Microorganisms

16 pages, 1148 KB

Open AccessSystematic Review

Torque Teno Virus (TTV) Plasma Load and Immune Reconstitution in People Living with HIV: A Systematic Review

by Federico Cesanelli, Ottavia Nozza, Martina Salvi, Maria Alberti, Irene Scarvaglieri, Giorgio Tiecco, Francesca Mosti, Maria Antonia De Francesco and Eugenia Quiros-Roldan

Microorganisms 2026, 14(6), 1386; https://doi.org/10.3390/microorganisms14061386 - 22 Jun 2026

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Abstract

Background: Torque teno virus (TTV) is a ubiquitous, non-pathogenic component of the human virome whose role in people living with HIV (PLWH), particularly during antiretroviral therapy (ART)-mediated immune reconstitution, remains unclear. This systematic review aimed to synthesize available evidence on TTV viral load [...] Read more.

Background: Torque teno virus (TTV) is a ubiquitous, non-pathogenic component of the human virome whose role in people living with HIV (PLWH), particularly during antiretroviral therapy (ART)-mediated immune reconstitution, remains unclear. This systematic review aimed to synthesize available evidence on TTV viral load in PLWH, focusing on its relationship with immunological markers. Methods: This systematic review followed the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 guidelines. A comprehensive literature search was conducted in MEDLINE, Web of Science, and Scopus in January 2026 to identify studies assessing plasma TTV viral load before and/or during ART and reporting immunological outcomes. Eligible studies included prospective and retrospective longitudinal studies, cross-sectional studies, and mixed designs assessing plasma TTV viral load in relation to ART status and immune recovery markers. Results: Thirteen studies (n = 1700 PLWH) were included, predominantly observational and conducted in adult populations. Most studies (76.9%) reported a significant inverse association between TTV viral load and CD4 T-cell count, while all studies assessing HIV viral load found a direct correlation with TTV levels. An inverse relationship with the CD4/CD8 ratio was consistently observed where evaluated. Higher TTV loads were reported in ART-naïve individuals and in those with advanced immunosuppression, with longitudinal studies indicating a general decline during ART. Overall, methodological heterogeneity and moderate risk of bias were common. Conclusions: TTV viral load shows a consistent inverse association with CD4 cell count and may reflect global immune dysfunction in PLWH beyond conventional markers. However, its clinical utility remains investigational due to the heterogeneity in the study design, limited data on longitudinal dynamics, and lack of standardized assays and thresholds. Full article

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

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30 pages, 6179 KB

Open AccessArticle

Optimizing Bacteriophage Screening and Isolation Methods for Microbial Samples Derived from Different Body Sites of Cattle

by Gabriela Magossi, Godson Aryee and Samat Amat

Microorganisms 2026, 14(6), 1385; https://doi.org/10.3390/microorganisms14061385 - 22 Jun 2026

Viewed by 487

Abstract

Bacteriophages are increasingly investigated as tools for studying and manipulating microbial communities in cattle. However, phage isolation remains challenging because of host specificity, microbial ecosystem differences, and the lack of optimized screening approaches. The objectives of this study were to (i) optimize the [...] Read more.

Bacteriophages are increasingly investigated as tools for studying and manipulating microbial communities in cattle. However, phage isolation remains challenging because of host specificity, microbial ecosystem differences, and the lack of optimized screening approaches. The objectives of this study were to (i) optimize the phage-screening method for microbial samples obtained from different cattle body sites, (ii) isolate lytic phages against key bovine pathogens and commensal bacteria, and (iii) characterize the isolated phages and their bacterial hosts. A total of 1214 samples from different cattle body sites (n = 1194) and environmental sources (n = 20) were screened using 13 phage detection methods, including one high-throughput approach. Eighty-three phages were isolated, primarily from ruminal fluid (59), feces (15), vaginal (7) and nasopharyngeal swabs (1), and fetal ruminal fluid (1). The bacterial hosts inhibited by these phages were from 29 genera, with Bacillus (34), Escherichia/Shigella (8), Shouchella (5), Corynebacterium (4), and Lysinibacillus (4) being the most common. No phages were identified against bovine pathogens including Trueperella pyogenes, Mannheimia haemolytica, Pasteurella multocida, or Moraxella bovis. Method 12 demonstrated the highest efficiency in phage recovery, particularly from ruminal samples. The successful recovery of bacteriophages from gastrointestinal, reproductive, respiratory, and fetal bovine samples demonstrates the utility of the optimized screening methods for isolating phages from diverse cattle-associated microbial ecosystems. Further studies are needed to refine these approaches to improve the recovery of phages targeting bovine pathogens. Full article

(This article belongs to the Section Environmental Microbiology)

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21 pages, 4893 KB

Open AccessArticle

Enhanced Biphenyl Degradation by Rhodococcus sp. TG-1 Under Cr(VI) Stress via Modified Biochar Immobilization

by Ying Zhai, Lei Huang, Xiuwei Hou, Yuefeng Zou, Xin Zhao and Meitong Li

Microorganisms 2026, 14(6), 1384; https://doi.org/10.3390/microorganisms14061384 - 22 Jun 2026

Viewed by 424

Abstract

Co-contamination of biphenyl and heavy metals is widespread in industrial environments, but systematic studies on the simultaneous treatment of both pollutants using a single microbial strategy remain limited. In this study, we characterized the biphenyl degradation performance, metabolic pathway, transcriptomic response, and Cr(VI) [...] Read more.

Co-contamination of biphenyl and heavy metals is widespread in industrial environments, but systematic studies on the simultaneous treatment of both pollutants using a single microbial strategy remain limited. In this study, we characterized the biphenyl degradation performance, metabolic pathway, transcriptomic response, and Cr(VI) tolerance of Rhodococcus sp. TG-1, and developed an alkali-modified biochar immobilization system to enhance its degradation efficiency for biphenyl under Cr(VI) stress. Degradation experiments were carried out under optimal conditions (30 °C, pH 7.0), and it was found that strain TG-1 degraded 76.84% of 300 mg/L biphenyl within 3 days. Intermediate metabolites were identified by LC-MS, and five key intermediates were detected, confirming that TG-1 metabolizes biphenyl via the classical 2,3-dihydroxybiphenyl dioxygenase pathway, with subsequent entry into the tricarboxylic acid cycle. Transcriptomic analysis was performed to profile gene expression, revealing 845 differentially expressed genes under biphenyl stress, including 672 upregulated genes significantly enriched in aromatic degradation pathways. Seven complete bph gene clusters responsible for biphenyl catabolism were also identified. Strain TG-1 exhibited high tolerance to Cr(VI), with a minimum inhibitory concentration (MIC) of 500 mg/L. However, its biphenyl degradation efficiency dropped to 51.32% in the presence of 200 mg/L Cr(VI). After immobilization using alkali-modified straw biochar (JBC), heavy metal toxicity was alleviated, and the biphenyl removal rate increased to 99.30% under co-contamination conditions. Scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FTIR) analyses confirmed that TG-1 was stably loaded onto the biochar surface through hydrogen bonding and electrostatic interactions. Altogether, this study provides a promising bacterial strain and a green immobilization strategy for enhancing biphenyl removal in the presence of Cr(VI), offering a practical approach for the treatment of environments co-contaminated with aromatic compounds and heavy metals. Full article

(This article belongs to the Section Environmental Microbiology)

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11 pages, 780 KB

Open AccessArticle

In Vitro Detection of Biologically Active Staphylococcal Enterotoxins Type B and C1 as an Alternative to In Vivo Testing

by Reuven Rasooly and Naomi Balaban

Microorganisms 2026, 14(6), 1383; https://doi.org/10.3390/microorganisms14061383 - 22 Jun 2026

Viewed by 398

Abstract

Staphylococcus aureus is a major bacterial pathogen that can cause clinical infections and foodborne illnesses through the production of 25 exotoxin types. The most frequently implicated toxins in food poisoning outbreaks are Staphylococcal enterotoxins type A–E (SEA-SEE), which are the first enterotoxins discovered. [...] Read more.

Staphylococcus aureus is a major bacterial pathogen that can cause clinical infections and foodborne illnesses through the production of 25 exotoxin types. The most frequently implicated toxins in food poisoning outbreaks are Staphylococcal enterotoxins type A–E (SEA-SEE), which are the first enterotoxins discovered. While in vitro detection methods are available to identify the presence of enterotoxins, they cannot distinguish between biologically active and inactive forms of the toxins. Detection of biologically active enterotoxins currently relies on in vivo testing, using the emetic response in kittens or monkeys. Here, we show the development of an in vitro assay to detect the active forms of SEB, a potential biological warfare agent and leading cause of food poisoning, and SEC1, a frequent cause of staphylococcal food poisoning. The novel assay involves the implementation of a genetically engineered Jurkat T-cell line expressing TCR Vβ3, resulting in a dose response of IL-2 production when exposed to active toxin. We also show that at a concentration of 100 ng/mL, the biological activity of SEB is significantly decreased at temperatures over 70 °C, while pasteurization at 63 °C only slightly reduces the biological activity of the toxin. Our studies provide an alternative method to animal testing to determine the presence of active toxins and provide possible inactivation methods of the toxins. Full article

(This article belongs to the Special Issue Emerging Technologies for Pathogen Detection in Agriculture, Medicine, and Food Safety)

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19 pages, 1234 KB

Open AccessArticle

Monitoring Hygiene Protocols and Exploring Alternatives to Counteract Resistant Pathogens: A Case Study from Southern Italy on Healthcare-Associated Infection Control

by Enza Mallardo, Claudio Attilio Baliano, Valeria Pedata, Rosita Zinzi, Federica Mayella, Mauro Murano, Antonio Fascione, Giuseppina Forgione, Daniela Sateriale and Caterina Pagliarulo

Microorganisms 2026, 14(6), 1382; https://doi.org/10.3390/microorganisms14061382 - 22 Jun 2026

Viewed by 377

Abstract

Healthcare-associated infections (HAIs) remain a major public health concern, contributing to increased morbidity, mortality, and antimicrobial resistance. Healthcare workers (HCWs) are recognized as key vehicles in the transmission of nosocomial pathogens, primarily via contaminated hands and medical devices. This study assessed the effectiveness [...] Read more.

Healthcare-associated infections (HAIs) remain a major public health concern, contributing to increased morbidity, mortality, and antimicrobial resistance. Healthcare workers (HCWs) are recognized as key vehicles in the transmission of nosocomial pathogens, primarily via contaminated hands and medical devices. This study assessed the effectiveness of hand hygiene protocols among HCWs, their correlation with bloodstream infections, and the potential of natural antimicrobial agents as complementary preventive measures. Between January and June 2025, 128 hand samples were collected from HCWs in surgical, intensive care, and internal medicine units of hospitals managed by ASL Caserta (Marcianise, n = 65; Piedimonte Matese, n = 30; Sessa Aurunca, n = 18; Maddaloni, n = 15). Sampling was performed upon entry to clinical areas and after antiseptic handwashing, using Rodac TSA plates to quantify microbial load (CFU/cm²). Isolates were identified via MALDI-TOF, and multidrug resistance was confirmed using the Phoenix BD system. Microbial growth was detected in 54.7% of samples. Coagulase-negative staphylococci, mainly Staphylococcus epidermidis and S. hominis, accounted for 67.1% of positive cultures, followed by Enterobacteriaceae (28.6%). Comparison with concurrently collected blood cultures revealed potential overlapping pathogens, with Staphylococcus spp. prevalence ranging from 35 to 56% and Gram-negatives from 18 to 39. Selected isolates were further tested for susceptibility to natural antimicrobial agents, derived from hop, red vine leaf, green tea, and pomegranate fruit, as well as thyme essential oil. Thyme essential oil (Thymus vulgaris) demonstrated notable antimicrobial activity, in several cases surpassing that of standard hygiene agents. These findings highlight not only that maintaining high standards of hand hygiene, proper care of invasive devices, and continuous microbiological surveillance is critical for preventing HAIs, but also that incorporating natural antimicrobial compounds into hygiene protocols may provide an effective and sustainable adjunct to reduce microbial contamination and combat infections caused by multidrug-resistant organisms. Full article

(This article belongs to the Special Issue Antimicrobial Resistance in Italy: Current Situation and New Effective Solutions)

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17 pages, 7822 KB

Open AccessArticle

Characteristics of the Tongue Coating Microbiome and Its Subtype Differences in Patients with Inflammatory Bowel Disease

by Jiaxin Shen, Xing Yu, Jinni Xu, Zhihua Zheng and Weiwei Zheng

Microorganisms 2026, 14(6), 1381; https://doi.org/10.3390/microorganisms14061381 - 22 Jun 2026

Viewed by 501

Abstract

Inflammatory bowel disease (IBD) is associated with microbial dysbiosis, yet subtype-specific alterations in the tongue-coating microbiome remain insufficiently characterized. In this cross-sectional study, tongue-coating samples from 158 participants (94 healthy controls [HC], 19 ulcerative colitis [UC] patients, and 45 Crohn’s disease [CD] patients) [...] Read more.

Inflammatory bowel disease (IBD) is associated with microbial dysbiosis, yet subtype-specific alterations in the tongue-coating microbiome remain insufficiently characterized. In this cross-sectional study, tongue-coating samples from 158 participants (94 healthy controls [HC], 19 ulcerative colitis [UC] patients, and 45 Crohn’s disease [CD] patients) were analyzed by 16S rRNA gene amplicon sequencing. We compared alpha and beta diversity, taxonomic composition, differential taxa, exploratory random-forest feature rankings, and SPIEC-EASI co-occurrence networks. Species richness did not differ significantly among groups, whereas Shannon and Simpson indices were lower in UC than in HC and CD. Bray–Curtis and Jaccard ordinations showed significant but partially overlapping community differences among the three groups. UC was characterized by enrichment of Proteobacteria, Neisseria, and Porphyromonass (p < 0.001), whereas CD showed higher relative abundances of Prevotella, Veillonella, Leptotrichia, and TM7x. Random forest and LEfSe analyses yielded concordant candidate discriminative taxa, but no independent validation cohort was available. Network analysis suggested group-specific co-occurrence patterns, with results interpreted as statistical associations rather than direct microbial interactions. These findings support the presence of subtype-associated tongue-coating dysbiosis in IBD and identify candidate taxa for future validation. Full article

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

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21 pages, 3954 KB

Open AccessArticle

Microbial Necromass and Extracellular Enzyme Activities Are Associated with Depth-Dependent Soil Carbon Stabilization Along a Wildfire-Severity Gradient

by Shaqian Liu and Rui Yang

Microorganisms 2026, 14(6), 1380; https://doi.org/10.3390/microorganisms14061380 - 22 Jun 2026

Viewed by 392

Abstract

Wildfire can alter soil organic carbon (SOC) pools and microbial pathways of carbon stabilization, but depth-dependent links between microbial necromass and stable carbon pools remain unclear. We investigated a wildfire-severity gradient in a subtropical coniferous forest in Guizhou, China, including four severity classes [...] Read more.

Wildfire can alter soil organic carbon (SOC) pools and microbial pathways of carbon stabilization, but depth-dependent links between microbial necromass and stable carbon pools remain unclear. We investigated a wildfire-severity gradient in a subtropical coniferous forest in Guizhou, China, including four severity classes (unburned, light, moderate, and severe) and two soil layers (0–20 and 20–40 cm). We measured easily oxidizable organic carbon (EOC), recalcitrant organic carbon (ROC), SOC, amino sugars, microbial necromass carbon (MNC), extracellular enzyme activities, and carbohydrate-active enzyme (CAZy) functional indices. MNC peaked under moderate wildfire in both layers, increasing by 73.8% and 85.1% in the topsoil and subsoil, respectively, relative to unburned plots. After accounting for soil physicochemical properties and wildfire severity, MNC was more strongly associated with ROC and SOC in the topsoil than in the subsoil. Extracellular enzyme activities were positively associated with amino sugars and necromass pools, whereas CAZy composite indices showed weaker relationships that did not persist after false discovery rate correction. Exploratory path analysis suggested that the EOC–NAG–MNC–ROC–SOC chain was more pronounced in the topsoil, while the subsoil showed weaker chained associations and stronger direct EOC–MNC and EOC–ROC links. Overall, microbial necromass was associated with depth-dependent post-fire carbon stabilization. Full article

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

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18 pages, 4890 KB

Open AccessArticle

Biosurfactants as Stabilizers of Silver Nanoparticles: A Sustainable Approach for Antimicrobial Applications

by Renata R. Silva, Hugo M. Meira, Marcos Antonio B. Lima, Jaciana dos S. Aguiar, Leonie A. Sarubbo and Juliana M. Luna

Microorganisms 2026, 14(6), 1379; https://doi.org/10.3390/microorganisms14061379 - 22 Jun 2026

Viewed by 456

Abstract

Microbial resistance to conventional antimicrobials is a growing public health challenge, driving the search for effective and sustainable alternatives. Among emerging strategies, the combination of silver nanoparticles (AgNPs), recognized for their potent antimicrobial action, with biosurfactants, natural, biodegradable compounds capable of interacting with [...] Read more.

Microbial resistance to conventional antimicrobials is a growing public health challenge, driving the search for effective and sustainable alternatives. Among emerging strategies, the combination of silver nanoparticles (AgNPs), recognized for their potent antimicrobial action, with biosurfactants, natural, biodegradable compounds capable of interacting with microbial cell membranes and promoting their stabilization stands out. In this context, the aim of this study was to produce a biosurfactant by Candida glabrata UCP 1002 from agroindustrial residues, reducing costs and environmental impacts. The compound exhibited a surface tension of 29 mN/m, a critical micellar concentration of 0.3%, and a yield of 9 g/L; furthermore, it demonstrated stability across wide ranges of temperature, pH, and salinity. The AgNPs were synthesized using the biosurfactant as a stabilizing agent and ascorbic acid as a reducing agent, resulting in stable particles. In antimicrobial assays, the formulation inhibited Gram-positive microorganisms, Gram-negative microorganisms, and fungi. The best results were obtained against Pseudomonas aeruginosa (26.63%) and Candida albicans (28.11%), followed by Staphylococcus aureus (17.58%), Enterobacter sp. (14.42%), and Escherichia coli (13.68%). Although less effective than commercial antibiotics such as streptomycin and moxifloxacin, it showed potential as a complementary alternative in combating multidrug-resistant pathogens. Cytotoxicity assays revealed low toxicity toward normal cells (28.42% inhibition in Vero CCL-81) and minimal activity against tumor cells. The results demonstrate that the BS-AgNPs association combines relevant antimicrobial activity with environmental safety and biocompatibility, establishing itself as a promising and sustainable approach for application in health, industry, and the environment, with potential for scale-up production from low-cost raw materials. Full article

(This article belongs to the Special Issue Antimicrobial Ability of Natural Products)

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34 pages, 2207 KB

Open AccessReview

Beyond Taxonomy: A Matrix–Trait–Function Framework for Predictive Selection of Non-Saccharomyces Yeasts in Food Fermentation

by Nora Haring, Milan Chňapek and Blažena Drábová

Microorganisms 2026, 14(6), 1378; https://doi.org/10.3390/microorganisms14061378 - 22 Jun 2026

Viewed by 563

Abstract

The growing diversity of food fermentation systems has intensified interest in non-Saccharomyces yeasts due to their broad metabolic capabilities and technological potential. However, current understanding of yeast functionality remains fragmented and frequently relies on taxonomy-centered classification, which often provides limited predictive value [...] Read more.

The growing diversity of food fermentation systems has intensified interest in non-Saccharomyces yeasts due to their broad metabolic capabilities and technological potential. However, current understanding of yeast functionality remains fragmented and frequently relies on taxonomy-centered classification, which often provides limited predictive value across fermentation systems. This review critically examines how strain-specific microbial traits, food matrix composition, and process conditions collectively shape fermentation performance across brewing, wine, cereal, plant-based, and functional fermentation systems. Particular emphasis is placed on key determinants of microbial functionality, including carbon metabolism, aroma biogenesis, acidification, enzymatic activity, microbial interactions, and transformation of food-associated bioactive compounds such as glycosides, phenolics, terpenes, and matrix-bound metabolites. The available evidence demonstrates that fermentation-relevant functionality cannot be reliably inferred from species identity alone because microbial performance is strongly modulated by strain variability and matrix-dependent environmental constraints. To address these limitations, this review proposes a matrix–trait–function framework that integrates microbial metabolic capabilities with food matrix characteristics and technological objectives to support a more predictive and application-oriented approach to yeast selection in food fermentation systems. Full article

(This article belongs to the Special Issue Diversity and Applications of Yeasts: Food, Plant and Human Health)

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13 pages, 4558 KB

Open AccessArticle

Inhibitors of the Machupo Virus L Endonuclease for Bolivian Hemorrhagic Fever Treatments

by Oluwafoyinsola O. Faniyi, Kristin V. Lyles, Neva Agarwala, Haozhe Cheng, Elise Copeland, Teri Tran, Shuyue Yang, Bingchen Yu, Binghe Wang, Xiaoxiao Yang and Ming Luo

Microorganisms 2026, 14(6), 1377; https://doi.org/10.3390/microorganisms14061377 - 22 Jun 2026

Viewed by 922

Abstract

Machupo virus (MACV) is the causal agent of Bolivian Hemorrhagic fever. It is highly pathogenic, has a high mortality rate, and currently lacks specific treatments or vaccines. MACV belongs to the Arenaviridae family, which uses a cap-snatching mechanism during the transcription process. Its [...] Read more.

Machupo virus (MACV) is the causal agent of Bolivian Hemorrhagic fever. It is highly pathogenic, has a high mortality rate, and currently lacks specific treatments or vaccines. MACV belongs to the Arenaviridae family, which uses a cap-snatching mechanism during the transcription process. Its viral polymerase, the L protein, harbors the endonuclease activity required for cap snatching, making it a suitable target for the development of antiviral therapeutics. We combined experimental and computational methods to characterize MACV endonuclease activity and evaluate inhibitors. A fluorescence resonance energy transfer (FRET) assay was used to measure the enzymatic activity of endonuclease and identify potent inhibitors via high-throughput screening. FRET assays identified BW-148, an inhibitor with a 48.4 µM (95% CI: 37.3–59.3 µM; R² = 0.98) IC₅₀, and a K_D of 13.7 µM (95% CI: 8.2–19.2 µM, n = 3). Docking studies reveal that BW-148 may bind near the MACV endonuclease catalytic site, inhibiting enzymatic activities by metal chelating. BW-148 is a useful lead compound for further optimization of Machupo endonuclease inhibitors. Full article

(This article belongs to the Special Issue Advances in Arenaviruses Research)

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34 pages, 4538 KB

Open AccessArticle

Molecular Characterization of Plant Growth-Promoting Bacteria Associated with Opuntia dillenii (Ker Gawl.) Haw (Cactaceae) in the Coastal Zone of Benin

by Yves Kévin Brun, Agossou Damien Pacôme Noumavo, Julien Colombet, Etienne Bankolé Atchadé, Lamine Baba-Moussa and François Lefort

Microorganisms 2026, 14(6), 1376; https://doi.org/10.3390/microorganisms14061376 - 21 Jun 2026

Cited by 1 | Viewed by 662

Abstract

Cacti thrive in arid and coastal environments partly through associations with beneficial endophytic and rhizosphere bacteria; however, current knowledge remains limited. This study aimed to assess the diversity of cultivable bacteria associated with Opuntia dillenii and evaluate their potential as Plant Growth-Promoting (PGP) [...] Read more.

Cacti thrive in arid and coastal environments partly through associations with beneficial endophytic and rhizosphere bacteria; however, current knowledge remains limited. This study aimed to assess the diversity of cultivable bacteria associated with Opuntia dillenii and evaluate their potential as Plant Growth-Promoting (PGP) agents. Endophytic bacteria were isolated from cladodes and roots, while rhizobacteria were recovered from rhizosphere soil. Bacterial isolates were identified using morphological characteristics and 16S rRNA/gyrB sequencing, followed by screening for PGP traits, pH and temperature tolerance. A total of 31 isolates were obtained, including 23 endophytes and 8 rhizobacteria, mainly affiliated with Firmicutes, Actinobacteria, and Proteobacteria. Bacillus (35.48%) and Priestia (32.25%) predominated, with Priestia flexa as the most prevalent species. The most frequent PGP traits were phosphate solubilization (80.65%), proteolytic activity (70.97%), siderophore production (67.74%), and nitrogenase activity (64.52%). The highest phosphate solubilization indices were observed for strain R3 (3.41), R6 (3.39) and S6 (3.21), whilst the highest indole-3-acetic acid yields were recorded for C9 (172.88 µg/mL), R11 (96.22 µg/mL) and C3 (90.94 µg/mL), and the strongest siderophore production for C3 (30.37 mm), C7 (27.96 mm) and S7 (27.88 mm). These findings highlight O. dillenii-associated coastal bacteria as promising resources for plant growth and plant stress resilience. Full article

(This article belongs to the Special Issue Advances in the Plant Microbiome: Rhizosphere, Endosphere and Phyllosphere, Second Edition)

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18 pages, 11246 KB

Open AccessArticle

Chlorogenic Acid Ameliorates CVB3-Induced Viral Myocarditis by Suppressing Viral Replication and ZBP1-Mediated PANoptosis

by Junbo Huang, Qing Song, Yanjun Di, Hao Wu, Zhiyun Cheng, Haoyi Zhan, Kaiyuan Huang, Yachen Wang, Lijuan Xie, Jieqing Liu and Lei Tong

Microorganisms 2026, 14(6), 1375; https://doi.org/10.3390/microorganisms14061375 - 21 Jun 2026

Viewed by 481

Abstract

Viral myocarditis (VMC), predominantly driven by Coxsackievirus B3 (CVB3) infection and the resultant excessive immune response, lacks effective treatments and specific antiviral drugs in clinical practice. Chlorogenic acid (CGA) has been proven to have significant antiviral and anti-inflammatory properties. This study evaluated the [...] Read more.

Viral myocarditis (VMC), predominantly driven by Coxsackievirus B3 (CVB3) infection and the resultant excessive immune response, lacks effective treatments and specific antiviral drugs in clinical practice. Chlorogenic acid (CGA) has been proven to have significant antiviral and anti-inflammatory properties. This study evaluated the potential and mechanism of action of CGA against CVB3-induced viral myocarditis. Our research results showed that CGA significantly alleviated myocardial tissue damage in vivo. This protective effect was accompanied by effective inhibition of myocardial inflammatory responses and viral replication. Further in vitro experiments confirmed that CGA significantly inhibited the replication of CVB3 in a dose-dependent manner, and its inhibitory effect mainly targeted the replication stage of the viral life cycle. Mechanistically, CGA treatment correlates with reduced ZBP1 expression and accelerated ZBP1 degradation involving the ubiquitin–proteasome pathway, accompanied by suppressed activation of PANoptosis markers. These findings suggest that CGA alleviates CVB3-induced myocarditis through concerted antiviral and anti-inflammatory effects, with ZBP1-mediated PANoptosis as a potential contributing mechanism. Full article

(This article belongs to the Special Issue Viral Infection and Antiviral Drug Development)

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17 pages, 5662 KB

Open AccessArticle

Characterization of Nasopharyngeal Microbiota Dysbiosis in Children with Mycoplasma pneumoniae Pneumonia

by Jing Bi, Bo Yu, Yang Zhang, Guotong Zheng, Yiyuan Han, Yangyan Yan, Wen Wang, Lei Wu, Yingshuo Wang and Zhengkai Yi

Microorganisms 2026, 14(6), 1374; https://doi.org/10.3390/microorganisms14061374 - 21 Jun 2026

Viewed by 413

Abstract

Mycoplasma pneumoniae pneumonia (MPP) is a leading cause of community-acquired pneumonia in children, yet little is known about the role of nasopharyngeal microbiota dysbiosis in susceptibility to infection and disease subtype. In this study, we performed 16S rRNA sequencing on nasopharyngeal samples from [...] Read more.

Mycoplasma pneumoniae pneumonia (MPP) is a leading cause of community-acquired pneumonia in children, yet little is known about the role of nasopharyngeal microbiota dysbiosis in susceptibility to infection and disease subtype. In this study, we performed 16S rRNA sequencing on nasopharyngeal samples from 102 pediatric MPP patients, 104 influenza A patients, and 103 healthy controls and compared the microbial diversity, composition, and functional profiles across groups. The MPP group exhibits an altered nasopharyngeal microbial composition, characterized by reduced microbial diversity and an increased relative abundance of genera including Mycoplasma, Pseudomonas, Acinetobacter, and Tannerella. Distinct microbiota profiles were identified for the MPP subtypes, with Mycoplasma more abundant in bronchopneumonia (BP) than in lobar pneumonia (LP). A microbial classifier based on the relative abundance of the nasopharyngeal microbiota was established to distinguish MPP patients from both influenza patients and healthy controls, with an area under the receiver operating characteristic curves of 0.978. Key microbial features associated with MPP included Mycoplasma, Mycobacterium, Aeromonas, and Acinetobacter. In addition, PICRUSt2-based functional predictions suggested alterations in amino acid metabolism and predicted functional pathways associated with bacterial infection and antimicrobial resistance in MPP patients. In conclusion, this study provides comprehensive insights into alterations in the nasopharyngeal microbiota in pediatric MPP. These findings highlight the potential role of dysbiosis in disease progression and suggest that changes in microbiota composition and functional profiles are associated with MPP infection. Full article

(This article belongs to the Special Issue Human Airway Microbiome and Immunity)

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21 pages, 8642 KB

Open AccessArticle

Enhancing Phosphorus Availability Through Bagasse Biochar Addition and Changes in phoD Bacterial Communities of Karst and Non-Karst Forest Soils

by Yanjun Chen, Xinyu He, Yueming Liang, Fujing Pan, Cheng Zeng, Haijun Tan, Qiang Li and Zeyan Wu

Microorganisms 2026, 14(6), 1373; https://doi.org/10.3390/microorganisms14061373 - 21 Jun 2026

Viewed by 397

Abstract

Biochar can enhance microbial-mediated organic phosphorus mineralization, but the underlying mechanisms remain unknown in forest soils with varying pH values. An incubation experiment was conducted using karst (alkaline) and non-karst (acidic) forest soils. Four amounts of bagasse biochar were applied (0, 5, 10, [...] Read more.

Biochar can enhance microbial-mediated organic phosphorus mineralization, but the underlying mechanisms remain unknown in forest soils with varying pH values. An incubation experiment was conducted using karst (alkaline) and non-karst (acidic) forest soils. Four amounts of bagasse biochar were applied (0, 5, 10, and 15 t·hm⁻²) to assess their effects on soil phosphorus availability and microbial community structure. Olsen-P content of alkaline and acidic forest soils increased with increasing bagasse biochar addition and incubation time, especially in non-karst forest soil. The structure and diversity of phoD-harboring bacterial community of acidic forest soil were significantly altered by the amount of bagasse biochar added and the incubation time, whereas those in alkaline karst forest soil were not significantly affected. The relative abundance of the dominant order Burkholderiales reached (43%) in acidic forest soil, significantly exceeding the (9%) recorded in alkaline karst forest soil. The phoD bacteria in acidic forest soil had more complex microbial networks and were more closely related to phosphorus fractions than those in alkaline forest soil. Structural equation modeling indicated that soil phosphorus availability was directly controlled by bagasse biochar input in acidic forest soil, with an indirect pathway linked to phoD bacterial community structure. The contribution of phoD bacteria to the variation in phosphorus availability was higher in acidic forest soil than in alkaline forest soil based on variance partitioning, indicating that enhancing soil phosphorus availability with bagasse biochar depends on the amount added, soil type, and its regulation of phoD bacterial communities. Full article

(This article belongs to the Special Issue Soil Microbial Carbon/Nitrogen/Phosphorus Cycling: 2nd Edition)

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29 pages, 5867 KB

Open AccessArticle

Municipal Solid Waste (MSW)-Compost Amendment Increases Diversity, Functional Activities, and Network Connectivity of a Vineyard Soil Microbiota

by Massimiliano Cardinale, Fabio Minervini, Francesco Maria Calabrese, Margherita Chiarini, Matteo Bernardi, Maria Calasso, Mohammad Yaghoubi Khanghahi, Piergiorgio Romano, Gianni Zorzi, Maria De Angelis and Laura Rustioni

Microorganisms 2026, 14(6), 1372; https://doi.org/10.3390/microorganisms14061372 - 21 Jun 2026

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Abstract

Sustainable agriculture increasingly relies on organic amendments that integrate circular economy principles. Municipal Solid Waste (MSW)-derived compost (MSW-compost) represents a promising candidate as soil amendment in viticulture, yet its impact on soil microbiota remains poorly investigated. This study assessed the effects of MSW-compost [...] Read more.

Sustainable agriculture increasingly relies on organic amendments that integrate circular economy principles. Municipal Solid Waste (MSW)-derived compost (MSW-compost) represents a promising candidate as soil amendment in viticulture, yet its impact on soil microbiota remains poorly investigated. This study assessed the effects of MSW-compost application on the bacterial microbiota of a Mediterranean vineyard soil over a twelve-month period, comparing two application methods (surface mulching and tillage incorporation). Soil DNA was analyzed by 16S rRNA gene metabarcoding, complemented by functional prediction (Picrust2) and the Tea Bag Index to assess soil decomposition activity. MSW-compost significantly increased alpha-diversity and affected beta-diversity (p = 0.001) of the microbiota, regardless of the application method, with significant effects persisting throughout the entire observation period despite a clearly diminishing trend. Devosia emerged as the hub taxon of the co-occurrence network and was increased by compost addition. MSW-compost application mode remarkably affected the microbial network, with mulched treatment leading to a more complex, denser, and more interconnected network. While a similar number of taxa were increased or decreased, functional prediction revealed a notable enrichment of metabolic pathways, both synthetic and degradative, in the MSW-compost amended samples; this finding was supported by the enhanced red tea decomposition data (p = 0.007). Our results indicate that MSW-compost acts as a beneficial soil amendment, simultaneously enhancing microbial diversity and soil decomposition activity. This study provides novel evidence supporting the use of MSW-compost as a sustainable tool for improving soil microbiological quality in productive vineyards. Full article

(This article belongs to the Topic Recent Advances in Soil Health Management)

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21 pages, 9316 KB

Open AccessArticle

Understanding Repression Under Secretion Stress in Trichoderma reesei During Cellulase Expression

by Reshma Jadhav, Güler Demirbas Uzel, Julien Charest, Igor Nikolaev, Sharief Barends, Robert Ludwig Mach and Astrid Rosa Mach-Aigner

Microorganisms 2026, 14(6), 1371; https://doi.org/10.3390/microorganisms14061371 - 21 Jun 2026

Viewed by 511

Abstract

The filamentous fungus Trichoderma reesei is one of the most important workhorses for industrial enzyme production, but the cellular mechanisms that balance protein folding stress with secretion, such as the unfolded protein response (UPR) and repression under secretion stress (RESS), are still not [...] Read more.

The filamentous fungus Trichoderma reesei is one of the most important workhorses for industrial enzyme production, but the cellular mechanisms that balance protein folding stress with secretion, such as the unfolded protein response (UPR) and repression under secretion stress (RESS), are still not fully understood. In this study, we set out to clarify how these pathways contribute to secretion in both laboratory settings and industrial-scale fermentations. Exposure to the reductive agent dithiothreitol for 5 h increased transcript levels of UPR-related genes at least 6-fold, and, simultaneously, transcript levels of target genes cbh1 and egl2 were reduced at least 5- or 6-fold, respectively. Interestingly, RESS was detected even when UPR was suppressed by the prevention of protein de novo synthesis, pointing to a non-hierarchical relation of the two mechanisms. With the aim to understand on which levels RESS is acting, in particular, whether it is transcription initiation or transcript stability, an experiment involving blocking the transcription was performed. Further, a recombinant strain with an exchanged promoter had an at least 45-fold-increased cbh1 transcript level, while a terminator exchange did not increase chb1 transcript levels, indicating that RESS operates mainly at the level of transcription initiation. Importantly, whole transcriptome data from industrial cellulase production did not reveal the signatures of UPR or RESS despite the heavy secretory load. Instead, expression profiles highlighted the induction of diverse hydrolytic enzymes and pathway adjustments that support efficient production. Full article

(This article belongs to the Section Microbial Biotechnology)

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18 pages, 4918 KB

Open AccessArticle

Fecal Microbiota Transplantation Improves Biota and Hepatic Metabolism, Promoting Growth in SD Rats Under Hypobaric Hypoxia Exposure

by Shuting Bao, Shengchun Xu, Zhilong Wang, Shatuo Chai, Shuxiang Wang, Dongwen Dai, Xun Wang and Jiaying Lv

Microorganisms 2026, 14(6), 1370; https://doi.org/10.3390/microorganisms14061370 - 20 Jun 2026

Viewed by 464

Abstract

Hypobaric hypoxia poses a serious threat to growth and development and can induce pronounced inflammatory responses. These effects are closely associated with the gut microbiota. However, the underlying mechanisms, particularly the role of gut microbiota in regulating hepatic metabolism under chronic hypoxic conditions, [...] Read more.

Hypobaric hypoxia poses a serious threat to growth and development and can induce pronounced inflammatory responses. These effects are closely associated with the gut microbiota. However, the underlying mechanisms, particularly the role of gut microbiota in regulating hepatic metabolism under chronic hypoxic conditions, remain poorly understood. In this study, SD rats were used as recipients and assigned to three groups: a hypobaric hypoxia group (H), an antibiotic-treated group (HA), and an antibiotic-treated group receiving fecal microbiota transplantation from plateau zokors (HAM). All rats were maintained in a hypobaric hypoxia chamber simulating an altitude of 6000 m for 30 days. Subsequently, growth performance, routine hematological parameters, and multi-omics profiles were evaluated. Compared with the H group, both the HAM and HA groups showed significantly increased average daily gain (ADG) (p < 0.05), while the ADG/ADFI ratio was significantly higher in the HAM group than in the H group (p < 0.05). Monocyte count (Mon#) and monocyte percentage (Mon%) were significantly higher in the HA group than in both the H and HAM groups (p < 0.05). Microbiota analysis revealed significant enrichment of Lachnospiraceae_NK4A136_group in the HAM group, whereas Desulfovibrio was significantly enriched in the HA group (p < 0.05). Fecal metabolomics showed that ursodeoxycholic acid (UDCA) was significantly increased in the HAM group (p < 0.05). In the liver metabolome, the anti-inflammatory lipid FAHFA 18:1/20:3 was significantly elevated in the HAM group, whereas pro-inflammatory factors, including uric acid and leukotriene D4, were significantly reduced (p < 0.05). Correlation analysis further demonstrated that the abundance of Lachnospiraceae was positively correlated with FAHFA 18:1/20:3 and negatively correlated with uric acid and creatinine (p < 0.05). Collectively, these findings indicate that the gut microbiota can modulate gut–liver metabolism, alleviate inflammatory responses, and enhance the adaptation of rats to hypoxic environments. This study provides valuable insights into potential strategies for promoting sustainable animal health and adaptation under hypoxic conditions. Full article

(This article belongs to the Section Gut Microbiota)

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17 pages, 5869 KB

Open AccessArticle

Variation in Soil Microbial Communities Across Plantation Types in the Yellow River Floodplain of Western Shandong, China

by Ke Xie, Tianxu Sun, Yongjie Miu, Ying Li, Yue Xu, Yun Cheng and Xinghui Lu

Microorganisms 2026, 14(6), 1369; https://doi.org/10.3390/microorganisms14061369 - 20 Jun 2026

Viewed by 356

Abstract

The Yellow River floodplain relies on plantations for ecological restoration, yet the key factors influencing soil microbial communities remain poorly elucidated. In this study, we investigated soil microbial communities under four representative stand types (Populus tomentosa monoculture (PP), Salix matsudana monoculture (PS), [...] Read more.

The Yellow River floodplain relies on plantations for ecological restoration, yet the key factors influencing soil microbial communities remain poorly elucidated. In this study, we investigated soil microbial communities under four representative stand types (Populus tomentosa monoculture (PP), Salix matsudana monoculture (PS), Populus tomentosa-Robinia pseudoacacia mixed plantation (MPR), and Salix matsudana-Populus tomentosa mixed plantation (MSP)) in this region. Using high-throughput sequencing, we compared the soil microbial community composition and diversity across stands, and combined soil physicochemical measurements to evaluate the relationships between community variation and soil factors. The results indicated that soil physicochemical properties differed significantly among stand types, except for available phosphorus. Bacterial α-diversity was highest in MPR, whereas fungal α-diversity was highest in MSP. Variation in microbial community structure (β-diversity) was primarily explained by soil organic carbon, total nitrogen, pH, water content, and electrical conductivity, as indicated by redundancy analysis and Mantel tests. The dominant bacterial phyla were Acidobacteriota, Pseudomonadota (formerly Proteobacteria), and Actinomycetota, while the dominant fungal phyla were Ascomycota, Basidiomycota, and Mortierellomycota. These findings demonstrate significant variation in soil microbial communities among plantation types and highlight the important role of soil physicochemical properties in shaping microbial community composition. Full article

(This article belongs to the Section Environmental Microbiology)

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3 pages, 161 KB

Open AccessEditorial

Editorial for the Special Issue “Advances in Metabolic Engineering of Industrial Microorganisms”

by Shuobo Shi

Microorganisms 2026, 14(6), 1368; https://doi.org/10.3390/microorganisms14061368 - 20 Jun 2026

Viewed by 444

Abstract

The past decade has witnessed transformative progress in metabolic engineering, driven by the convergence of synthetic biology, CRISPR-based genome editing, systems biology, and high-throughput omics technologies [...] Full article

(This article belongs to the Special Issue Advances in Metabolic Engineering of Industrial Microorganisms)

27 pages, 2415 KB

Open AccessArticle

Dietary Sporolactobacillus laevolacticus Improves Growth Performance, Intestinal Health, and Immune-Antioxidant Related Responses in Juvenile Coho Salmon (Oncorhynchus kisutch)

by Qin Zhang, Lan Li, Xin Guo, Yuping Xia, Shanping Xiong, Xinjing Wei, Rongkai Zhu, Weiguang Kong, Yongqiang Liu and Tong Tong

Microorganisms 2026, 14(6), 1367; https://doi.org/10.3390/microorganisms14061367 - 20 Jun 2026

Viewed by 516

Abstract

Probiotics are considered promising feed additives for enhancing fish health and production performance in aquaculture. This study evaluated the effects of dietary supplementation with Sporolactobacillus laevolacticus on growth performance, feed utilization, intestinal health, and physiological responses in juvenile coho salmon (Oncorhynchus kisutch [...] Read more.

Probiotics are considered promising feed additives for enhancing fish health and production performance in aquaculture. This study evaluated the effects of dietary supplementation with Sporolactobacillus laevolacticus on growth performance, feed utilization, intestinal health, and physiological responses in juvenile coho salmon (Oncorhynchus kisutch). Fish were fed a control diet or diets supplemented with S. laevolacticus at 0.89 × 10⁷, 0.90 × 10⁹, or 0.87 × 10¹¹ CFU/g for 10 weeks. Compared with the control, S. laevolacticus supplementation significantly increased final body weight, weight gain rate, specific growth rate, and protein efficiency ratio, while decreasing the feed conversion ratio (p < 0.05). It also significantly enhanced intestinal protease and α-amylase activities, improved serum biochemical and immune-related parameters, and promoted better intestinal morphology (p < 0.05). Additionally, S. laevolacticus supplementation led to elevated expression of antioxidant-related genes, reduced expression of pro-inflammatory genes, and altered gut microbial composition, characterized by a decrease in Proteobacteria and increases in Firmicutes and Lactobacillales. Among the tested dosages, 0.90 × 10⁹ CFU/g produced the most consistent improvements in growth performance, digestive function, intestinal health, antioxidant and immune responses, and gut microbial composition, and was therefore identified as the optimal supplementation level. Collectively, dietary S. laevolacticus at 0.90 × 10⁹ CFU/g improved growth performance and intestinal health in juvenile coho salmon, highlighting its potential as a probiotic candidate for coho salmon aquaculture. Full article

(This article belongs to the Special Issue Microbiome in Fish and Their Living Environment, Second Edition)

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19 pages, 2618 KB

Open AccessReview

The Gut–Brain–Muscle Axis: Microbial Regulation of Neuromuscular Aging and Cognitive Frailty

by Nurpudji Astuti Taslim, Jeremy Nicolas Sibarani, Ricky Indra Alfaray, Nelly Mayulu, Arifa Mustika, Dian Aruni Kumalawati, Happy Kurnia Permatasari, Raymond Rubianto Tjandrawinata and Fahrul Nurkolis

Microorganisms 2026, 14(6), 1366; https://doi.org/10.3390/microorganisms14061366 - 19 Jun 2026

Viewed by 2136

Abstract

Cognitive frailty, characterized by the coexistence of physical frailty and cognitive impairment, has emerged as a major challenge in aging populations and is closely linked to sarcopenia, neurodegeneration, and chronic inflammation. Increasing evidence suggests that the gut microbiota acts as a central regulator [...] Read more.

Cognitive frailty, characterized by the coexistence of physical frailty and cognitive impairment, has emerged as a major challenge in aging populations and is closely linked to sarcopenia, neurodegeneration, and chronic inflammation. Increasing evidence suggests that the gut microbiota acts as a central regulator of neuromuscular and neurocognitive aging through the integrated gut–brain–muscle axis. This review highlights how microbial dysbiosis, reduced short-chain fatty acid (SCFA) production, systemic endotoxemia, and altered microbial metabolites contribute to mitochondrial dysfunction, neuroinflammation, anabolic resistance, and impaired neuroplasticity. Key signaling mediators, including SCFAs, bile acids, tryptophan-derived metabolites, cytokines, and myokines such as irisin, brain-derived neurotrophic factor (BDNF), and cathepsin B, orchestrate bidirectional communication among the gut, skeletal muscle, and brain. We further discuss the role of exercise-induced microbiota remodeling and muscle endocrine signaling in promoting mitochondrial biogenesis and cognitive resilience. In addition, emerging translational strategies including probiotics, prebiotics, postbiotics, polyphenol-rich functional foods, marine bioactives, and precision nutrition are explored as potential interventions targeting this axis. Collectively, the gut–brain–muscle axis provides a novel systems biology framework for understanding cognitive frailty and developing integrated therapeutic strategies for healthy longevity. Full article

(This article belongs to the Special Issue Probiotics and Gut Microbiome Dynamics in Health and Disease)

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21 pages, 647 KB

Open AccessReview

Clinical Significance of Intestinal Fungal Overgrowth: Integrating the Gut Mycobiome into Modern Gastroenterology

by Jisoon Im, Kyucheol Lee, Sang-Hoon Lee, Soohwan Jung, Kyu-Nam Kim and Jiyoung Lee

Microorganisms 2026, 14(6), 1365; https://doi.org/10.3390/microorganisms14061365 - 19 Jun 2026

Viewed by 1854

Abstract

Intestinal fungal overgrowth (IFO) is an increasingly recognized yet underexplored component of gut dysbiosis with potential implications for gastrointestinal and systemic disease. While bacterial microbiota have historically garnered research attention, recent advances in sequencing technologies have highlighted the importance of the gut mycobiome [...] Read more.

Intestinal fungal overgrowth (IFO) is an increasingly recognized yet underexplored component of gut dysbiosis with potential implications for gastrointestinal and systemic disease. While bacterial microbiota have historically garnered research attention, recent advances in sequencing technologies have highlighted the importance of the gut mycobiome in maintaining intestinal homeostasis. Disruption of fungal–bacterial balance, particularly involving Candida albicans, C. tropicalis, and C. glabrata, may contribute to symptom generation through immune activation, epithelial barrier dysfunction, biofilm formation, and the production of toxic metabolites such as acetaldehyde and candidalysin. Emerging clinical evidence suggests that IFO is associated with persistent gastrointestinal symptoms, including bloating, abdominal discomfort, and altered bowel habits, particularly in patients who do not respond to conventional therapies targeting bacterial overgrowth. Furthermore, fungal dysbiosis involving Malassezia restricta and Saccharomyces cerevisiae has been associated with inflammatory bowel disease, metabolic disorders, and systemic immune dysregulation; however, the nature and directionality of these relationships remain incompletely understood. Despite increasing recognition, the diagnosis of IFO remains challenging due to a lack of standardized criteria and validated non-invasive tools. Therapeutic strategies, including antifungal agents such as fluconazole and nystatin, as well as microbiome-targeted interventions, show promise but require further validation. This review provides a comprehensive synthesis of current evidence regarding the epidemiology, pathophysiology, clinical manifestations, diagnostic challenges, and therapeutic implications of IFO, with particular emphasis on species-specific mechanisms. Recognition of the intestinal mycobiome as a potentially important component of gut health may provide new perspectives for understanding gastrointestinal disorders and inform future precision medicine approaches. Full article

(This article belongs to the Special Issue Gut Microbiota and Diseases)

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25 pages, 3010 KB

Open AccessSystematic Review

Leptospira santarosai: A Systematic Review on Its Serological Diversity, Geographical Distribution, Natural Sources of Infection, and Human Leptospirosis

by Ronald Guillermo Peláez Sánchez, Jorge Emilio Salazar Flórez, Luz Estella Giraldo Cardona, Lina Paola Cifuentes, Daniela Sánchez Mejía, Santiago Pineda, Mariana Ossa-Yepes, Marco Torres-Castro, Alejandro Suarez-Galaz, Rodrigo Urrego, Luis Ernesto López-Rojas, Sergio Agudelo-Pérez and Fernando P. Monroy

Microorganisms 2026, 14(6), 1364; https://doi.org/10.3390/microorganisms14061364 - 18 Jun 2026

Cited by 1 | Viewed by 669

Abstract

Leptospirosis is a globally distributed zoonotic disease caused by pathogenic bacteria of the Leptospira genus. Currently, 77 genomic species have been described. Leptospira interrogans is the most extensively studied species due to its high prevalence worldwide and the severity of the disease it [...] Read more.

Leptospirosis is a globally distributed zoonotic disease caused by pathogenic bacteria of the Leptospira genus. Currently, 77 genomic species have been described. Leptospira interrogans is the most extensively studied species due to its high prevalence worldwide and the severity of the disease it causes in humans and animals. However, Leptospira santarosai is an important pathogenic species in the Americas, the Caribbean islands, and Taiwan. This species has a high serological diversity: it can infect domestic, wild, and agricultural production animals, causing reproductive problems and substantial economic losses. Additionally, Leptospira santarosai has been detected in water sources and wet soils. In humans, infection with this species can lead to a wide range of clinical manifestations and severe complications. Therefore, this study aimed to synthesize available information on the serological diversity, geographical distribution, natural sources of infection, and human leptospirosis caused by Leptospira santarosai to better understand their role in the leptospirosis transmission cycle. Methods: A systematic review of the literature was conducted, following the criteria established by the PRISMA-2020 guide, the search for scientific articles was conducted in five specialized and multidisciplinary databases (PubMed, Scopus, Web of Science, SciELO, and LILACS), and a search engine (Google Scholar). Two different search strategies (Leptospira santarosai OR L. santarosai) were used. Result: Once the search was carried out in the databases, 2989 scientific articles were identified. These articles underwent a process of identification, screening, eligibility, and inclusion, resulting in 84 articles that met all established inclusion criteria. These articles were included in the qualitative synthesis and elaboration of the systematic review. Conclusions: Leptospira santarosai shows a high serological diversity, with 14 serogroups and 59 serovars. The species has a wide geographic distribution, having been reported on five continents and in 26 countries, and has been described as an infectious agent in at least 24 host animals. It has also been detected in environmental sources such as water and wet soils; 24 serovars have been identified as the causative agents of human leptospirosis, causing clinical manifestations that range from mild to severe forms of the disease and clinical complications such as myocarditis, uveitis, and neuroleptospirosis. Although L. santarosai is considered native to the Americas, it shows an expansion pattern to other continents and countries. Therefore, this pathogenic species of the Leptospira genus represents an important public health problem worldwide. Full article

(This article belongs to the Section Medical Microbiology)

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25 pages, 8457 KB

Open AccessArticle

Coupled Hydrological and Biogeochemical Forcings Structure Phytoplankton Community Assembly in a Eutrophic Estuary

by Liang-Gen Wang, Peng-Bing Pei, Tang-Cheng Li, Xiu-Li Yan, Fei-Yan Du and Hong Du

Microorganisms 2026, 14(6), 1363; https://doi.org/10.3390/microorganisms14061363 - 18 Jun 2026

Viewed by 463

Abstract

The seasonal monsoon reversal drives runoff and current variability along the East Asian coast, intensifying eutrophication from terrestrial nutrients. However, phytoplankton responses to these combined pressures remain poorly understood. This study analyzed their effects using partial least-squares path modeling (PLS-PM) and generalized additive [...] Read more.

The seasonal monsoon reversal drives runoff and current variability along the East Asian coast, intensifying eutrophication from terrestrial nutrients. However, phytoplankton responses to these combined pressures remain poorly understood. This study analyzed their effects using partial least-squares path modeling (PLS-PM) and generalized additive models (GAMs), based on 2021 data from Shantou Bay in the Taiwan Strait, a region with complex currents and significant nutrient inputs. A total of 359 phytoplankton species were identified, with seasonal mean abundances ranging from 6.76 × 10⁶ to 57.36 × 10⁶ cells m⁻³. Ocean currents and riverine runoff drive the seasonal turnover of dominant species by modulating the temperature and salinity. In summer, the exceptionally high phytoplankton abundance in the southwestern Taiwan Strait is driven by nutrient-rich terrestrial inputs, upwelling-induced thermal inhibition, and thermocline stratification from upwelling and offshore warm waters. The phytoplankton abundance and distribution were strongly correlated with the seasonal current and runoff-driven water masses. The PLS-PM results confirm that phytoplankton dynamics are regulated by currents and terrestrial nutrient inputs altering the hydrological and chemical environments, highlighting temperature and salinity as dominant controlling factors in eutrophic coastal zones. Full article

(This article belongs to the Special Issue Microbial Responses and Adaptations to Environmental Changes)

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17 pages, 1169 KB

Open AccessReview

Bacterial Extracellular Vesicles in the Strategic Interplay Between Pathogens and Hosts

by Jiahui Liang, Mi Li, Jingjing Xu and Shengxia Chen

Microorganisms 2026, 14(6), 1362; https://doi.org/10.3390/microorganisms14061362 - 18 Jun 2026

Viewed by 614

Abstract

Bacterial extracellular vesicles (BEVs) are nanoscale spherical lipid bilayer structures secreted by bacteria, including outer membrane vesicles (OMVs) released by Gram-negative bacteria and membrane vesicles (MVs) produced by Gram-positive bacteria. Although the biogenesis of BEVs requires substantial energy expenditure, these vesicles provide bacteria [...] Read more.

Bacterial extracellular vesicles (BEVs) are nanoscale spherical lipid bilayer structures secreted by bacteria, including outer membrane vesicles (OMVs) released by Gram-negative bacteria and membrane vesicles (MVs) produced by Gram-positive bacteria. Although the biogenesis of BEVs requires substantial energy expenditure, these vesicles provide bacteria with strategic advantages in the evolutionary interplay between pathogens and hosts. BEVs contribute to bacterial adaptation to environmental stress by remodeling membrane components, eliminating toxic substances, promoting biofilm formation, and mediating the interbacterial transfer of antibiotic resistance determinants. They can also function as decoys to protect bacteria from bacteriophage or antibiotic attack, deliver virulence factors, modulate host immune responses to facilitate bacterial colonization, and mediate interspecies competition. This review summarizes the central roles of BEVs as bacterial mediators of environmental responses, with particular emphasis on their involvement in immune regulation, environmental adaptation, and interspecies competition, thereby providing new insights into pathogen evolutionary strategies. Full article

(This article belongs to the Collection Feature Papers in Medical Microbiology)

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17 pages, 2733 KB

Open AccessArticle

Combined Mechanisms of Streptomyces sp. HU2014 and Coronatine in Promoting Maize Seedling

by Linfeng Hu, Xiaoyu Wang, Jiangsheng Meng, Qian Su, Wenhui Shi, Jungao Zhang and Hongxia Zhu

Microorganisms 2026, 14(6), 1361; https://doi.org/10.3390/microorganisms14061361 - 17 Jun 2026

Viewed by 469

Abstract

The rhizosphere microbiome and phytohormone signaling are critical determinants of plant growth and stress resilience. This study evaluated the combined effects of Streptomyces sp. HU2014 and coronatine (COR) on maize (Zea mays L.) seedlings. Four treatments were established: control (CK), COR seed [...] Read more.

The rhizosphere microbiome and phytohormone signaling are critical determinants of plant growth and stress resilience. This study evaluated the combined effects of Streptomyces sp. HU2014 and coronatine (COR) on maize (Zea mays L.) seedlings. Four treatments were established: control (CK), COR seed soaking (Cor), HU2014 soil inoculation (S), and combined S + Cor (SCor). Growth parameters, chlorophyll content, and antioxidant/oxidative stress markers were measured, and root and leaf transcriptomes, together with root metabolomes, were compared between SCor and CK, followed by qRT-PCR validation. Compared with CK, SCor treatment significantly increased stem diameter (~60%), plant height (~20%), and relative chlorophyll content (SPAD, ~50%). Soluble sugar levels were elevated by over 40% in both leaves and roots, accompanied by tissue-specific modulation of antioxidant enzymes. Transcriptomic analysis of SCor vs. CK revealed 2459 differentially expressed genes (DEGs) in leaves and 3444 DEGs in roots; leaves exhibited upregulation of photosynthetic pigment metabolism (porphyrin and carotenoid pathways) and volatile defense compounds (alkaloids and monoterpenoids), whereas roots showed enrichment in phenylpropanoid/flavonoid biosynthesis, benzoxazinoid synthesis, and starch/sucrose metabolism. Metabolomics of SCor vs. CK identified 526 differentially accumulated metabolites (DAMs) in roots, with significant enrichment in aminoacyl-tRNA biosynthesis, phenylalanine metabolism, and linoleic acid metabolism. Integrative multi-omics analysis further revealed that the JA precursor 13-epi-12-oxo-phytodienoic acid co-clustered with stress-responsive transcription factors (e.g., DREB1C), while tricarboxylic acid (TCA) intermediates and phenylpropanoid metabolites were linked to energy and lignin biosynthesis genes. qRT-PCR confirmed the expression trends of 14 out of 15 tested genes. Collectively, combined HU2014 and COR application triggers tissue-specific transcriptional and metabolic reprogramming in maize, coupling JA-mediated stress signaling with enhanced carbon metabolism and secondary defense compound synthesis to promote rhizosphere adaptation and seedling vigor. Full article

(This article belongs to the Section Plant Microbe Interactions)

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20 pages, 2055 KB

Open AccessReview

Therapeutic Management of Probiotics and Prebiotic Products to Modulate Gut Microbiome by Healthcare Services

by Rawan Bajoudah, Li Li and Malik Altaf Hussain

Microorganisms 2026, 14(6), 1360; https://doi.org/10.3390/microorganisms14061360 - 17 Jun 2026

Viewed by 785

Abstract

The prescription and recommendation of prebiotics and probiotics by healthcare professionals remain an evolving area of research. Despite increasing recognition of their benefits in modulating the gut microbiome, healthcare professionals including dietitians, often lack standardised guidelines and sufficient training to integrate them into [...] Read more.

The prescription and recommendation of prebiotics and probiotics by healthcare professionals remain an evolving area of research. Despite increasing recognition of their benefits in modulating the gut microbiome, healthcare professionals including dietitians, often lack standardised guidelines and sufficient training to integrate them into practice. Barriers to implementation include insufficient clinical evidence, cost, uncertainty regarding strain-specific efficacy, and a lack of consensus on appropriate therapeutic applications. Studies indicate that while many healthcare professionals acknowledge the potential benefits of these products, their hesitancy arises from insufficient supporting research evidence and associated education. Future efforts should concentrate on enhancing clinical guidelines, improving educational programs for healthcare professionals, and conducting large-scale trails to establish evidence-based recommendations. Additionally, integrating gut microbiome sequencing into clinical decision-making could improve personalised nutrition and optimise the prescription of prebiotics and probiotics. Further research is necessary to address knowledge gaps and promote effective, evidence-based use of these interventions by healthcare professionals. This review explores current prescribing practices, knowledge, and perceptions of healthcare professionals regarding prebiotics and probiotics with a particular focus on the evidence, education, and implementation gaps that may influence their clinical application. Full article

(This article belongs to the Special Issue Probiotics in Human Health and Disease)

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22 pages, 18834 KB

Open AccessArticle

Spatiotemporal Dynamics and Assembly Mechanisms of Bacterial Communities in Tropical-Subtropical Coastal Waters of the Leizhou Peninsula, China

by Junyu Wei, Menghan Gao, Yingyi Fan, Sen Ai, Mi Zhang, Yulei Zhang, Huaming Wu and Zhangxi Hu

Microorganisms 2026, 14(6), 1359; https://doi.org/10.3390/microorganisms14061359 - 17 Jun 2026

Viewed by 365

Abstract

Bacterial communities play vital roles in coastal biogeochemical cycling and ecological stability. Despite their importance, a significant knowledge gap exists regarding their spatiotemporal dynamics and assembly mechanisms in the tropical coastal waters of the Leizhou Peninsula, China. To investigate the bacterial community structure, [...] Read more.

Bacterial communities play vital roles in coastal biogeochemical cycling and ecological stability. Despite their importance, a significant knowledge gap exists regarding their spatiotemporal dynamics and assembly mechanisms in the tropical coastal waters of the Leizhou Peninsula, China. To investigate the bacterial community structure, co-occurrence networks, and assembly processes, we conducted 16S rRNA gene amplicon sequencing on water samples collected seasonally from August 2022 to June 2023. The bacterial communities were dominated by Proteobacteria and Cyanobacteria, and were characterized by a distinct warm-season peak in the relative of Cyanobium. Alpha diversity indices exhibited significant seasonal fluctuations, reaching a minimum in August (autumn) and a maximum in December (winter). These variations were strongly regulated by water temperature and phosphate availability. Redundancy analysis (RDA) identified salinity as the primary deterministic factor shaping community composition. Seasonal environmental heterogeneity, rather than spatial variation, primarily governed bacterial community dynamics. We also observed a seasonal succession in community assembly mechanisms with deterministic filtering dominated in autumn, whereas stochastic processes prevailed in other seasons. Predicted functional profiles indicated a stable core metabolism, although local anthropogenic inputs stimulated specific metabolic adaptations in industrial and aquaculture zones. Our findings reveal that seasonal environmental filtering (especially temperature and salinity) and a shifting balance between stochastic and deterministic assembly processes govern bacterial dynamics in this tropical coastal ecosystem, with anthropogenic inputs modulating local metabolic functions. This study provides fundamental insights into the mechanisms maintaining microbial diversity and stability in tropical coastal waters facing seasonal and human pressures. Full article

(This article belongs to the Special Issue Microbial Taxonomy and Environmental Metagenomics: Diversity, Dynamics, and Functional Genes)

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16 pages, 5399 KB

Open AccessArticle

Screening of Plant-Derived Lactic Acid Bacteria for Faba Bean Fermentation and Their Mycotoxin Removal Capacity

by Hang Xiao, Kristóf Kajdi, Reinhard Wimmer and Claus Heiner Bang-Berthelsen

Microorganisms 2026, 14(6), 1358; https://doi.org/10.3390/microorganisms14061358 - 17 Jun 2026

Viewed by 511

Abstract

The development of novel plant-based products using unconventional food matrices increases the risk of introducing mycotoxins into the food system. Biological detoxification methods, particularly those involving lactic acid bacteria (LAB), are considered sustainable and safe strategies. In this study, we screened 142 plant-derived [...] Read more.

The development of novel plant-based products using unconventional food matrices increases the risk of introducing mycotoxins into the food system. Biological detoxification methods, particularly those involving lactic acid bacteria (LAB), are considered sustainable and safe strategies. In this study, we screened 142 plant-derived LAB strains across 17 species for their fermentation performance and mycotoxin removal capacity during faba fermentation. Among them, 84 strains showed rapid acidification. The plating of 11 selected strains confirmed robust growth with cell densities ranging from 4 × 10⁸ to 2.18 × 10⁹ CFU/mL. Screening for aflatoxin B1 (AFB1) removal in complex medium identified several strains that could reduce AFB1 in the supernatant. However, complete toxin extraction after faba fermentation indicated that AFB1 was not enzymatically degraded. Similarly, no significant degradation of ochratoxin A or zearalenone was observed during faba fermentation. Additionally, a cell binding test with 11 selected strains showed that all strains bound AFB1, with efficiencies from about 10% to 35%. Notably, Lentilactobacillus hilgardii NFICC857 demonstrated the highest binding capacity, which has never been reported before. Our study provides preliminary insight into plant-derived LAB in mycotoxin removal. Given the vast unexplored diversity of LAB in nature, the discovery of novel strains with enhanced mycotoxin-binding capacity and potential enzymatic degradation remains promising. Full article

(This article belongs to the Special Issue Microbial Biotechnology in the Food Industry: Innovations, Applications, and Future Perspectives)

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18 pages, 30426 KB

Open AccessArticle

Molecular Visualization of α-Proteobacterial RNA Using a Newly Developed Probe in Extracted Samples, Bacterial Cells, and Rice Root Tissues

by Juan Xia, Sora Muramatsu and Isamu Maeda

Microorganisms 2026, 14(6), 1357; https://doi.org/10.3390/microorganisms14061357 - 17 Jun 2026

Viewed by 562

Abstract

Purple non-sulfur bacteria (PNSB) have attracted attention as a group of microorganisms with plant growth-promoting abilities. Notably, agriculturally important PNSB, including members of the genera Rhodopseudomonas and Rhodobacter, are classified within the class α-Proteobacteria. However, molecular visualization of these bacteria in plant tissues [...] Read more.

Purple non-sulfur bacteria (PNSB) have attracted attention as a group of microorganisms with plant growth-promoting abilities. Notably, agriculturally important PNSB, including members of the genera Rhodopseudomonas and Rhodobacter, are classified within the class α-Proteobacteria. However, molecular visualization of these bacteria in plant tissues remains challenging without bacterial genetic manipulation. In this study, a DIG-labeled RNA probe was developed from a 16S rRNA region showing relatively high sequence conservation among the tested α-Proteobacterial strains. Northern blot analysis using RNA extracted from 13 bacterial strains demonstrated preferential hybridization of the probe to the tested α-Proteobacterial strains. Then, in situ hybridization (ISH) of fixed bacterial cells produced positive signals only in the tested α-Proteobacterial strains. Finally, after inoculation of Rhodopseudomonas palustris C2 during rice seed priming and seedling hydroponic cultivation, ISH analysis of rice roots revealed probe-positive bacterial structures in root epidermal and root hair-associated regions. Collectively, these results demonstrate the applicability of the developed RNA probe for molecular visualization from extracted RNA and bacterial cells to rice root tissues under controlled inoculation conditions and provide a useful approach for investigating bacterial localization and plant–bacteria interactions in rice roots. Full article

(This article belongs to the Section Plant Microbe Interactions)

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Microorganisms, Volume 14, Issue 6 (June 2026) – 220 articles

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