Microorganisms

15 pages, 815 KB

Open AccessArticle

Synergistic Antimicrobial Activity of Juniperus excelsa Essential Oil and Streptococcus thermophilus Postbiotic in Inhibiting Foodborne Pathogens in Chicken Meat During Refrigerated Storage (4 °C)

by Nuri Gungor, Hatice Yazgan, Tülin Guven Gokmen, Esmeray Kuley and Nur Sima Uprak

Microorganisms 2026, 14(2), 399; https://doi.org/10.3390/microorganisms14020399 (registering DOI) - 7 Feb 2026

Abstract

The objective of this study was to evaluate the individual and synergistic antimicrobial efficacy of Juniperus excelsa berry essential oil (JEO) and the cell-free supernatant (CFS) from Streptococcus thermophilus against Escherichia coli (ATCC 43888), Staphylococcus aureus (ATCC 25923), and multidrug-resistant Salmonella enterica serovar [...] Read more.

The objective of this study was to evaluate the individual and synergistic antimicrobial efficacy of Juniperus excelsa berry essential oil (JEO) and the cell-free supernatant (CFS) from Streptococcus thermophilus against Escherichia coli (ATCC 43888), Staphylococcus aureus (ATCC 25923), and multidrug-resistant Salmonella enterica serovar Infantis S2 isolated from chicken meat. In vitro antimicrobial effects were assessed using the agar well diffusion and microdilution methods (MIC and MBC assays). The in vivo antimicrobial effect of these natural bioactive substances in controlling microbial growth in chicken meat stored at 4 °C for 48 h was also evaluated. Bioactive components of JEO were determined via GC–MS, identifying alpha-pinene (84.56%) as the primary compound. In vitro assays revealed that JEO showed high antimicrobial activity against Gram-positive S. aureus with a zone diameter of 35.50 mm (p < 0.05). JEOCFS treatment, which is the combination of CFS and JEO, demonstrated a significant synergistic interaction against S. aureus, resulting in an MIC value of 25 mg/mL. CFS alone exerted a measurable inhibitory effect on S. aureus, with an MIC of 50 mg/mL, indicating its potential antimicrobial capability. Further evaluation of the in vivo antimicrobial efficacy using chicken meat stored at 4 °C revealed that the JEOCFS treatment significantly inhibited microbial growth (p < 0.05). After 48 h of storage under refrigerated conditions, the number of psychrophilic bacteria in the control group reached 8.40 log cfu/g, while it remained significantly lower at 6.44, 5.37, and 6.74 log cfu/g in the JEO, JEOCFS, and CFS treatments, respectively. These results indicate that the synergistic application of JEO and CFS effectively suppresses foodborne pathogens, particularly S. aureus, and extends the microbiological shelf life of refrigerated chicken meat. Full article

(This article belongs to the Special Issue Microbial Safety of Animal-Derived Foods)

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21 pages, 664 KB

Open AccessReview

Perioperative Management of Biologic and Targeted Synthetic DMARDs in Orthopedic Surgery: Balancing Infection Risk and Disease Control

by Francesco Mancuso, Jacopo Angelini, Alen Zabotti, Francesco Russiani, Massimo Baraldo, Luca Quartuccio, Hemant Pandit, Paolo Di Benedetto and Araldo Causero

Microorganisms 2026, 14(2), 398; https://doi.org/10.3390/microorganisms14020398 (registering DOI) - 7 Feb 2026

Abstract

The perioperative management of biologic and immunomodulatory therapies in patients undergoing orthopedic surgery poses a clinical challenge, primarily due to the increased risk of postoperative infections. Biologic agents, particularly TNF inhibitors and interleukin-targeting drugs, may impair host immune responses, potentially increasing the risk [...] Read more.

The perioperative management of biologic and immunomodulatory therapies in patients undergoing orthopedic surgery poses a clinical challenge, primarily due to the increased risk of postoperative infections. Biologic agents, particularly TNF inhibitors and interleukin-targeting drugs, may impair host immune responses, potentially increasing the risk of surgical site infections (SSIs), delayed wound healing, and systemic infections. However, abrupt discontinuation of these therapies can lead to disease flare-ups, which themselves may complicate recovery and rehabilitation. In addition, discontinuation of biologics can lead to drug tolerance and unresponsiveness when they are restarted and thereby need switching to another biologic. Recent studies suggest that the infection risk is particularly elevated with ongoing biologic therapy during major surgeries, especially in procedures involving prosthetic implants. Guidelines generally recommend withholding biological disease-modifying antirheumatic drugs (bDMARDs) for at least one dosing cycle prior to surgery, when feasible, while maintaining non-biologic DMARDs in most cases. The decision must be individualized, taking into account the pharmacokinetics of each drug, the type of surgery, the patient’s comorbidities, and the activity of the underlying disease. Close coordination among rheumatologists, orthopedic surgeons, and infectious disease specialists is essential to minimize perioperative complications and optimize patient outcomes. Full article

(This article belongs to the Special Issue Advances in Microbial Infections and Rheumatic Diseases)

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16 pages, 1062 KB

Open AccessArticle

Comparative Transcriptomics Reveals Metabolic Adaptations of Priestia megaterium BZ-95 to Different Nitrogen Sources

by Hao Chen Jiang, Zi Yan Jin, Yan Zhao and Xiang Shan Ji

Microorganisms 2026, 14(2), 397; https://doi.org/10.3390/microorganisms14020397 - 6 Feb 2026

Abstract

While intensive aquaculture has developed rapidly, the consequent buildup of nitrogenous compounds, poses a critical threat to aquatic organisms. Microbial degradation offers an environmentally sustainable solution. We investigated the metabolic regulatory capacity of Priestia megaterium BZ-95 under four nitrogen regimes—ammonium (NH₄⁺ [...] Read more.

While intensive aquaculture has developed rapidly, the consequent buildup of nitrogenous compounds, poses a critical threat to aquatic organisms. Microbial degradation offers an environmentally sustainable solution. We investigated the metabolic regulatory capacity of Priestia megaterium BZ-95 under four nitrogen regimes—ammonium (NH₄⁺-N), nitrite (NO₂⁻-N), nitrate (NO₃⁻-N), and a mixture of them (Mix)—using comparative transcriptomics. We revealed that BZ-95 in NH₄⁺-N activated a direct assimilation program prioritizing branched-chain amino acid biosynthesis. Conversely, under nitrate, BZ-95 enhanced membrane transport and 2-oxocarboxylic acid metabolism to facilitate the rapid incorporation of nitrate-derived ammonium into biomass. Nitrite stress triggered a coordinated response involving the assimilatory nir module (nirC-nirB-nirD) and enhanced energy metabolism to meet the heightened demand for reducing power during its rapid reduction. Under mixed nitrogen sources, BZ-95 established a highly synergistic carbon-nitrogen network, simultaneously processing multiple nitrogen inputs without a hierarchical preference, highlighting its remarkable metabolic plasticity. Intersection analysis defined a refined core of 692 nitrite-specific DEGs and revealed broad transcriptional activation under nitrite stress. Analysis of the NO₂⁻-specific core identified enhanced transmembrane transport capacity, coupled with auxiliary metabolic tuning, as central adaptive strategies for nitrite processing. Collectively, these findings provide crucial insights into the molecular basis of nitrogen coordination in P. megaterium BZ-95. Full article

(This article belongs to the Special Issue Bioinformatics and Omic Data Analysis in Microbial Research, 2nd Edition)

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17 pages, 3148 KB

Open AccessArticle

Molecular Evolution of the Fusion (F) Genes in Human Metapneumovirus Genotype B

by Tatsuya Shirai, Fuminori Mizukoshi, Mitsuru Sada, Kazuya Shirato, Takeshi Saraya, Haruyuki Ishii, Ryusuke Kimura, Toshiyuki Sugai, Akihide Ryo and Hirokazu Kimura

Microorganisms 2026, 14(2), 396; https://doi.org/10.3390/microorganisms14020396 - 6 Feb 2026

Abstract

Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epitope [...] Read more.

Human metapneumovirus genotype B (HMPV-B) is an important respiratory pathogen, requiring detailed elucidation of the evolutionary and antigenic features of its fusion (F) gene. Using 500 sequences collected between 1982 and 2024, we investigated the molecular evolution, phylodynamics, and structural epitope landscape of the HMPV-B F gene. Time-scaled phylogeny dated the divergence of sublineages B1 and B2 to around 1937, and Bayesian Skyline Plot analysis showed that these sublineages exhibited distinct demographic trajectories over time. The F gene evolved at a rate of 1.01 × 10⁻³ substitutions/site/year; however, amino acid variation remained limited, consistent with pervasive purifying selection, with 39% of codons under strong negative selection and little consensus evidence for positive selection. Conformational B-cell epitope prediction demonstrated a high degree of conservation across neutralizing antibody binding regions (sites Ø and I–V), and amino acid substitutions occurring within these sites were not predicted to substantially alter epitope architecture. Together, these findings indicate that the HMPV-B F gene evolves under strong evolutionary constraint while maintaining stable antigenic features, supporting the potential for antibody-based strategies that target neutralizing antibody binding regions of the F protein. Full article

(This article belongs to the Section Public Health Microbiology)

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16 pages, 1084 KB

Open AccessArticle

Early-Stage Growth Restriction of Hymenoscyphus fraxineus on Tolerant Fraxinus excelsior Is Associated with Constitutive Chemical Defenses

by Akira Hattori, Shunsuke Masuo, Yasuhiro Ishiga, Yutaka Tamai, Yuichi Yamaoka and Izumi Okane

Microorganisms 2026, 14(2), 395; https://doi.org/10.3390/microorganisms14020395 - 6 Feb 2026

Abstract

Hymenoscyphus fraxineus is the causal agent of ash dieback, a devastating disease of European ash (Fraxinus excelsior). Although the pathogen is believed to have originated in East Asia and has been confirmed in Japan, European ash trees cultivated in the Sapporo [...] Read more.

Hymenoscyphus fraxineus is the causal agent of ash dieback, a devastating disease of European ash (Fraxinus excelsior). Although the pathogen is believed to have originated in East Asia and has been confirmed in Japan, European ash trees cultivated in the Sapporo Experimental Forest of Hokkaido University remain asymptomatic despite the presence of H. fraxineus. In this study, we investigated the early infection behavior of H. fraxineus and associated host defense responses by comparing asymptomatic F. excelsior with the susceptible control species F. angustifolia. Leaflets were inoculated with ascospores, and fungal development as well as host responses were examined microscopically during early infection stages. In addition, we analyzed the accumulation of selected coumarins, which have been proposed as candidate compounds associated with ash dieback tolerance, and assessed their effects on ascospore germination. We found that fungal growth was consistently restricted on F. excelsior at 7 days post inoculation, particularly at the stage of invasion into adjacent epidermal cells. Fraxetin was detected in F. excelsior leaflets but not in F. angustifolia, and fraxetin treatment significantly reduced ascospore germination in vitro. While typical markers of induced resistance were not clearly detected at the examined time points, these results indicate that constitutive chemical traits, including fraxetin accumulation, may contribute to early-stage suppression of H. fraxineus growth in F. excelsior. Together, our findings provide insight into early host–pathogen interactions associated with ash dieback tolerance and highlight the potential role of constitutive defenses during initial infection. Full article

(This article belongs to the Special Issue Fungal Diversity and Bioactive Potential: From Taxonomy to Therapeutic Applications)

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30 pages, 4048 KB

Open AccessReview

Artificial Intelligence as a Catalyst for Antimicrobial Discovery: From Predictive Models to De Novo Design

by Romaisaa Boudza, Salim Bounou, Jaume Segura-Garcia, Ismail Moukadiri and Sergi Maicas

Microorganisms 2026, 14(2), 394; https://doi.org/10.3390/microorganisms14020394 (registering DOI) - 6 Feb 2026

Abstract

Antimicrobial resistance represents one of the most critical global health challenges of the 21st century, urgently demanding innovative strategies for antimicrobial discovery. Traditional antibiotic development pipelines are slow, costly, and increasingly ineffective against multidrug-resistant pathogens. In this context, recent advances in artificial intelligence [...] Read more.

Antimicrobial resistance represents one of the most critical global health challenges of the 21st century, urgently demanding innovative strategies for antimicrobial discovery. Traditional antibiotic development pipelines are slow, costly, and increasingly ineffective against multidrug-resistant pathogens. In this context, recent advances in artificial intelligence have emerged as transformative tools capable of accelerating antimicrobial discovery and expanding accessible chemical and biological space. This comprehensive review critically synthesizes recent progress in AI-driven approaches applied to the discovery and design of both small-molecule antibiotics and antimicrobial peptides. We examine how machine learning, deep learning, and generative models are being leveraged for virtual screening, activity prediction, mechanism-informed prioritization, and de novo antimicrobial design. Particular emphasis is placed on graph-based neural networks, attention-based and transformer architectures, and generative frameworks such as variational autoencoders and large language model-based generators. Across these approaches, AI has enabled the identification of structurally novel compounds, facilitated narrow-spectrum antimicrobial strategies, and improved interpretability in peptide prediction. However, significant challenges remain, including data scarcity and imbalance, limited experimental validation, and barriers to clinical translation. By integrating methodological advances with a critical analysis of the current limitations, this review highlights emerging trends and outlines future directions aimed at bridging the gap between in silico discovery and real-world therapeutic development. Full article

(This article belongs to the Special Issue Artificial Intelligence as a Tool for Combating Antimicrobial Resistance)

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19 pages, 5101 KB

Open AccessReview

Revealing Microbial Siderophores: From Genes to Applications

by Jionglin Cai, Yuting Fang, Xia Liu, Mark Owusu Adjei and Ben Fan

Microorganisms 2026, 14(2), 393; https://doi.org/10.3390/microorganisms14020393 - 6 Feb 2026

Abstract

Iron is an essential micronutrient for nearly all microorganisms, yet its bioavailability is severely limited in most environments. To overcome this restriction, microorganisms produce siderophores, high-affinity iron-chelating molecules that play pivotal roles in microbial iron homeostasis, interspecies competition, and host–pathogen interactions. Despite extensive [...] Read more.

Iron is an essential micronutrient for nearly all microorganisms, yet its bioavailability is severely limited in most environments. To overcome this restriction, microorganisms produce siderophores, high-affinity iron-chelating molecules that play pivotal roles in microbial iron homeostasis, interspecies competition, and host–pathogen interactions. Despite extensive research, current understanding of siderophore biosynthetic and regulatory diversity remains largely limited to specific models, with comprehensive cross-taxonomic frameworks only beginning to emerge. This review systematically integrates recent advances in the genetic and biochemical foundations of microbial siderophore production, focusing on the two major biosynthetic pathways: nonribosomal peptide synthetase (NRPS)-dependent and NRPS-independent synthetase (NIS). We further elaborate on the diverse transport systems in Gram-negative and Gram-positive bacteria, as well as fungi, alongside the iron-responsive regulators (e.g., Fur) and gene clusters that coordinate iron uptake and utilization. Beyond physiological mechanisms, we discuss how these insights inform emerging applications of siderophores across multiple fields: in medicine, enabling “Trojan horse” antimicrobial strategies; in agriculture, enhancing plant iron uptake and serving as biocontrol agents; in environmental remediation, facilitating heavy-metal detoxification; and in biosensing, acting as selective probes for metals and pathogens. By bridging fundamental mechanisms with practical applications, this review aims to provide an integrative perspective for future exploration of microbial iron homeostasis and its biotechnological potential. Full article

(This article belongs to the Special Issue Resource Utilization of Microorganisms: Fermentation and Biosynthesis)

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11 pages, 481 KB

Open AccessCommunication

Preliminary Screening for Ophidiomyces ophidiicola in Pet Snakes from Italy and Exploratory Evaluation of Droplet Digital PCR Assay

by Matteo Riccardo Di Nicola, Simona Sciuto, Daniele Marini, Luca Colla, Giacomo Vanzo, Gabriele Carsana, Emanuele Scanarini, Luana Dell’Atti, Giulia Milanese, Martina Alessandra Gini, Maria Claudia Palazzolo, Jean-Lou C. M. Dorne, Maria Goria, Silvia Colussi and Pier Luigi Acutis

Microorganisms 2026, 14(2), 392; https://doi.org/10.3390/microorganisms14020392 - 6 Feb 2026

Abstract

Ophidiomyces ophidiicola, the agent of ophidiomycosis, has recently been reported in wild snakes in Italy, but the status of captive populations remains unknown. We carried out an opportunistic survey of pet snakes from private collections and, in parallel, performed an exploratory [...] Read more.

Ophidiomyces ophidiicola, the agent of ophidiomycosis, has recently been reported in wild snakes in Italy, but the status of captive populations remains unknown. We carried out an opportunistic survey of pet snakes from private collections and, in parallel, performed an exploratory evaluation of a droplet digital PCR (ddPCR) assay adapted from an established probe-based real-time PCR. Non-invasive skin swabs were collected by 32 private owners from 97 snakes, representing 31 species across ten Italian regions. All swabs tested negative for O. ophidiicola by both methods, including samples from four snakes that showed cutaneous lesions at the time of sampling. Both assays yielded consistent amplification up to the 1:1000 dilution (ddPCR 0.38 to 0.94 copies/µL for the culture-derived control and 0.24 to 0.33 copies/µL for the field-derived control at 1:1000), while ddPCR retained positive partitions in some replicates at higher dilutions (up to 1:8000). These results provide preliminary screening data for O. ophidiicola in an opportunistic sample of Italian pet snakes and suggest potential applicability of ddPCR as a complementary tool for low-template diagnostics, while highlighting the need for larger, standardised surveys and formal assay validation. Full article

(This article belongs to the Section Veterinary Microbiology)

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20 pages, 1010 KB

Open AccessArticle

Fertility-Associated Soil Chemistry Predominantly Influence Gut Microbiota Diversity in Goitered Gazelles of the Qaidam Basin, China

by Qing Zhao, Bin Li, Chengbo Liang, Jiaxin Wei, Juan Ma and Wen Qin

Microorganisms 2026, 14(2), 391; https://doi.org/10.3390/microorganisms14020391 - 6 Feb 2026

Abstract

This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) [...] Read more.

This study focused on the links between soil physicochemical properties and the gut microbiota of goitered gazelles (Gazella subgutturosa) in the hyper-arid Qaidam Basin. By integrating 16S rRNA gene sequencing, soil physicochemical analysis (11 soil indicators), and microbial source tracking (FEAST) on samples of feces (n = 58), soil (n = 35), and water (n = 35) collected from six typical regions. We systematically revealed the mechanisms by which soil properties influence the gut microbiome of wildlife in an arid desert ecosystem based on source tracking and Multiple Regression on distance Matrices (MRM) analysis. The results showed that soil total phosphorus (TP) was significantly positively correlated with the α-diversity of gut microbiota (coefficient = 0.4/0.23/0.332; p < 0.05), while soil organic carbon (SOC) was significantly negatively correlated (coefficient = −0.44/−0.436; p < 0.05), indicating that soil nutrients indirectly predict host microbial diversity by regulating vegetation productivity and forage quality. β-diversity analysis further demonstrated that spatial heterogeneity in soil pH (coefficient = 0.3083; p < 0.05) and TP (coefficient = 0.227; p < 0.05) significantly drove the structural differentiation of gut microbial communities. Source-tracking results based on FEAST revealed significant regional differences in the proportional contribution of environmental microorganisms to the gut microbiota, with individuals in resource-poor habitats (ALK region) exhibiting higher input from soil microbes (8.0672% ± 6.9291%; p < 0.05). In conclusion, this study clarifies the ecological mechanism by which soil physicochemical properties regulate the diversity and composition of herbivore gut microbiota through a “soil–plant–food–gut microbiota” cascading pathway, providing important empirical evidence for understanding animal–microbe–environment interactions and adaptive evolution in extreme environments. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 750 KB

Open AccessArticle

Optimizing Salvage ART: Real-World Outcomes of Doravirine Plus DTG or BIC in Heavily Treatment-Experienced Persons Living with HIV

by Irina Ianache, Roxana Radoi, Gratiela Tardei, Mike Youle and Cristiana Oprea

Microorganisms 2026, 14(2), 390; https://doi.org/10.3390/microorganisms14020390 - 6 Feb 2026

Abstract

Management of heavily treatment-experienced people living with HIV (HTE-PWH) remains challenging due to long antiretroviral therapy (ART) exposure and limited treatment options. We conducted an observational, real-world-data study on HTE-PWH in active care at the “Victor Babeș” Hospital, Bucharest, receiving doravirine (DOR)-based salvage [...] Read more.

Management of heavily treatment-experienced people living with HIV (HTE-PWH) remains challenging due to long antiretroviral therapy (ART) exposure and limited treatment options. We conducted an observational, real-world-data study on HTE-PWH in active care at the “Victor Babeș” Hospital, Bucharest, receiving doravirine (DOR)-based salvage regimens combined with dolutegravir (DTG) or bictegravir (BIC). Epidemiological, clinical, and laboratory variables were analyzed according to HIV acquisition mode and salvage regimen. Sixty-nine PWH were included; 57.9% male, with a median age of 36 years. Median ART duration before switch was 21.5 years. HIV was acquired parenterally in childhood (PM) in 64.7% cases. Salvage regimens included BIC/FTC/TAF + DOR (50.0%), 3TC/TDF/DOR + DTG (35.2%), and 3TC/DTG + DOR (14.7%). The median nadir CD4 count was 37 cells/µL, and the median viral load at diagnosis was 5.24 log10 copies/mL. Switching was performed for regimen simplification (n = 32) or non-adherence-related virological failure (n = 37). At switch, 53.6% had detectable viremia. Viral suppression was achieved in 68.3% at 6 months and 75.0% at 12 months. Individuals with PM infection were younger and had longer ART exposure than those with heterosexual acquisition. DOR-based salvage regimens combined with DTG or BIC were effective in adherent HTE-PWH, particularly those with extensive ART histories. Full article

(This article belongs to the Special Issue HIV Infections: Comorbidities, Clinical Challenges, and Antiretroviral Advances)

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11 pages, 491 KB

Open AccessArticle

Helicobacterpylori Infection and Antimicrobial Resistance Surveillance over 25 Years in Children in Gipuzkoa, Northern Spain

by Itsaso Jimenez, Iñigo Ansa, Pedro Vallejo and Milagrosa Montes

Microorganisms 2026, 14(2), 389; https://doi.org/10.3390/microorganisms14020389 - 6 Feb 2026

Abstract

The diagnosis and treatment of Helicobacter pylori infection in children represent a major public health problem worldwide, and although prevalence in developed countries has declined, concern about antibiotic resistance continues to grow. This retrospective study aimed to analyze H. pylori infections in children [...] Read more.

The diagnosis and treatment of Helicobacter pylori infection in children represent a major public health problem worldwide, and although prevalence in developed countries has declined, concern about antibiotic resistance continues to grow. This retrospective study aimed to analyze H. pylori infections in children under 15 years of age in Gipuzkoa (Basque Country, Spain) over a 25-year period and to describe patterns of primary and secondary antimicrobial resistance. All diagnostic tests received at a tertiary referral hospital between 2000 and 2024 were reviewed: urea breath test, gastric biopsy culture, string test, and stool antigen detection. Antimicrobial susceptibility testing was performed using the E-test gradient diffusion method. Out of 2855 children investigated, 26.9 were infected with H. pylori. Eradication control was performed in 62.5% (n = 480) of cases. Antimicrobial susceptibility testing was achieved in 96.5% out of the 400 isolates studied. All isolates were sensitive to amoxicillin and tetracyclines. Primary resistance to clarithromycin, metronidazole, and levofloxacin was 28.9%, 19.4%, and 8.9%, respectively, and secondary resistance was 38.7%, 29.7%, and 5.9%, respectively. H.pylori infection remains a challenge in pediatric patients, and the high resistance observed to clarithromycin and metronidazole makes it necessary to monitor the susceptibility of H.pylori and confirms the need for targeted treatment. Full article

(This article belongs to the Special Issue Helicobacter pylori and Related Gastrointestinal Diseases: Infection, Treatment, Prevention, and Beyond)

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20 pages, 7060 KB

Open AccessArticle

Tree Species Mixing Regulates Soil Multi-Nutrient Cycling by Altering Microbial Network Complexity and Assembly Processes in Larix olgensis

by Yue Liu, Chunjing Jiao, Wanju Feng, Yuchun Yang, Bing Yang, Fang Wang and Jun Wang

Microorganisms 2026, 14(2), 388; https://doi.org/10.3390/microorganisms14020388 - 6 Feb 2026

Abstract

Establishing mixed conifer–broadleaf forests enhances soil multi-nutrient cycling (SMC), yet the underlying mechanisms, particularly the role of rhizosphere microbial communities, remain poorly understood. This study investigated how bacterial and fungal communities in the rhizosphere soil of Larix olgensis drive SMC in both pure [...] Read more.

Establishing mixed conifer–broadleaf forests enhances soil multi-nutrient cycling (SMC), yet the underlying mechanisms, particularly the role of rhizosphere microbial communities, remain poorly understood. This study investigated how bacterial and fungal communities in the rhizosphere soil of Larix olgensis drive SMC in both pure and mixed plantations with Fraxinus mandshurica, elucidating the microbial pathways for nutrient supply in mixed stands. Our results indicated that SMC in the L. olgensis rhizosphere soil was significantly greater in mixed stands (0.43) than in pure stands (−0.51). Tree species mixing significantly enhanced microbial diversity, increased the stochasticity of community assembly, and reduced dispersal limitation. Cross-kingdom (bacteria–fungi) co-occurrence networks in mixed stands showed a 19.7% increase in positive correlations, indicating stronger microbial cooperation. Random forest analysis identified microbial diversity, network complexity, and bacterial assembly processes as the main predictors of SMC. Structural equation modeling indicated that microbial diversity indirectly promoted SMC via increased network complexity, while bacterial assembly processes directly influenced SMC. These findings demonstrate that mixed conifer–broadleaf plantations improve soil microbial functioning and nutrient cycling by modifying microbial diversity, assembly processes, and interaction networks. Full article

(This article belongs to the Special Issue Advances in Plant–Soil–Microbe Interactions)

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42 pages, 1129 KB

Open AccessReview

Basic Microbiome Analysis: Analytical Steps from Sampling to Sequencing

by Gülfem Ece, Ahmet Aktaş, Özlem Koyuncu Özyurt, Hadiye Demirbakan, Hikmet Eda Alışkan, İmran Sağlık, Orçun Zorbozan, Alev Çetin Duran, Ayşe Rüveyda Uğur, Duygu Öcal, Emel Uzunoğlu, Esra Kaya, Fatma Mutlu Sarıgüzel, Fulya Bayındır, Gülay Yetkin, Mustafa Altındiş, Sevinç Yenice Aktaş and Tuba Kula Atik

Microorganisms 2026, 14(2), 387; https://doi.org/10.3390/microorganisms14020387 - 6 Feb 2026

Abstract

The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and [...] Read more.

The human microbiome is increasingly recognized as a key determinant of health and disease, yet methodological variability continues to limit reproducibility and clinical translation of findings. This review synthesizes current approaches in microbiome research, critically evaluating each step from sampling to sequencing and downstream bioinformatics. Pre-analytical factors such as sample type, collection method, preservation, and storage conditions profoundly affect microbial community profiles and remain a major source of bias. Nucleic acid extraction protocols and quality assessment strategies are discussed with emphasis on optimized lysis techniques, contamination controls, and DNA yield evaluation. Advances in sequencing technologies are highlighted, including 16S rRNA amplicon sequencing, shotgun metagenomics, third-generation long-read platforms, and emerging single-cell and minimal-input methods, each with specific advantages and limitations in taxonomic and functional resolution. Bioinformatics pipelines for taxonomic profiling, variant detection, phylogenetic inference, and functional annotation are compared, with attention to widely used reference databases such as RefSeq, GTDB, and SILVA. Integrative multi-omics approaches, including metatranscriptomics, metabolomics, and genome-scale metabolic modeling, are presented as powerful tools for linking microbial community structure to host physiology and disease mechanisms. Despite these advances, the lack of standardized workflows across pre-analytical, sequencing, and computational steps continues to hinder inter-study comparability and biomarker validation. This review aims to provide a methodological framework that highlights both strengths and limitations of current technologies while underlining the need for harmonized protocols to ensure reproducibility and accelerate the translation of microbiome research into clinical practice. Full article

(This article belongs to the Section Microbiomes)

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28 pages, 732 KB

Open AccessReview

Chronic Rhinosinusitis at the Interface of Type 2 Inflammation, Epithelial Barrier Dysfunction, and Microbiome Dysbiosis

by Konstantinos Petalas and George N. Konstantinou

Microorganisms 2026, 14(2), 386; https://doi.org/10.3390/microorganisms14020386 - 6 Feb 2026

Abstract

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease of the nasal and paranasal sinus mucosa with substantial impact on quality of life. Although atopy and/or allergic rhinitis frequently coexist with CRS, often alongside type 2-skewed inflammation, the extent to which allergic mechanisms define [...] Read more.

Chronic rhinosinusitis (CRS) is a heterogeneous inflammatory disease of the nasal and paranasal sinus mucosa with substantial impact on quality of life. Although atopy and/or allergic rhinitis frequently coexist with CRS, often alongside type 2-skewed inflammation, the extent to which allergic mechanisms define a discrete CRS entity remains debated, in part due to inconsistent operational definitions and overlapping clinical phenotypes. In parallel, culture-independent sequencing studies have reframed CRS as a disorder of host–microbe interactions, with many cohorts reporting reduced sinonasal microbial diversity, enrichment of potentially pathogen taxa (including Staphylococcus aureus), and biofilm-associated community states. However, causality and directionality remain uncertain. In this narrative review, we synthesize evidence at the interface of epithelial barrier dysfunction, type 2 cytokine networks (IL-4/IL-13/IL-5), and microbiome dysbiosis, highlighting where data are consistent across studies versus where findings are heterogeneous or predominantly associative. We discuss representative allergy-associated CRS prototypes such as allergic fungal rhinosinusitis and central compartment atopic disease as clinical models to interrogate these interactions, while distinguishing them from non–IgE-mediated type 2 entities such as aspirin-exacerbated respiratory disease. We also summarize current data linking atopy to sinonasal microbial signatures and discuss emerging microbiome-directed interventions (topical probiotics, bacteriophages, and microbiota transfer concepts) alongside biologics and precision anti-inflammatory therapies. Finally, we highlight key knowledge gaps, including the limited endotype-resolved and longitudinal studies, variable allergic phenotyping in microbiome research, and the need for standardized definitions and biomarker-driven stratification to clarify clinical utility and to guide mechanism-informed therapeutic trials. Full article

(This article belongs to the Special Issue Respiratory Diseases and Microbiome Dysbiosis)

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20 pages, 1166 KB

Open AccessArticle

Novel Skin- and Oral-Derived Probiotic Candidates: Functional Evaluation and Application Perspectives

by Ivana Repić, Nina Čuljak, Matea Hrupački, Iva Čanak, Ksenija Markov and Jadranka Frece

Microorganisms 2026, 14(2), 385; https://doi.org/10.3390/microorganisms14020385 - 6 Feb 2026

Abstract

The skin and oral environment represent complex microbial ecosystems that host diverse bacterial communities with potential health-promoting properties beyond the gastrointestinal tract (GIT). In this study, four bacterial and three yeast isolates were obtained from saliva (S1, S3, S5, and S6) and human [...] Read more.

The skin and oral environment represent complex microbial ecosystems that host diverse bacterial communities with potential health-promoting properties beyond the gastrointestinal tract (GIT). In this study, four bacterial and three yeast isolates were obtained from saliva (S1, S3, S5, and S6) and human skin (A1, A2, and A3) and subjected to identification and functional characterization. Phenotypic identification by API and MALDI-TOF mass spectrometry identified bacterial isolates as Limosilactobacillus sp. (S1) and Lacticaseibacillus rhamnosus (S3, S5, and S6), while the yeasts were identified as Saccharomyces cerevisiae (A1, A2, and A3). The isolates were evaluated for their functional properties, including antimicrobial activity, autoaggregation, antioxidative potential, resistance to freeze-drying, survival in simulated saliva and GIT conditions, adhesion to Caco-2 and HaCaT cell lines, and biofilm-forming ability. Lcb. rhamnosus S3 demonstrated the highest probiotic potential, characterized by strong inhibition of S. aureus, high autoaggregation capacity, substantial survival following freeze-drying, and good tolerance to simulated saliva and GIT conditions. Limosilactobacillus sp. (S1) demonstrated the strongest antimicrobial activity against C. acnes and the highest adhesion capacity to HaCaT cells, indicating its suitability for topical dermatological applications. Although S. cerevisiae isolates did not exhibit antimicrobial activity, they showed strong autoaggregation and notable antioxidant capacity. However, their low resistance to freeze-drying limits their applicability in probiotic formulation development. Full article

(This article belongs to the Section Food Microbiology)

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18 pages, 2293 KB

Open AccessArticle

Serum Uric Acid-Reducing Effect and Intestinal Mucosal Barrier-Repairing Function of Limosilactobacillus reuteri MBHC10138

by Jinhua Cheng, Youjin Lee, Joo-Hyung Cho and Joo-Won Suh

Microorganisms 2026, 14(2), 384; https://doi.org/10.3390/microorganisms14020384 - 5 Feb 2026

Abstract

Hyperuricemia is a metabolic disorder characterized by elevated serum uric acid levels and is increasingly linked to alterations in intestinal mucosal condition and gut microbiota composition. Probiotics have been proposed as safe, non-pharmacological approaches for managing hyperuricemia, but strain-specific evidence remains limited. This [...] Read more.

Hyperuricemia is a metabolic disorder characterized by elevated serum uric acid levels and is increasingly linked to alterations in intestinal mucosal condition and gut microbiota composition. Probiotics have been proposed as safe, non-pharmacological approaches for managing hyperuricemia, but strain-specific evidence remains limited. This study aimed to evaluate the anti-hyperuricemic potential of Limosilactobacillus reuteri MBHC10138, isolated from human breast milk, and to examine its association with purine metabolism–related parameters, renal morphological features, intestinal barrier-associated markers, and gut microbiota composition. In vitro, MBHC10138 effectively degraded purine nucleosides that are metabolized into uric acid, suggesting its potential to reduce uric acid production in the host. In a mouse model of diet- and oxonate-induced hyperuricemia, oral administration of MBHC10138 significantly lowered serum uric acid levels to a level comparable with allopurinol treatment, while improving renal morphology. Histological and molecular analyses demonstrated restoration of the tight junction proteins zonula occludens-1 and occludin, indicative of enhanced intestinal barrier integrity. Furthermore, MBHC10138 administration modulated the gut microbiota by restoring microbial α-diversity and significantly increasing the relative abundances of the Clostridia vadinBB60 group and Oscillospiraceae, taxa associated with butyrate production, compared with the allopurinol-treated group. Collectively, these findings indicate that MBHC10138 exerts dual actions against hyperuricemia and intestinal barrier dysfunction through the regulation of purine metabolism, promotion of renal urate excretion, and modulation of gut microbial composition. MBHC10138 may thus represent a promising probiotic candidate for the prevention and adjunctive management of hyperuricemia-related metabolic disorders. Full article

(This article belongs to the Special Issue Advances in Host Gut Microbiota—2nd Edition)

23 pages, 799 KB

Open AccessReview

Exploring the Diversity and Applications of Lactic Acid Bacteria from Tunisian Traditional Fermented Foods

by Sabrine Alebidi, Hana Mallek, Mariagiovanna Fragasso, Vittorio Capozzi, Ferid Abidi, Ines Essid, Giuseppe Spano and Hiba Selmi

Microorganisms 2026, 14(2), 383; https://doi.org/10.3390/microorganisms14020383 - 5 Feb 2026

Abstract

Tunisian traditional fermented foods represent a valuable cultural heritage transmitted across generations and are highly appreciated by consumers for their distinctive flavours, textures, and nutraceutical value. This review provides the first comprehensive and exclusive overview of lactic acid bacteria (LAB) associated with Tunisian [...] Read more.

Tunisian traditional fermented foods represent a valuable cultural heritage transmitted across generations and are highly appreciated by consumers for their distinctive flavours, textures, and nutraceutical value. This review provides the first comprehensive and exclusive overview of lactic acid bacteria (LAB) associated with Tunisian traditional fermented foods, both plant- and animal-based. The overview integrates data across dairy, meat, fish, vegetable, and cereal matrices, highlighting the central role that LAB play in the processing of these foods, driving fermentation and shaping the quality and safety of final products. During fermentation, LAB produce a variety of bioactive metabolites, including organic acids, antimicrobial compounds, exopolysaccharides, enzymes, and vitamins, which enhance food safety, shelf life, nutritional quality, and health-promoting potential. The studies include evidence of LAB’s long history of safe use by humans, including the characterisation of autochthonous strains with protechnological, bioprotective, and probiotic properties, providing candidates for the design of starter, protective and probiotic cultures. By consolidating evidence on the relevance of microbial diversity, this review positions Tunisian LAB as valuable resources for both traditional food valorisation and innovative food system development. Importantly, key knowledge gaps are identified, including the limited application of omics-based tools, insufficient genomic safety assessments, and the lack of systematic analysis linking LAB diversity with the desired attributes to promote innovations. Overall, this review provides a structured framework for the valorisation of Tunisian agrofood heritage, bridging artisanal knowledge with modern food microbiology and offering strategic directions for future research, industrial translation, and sustainable innovation in fermented foods. Full article

(This article belongs to the Special Issue Microbial Fermentation, Food and Food Sustainability, 2nd Edition)

19 pages, 2785 KB

Open AccessArticle

Siderophore-Producing Bacteria from the Santiago River: A Quantitative Study and Biocomposite Applications

by Mariana R. Corona-Ramírez, Nidia N. García-Valdez, Luis A. Romero-Cano, Camila S. Gómez-Navarro, Ma Isidora Bautista-Toledo, Francisco Carrasco-Marín, Fabiola Padilla-Arizmendi, Karina Sandoval-García and Marco A. Zárate-Navarro

Microorganisms 2026, 14(2), 382; https://doi.org/10.3390/microorganisms14020382 - 5 Feb 2026

Abstract

The Santiago River near the Guadalajara Metropolitan Area is one of the most contaminated water bodies in Mexico, where heavy metals pose a major threat to aquatic ecosystems. Chronic metal pollution has promoted the adaptation of native microbial communities, including the production of [...] Read more.

The Santiago River near the Guadalajara Metropolitan Area is one of the most contaminated water bodies in Mexico, where heavy metals pose a major threat to aquatic ecosystems. Chronic metal pollution has promoted the adaptation of native microbial communities, including the production of metal-chelating metabolites such as siderophores, which represent a valuable resource for remediation-oriented biomaterials. In this study, bacterial strains were isolated from water and sediment samples, then screened for siderophore production using the Chrome Azurol S assay (CAS), complemented by a MATLAB-based image processing approach for semi-quantitative ranking prior to taxonomic identification by MALDI-TOF MS. Based on biosafety considerations and cultivation robustness, Bacillus thuringiensis was selected as a benchmark case, being immobilized onto activated carbon to produce a carbon–bacteria biocomposite (CBM). To evaluate the performance of CBM, Cu(II) was used as a model contaminant due to its industrial relevance, persistence, toxicity, and strong complexation behavior. Batch adsorption experiments showed that the CBM exhibited a 23.9% higher maximum Cu(II) sorption capacity than pristine activated carbon. Acute toxicity assays using Vibrio fischeri further indicated reduced toxicity in CBM-treated effluents, supporting the feasibility of this contained biocomposite for heavy metal remediation. Full article

(This article belongs to the Special Issue Effect of Microbial Communities for Environmental Protection and Development of Agriculture, Second Edition)

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19 pages, 6325 KB

Open AccessArticle

Genomic Characterization, Safety Assessment, and Probiotic Potential of a Novel Human-Derived Enterococcus lactis IOBRA9746

by Dongxiong Hu, Jiao Yan, Yuxin Li, Jun Wu, Yifan Xie, Lirong Peng, Erhong Zhang, Hao Jiang, Qinmiao Sun and Xiao Chu

Microorganisms 2026, 14(2), 381; https://doi.org/10.3390/microorganisms14020381 - 5 Feb 2026

Abstract

Probiotic strains exhibiting bile salt hydrolase (BSH) activity represent a promising therapeutic strategy for ameliorating metabolic disorders via targeting the gut–liver axis. Herein, we characterized a newly isolated human-derived Enterococcus strain and investigated its therapeutic potential. Genomic analysis confirmed its safety profile, while [...] Read more.

Probiotic strains exhibiting bile salt hydrolase (BSH) activity represent a promising therapeutic strategy for ameliorating metabolic disorders via targeting the gut–liver axis. Herein, we characterized a newly isolated human-derived Enterococcus strain and investigated its therapeutic potential. Genomic analysis confirmed its safety profile, while in vitro assays demonstrated potent BSH activity. Subsequently, C57BL/6J mice fed a high-cholesterol diet were orally administered this strain over an eight-week intervention period. Although the treatment did not significantly reduce serum cholesterol levels, a marked reduction in hepatic lipid droplet accumulation was confirmed by H&E and Oil Red O staining. Mechanistically, the strain’s potent BSH activity likely modulates bile acid metabolism within the gut–liver axis, thereby specifically inhibiting hepatic lipid deposition. Comprehensive histopathological examination of major organs revealed no signs of toxicity, affirming its excellent in vivo safety profile. In summary, E. lactis IOBRA9746 constitutes a safe and BSH-active probiotic candidate, whose primary beneficial effect lies in directly alleviating hepatic lipid accumulation independent of systemic cholesterol modulation. These findings highlight its potential as a novel liver-targeted intervention for preventing metabolic diseases induced by suboptimal dietary patterns. Full article

(This article belongs to the Special Issue Microbe–Host Interactions: Molecular Mechanisms and Applications)

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