based on 16S rRNA gene sequencing and phylogenetic analysis, the isolates were identified as Bacillus aerophilus, Bacillus inaquosorum, Bacillus subtilis, Bradyrhizobium yuanmingense, Burkholderia lata, and Rhizobium tropici. Nodules from herbicide-treated plants yielded exclusively Bacillus spp., whereas those from non-treated plants showed greater taxonomic diversity. Molecular screening detected genes associated with biological nitrogen fixation (nifH) and nodulation (nodA, nodB, nodC, nodD), indicating potential functional capacity. In greenhouse assays, the isolates showed strain-dependent effects on early plant development, with pronounced responses in root growth and nodulation. Burkholderia lata and bacterial consortia enhanced root development and nodulation, with performance comparable to the commercial inoculant SEMIA 6144. Herbicide management shapes the cultivable nodule microbiota, and selected isolates show potential as bioinoculants for peanut production systems.

Microorganisms doi: 10.3390/microorganisms14051003

Authors: Yan Zhang Yingfei Xu Bin Peng Xun Li Hongliang Ma

Under-forest cultivation of morels is increasingly constrained by soil ecological deterioration, which has become a major obstacle to its sustainable development. This study characterized hyphosphere soil microbiomes of Morchella sextelata M. Kuo under pine canopy at four distances from the fruiting body: 0 cm (R), 20 cm (R20), 40 cm (R40), and uncultivated control (CK). Bacterial and fungal community composition and diversity were analyzed using Illumina NovaSeq high-throughput sequencing. Results showed that the dominant bacterial phyla were Proteobacteria and Acidobacteriota, with RB41, Sphingomonas, and Dongia as the dominant genera. Relative to CK, the abundances of Acidobacteriota and RB41 in R increased by 4.45% and 6.16%, respectively, whereas R20 was enriched in Proteobacteria (+7.77%), Sphingomonas (+0.95%), Dongia, and Bradyrhizobium. For fungi, Ascomycota and Basidiomycota were the dominant phyla, with the principal genera being Sebacina, Microbotryales_gen_Incertae_sedis, and Oidiodendron. Compared with CK, morel cultivation decreased the abundances of Ascomycota and Oidiodendron, with the greatest reductions in R20 (by 8.73% and 3.67%, respectively), while increasing the abundances of Basidiomycota, Sebacina, and Microbotryales_gen_Incertae_sedis, again most markedly in R20, by 17.56%, 14.82%, and 5.74%, respectively. Morel cultivation significantly reduced microbial diversity and evenness (Shannon, Simpson, and Pielou), with the lowest diversity and highest dominance in Zone R. Partial least squares structural equation modeling (PLS-SEM) revealed that soil chemical properties and enzyme activities negatively drove dominant bacterial genera but positively drove dominant fungal genera. Overall, under-forest cultivation of M. sextelata significantly reduced hyphosphere microbial diversity and reshaped microbial community structure in a distance-dependent manner: Zone R was dominated by Acidobacteriota; Zone R20 was enriched with nitrogen-cycling beneficial bacteria (Dongia, Sphingomonas, and Bradyrhizobium) and beneficial fungi (Sebacina and Microbotryales_gen_Incertae_sedis); Zone R40 exhibited relatively optimal fungal diversity.

Microorganisms doi: 10.3390/microorganisms14051002

Authors: Xin-Yu Gao Yan Wang Yu-Hui Wang Hao Yu Liang Liu Xing-Hua Zhang Hong-Tao Xu Yao Meng Randal N. Johnston Gui-Rong Liu Shu-Lin Liu

Ulcerative colitis (UC) is a type of inflammatory bowel disease without curative therapeutics. Recent studies demonstrate that Akkermansia muciniphila exerts mitigating effects on UC, but the underlying mechanisms remain unclear. In this study, we isolated a strain of A. muciniphila, designated NND9, from the feces of DSS-induced ulcerative colitis model mice and investigated its effects on UC of the mouse model. NND9 significantly alleviated UC severity in the mice by restoring gut barrier integrity through improving colonic mucus layer thickness, mitigating goblet cell depletion, and halting epithelial cell death. Mechanistically, NND9 suppressed the expression of the Tnfrsf10b gene encoding death receptor 5 (DR5) on the surface of colonic epithelial cells. Additionally, NND9 inhibited the phosphorylation of kinase 3 (RIPK3) and the pseudokinase mixed-lineage kinase domain-like protein (MLKL) associated with the necrotic apoptosis pathway, thereby reducing gut epithelial cell death. NND9 also markedly ameliorated the gut microbiome of the colitis mice. Untargeted metabolomics analysis demonstrated that NND9 modulated both tryptophan and bile acid metabolism. In conclusion, NND9 exhibits curative effects on UC by resolving inflammatory reactions of the gut mucosa through the DR5-RIPK3/p-RIPK3-MLKL/p-MLKL pathway and redressing gut dysbiosis. This study provides valuable information for the development of innovative therapeutic strategies for the treatment of UC.

Microorganisms doi: 10.3390/microorganisms14051001

Authors: Aikaterini Gropali Ioannis Stavrakakis Nikolaos Remmas Shereen Basiouni George Tsiamis Asma Ben Salem Salma Lasram Mete Yilmaz Mevlut Emekci Fatma Acheuk Awad A. Shehata Wolfgang Eisenreich Paraschos Melidis Spyridon Ntougias

The transition toward a sustainable agri-food system, aligned with agricultural and environmental policy objectives, has increased interest in aromatic plants as non-synthetic pesticide alternatives. This study focused on evaluating the antifungal potential of five specific aromatic plant species, particularly Lavandula dentata, Origanum vulgare, Thymus vulgaris, Salvia officinalis and Rosmarinus officinalis, against the phytopathogenic soil-borne fungi Fusarium oxysporum f.sp. radicis-lycopersici and Verticillium dahliae. During screening, L. dentata and T. vulgaris extracts exhibited strong in vitro fungicidal activity. Bioactive compounds previously detected in both lavender and thyme were identified in their extracts using a triple quadrupole/linear ion trap mass spectrometer. Assessment of in vitro phytoprotective action of L. dentata extract in solid and liquid growth media demonstrated inhibitory effects against F. oxysporum f.sp. radicis-lycopersici at concentrations above 1% v/v, with inhibitory effects of L. dentata extract being observed at concentrations equal to or above 2% v/v. T. vulgaris extract inhibited V. dahliae growth on solid media at concentrations at 1% v/v or above, while inhibitory effects were observed in broth media containing 2% v/v thyme extract. Seed germination tests of both L. dentata and T. vulgaris revealed a concentration-dependent reduction in their germination index (GI) at concentrations equal or above 2% v/v, apart from the effect of lavender extract on cress, where inhibition occurred at dose application above 5% v/v. In planta experiments demonstrated the complete phytoprotective action of lavender extract against F. oxysporum f.sp. radicis-lycopersici, while a marginal improvement in plant survival was observed during application of T. vulgaris extract.

Microorganisms doi: 10.3390/microorganisms14051000

Authors: Sisi Chen Rui Li Yanyan Zhu Jie Sun Jia Chen

Toxoplasma gondii is an obligate intracellular protozoan parasite that causes toxoplasmosis, posing a significant threat to human health and livestock production worldwide. Although monovalent DNA or mRNA vaccines often confer only partial protection, whether these platforms can be effectively integrated into a heterologous prime–boost regimen against T. gondii remains to be fully elucidated. Here, we constructed GRA35-encoding DNA and mRNA vaccines and evaluated their immunogenicity and protective efficacy, administered either alone or in heterologous prime–boost combinations, in C57BL/6 and BALB/c mice. Both vaccines induced strong antigen-specific immune responses, with the heterologous prime–boost regimen eliciting the strongest effects and conferring the most robust and consistent protection across both mouse strains. Immunization triggered a predominantly Th1-skewed response characterized by significantly elevated IFN-γ production, accompanied by balanced antigen-specific IgG responses. Moreover, vaccinated mice developed rapid and potent cytotoxic T lymphocyte (CTL) responses. Following challenge with the RH and PRU strains, vaccinated mice exhibited prolonged survival and significantly reduced brain cyst burdens following PRU challenge compared with control groups. Collectively, these findings indicate that GRA35-based nucleic acid vaccines, particularly when administered in a heterologous prime–boost regimen, elicit multifaceted protective immune responses and represent promising vaccine candidates against T. gondii infection.

Microorganisms doi: 10.3390/microorganisms14050999

Authors: Zhongliang Sun Weixian Chen Yu Xie Shoukai Guo Liqin Sun Qiang Wang

Microalgae are among the most efficient photosynthetic organisms on Earth, and their capacity for CO2 fixation directly links the global carbon cycle with green energy conversion, positioning them as strategic biological platforms for achieving carbon neutrality. This review provides a comprehensive and multiscale synthesis of the engineering and biological mechanisms underlying microalgal CO2 fixation, integrating perspectives from gas–liquid mass transfer, CO2 assimilation pathways, key enzymatic systems, metabolic regulation, and environmental control. From an engineering standpoint, we analyze the limitations governing CO2 transfer from the gas phase to the aqueous phase and critically evaluate intensification strategies aimed at enhancing inorganic carbon availability in cultivation systems. At the biological and biochemical levels, we dissect carbon concentrating mechanisms (CCMs), including C4-like pathways, and elucidate the structural organization, regulatory properties, and functional coordination of Rubisco and carbonic anhydrase systems. Particular emphasis is placed on the coupling between enzyme-level regulation and metabolic flux redistribution, supported by insights from metabolic flux analysis and systems-level modeling, to establish theoretical and engineering foundations for improving carboxylation efficiency. Finally, we propose an integrated roadmap for the future development of microalgal CO2 fixation technologies, highlighting the convergence of synthetic biology, artificial intelligence, and systems engineering to achieve end-to-end optimization from molecular mechanisms to reactor-scale performance, while enabling the valorization of waste gas streams and circular carbon utilization. This review aims to provide a coherent theoretical framework and forward looking perspective for the development of efficient, intelligent, and sustainable microalgal CO2 fixation systems.