Microorganisms

19 pages, 12799 KB

Open AccessArticle

Genotype–Phenotype Links Between Aminoglycoside-Modifying Enzymes and Aminoglycoside MICs in Aminoglycoside-Resistant Klebsiella pneumoniae in a Southern Vietnam Tertiary Hospital

by Tuan Huu Ngoc Nguyen, Huy Quang Nguyen, Tham Thi Hong Ho, Hung Cao Dinh, Huong Thi Nguyen, Tam Bui Thanh Pham and Ha Minh Nguyen

Microorganisms 2026, 14(2), 463; https://doi.org/10.3390/microorganisms14020463 - 13 Feb 2026

Abstract

Aminoglycosides remain important components of combination therapy for complicated Klebsiella pneumoniae infections in Vietnam; however, gene-level evidence linking aminoglycoside-modifying enzymes (AMEs) with minimum inhibitory concentrations (MICs) and multidrug resistance is limited, particularly in tertiary-care settings in southern Vietnam. A cross-sectional analysis was conducted [...] Read more.

Aminoglycosides remain important components of combination therapy for complicated Klebsiella pneumoniae infections in Vietnam; however, gene-level evidence linking aminoglycoside-modifying enzymes (AMEs) with minimum inhibitory concentrations (MICs) and multidrug resistance is limited, particularly in tertiary-care settings in southern Vietnam. A cross-sectional analysis was conducted on 186 non-duplicate aminoglycoside-resistant Klebsiella pneumoniae clinical isolates collected in a tertiary-care hospital in Ho Chi Minh City. Species identity was reconfirmed using ZKIR qPCR. MICs for amikacin, gentamicin, and tobramycin were determined by broth microdilution according to Clinical and Laboratory Standards Institute (CLSI) guidelines, and 14 AME genes were detected using targeted qPCR. Associations between AME genes, aminoglycoside MICs or susceptibility categories, and co-resistance to major antibiotic classes were assessed using non-parametric and exact tests with Benjamini–Hochberg false discovery rate correction, with emphasis on effect direction and clinically interpretable genotype–phenotype patterns beyond statistical significance alone. AME genes were highly prevalent, with ant(2″)-Ia, aac(6′)-Ir, and aac(6′)-Ib detected in 97.3%, 91.9%, and 89.8% of isolates, respectively. The presence of aac(6′)-Ib and aac(6′)-Ih_v was associated with higher aminoglycoside MICs, resistance to amikacin and tobramycin, and broader multidrug resistance, including carbapenem resistance, whereas several other AMEs were linked to lower MICs. These findings indicate that specific AME profiles, particularly aac(6′)-Ib and aac(6′)-Ih_v, are associated with intensified aminoglycoside resistance in this setting and support the need for gene-informed surveillance to prioritise confirmatory MIC-based Antimicrobial Susceptibility Testing (AST) to guide local antimicrobial stewardship. Full article

(This article belongs to the Special Issue Advances in Clinical Infections and Antimicrobial Resistance)

► Show Figures

Figure 1

17 pages, 6558 KB

Open AccessArticle

Secretome-Wide Lysine Acetylation Profiling of Fusarium oxysporum Reveals Potential Virulence Factors in Sugarcane Pokkah Boeng Disease

by Gege Wang, Jie Zheng, Chi Zhang, Sehrish Akbar, Yibin Wei, Yu Zhou, Muqing Zhang and Yixue Bao

Microorganisms 2026, 14(2), 462; https://doi.org/10.3390/microorganisms14020462 - 13 Feb 2026

Abstract

Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its [...] Read more.

Fusarium oxysporum is the causal agent of Pokkah Boeng disease (PBD) in sugarcane. Lysine acetylation (Kac) is a dynamic and reversible post-translational modification that plays a critical role in regulating diverse cellular processes. Although Kac is known to significantly influence protein function, its specific role within the F. oxysporum secretome during PBD pathogenesis remains poorly understood. In this study, we conducted a comprehensive analysis of the lysine acetylome across the F. oxysporum secretome. Utilizing highly sensitive immunoaffinity purification coupled with high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS), we identified 291 acetylation sites within 85 potentially secreted proteins. Bioinformatics analysis revealed that these acetylated proteins are involved in a wide array of biological functions and exhibit diverse subcellular localizations. Notably, these secreted proteins represent a valuable resource for identifying novel effectors; specifically, eight upregulated genes encoding Kac proteins were identified as potential players during the initial asymptomatic stages of infection. Collectively, these findings provide a global overview of the F. oxysporum secretome acetylome and offer a foundational resource for elucidating the functional significance of lysine acetylation in sugarcane PBD pathogenesis. Full article

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

► Show Figures

Figure 1

12 pages, 1571 KB

Open AccessArticle

Common Serum Biomarkers and Combination Ratios in the Diagnosis of Periprosthetic Joint Infection Following Total Hip Arthroplasty

by Jason M. Dayan, Don H. Le, Anzar Sarfraz, Theodor Di Pauli von Treuheim, Farouk J. Khury, Sallie Yassin, Vinay K. Aggarwal, Ran Schwarzkopf and Alan J. Dayan

Microorganisms 2026, 14(2), 461; https://doi.org/10.3390/microorganisms14020461 - 13 Feb 2026

Abstract

Accurate preoperative diagnosis of periprosthetic joint infection (PJI) is difficult, complicating distinction between septic and aseptic failures. This study assessed the value of common serum biomarkers and three calculated ratios—albumin–globulin ratio (AGR), C-reactive protein–albumin ratio (CAR), and C-reactive protein–AGR ratio (CAGR)—in diagnosing PJI [...] Read more.

Accurate preoperative diagnosis of periprosthetic joint infection (PJI) is difficult, complicating distinction between septic and aseptic failures. This study assessed the value of common serum biomarkers and three calculated ratios—albumin–globulin ratio (AGR), C-reactive protein–albumin ratio (CAR), and C-reactive protein–AGR ratio (CAGR)—in diagnosing PJI after primary total hip arthroplasty (THA). We retrospectively reviewed patients undergoing revision THA for PJI or aseptic failure from 2011 to 2021 at a single institution. Inclusion required reported serum white blood cell count (WBC), C-reactive protein (CRP), erythrocyte sedimentation rate (ESR), albumin (Alb), and total protein (TP). Diagnostic performance was evaluated using areas under the curve (AUCs), with higher values indicating better accuracy. Ratios were defined as: AGR = Alb/[TP − Alb], CAR = CRP/Alb, and CAGR = CRP/AGR. Among 128 cases, 67 were PJI and 61 aseptic. AUCs were: WBC (0.53), CRP (0.69), ESR (0.75), Alb (0.69), Glb (0.63), TP (0.53), AGR (0.72), CAR (0.70), and CAGR (0.71). Optimal cutoff, sensitivity, and specificity were: CRP (10.5, 0.76, 0.59), ESR (41.0, 0.70, 0.72), AGR (1.10, 0.64, 0.75), CAR (3.37, 0.73, 0.64), and CAGR (10.9, 0.75, 0.66). ESR, AGR, CAR, and CAGR demonstrated acceptable accuracy. These readily available markers and ratios may aid PJI diagnosis, supporting improved clinical decision-making. Full article

(This article belongs to the Special Issue Clinical Microbiology and Related Diseases)

► Show Figures

Figure 1

18 pages, 3734 KB

Open AccessArticle

Characterization of a Novel Cyclized Prodigiosin Derivative from Termite Mound-Associated Streptomyces and Its Potential in Cosmetic Applications

by Pisit Poolprasert, Tawatchai Sumpradit, Kanjana Wongkrajang, Katekan Dajanta, Sittichai Urtgam, Chaowalit Puengtang and Naruemol Thurnkul

Microorganisms 2026, 14(2), 460; https://doi.org/10.3390/microorganisms14020460 - 13 Feb 2026

Abstract

Termite mounds are rich, underexplored reservoirs of bioactive Streptomyces. This study focuses on the isolation and metabolic characterization of pigment-producing Streptomyces from Macrotermes gilvus mounds in Thailand. Four pigment-producing strains related to S. violarus, S. aureofaciens, S. roseoverticillatus, and [...] Read more.

Termite mounds are rich, underexplored reservoirs of bioactive Streptomyces. This study focuses on the isolation and metabolic characterization of pigment-producing Streptomyces from Macrotermes gilvus mounds in Thailand. Four pigment-producing strains related to S. violarus, S. aureofaciens, S. roseoverticillatus, and S. flavofungini were analyzed. These strains exhibited robust antibacterial properties, primarily against Gram-positive bacteria, and significant antioxidant capacity. Structural elucidation using HRMS and NMR identified a stable pink pigment from strain A2 as a novel cyclized prodigiosin derivative (C₃₆H₄₆N₄O₅). To our knowledge, this is the first report of a novel prodiginine sourced from termite-associated actinobacteria. Feasibility trials in cosmetic formulations confirmed the pigment’s stability, suggesting significant potential for industrial use. These results underscore the value of exploring termite-associated microbes for the discovery of unique, functional natural products. Full article

(This article belongs to the Section Microbial Biotechnology)

► Show Figures

Graphical abstract

14 pages, 3975 KB

Open AccessArticle

LncRNA SBF2-AS1 Regulates Pyroptosis to Promote Chlamydia trachomatis Growth Through miR-196b-5p/RIPK2 Axis

by Hongrong Wu, Shan Cheng, Yewei Yang, Wenbo Lei, Yu Zhou and Zhongyu Li

Microorganisms 2026, 14(2), 459; https://doi.org/10.3390/microorganisms14020459 - 13 Feb 2026

Abstract

Pyroptosis enables host cells to eliminate intracellular pathogens effectively. However, how Chlamydia trachomatis (C. trachomatis) evades host pyroptosis remains unclear. This study reveals that C. trachomatis exploits the host Long non-coding RNA (lncRNA) SBF2-AS1 as a key factor to regulate the [...] Read more.

Pyroptosis enables host cells to eliminate intracellular pathogens effectively. However, how Chlamydia trachomatis (C. trachomatis) evades host pyroptosis remains unclear. This study reveals that C. trachomatis exploits the host Long non-coding RNA (lncRNA) SBF2-AS1 as a key factor to regulate the host pyroptosis. The SBF2-AS1 was significantly upregulated during C. trachomatis infection. Knockdown of SBF2-AS1 activated NLRP3/caspase-1/GSDMD pyroptosis pathway. Mechanistically, it verified that SBF2-AS1 functions as a competing endogenous RNA for miR-196b-5p targeting RIPK2 through dual-luciferase reporter gene assay. We further identified the interaction between RIPK2 and Caspase-1 by Co-immunoprecipitation (Co-IP). Silencing SBF2-AS1 or RIPK2, as well as overexpressing miR-196b-5p, triggered pyroptosis and suppressed the replication of C. trachomatis. In conclusion, C. trachomatis upregulates SBF2-AS1 to increase RIPK2 by binding miR-196b-5p, which shields against pyroptosis mediated by Caspase-1 to promote its proliferation. These results uncover a novel mechanism of pathogen–host interaction and provide insights for developing new therapeutic strategies against C. trachomatis infection. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

► Show Figures

Figure 1

14 pages, 3513 KB

Open AccessArticle

Transcriptome Analysis Reveals the Potential Mechanism of MAP34-B Targeting Pasteurella multocida

by Junnan Dai, Yue Peng, Fan Zheng, Qing Pan, Zihui Chen, Baowei Zhang and Aili Wang

Microorganisms 2026, 14(2), 458; https://doi.org/10.3390/microorganisms14020458 - 13 Feb 2026

Abstract

Pasteurella multocida is a widespread zoonotic pathogen responsible for substantial economic losses in the poultry industry. The antimicrobial peptide MAP34-B has been shown to exhibit potent antibacterial activity against Pasteurella multocida, while the mechanism of action remains unclear. To elucidate the antibacterial mechanism [...] Read more.

Pasteurella multocida is a widespread zoonotic pathogen responsible for substantial economic losses in the poultry industry. The antimicrobial peptide MAP34-B has been shown to exhibit potent antibacterial activity against Pasteurella multocida, while the mechanism of action remains unclear. To elucidate the antibacterial mechanism of MAP34-B, we performed transcriptomic profiling via RNA sequencing (RNA-seq) on clinical strain HB03 treated with or without 47.4 µM MAP34-B for one hour. The results showed that, after treatment with MAP34-B, 281 differentially expressed genes were identified, including 161 upregulated genes and 120 downregulated genes. KEGG pathway enrichment analysis revealed that the Ribosome pathway had the highest proportion of affected genes. After treatment with MAP34-B, the gene expressions of rps2, rps3, rps9, rps16, rpl3, rpl9, rpl22, and rpl23 were upregulated, which may affect bacterial protein synthesis. Additionally, the expression levels of membrane-associated genes, such as SecE, SecG, lolB, and ompR, were also altered, indicating disruption of bacterial membrane integrity. Thus, the antibacterial activity of MAP34-B against Pasteurella multocida primarily involves impairment of cell membrane integrity and inhibition of protein synthesis, providing a theoretical foundation for its potential application in treating bacterial infections. Full article

(This article belongs to the Section Molecular Microbiology and Immunology)

► Show Figures

Figure 1

16 pages, 2398 KB

Open AccessArticle

Dietary Energy Levels Impact on Skin Microbiota and Metabolites of Yaks

by Pengcheng Zhao, Bingang Shi, Xuelan Zhou, Zhidong Zhao, Jiang Hu and Xiaolan Zhang

Microorganisms 2026, 14(2), 457; https://doi.org/10.3390/microorganisms14020457 - 13 Feb 2026

Abstract

The study aims to investigate the skin microbiome composition of Yaks and the effects of different dietary nutrient levels on the skin microbiome diversity and metabolites. A total of 19 healthy Tianzhu White Yaks at two age stages (2.5 and 4.5 years old) [...] Read more.

The study aims to investigate the skin microbiome composition of Yaks and the effects of different dietary nutrient levels on the skin microbiome diversity and metabolites. A total of 19 healthy Tianzhu White Yaks at two age stages (2.5 and 4.5 years old) were selected and fed either a high-energy diet (n = 9) or a low-energy diet (n = 10). After 90 days of feeding, skin microbiota and skin tissue metabolites were detected using 16S rRNA sequencing and LC-MS/MS untargeted metabolomics, respectively. The results showed: (1) the phyla Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidetes exhibited relatively high abundances in the skin of yaks, and the total abundance of these four phyla reached as high as 99.3%. Alpha diversity analysis indicated that the alpha diversity index of yak skin microbiota was significantly higher (p < 0.05) in the low-energy nutritional level group than in the high-energy nutritional level group in yaks of both 2.5 and 4.5 years of age. Principal coordinate analysis (PCoA) revealed a distinct separation of all skin microbiota samples into two clusters: the high-energy (H) and low-energy (L) groups. (2) A total of 114 differentially expressed metabolites were screened across both groups, significantly enriched (p < 0.05) in pathways including synaptic vesicle trafficking and glycerophospholipid metabolism; (3) Correlation analysis between microbiota and metabolites revealed significant positive correlations (p < 0.01) between Psychrobacter and choline, and between Corynebacterium and palmitic acid. In conclusion, A low-energy diet increases skin microbial diversity, which is beneficial for maintaining community stability; In contrast, a high-energy diet enriches bacterial genera such as Corynebacterium and Psychrobacter, enhancing functions related to antibacterial activity and barrier protection. Full article

(This article belongs to the Section Veterinary Microbiology)

► Show Figures

Figure 1

19 pages, 760 KB

Open AccessReview

Beyond the Single Isolate: Leveraging Plant-Associated Microbial Communities for Crop Resilience

by Ashish Kumar Sarker, Karishma D. Kuar, Esha Kuriakose, C. Oliver Morton, Colin M. Stack and Michelle C. Moffitt

Microorganisms 2026, 14(2), 456; https://doi.org/10.3390/microorganisms14020456 - 13 Feb 2026

Abstract

The future of sustainable agriculture will require practical microbial solutions that reduce chemical inputs while maintaining productivity. While existing literature reviews focus on laboratory science, they rarely address the practicalities of farm implementation. Low rates of adoption suggest a translational gap. This review [...] Read more.

The future of sustainable agriculture will require practical microbial solutions that reduce chemical inputs while maintaining productivity. While existing literature reviews focus on laboratory science, they rarely address the practicalities of farm implementation. Low rates of adoption suggest a translational gap. This review translates current scientific insights for the relevant end user (farmers). Pesticides and fertilisers disrupt naturally occurring microbial communities that maintain plant health and resilience. Applications of beneficial microbes to restore plant health or improve productivity currently employ single-strain inoculants. The targeted application of a consortium of multiple microorganisms, a “synthetic community” (SynCom), including biocontrol agents, biostimulants and biofertilisers, is superior. The “SynCom” approach could be considered the Swiss army knife of sustainable agriculture, with each member of the community performing overlapping functions. While SymComs have shown success in laboratory and greenhouse trials, field reliability has been inconsistent, either due to variability in production or stability issues in the field. The future of sustainable agriculture will require greater collaboration between scientists and farmers at a local level, specifically, the application of microbes from local soils that are adapted to local environmental conditions, investment in monitoring successes and failures, and application via seed coating using currently available infrastructure. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

► Show Figures

Graphical abstract

22 pages, 6458 KB

Open AccessArticle

Differential Responses to Heat Stress Between Freshly Isolated and Long-Term Cultured Symbiodinium

by 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 and Carlos Manuel Duarte

Microorganisms 2026, 14(2), 455; https://doi.org/10.3390/microorganisms14020455 - 13 Feb 2026

Abstract

Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. [...] Read more.

Symbiotic dinoflagellates from the family Symbiodiniaceae play a central role in coral reef ecosystems by forming mutualistic relationships with reef invertebrates, particularly stony corals. These relationships underpin reef productivity in nutrient-poor waters but are vulnerable to disruption from marine heatwaves and climate change. While laboratory culturing of symbionts has enabled controlled studies of thermal stress, prolonged culturing may lead to physiological changes that do not reflect in hospite conditions. Here, we examined the thermal stress responses of two axenic cultures of Symbiodinium A1, freshly isolated and long-term cultured (2.5 years), originally from the jellyfish Cassiopea andromeda in the Red Sea. Both cultures were exposed to a daily temperature increase of 1 °C, up to 37 °C. Freshly isolated symbionts consistently showed higher photochemical efficiency (0.515 ± 0.007) and growth rates (1.68 ± 0.60 µ day⁻¹) compared to long-term cultured cells (0.401 ± 0.007; −2.25 ± 0.38 µ day⁻¹), which collapsed at 37 °C. Heat stress also led to decreases in O₂ and increases in pCO₂ across treatments. Long-term cultured symbionts exhibited greater lipid body accumulation, suggesting a shift to anaerobic metabolism. These findings demonstrate that extended batch culturing alters symbiont physiology and stress responses, highlighting the need to consider culture history in experimental designs to avoid bias in interpreting holobiont resilience. Full article

(This article belongs to the Special Issue Coral Microbiome and Microbial Ecology)

► Show Figures

Figure 1

13 pages, 820 KB

Open AccessArticle

Riparian Forest Restoration Drives the Recovery of Soil Chemistry, Microbial Community Structure, and Enzymatic Activity in the Itaipu Reservoir Protection Zone

by Gabriela da Silva Machineski, Andrea Scaramal Menoncin, Hudson Carlos Lissoni Leonardo and Arnaldo Colozzi Filho

Microorganisms 2026, 14(2), 454; https://doi.org/10.3390/microorganisms14020454 - 13 Feb 2026

Abstract

Riparian forests play a critical role in protecting soil and water resources and maintaining ecosystem stability. In this study, we evaluated the response of soil chemical and microbial attributes to different stages of riparian forest restoration in the protection zone of the Itaipu [...] Read more.

Riparian forests play a critical role in protecting soil and water resources and maintaining ecosystem stability. In this study, we evaluated the response of soil chemical and microbial attributes to different stages of riparian forest restoration in the protection zone of the Itaipu Reservoir (Brazil). Soil samples were collected during summer and winter from sites representing four restoration stages (initial, 3, 19, and 30 years), as well as from an adjacent agricultural field and a native forest used as reference systems. We assessed soil chemical properties, microbial biomass carbon, basal respiration, enzymatic activities, and the soil microbial community structure using 16S rRNA gene sequencing. Principal component analysis (PCA) revealed a clear restoration gradient, with older restored sites progressively converging toward the native forest condition. Soil chemical properties showed gradual recovery along the restoration trajectory, with increases in soil organic carbon, cation exchange capacity, and base saturation. In contrast, the availability of P, K, Ca, and Mg declined at early restoration stages and increased with restoration age. Microbial biomass carbon increased by approximately 60% from early restoration to native forest conditions, while metabolic quotients (qCO₂) decreased, indicating greater microbial efficiency and reduced metabolic stress. Enzyme activities related to C, P, and S cycling increased by 1.5- to 3-fold with restoration age. Sequencing analyses indicated a progressive convergence of microbial community composition toward that of the native forest, driven by shifts in relative abundance and the enrichment of forest-associated taxa, such as Verrucomicrobia and Acidobacteria, at advanced restoration stages. Overall, long-term riparian forest restoration promoted substantial recovery of soil chemical fertility and microbial community structure and functioning, reinforcing the role of soil microbiota as a sensitive indicator of ecosystem resilience and restoration success. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

11 pages, 282 KB

Open AccessArticle

Molecular Diagnosis of Syphilis in Brazilian Ambulatory Patients: Detection of Treponema pallidum subsp. pallidum in Serum Using Ancient DNA Protocols

by Lorrayne Samille Santos de Brito, Mauro Romero Leal Passos and Alena Mayo Iñiguez

Microorganisms 2026, 14(2), 453; https://doi.org/10.3390/microorganisms14020453 - 12 Feb 2026

Abstract

The rising incidence of syphilis in recent decades underscores the need to improve diagnostic and control strategies. The infection caused by Treponema pallidum subsp. pallidum is commonly diagnosed using serological tests. However, these methods exhibit limitations in the early or late stages of [...] Read more.

The rising incidence of syphilis in recent decades underscores the need to improve diagnostic and control strategies. The infection caused by Treponema pallidum subsp. pallidum is commonly diagnosed using serological tests. However, these methods exhibit limitations in the early or late stages of disease, when antibody responses and/or bacterial loads are low. Molecular biology detection using serum samples is also hampered by low circulating bacterial loads during asymptomatic periods. Ancient DNA (aDNA) studies apply methods adapted to recovering low concentrations and degraded DNA. In this study, we evaluated the effectiveness of aDNA protocols applied to the molecular diagnosis of T. p. subsp. pallidum in serum samples from ambulatory patients from Rio de Janeiro, Brazil. A PRISMA-based systematic review was also performed to identify studies using molecular biology diagnosis from serum. Twenty serums screened by TPHA (Treponema pallidum Hemagglutination assay) and with different VDRL titers (Venereal Disease Research Laboratory test) were analyzed. Amplification of tpp15 gene was observed in 14/17 (82.35%) samples; T. pallidum sequence was confirmed in 12/17 (70.59%). The findings demonstrate the potential of molecular approaches based on aDNA-adapted protocols as alternatives to conventional serological diagnosis, contributing to improved detection of infection and strengthening epidemiological surveillance of syphilis. Full article

(This article belongs to the Section Public Health Microbiology)

20 pages, 5555 KB

Open AccessArticle

Isolation of Siderophore-Producing Bacteria from Extreme Environments and Their Role in Improving Maize Salinity–Alkalinity Tolerance

by Yuanyuan Huang, Yuansheng Xu, Zhe Chen, Xiaomei Dong, Yuxia Mei, Zhufeng Zhang and Min Ren

Microorganisms 2026, 14(2), 452; https://doi.org/10.3390/microorganisms14020452 - 12 Feb 2026

Abstract

Soil salinization represents a significant abiotic constraint to global agricultural sustainability. The potential of extremophile plant growth-promoting bacteria (PGPB) to alleviate such stress in maize was investigated in this study. Siderophore-producing PGPB enhance plant growth and improve the rhizosphere microenvironment by increasing nutrient [...] Read more.

Soil salinization represents a significant abiotic constraint to global agricultural sustainability. The potential of extremophile plant growth-promoting bacteria (PGPB) to alleviate such stress in maize was investigated in this study. Siderophore-producing PGPB enhance plant growth and improve the rhizosphere microenvironment by increasing nutrient availability and inducing systemic resistance. Two salt-tolerant, high-siderophore-producing PGPB strains, Bacillus toyonensis TRM58010 and Peribacillus frigoritolerans TRM58009, were isolated and identified from soil samples collected on the Pamir Plateau. In this study, we found that B. toyonensis TRM58010 synthesized catechol-type siderophores, which enhanced iron availability for maize in saline–alkaline conditions, thereby improving iron nutrition and directly promoting root and stem growth under salt stress. P. frigoritolerans TRM58009 produced hydroxamate-type siderophores, which increased maize iron uptake and stimulated antioxidant enzyme activity, mitigating oxidative stress caused by salinity and alkalinity and supporting overall plant health. Both strains demonstrated robust tolerance to extreme alkaline and saline conditions. Hydroponic and pot experiments showed that these strains significantly improved maize germination rate, root and stem development, plant height, leaf growth, antioxidant enzyme activities, and chlorophyll content under saline–alkaline stress. Notably, the application of P. frigoritolerans TRM58009 bacterial suspension increased maize leaf catalase, peroxidase, and superoxide dismutase activities by 15.712%, 11.584%, and 2.820%, respectively (all p < 0.05), while decreasing malondialdehyde (MDA) content by 15.685% (p < 0.05). P. frigoritolerans TRM58009 elevated chlorophyll a content by 23.4% (p < 0.05). These findings demonstrate the potential of extremophile PGPB strains to mitigate the impact of saline–alkaline stress on maize growth. The distinct growth-promoting effects of these strains, isolated from Pamir Plateau meadow soils, present a promising strategy for bioremediation of saline–alkaline lands and the development of efficient microbial fertilizers. By advancing the use of salt-tolerant siderophore-producing bacteria, this study lays the foundation for innovative approaches to enhance crop resilience and productivity in challenging environments. Full article

(This article belongs to the Special Issue Beneficial Microorganisms for Sustainable Agriculture)

► Show Figures

Figure 1

21 pages, 5382 KB

Open AccessArticle

Transplantation-Driven Microbial Shifts and Keystone Taxa Enhance Medicinal Ingredients in Astragalus mongholicus

by Yanmei Li, Jiangying Huang, Xinrui Wang, Chenyuan Wang, Gehong Wei and Zhefei Li

Microorganisms 2026, 14(2), 451; https://doi.org/10.3390/microorganisms14020451 - 12 Feb 2026

Abstract

Root-associated microbes play a crucial role in plant growth, stress resistance and the accumulation of secondary metabolites. In this study, LC-MS analysis revealed that soil provenance exerts a decisive influence on the content of flavonoids and astragalosides in Astragalus membranaceus. Transplant assays [...] Read more.

Root-associated microbes play a crucial role in plant growth, stress resistance and the accumulation of secondary metabolites. In this study, LC-MS analysis revealed that soil provenance exerts a decisive influence on the content of flavonoids and astragalosides in Astragalus membranaceus. Transplant assays revealed that each soil type acted as a selective filter, assembling distinct microbial communities in both the rhizosphere and root of Astragalus membranaceus. The rhizosphere taxa selected from Yangling soil specifically enhanced flavonoid levels, whereas the root taxa selected from TanChang soil drove higher astragaloside accumulation. SourceTracker revealed that seedling root-endosphere ASVs served as the primary inoculum for later communities, confirming strong priority effects among early colonizers. Keystones tightly linked to both metabolite contents and biomass belonging to Caulobacteraceae, Acidimicrobiia, Sutterellaceae, Bradyrhizobium, Sphingomonas and Mesorhizobium were isolated, and the SynComs were constructed. In Tanchang soil, SynComs inoculation raised Astragaloside IV (AST IV) and Calycosin-7-glucoside (CAG) contents by 52.30% and 55.73%, respectively; in Yangling soil, the same consortium increased Astragaloside I (AST I), Astragaloside II (AST II), AST IV and CAG by 29.38%, 39.04%, 54.97% and 58.98% compared to the uninoculated controls. Collectively, our work charts the transplantation-driven dynamics of root-associated bacterial communities and medicinal metabolites, pinpoints keystones that govern ingredient accumulation and delivers validated microbial strains for enhancing the quality and pharmaceutical value of Astragalus mongholicus. Full article

(This article belongs to the Section Environmental Microbiology)

► Show Figures

Figure 1

12 pages, 1377 KB

Open AccessArticle

Fungal–Bacterial Crosstalk Modulates Glucocorticoid-Primed TLR2 Signaling in the Human Skin

by Otomi Cho, Kanako Watanabe and Takashi Sugita

Microorganisms 2026, 14(2), 450; https://doi.org/10.3390/microorganisms14020450 - 12 Feb 2026

Abstract

Cutibacterium acnes, a major skin commensal bacterium, induces inflammatory cytokine production in keratinocytes through Toll-like receptor 2 (TLR2) signaling and contributes to acne vulgaris pathogenesis. Although glucocorticoids, e.g., dexamethasone (Dex), exert anti-inflammatory effects in related treatments, prolonged glucocorticoid exposure paradoxically induces acneiform [...] Read more.

Cutibacterium acnes, a major skin commensal bacterium, induces inflammatory cytokine production in keratinocytes through Toll-like receptor 2 (TLR2) signaling and contributes to acne vulgaris pathogenesis. Although glucocorticoids, e.g., dexamethasone (Dex), exert anti-inflammatory effects in related treatments, prolonged glucocorticoid exposure paradoxically induces acneiform eruptions, a phenomenon referred to as steroid-induced acne. Moreover, how commensal fungi influence bacterial-driven inflammatory signaling under glucocorticoid treatment remains unclear. In this study, we investigated how the lipophilic skin yeast Malassezia restricta affects C. acnes-induced TLR2 expression under Dex treatment using normal human epidermal keratinocytes. We discovered that M. restricta selectively suppressed Dex-enhanced C. acnes-induced TLR2 expression both at the transcriptional level and cell surface. Mechanistically, M. restricta enhanced p38 MAPK phosphorylation and inhibited NF-κB p65 nuclear translocation, indicating context-dependent glucocorticoid-primed TLR2 signaling modulation rather than simple inhibition. These results demonstrate that M. restricta modulates bacterial-induced inflammatory responsiveness in keratinocytes under glucocorticoid exposure and highlight the importance of fungal–bacterial interactions in shaping host immune signaling in steroid-treated skin. Our study provides new insight into the mechanistic basis of steroid-induced acne and the polymicrobial regulation of cutaneous innate immunity. Full article

(This article belongs to the Section Medical Microbiology)

► Show Figures

Figure 1

16 pages, 2329 KB

Open AccessArticle

Microbial Biomarkers for the Prevention and Diagnosis of Alcoholic Liver Disease

by Goo Hyun Kwon, Hyunjoon Park, Hyeong Seop Kim, Ki Kwang Oh, Jung A Eom, Kyeong Jin Lee, Min Ju Kim, Minsoo Kim, Jeong Su Kim, Sang Hak Han, Young Lim Ham and Ki Tae Suk

Microorganisms 2026, 14(2), 449; https://doi.org/10.3390/microorganisms14020449 - 12 Feb 2026

Abstract

Alterations in gut microbiota are closely associated with alcohol-associated liver disease (ALD) progression. We aimed to identify ALD-related bacterial strains with therapeutic or diagnostic potential. Human fecal samples were analyzed to screen candidate microbes, and an ALD mouse model was used to evaluate [...] Read more.

Alterations in gut microbiota are closely associated with alcohol-associated liver disease (ALD) progression. We aimed to identify ALD-related bacterial strains with therapeutic or diagnostic potential. Human fecal samples were analyzed to screen candidate microbes, and an ALD mouse model was used to evaluate their effects. We also assessed bacterial DNA levels in blood to explore diagnostic utility. Lactobacillus helveticus and L. lactis treatment improved gut dysbiosis and reduced hepatic inflammation and endotoxemia. In contrast, Veillonella dispar, which is significantly enriched in ALD patients, had no beneficial effects in vivo. Instead, V. dispar abundance in blood distinguished ALD patients from controls with an area under the ROC curve of 0.815. These findings suggest that L. helveticus and L. lactis may be effective probiotics for ALD, while V. dispar may serve as a non-invasive diagnostic biomarker. Targeting microbiota may offer a new approach for ALD prevention and diagnosis. Full article

(This article belongs to the Special Issue Advances in Gut Microbiota–Host Interactions: Microbial Mechanisms, Modulators, and Translational Perspectives)

► Show Figures

Figure 1

24 pages, 3109 KB

Open AccessArticle

Differential Immobilization of Pb²⁺ and Cd²⁺ by Marine Bacillus velezensis Hao 2023: Mechanisms and Fermentation Optimization for Enhanced Exopolysaccharide Production

by Rui Geng, Longyu Fang, Junfeng Chen, Jinghua Li, Shengbo Shi, Yuanyuan Wang, Maoyu Men, Xiangren Qiao, Xia Liu, Chunhua Mu and Lujiang Hao

Microorganisms 2026, 14(2), 448; https://doi.org/10.3390/microorganisms14020448 - 12 Feb 2026

Abstract

Soil contamination with lead (Pb) and cadmium (Cd) poses a severe threat to agricultural safety. This study explored the marine bacterium Bacillus velezensis Hao 2023 for bioremediation potential and EPS yield enhancement. Soil filtrate tests under metal stress revealed high tolerance to Pb [...] Read more.

Soil contamination with lead (Pb) and cadmium (Cd) poses a severe threat to agricultural safety. This study explored the marine bacterium Bacillus velezensis Hao 2023 for bioremediation potential and EPS yield enhancement. Soil filtrate tests under metal stress revealed high tolerance to Pb²⁺ (250 mg/L) and Cd²⁺ (2.5 mg/L), with distinct mechanisms: Cd²⁺ removal was strongly correlated with significant pH increase (up to 8.10), suggesting that immobilization likely occurred through precipitation, while Pb²⁺ was sequestered via EPS synthesis, achieving a yield of 1.62 g/L under stress. To decouple production from metal stress, fermentation was optimized using single-factor and response surface methodology. Key conditions (sucrose, ammonium sulfate, 45 g/L sea salt, 35 °C, pH 6.0, 8% inoculum, 150 rpm) achieved 1.081 g/L EPS under metal-free conditions. These results demonstrate strain Hao 2023’s metal-specific resistance and provide a scalable process for soil remediation agent development. Full article

(This article belongs to the Special Issue Environmental Microbes in Antimicrobial Resistance and Soil Pollution Mitigation)

► Show Figures

Figure 1

26 pages, 835 KB

Open AccessReview

Gut Microbiome Health in Farm Animals and Fish: Implications for Human Health and the Risk of Gastrointestinal Diseases

by Andrada Ihuț, Camelia Răducu, Mirela Ranta, Andreea Andrecan and Paul Uiuiu

Microorganisms 2026, 14(2), 447; https://doi.org/10.3390/microorganisms14020447 - 12 Feb 2026

Abstract

The gut microbiome is central to immune, metabolic, and gastrointestinal health across species. Dysbiosis disrupts microbial communities and is linked to inflammatory bowel disease, celiac disease, and other immune-mediated gastrointestinal disorders. This review addresses the central question of how diet- and environment-driven gut [...] Read more.

The gut microbiome is central to immune, metabolic, and gastrointestinal health across species. Dysbiosis disrupts microbial communities and is linked to inflammatory bowel disease, celiac disease, and other immune-mediated gastrointestinal disorders. This review addresses the central question of how diet- and environment-driven gut dysbiosis in farm animals and fish is transmitted through the food chain to influence human gastrointestinal health within a One Health framework. This review synthesizes recent evidence within the One Health framework, focusing on how diet- and environment-induced dysbiosis in farm animals and fish can influence human gastrointestinal health via the food chain. We highlight mechanisms of immune modulation, alterations in food products, and the risks of pathogen transmission and antimicrobial resistance. An important limitation of the current body of evidence is the lack of studies that comprehensively trace the proposed axis from animal gut dysbiosis to human health outcomes. Emerging interventions, including precision nutrition, probiotics, and microbiota-targeted therapies, show potential for restoring microbial balance, though translating these findings into clinical practice remains challenging. By integrating human, veterinary, and environmental perspectives, this work proposes a novel cross-species microbiome–diet–immune framework to guide future research and interventions, advancing One Health strategies for disease prevention, antimicrobial resistance mitigation, and sustainable gastrointestinal health. Full article

(This article belongs to the Special Issue Intestinal Dysbiosis: 2nd Edition)

► Show Figures

Figure 1

18 pages, 2308 KB

Open AccessArticle

The Phenotypic Divergence and Potential Microevolution of a Dominant Mycoplasmopsis bovis ST-52 Clone Within a Closed Dairy Herd in China

by Zhiyong Wu, Liang Zhang, Shaohua Yang, Zhaizhuo Yu, Tingwei Wang and Hongjun Yang

Microorganisms 2026, 14(2), 446; https://doi.org/10.3390/microorganisms14020446 - 12 Feb 2026

Abstract

Mycoplasmopsis bovis is a significant pathogen causing substantial economic losses in cattle, yet its within-herd microevolution remains poorly understood. This study aimed to characterize phenotypic and genomic variations within a dominant ST-52 clone circulating in a closed dairy herd. We isolated M. bovis [...] Read more.

Mycoplasmopsis bovis is a significant pathogen causing substantial economic losses in cattle, yet its within-herd microevolution remains poorly understood. This study aimed to characterize phenotypic and genomic variations within a dominant ST-52 clone circulating in a closed dairy herd. We isolated M. bovis from respiratory (n = 11) and milk (n = 5) samples. Phenotypic characterization included biofilm formation, antimicrobial susceptibility testing, and cellular invasion assays. Whole-genome sequencing was performed on four representative isolates to identify genetic variations. All isolates were genetically identical according to MLST (ST-52). However, significant phenotypic diversity was observed. Biofilm formation capacity varied significantly (OD595 from 0.25 to 1.10), and resistance to doxycycline was higher in nose swabs (100%) than milk isolates (20%). Cellular invasion assays demonstrated that all isolates could invade bovine-derived cells (MDBK, MAC-T, EBL, and PBMC), but the invasion efficiency differed by strain and cell type. These findings confirm the circulation of a single genetic lineage within a closed herd while highlighting significant phenotypic diversification in biofilm formation, antibiotic resistance, and cellular invasiveness. The results provide evidence consistent with microevolution and underscore the adaptive potential of M. bovis. This study underscores the adaptive potential of M. bovis during within-host colonization and cross-tissue transmission, providing critical insights for optimizing herd management and treatment strategies. Full article

(This article belongs to the Section Veterinary Microbiology)

► Show Figures

Figure 1

19 pages, 2429 KB

Open AccessArticle

Feeding Type Shapes Infant Gut Microbiota and Metabolite Profiles in a Simulated Colonic Model

by Cristiane Mori, Christopher Pillidge and Harsharn Gill

Microorganisms 2026, 14(2), 445; https://doi.org/10.3390/microorganisms14020445 - 12 Feb 2026

Abstract

The establishment of the infant gut microbiota is strongly influenced by feeding type, with human milk (HM) and infant formula (IF) driving distinct microbial profiles. This study compared the effects of donated raw human milk (HM) and Holder-pasteurised HM (Past-HM) on microbial composition [...] Read more.

The establishment of the infant gut microbiota is strongly influenced by feeding type, with human milk (HM) and infant formula (IF) driving distinct microbial profiles. This study compared the effects of donated raw human milk (HM) and Holder-pasteurised HM (Past-HM) on microbial composition using a 4-stage in vitro gut model inoculated with pooled faecal samples from five healthy 3–6-month-old infants. Colonic digesta were sampled over a 48-h period following introduction of raw HM, Past-HM and IFs for microbial diversity by quantitative polymerase chain reaction (qPCR) and 16S rRNA gene sequencing, and short-chain fatty acid (SCFA) analysis by gas chromatography. Microbial profiling revealed 2026 operational taxonomic units (OTUs) across eight phyla and 165 genera. Past-HM and goat milk-based IF (GIF) promoted Bifidobacterium dominance and produced higher levels of total SCFA, especially acetic acid, compared to HM. Spearman correlation linked Bifidobacterium with acetic acid and Escherichia-Shigella with propionic acid. PCA showed OTU composition (Dim1, 72.6%) and SCFA profiles (Dim2, 19.8%) and distinguished control and milk-inoculated groups. Feeding type was the dominant factor shaping microbiota and metabolite profiles, exerting a stronger influence than incubation time (PERMANOVA p < 0.05). These findings underscore the pivotal role of early feeding choices in directing both microbial colonisation and microbial metabolic activity in the infant gut. Full article

(This article belongs to the Section Microbiomes)

► Show Figures

Figure 1

Journal Description

Microorganisms

Latest Articles

Journal Menu

Journal Browser

Highly Accessed Articles

Latest Books

E-Mail Alert

News

Topics

Conferences

Special Issues

Topical Collections

Further Information

Guidelines

MDPI Initiatives

Follow MDPI