@article {pmid41601032,
year = {2026},
author = {Wang, X and Yan, W and Fan, G and Han, Z and Xia, M and Liu, J and Wang, Y and Rensing, C and Augustyniak, M and Zhang, Z and Wu, H},
title = {Earthworms reduce the accumulation of soil-borne pathogens in strawberry by altering the gut microbiome and physiological characteristics.},
journal = {Ecotoxicology and environmental safety},
volume = {309},
number = {},
pages = {119595},
doi = {10.1016/j.ecoenv.2025.119595},
pmid = {41601032},
issn = {1090-2414},
mesh = {*Oligochaeta/physiology/microbiology ; Animals ; *Fragaria/microbiology ; *Gastrointestinal Microbiome ; *Soil Microbiology ; Fusarium/physiology ; Alternaria/physiology ; *Plant Diseases/microbiology/prevention & control ; Soil/chemistry ; },
abstract = {Pathogenic fungi cause economic loss to many crops including strawberry, highlighting the need for control using sustainable eco-friendly strategies. Earthworm casts effectively reduce the occurrence of soil-borne diseases. However, the interactions between earthworms and soil-borne pathogenic fungi and their underlying mechanisms remain insufficiently understood in strawberry. This study investigated the effects of the pathogenic fungi Fusarium oxysporum and Alternaria alstroemeriae on the structure and composition of the microbial communities in the drilosphere soil and earthworm gut using high-throughput sequencing. The impact of these pathogenic fungi on functional gene expression in earthworms was determined using transcriptomic analysis. Applying F. oxysporum and A. alstroemeriae with earthworms significantly altered the physicochemical properties of the drilosphere soil, reduced the fungal alpha diversity therein, and increased the abundance of potentially beneficial Pseudomonas spp. and Bacillus spp. The presence of the pathogenic fungi increased the alpha diversity and habitat niche breadth of the fungal community in the earthworm gut. However, there was a significant reduction in the relative abundance of potentially pathogenic fungi to plants and animals in the earthworm gut. Earthworms had a positive legacy effect on the abundance of beneficial bacteria in the rhizosphere and enhanced strawberry biomass. Transcriptomic analysis demonstrated that earthworms activated α-linolenic acid and glycerophospholipid metabolism but downregulated the Toll-like receptor pathway, mitigating excessive immune responses. In summary, earthworms suppress soil-borne pathogenic fungi in strawberry via an integrated mechanism involving the restructuring of the gut microbiota, enrichment of biocontrol agents in the drilosphere, and coordination of host immunity, offering a novel paradigm for pest management and sustainable means for strawberry cultivation.},
}

*Oligochaeta/physiology/microbiology
Animals
*Fragaria/microbiology
*Gastrointestinal Microbiome
*Soil Microbiology
Fusarium/physiology
Alternaria/physiology
*Plant Diseases/microbiology/prevention & control
Soil/chemistry

@article {pmid41600738,
year = {2026},
author = {Yachida, M and Itoh, M and Morita, Y},
title = {Comparative Effects of Raw Milk and Milk Replacer Feeding on Gut Microbiota Diversity and Function in Cryptosporidium parvum-Infected Neonatal Dairy Calves on a Japanese Farm.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010082},
pmid = {41600738},
issn = {2306-7381},
support = {24K09209//Japan Society for the Promotion of Science/ ; 5 chiku-ni-kyo hatsu dai 27//Japan Association for Livestock New Technology/ ; },
abstract = {Neonatal diarrhea is a major health concern in the livestock industry, and Cryptosporidium parvum is a key pathogen responsible for this condition in calves. Milk management and gut microbiome regulation may play important roles in preventing cryptosporidiosis symptoms. This study analyzed the gut microbiota of neonatal calves fed raw milk (BM) or milk replacer (MR) using a total of 58 fecal samples collected on the same farm in 2022 and 2024. In milk replacer-fed calves, alpha diversity was significantly higher in C. parvum-positive (P) calves without diarrhea (N) (PN, n = 5) than in C. parvum-positive calves with diarrhea(D) (PD, n = 18) (Shannon p = 0.0358; Chao1 p = 0.0598). Beta diversity also differed between PN and PD (PERMANOVA, R[2] = 0.1763, p = 0.0092). Predicted microbial taxa such as Faecalibacterium (ALDEx2, effect size = 2.31, p = 0.00003) and Butyricicoccus (effect size = 1.31, p = 0.0041) were enriched in PN calves in MR. Comparison between milk types (BM vs. MR) further showed higher species richness in PN calves in MR than in those (n = 5) in BM(Chao1, p = 0.0088), along with significant differences in beta diversity (R[2] = 0.4112, p = 0.0069). These findings suggest that microbial diversity and the presence of specific taxa may be associated with reduced diarrheal symptoms. Predicted metabolic pathway profiling using a computational functional profiling approach showed the distinct metabolic pathways, including amino acid, carbohydrate, lipid, and vitamin biosynthesis, were enriched in healthier calves in both groups. These results suggest certain functional features of the microbiome could be associated with anti-inflammatory activity and short-chain fatty acid production, potentially mitigating diarrheal symptoms.},
}

@article {pmid41600714,
year = {2026},
author = {Jin, A and Zhou, S and Cheng, S and Yang, Y and Sun, Y and Sun, Z and Zhao, Y and Chen, X},
title = {Effects of Dietary Supplementation with Whole Lamb Omasum on Gut Health and Metabolism in Shiba Inu Dogs.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010058},
pmid = {41600714},
issn = {2306-7381},
support = {CSTB2025TIAD-KPX0079//Chongqing Key Special Project for Technological Innovation and Application Development/ ; CQMAITS202513//Chongqing Herbivorous Livestock Industry Technology System/ ; },
abstract = {The growing pet economy boosts demand for fiber-enriched functional foods to improve canine gut motility and metabolic health. However, low-bioavailability commercial fibers often falter in high-energy diets. Whole lamb omasum-from grass-fed sheep omasum and gastric contents-repurposes a discarded byproduct for waste reduction and sustainable livestock production. This study evaluated the short-term effects of WLO supplementation on gut health and metabolism in healthy adult Shiba Inu dogs. Twelve dogs were randomly assigned to control or WLO groups in a randomized controlled trial. WLO supplementation significantly reduced fecal scores by 8.91% (p < 0.05), increased apparent crude fat and fiber digestibility by 3.70% and 11.55% (p < 0.05), and elevated serum IgA by 35.79-36.15% and T-AOC by 30.53-35.71% (p < 0.05). Serum metabolome revealed 13 between-group and 8 within-subject differences related to lipid and endocrine modulation. Fecal microbiota analysis indicated enrichment of the Bacillota phylum and Blautia genus (p < 0.05). These findings support WLO as a functional food that enhances gut and metabolic health in small-breed dogs.},
}

@article {pmid41600684,
year = {2025},
author = {Mgeni, MS and Zhang, L and Chen, Y and Dong, X and Xiu, Z and Zhang, J and Chen, J and Sun, Y},
title = {Effects of Dandelion Extracts on the Ruminal Microbiota, Metabolome, and Systemic Inflammation in Dairy Goats Fed a High-Concentrate Diet.},
journal = {Veterinary sciences},
volume = {13},
number = {1},
pages = {},
doi = {10.3390/vetsci13010028},
pmid = {41600684},
issn = {2306-7381},
support = {22532J//This research was funded by chongqing performance incentive guide special project 22532J/ ; },
abstract = {This study examined the effect of dandelion extracts on the ruminal microbiota, metabolome, and inflammatory response in dairy goats fed a high-concentrate diet. Eighteen Guanzhong dairy goats were assigned to three groups: low-concentrate diet group (L group, F:C = 60:40), high-concentrate diet group (H group, F:C = 35:65), and dandelion group (D) with 1% dandelion extracts based on the H group. Over six weeks, milk, blood, and ruminal fluid were collected to analyze pH, volatile fatty acids (VFAs), inflammatory markers, microbiome, and metabolome. Feed intake was significantly higher in the H and D groups than in the L group. Ruminal pH decreased in the H group, acetate was significantly higher in the L and D groups, and serum IgA was higher in D group. Bacteroidetes and Firmicutes were dominant rumen phyla, and dandelion supplementation significantly increased Proteobacteria. Prevotella abundance was enriched in the L and D groups and showed a positive correlation with acetate. Dandelion extracts also increased the production of trans-3-Hydroxy-L-proline and 7-Ethyl-5,6-dihydro-1,4-dimethylazulene in the rumen while improving amino acid and lipid metabolism. Overall, supplementation of dandelion extracts positively influenced rumen microbiota, enhanced production of beneficial metabolites, and positively influenced immune function in dairy goats fed high-concentrate diet.},
}

@article {pmid41600605,
year = {2026},
author = {De Rosa, M and Canepari, S and Tranfo, G and Giampaoli, O and Patriarca, A and Smolinska, A and Marini, F and Massimi, L and Sciubba, F and Spagnoli, M},
title = {Unveiling the Metabolic Fingerprint of Occupational Exposure in Ceramic Manufactory Workers.},
journal = {Toxics},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/toxics14010056},
pmid = {41600605},
issn = {2305-6304},
support = {BRIC ID 52//Istituto Nazionale per l'Assicurazione Contro gli Infortuni sul Lavoro/ ; },
abstract = {In this study, for the first time urinary NMR-based metabolomics was applied to investigate the physiological alterations associated with occupational exposure in ceramic manufacturing workers. Multivariate analysis revealed a distinctive metabolic signature with exposure, characterized by a depletion of both aliphatic and aromatic amino acids and a concomitant accumulation of branched-chain amino acid catabolites. Alterations in tricarboxylic acid (TCA) cycle intermediates, including citrate and succinate, suggest an involvement of mitochondrial energy metabolism, reflecting adaptive responses to oxidative stress and increased protein turnover. Notably, glycine levels were found increased, consistent with its central role in antioxidant defense and xenobiotic detoxification. Furthermore, changes in urinary host-microbiome co-metabolites, such as 4-hydroxyphenylacetate and phenylacetylglycine, indicate the potential modulation of gut microbial activity in response to occupational exposure. While limited by the small cohort, this study demonstrates the feasibility of NMR-based urinary metabolomics for the non-invasive biomonitoring of workers and suggests its potential as a useful tool for detecting subtle metabolic perturbations associated with complex occupational exposures.},
}

@article {pmid41600411,
year = {2026},
author = {Tiwari, AK and Gupta, MK and Mishra, SK and Meena, R and Patolsky, F and Narayan, RJ},
title = {Nanobiosensors: A Potential Tool to Decipher the Nexus Between SARS-CoV-2 Infection and Gut Dysbiosis.},
journal = {Sensors (Basel, Switzerland)},
volume = {26},
number = {2},
pages = {},
doi = {10.3390/s26020616},
pmid = {41600411},
issn = {1424-8220},
mesh = {*Dysbiosis/diagnosis/virology/microbiology ; Humans ; *COVID-19/diagnosis/virology/complications ; *Biosensing Techniques/methods ; *SARS-CoV-2/isolation & purification/pathogenicity ; *Gastrointestinal Microbiome ; *Nanotechnology/methods ; },
abstract = {The emergence of SARS-CoV-2 posed a great global threat and emphasized the urgent need for diagnostic tools that are rapid, reliable, sensitive and capable of real-time monitoring of SARS-CoV-2 infections. Recent investigations have identified a potential connection between SARS-CoV-2 infection and gut dysbiosis, highlighting the sophisticated interplay between the virus and the host microbiome. This review article discusses the eminence of nanobiosensors, as state-of-the-art tools, to investigate and clarify the connection between SARS-CoV-2 pathogenesis and gut microbiome imbalance. Nanobiosensors are uniquely advantageous owing to their sensitivity, selectivity, specificity, and reliable monitoring capabilities, making them well-suited for identifying both viral particles and microbial markers in biological samples. We explored a range of nanobiosensor platforms and their potential use for concurrently monitoring the gut dysbiosis induced by different pathological conditions. Additionally, we explore how advanced sensing technologies can shed light on the mechanisms driving virus-induced dysbiosis, and the implications for disease progression and patient outcomes. The integration of nanobiosensors with microfluidic devices and artificial intelligence algorithms has also been explored, highlighting the potential of developing point-of-care diagnostic tools that provide comprehensive insights into both viral infection and gut health. Utilizing nanotechnology, scientists and healthcare professionals may gain a more profound insight into the complex interaction dynamics between SARS-CoV-2 infection and the gut microenvironment. This could pave the way for enhanced diagnostic and prognostic approaches, treatment courses, and patient care for COVID-19.},
}

*Dysbiosis/diagnosis/virology/microbiology
Humans
*COVID-19/diagnosis/virology/complications
*Biosensing Techniques/methods
*SARS-CoV-2/isolation & purification/pathogenicity
*Gastrointestinal Microbiome
*Nanotechnology/methods

@article {pmid41600136,
year = {2026},
author = {Song, X and Xia, X and Yang, S and Hao, C and Sun, H and Li, F and Xu, X and Zhang, H and Lu, X},
title = {The Influence of Transgenic Insect-Resistance and Herbicide-Tolerance Soybean KM2208-23 on the Rhizosphere Micro-Biome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/plants15020329},
pmid = {41600136},
issn = {2223-7747},
support = {2023ZD04062//Biological Breeding-Major Projects/ ; 2024LZGC010//the Agricultural Variety Improvement Project of Shandong Province/ ; ZR2021QC207//Shan-dong Province Natural Science Foundation Young Project/ ; },
abstract = {The consequences of stacking multiple insect-resistance and herbicide-tolerance genes, particularly across the entire plant life cycle, remain inadequately understood. This study investigated the impact of stacked-trait transgenic soybeans on rhizosphere microbial communities across five growth stages (pre-sowing, V3, R3, R5, R8). Using 16S rRNA and ITS sequencing, we compared the rhizosphere microbiome of the transgenic modified soybean (GMO) with its non-transgenic control check (CK). Results showed transient but significant shifts in soil properties (e.g., available nitrogen) and microbial beta diversity during the V3 stages. However, plant developmental stage was the predominant factor shaping microbial succession, with its effect outweighing that of the transgene. No persistent changes in microbial alpha diversity were observed. We conclude that the influence of this stacked-trait soybean on the rhizosphere is growth-stage-specific and represents a minor, recoverable perturbation rather than a sustained ecological impact. These findings contribute to the ecological safety assessment of multi-gene transgenic crops.},
}

@article {pmid41599966,
year = {2026},
author = {Nedeva, I and Assyov, Y and Duleva, V and Karamfilova, V and Kamenov, Z and Naydenov, J and Handjieva-Darlenska, T and Denchev, V and Kolevski, A and Pencheva, V and Vodenicharov, V},
title = {Distinct Gut Microbiome Profiles Underlying Cardiometabolic Risk Phenotypes in Individuals with Obesity.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020353},
pmid = {41599966},
issn = {2072-6643},
support = {contract D-300/18.12/2023//Stimulating Excellence in Scientific research, Medical university Sofia/ ; 2025//National program " For Women in Science 2025"/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome ; *Obesity/microbiology/complications ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; Adult ; Phenotype ; *Metabolic Syndrome/microbiology ; Cardiometabolic Risk Factors ; *Cardiovascular Diseases/microbiology ; },
abstract = {Background: Obesity-related cardiometabolic disorders have been linked to alterations in selected gut microbiome components, yet clinically relevant microbial signatures remain incompletely defined. Objectives: This study investigated associations between selected gut bacterial taxa and cardiometabolic risk phenotypes in individuals with obesity. Methods: In this cross-sectional study, 100 adults with obesity were stratified according to metabolic syndrome status. Gut microbiome composition was assessed using targeted multiplex real-time PCR of functionally relevant bacterial taxa. Associations with anthropometric and cardiometabolic parameters were examined using correlation analysis, ROC curves, and multivariable logistic regression models. Results: Reduced relative abundance of Lachnospiraceae was associated with metabolic syndrome, lower Faecalibacterium abundance with arterial hypertension, and increased Prevotella abundance with dyslipidemia. ROC analyses identified cohort-specific discriminative thresholds with moderate accuracy. Conclusions: Selected taxon-specific gut microbiome signatures are associated with cardiometabolic risk phenotypes in obesity. These findings are exploratory and require validation in longitudinal and independent cohorts.},
}

Humans
*Gastrointestinal Microbiome
*Obesity/microbiology/complications
Male
Female
Cross-Sectional Studies
Middle Aged
Adult
Phenotype
*Metabolic Syndrome/microbiology
Cardiometabolic Risk Factors
*Cardiovascular Diseases/microbiology

@article {pmid41599961,
year = {2026},
author = {Lietz, A and Dapprich, J and Fischer, T},
title = {Carnivore Diet: A Scoping Review of the Current Evidence, Potential Benefits and Risks.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020348},
pmid = {41599961},
issn = {2072-6643},
mesh = {Humans ; Animals ; },
abstract = {Background: The Carnivore Diet (CD) is an almost exclusively animal-based dietary pattern that has gained increasing popularity on social media. Despite numerous health-related claims, a standardized definition is lacking, and scientific evidence regarding the long-term effects of this diet remains unclear. Methods: The literature search for this scoping review was conducted in accordance with PRISMA guidelines (PRISMA-ScR) using the databases PubMed, LIVIVO, Web of Science, and the Cochrane Library. Results: Nine human studies were included. Individual publications reported positive effects of the CD, such as weight reduction, increased satiety, and potential improvements in inflammatory or metabolic markers. At the same time, potential risks of nutrient deficiencies, particularly in vitamins C and D, calcium, magnesium, iodine, and dietary fiber, as well as elevated low-density-lipoprotein (LDL-) and total cholesterol (TC) levels, were identified, along with one case describing a deterioration in health status. Overall, the quality of evidence is very limited due to small sample sizes, short study durations, and the absence of control groups. Conclusions: The CD may offer short-term health benefits but carries substantial risks of nutrient deficiencies, reduced intake of health-promoting phytochemicals, and the development of cardiovascular disease. At this time, long-term adherence to a CD cannot be recommended.},
}

Humans
Animals

@article {pmid41599910,
year = {2026},
author = {Park, SH},
title = {Recent Research on the Role of Lactobacilli Probiotics in Cancer Management.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020297},
pmid = {41599910},
issn = {2072-6643},
mesh = {*Probiotics/therapeutic use ; Humans ; *Neoplasms/therapy/microbiology ; *Lactobacillus ; Gastrointestinal Microbiome ; Animals ; Apoptosis ; },
abstract = {Lactobacilli strains are one of the major groups belonging to probiotics. Lactobacilli strains are known to be beneficial microbes widely studied and utilized for their health benefits and applications in various fields. Recently, Lactobacilli strains have emerged as promising agents in cancer management due to their ability to influence various physiological processes. Lactobacilli strains have shown potential in producing tumor-suppressive compounds, enhancing immune responses, and reshaping gut microbiota balance for the management of various cancer types. Lactobacilli strains demonstrated tumor-suppressive activity through mechanisms including induction of apoptosis, inhibition of migration, and regulation of key oncogenic signaling pathways. However, the effects of Lactobacilli strains appear to be strain- and cancer-type-dependent, necessitating further research to identify the most effective strains for the proper cancer type with the optimal treatment regimens. In this review article, we focus on Lactobacilli strains studied between 2021 and 2025 that have demonstrated tumor-suppressive properties in various experimental models. In addition, this article explores the current limitations in research methodologies and proposes potential avenues for future investigations in this area of study.},
}

*Probiotics/therapeutic use
Humans
*Neoplasms/therapy/microbiology
*Lactobacillus
Gastrointestinal Microbiome
Animals
Apoptosis

@article {pmid41599902,
year = {2026},
author = {Plaza-Diaz, J and Herrera-Quintana, L and Olivares-Arancibia, J and Vázquez-Lorente, H},
title = {Personalized Nutrition Through the Gut Microbiome in Metabolic Syndrome and Related Comorbidities.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020290},
pmid = {41599902},
issn = {2072-6643},
mesh = {Humans ; *Metabolic Syndrome/microbiology/prevention & control/diet therapy/therapy ; *Gastrointestinal Microbiome/physiology ; Exercise ; *Precision Medicine/methods ; Comorbidity ; Diet ; },
abstract = {Background: Metabolic syndrome, a clinical condition defined by central obesity, impaired glucose regulation, elevated blood pressure, hypertriglyceridemia, and low high-density lipoprotein cholesterol across the lifespan, is now a major public health issue typically managed with lifestyle, behavioral, and dietary recommendations. However, "one-size-fits-all" recommendations often yield modest, heterogeneous responses and poor long-term adherence, creating a clinical need for more targeted and implementable preventive and therapeutic strategies. Objective: To synthesize evidence on how the gut microbiome can inform precision nutrition and exercise approaches for metabolic syndrome prevention and management, and to evaluate readiness for clinical translation. Key findings: The gut microbiome may influence cardiometabolic risk through microbe-derived metabolites and pathways involving short-chain fatty acids, bile acid signaling, gut barrier integrity, and low-grade systemic inflammation. Diet quality (e.g., Mediterranean-style patterns, higher fermentable fiber, or lower ultra-processed food intake) consistently relates to more favorable microbial functions, and intervention studies show that high-fiber/prebiotic strategies can improve glycemic control alongside microbiome shifts. Physical exercise can also modulate microbial diversity and metabolic outputs, although effects are typically subtle and may depend on baseline adiposity and sustained adherence. Emerging "microbiome-informed" personalization, especially algorithms predicting postprandial glycemic responses, has improved short-term glycemic outcomes compared with standard advice in controlled trials. Targeted microbiome-directed approaches (e.g., Akkermansia muciniphila-based supplementation and fecal microbiota transplantation) provide proof-of-concept signals, but durability and scalability remain key limitations. Conclusions: Microbiome-informed personalization is a promising next step beyond generic guidelines, with potential to improve adherence and durable metabolic outcomes. Clinical implementation will require standardized measurement, rigorous external validation on clinically meaningful endpoints, interpretable decision support, and equity-focused evaluation across diverse populations.},
}

Humans
*Metabolic Syndrome/microbiology/prevention & control/diet therapy/therapy
*Gastrointestinal Microbiome/physiology
Exercise
*Precision Medicine/methods
Comorbidity
Diet

@article {pmid41599892,
year = {2026},
author = {Guraka, A and Lush, M and Zouganelis, G and Waldron, J and Mekapothula, S and Masania, J and Cave, GWV and Conway, ME and Tripathi, G and Kermanizadeh, A},
title = {Investigating the Role of Diet-Manipulated Gut Bacteria in Pathogenesis of Type 2 Diabetes Mellitus-An In Vitro Approach.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020279},
pmid = {41599892},
issn = {2072-6643},
support = {NA//University of Derby/ ; NA//Animal Free Research UK/ ; },
mesh = {*Gastrointestinal Microbiome/physiology ; *Diabetes Mellitus, Type 2/microbiology/etiology/metabolism ; Humans ; Feces/microbiology ; Insulin/metabolism ; Diet, High-Fat/adverse effects ; Dietary Fiber ; Cell Line, Tumor ; *Limosilactobacillus fermentum/metabolism/isolation & purification ; *Diet ; Bacteroides/metabolism/isolation & purification ; Insulin Resistance ; Glucose/metabolism ; Insulin Secretion ; Male ; },
abstract = {Background: The human gut microbiome is highly complex, and its composition is strongly influenced by dietary patterns. Alterations in microbiome structure have been associated with a range of diseases, including type 2 diabetes mellitus. However, the underlying mechanisms for this remain poorly understood. In this study, a novel in vitro approach was utilized to investigate the interplay between gut bacteria, dietary metabolites, and metabolic dysfunction. Methods: Two representative gut bacterial species-Bacteroides thetaiotaomicron and Lactobacillus fermentum-were isolated from human faecal samples and subjected to controlled dietary manipulation to mimic eubiotic and dysbiotic conditions. Metabolites produced under these conditions were extracted, characterized, and quantified. To assess the functional impact of these metabolites, we utilized the INS-1 832/3 insulinoma cell line, evaluating insulin sensitivity through glucose-stimulated insulin secretion and ERK1/2 activation. Results: Our findings demonstrate that metabolites derived from high-carbohydrate/high-fat diets exacerbate metabolic dysfunction, whereas those generated under high-fibre conditions significantly enhance insulin secretion and glucose-dependent ERK1/2 activation in co-culture compared to monocultures. Conclusions: This work systematically disentangles the complex interactions between gut microbiota, diet, and disease, providing mechanistic insights into how microbial metabolites contribute to the onset of metabolic disorders.},
}

*Gastrointestinal Microbiome/physiology
*Diabetes Mellitus, Type 2/microbiology/etiology/metabolism
Humans
Feces/microbiology
Insulin/metabolism
Diet, High-Fat/adverse effects
Dietary Fiber
Cell Line, Tumor
*Limosilactobacillus fermentum/metabolism/isolation & purification
*Diet
Bacteroides/metabolism/isolation & purification
Insulin Resistance
Glucose/metabolism
Insulin Secretion
Male

@article {pmid41599868,
year = {2026},
author = {Allegretti, JR and Kassam, Z and Kelly, CR and Grinspan, A and El-Nachef, N and Van Den Elzen, C and Jäger, R and Feuerstadt, P},
title = {A Randomized, Placebo-Controlled Trial Evaluating Multi-Species Synbiotic Supplementation for Bloating, Gas, and Abdominal Discomfort.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020255},
pmid = {41599868},
issn = {2072-6643},
support = {N/A//Seed Health Inc./ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; Double-Blind Method ; Male ; Female ; *Abdominal Pain/therapy ; Adult ; Middle Aged ; *Flatulence/therapy ; Quality of Life ; *Dietary Supplements ; Probiotics/administration & dosage ; Gases ; Treatment Outcome ; Plant Extracts/administration & dosage ; Young Adult ; },
abstract = {Background: Bloating, gas, and abdominal discomfort are common in healthy individuals but lack effective interventions. Probiotics can alleviate some gastrointestinal (GI) symptoms; however, evidence for their impact on bloating, gas and abdominal discomfort in otherwise healthy populations remains limited. Mechanistic studies suggest that synbiotics may influence the underlying mechanisms of bloating, including increased gas production, impaired gut motility, and visceral hypersensitivity, but there is a paucity of data from large trials evaluating clinical outcomes. Accordingly, we evaluated the effects of a multi-species synbiotic on GI symptoms. Methods: In a randomized, double-blind, placebo-controlled, decentralized trial, participants (n = 350) with self-reported bloating/indigestion received either a multi-species synbiotic (53.6 billion AFU multi-species probiotic and 400 mg pomegranate extract; DS-01) or placebo daily for 6 weeks. Outcomes included GI quality-of-life (DQLQ), bloating and gas (PROMIS-GI 13a), abdominal discomfort (PROMIS-GI 5a), constipation, regularity, mood-related symptoms, and safety. Results: The multi-species synbiotic improved GI quality-of-life compared to placebo (0.80 vs. 1.20; p < 0.05) at Week 6. Bloating and gas were reduced in the synbiotic arm compared to placebo (16.0 vs. 21.0; p < 0.01), with more participants reporting never/rarely bloating (72.3% vs. 55.9%; p < 0.001). Abdominal discomfort also decreased (8.0 vs. 10.0; p < 0.01). Additionally, there was a statistically significant improvement in constipation symptoms and regularity in the synbiotic arm relative to placebo. Conclusions: Daily supplementation with this multi-species synbiotic significantly improved GI quality-of-life, bloating, gas, abdominal discomfort, and bowel habits. This is the first synbiotic to demonstrate meaningful improvements in bloating and gas in a generally healthy, diverse, real-world population.},
}

Humans
*Synbiotics/administration & dosage
Double-Blind Method
Male
Female
*Abdominal Pain/therapy
Adult
Middle Aged
*Flatulence/therapy
Quality of Life
*Dietary Supplements
Probiotics/administration & dosage
Gases
Treatment Outcome
Plant Extracts/administration & dosage
Young Adult

@article {pmid41599863,
year = {2026},
author = {Baek, HI and Kwon, SY and Noh, HJ and Park, SJ},
title = {Efficacy and Safety of CKDB-322, a Combination of Lactiplantibacillus plantarum Q180 and Phaeodactylum tricornutum, for Reducing Body Fat and Abdominal Adiposity in Overweight Adults.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020250},
pmid = {41599863},
issn = {2072-6643},
support = {20020268//Ministry of Trade, Industry and Energy/ ; 2025-RISE-13-WSU//Ministry of Education/ ; },
mesh = {Humans ; Female ; Male ; Adult ; Middle Aged ; Double-Blind Method ; *Probiotics/administration & dosage/adverse effects/therapeutic use ; *Overweight/therapy ; *Lactiplantibacillus plantarum ; *Adiposity ; *Abdominal Fat ; Aged ; Young Adult ; *Obesity, Abdominal/therapy ; *Diatoms ; Body Mass Index ; Treatment Outcome ; Adipose Tissue ; Waist Circumference ; },
abstract = {BACKGROUND: CKDB-322, a combination of Lactiplantibacillus plantarum Q180 and Phaeodactylum tricornutum, has shown anti-obesity potential in preclinical models, although human evidence is still limited. This randomized, double-blind, placebo-controlled, 12-week trial evaluated the efficacy and safety of CKDB-322 in overweight adults.

METHODS: Participants were aged 19-65 years; had a body mass index (BMI) of 25-30 kg/m[2], and a waist circumference of ≥90 cm for men or ≥85 cm for women. They were randomly assigned to receive either CKDB-322, which provided 1.0 × 10[9] CFU of L. plantarum Q180 and 200 mg of P. tricornutum daily (n = 50), or a placebo (n = 50).

RESULTS: CKDB-322 supplementation resulted in statistically significant reductions in body fat mass and body fat percentage, as measured by dual-energy X-ray absorptiometry (DEXA), compared to the placebo group (p < 0.05). Computed tomography (CT) analyses also revealed significant reductions in abdominal fat area in the CKDB-322 group (p < 0.05). Additional improvements were observed in body weight and anthropometric parameters. Among metabolic biomarkers, serum triglycerides and leptin levels decreased significantly in the CKDB-322 group compared to the placebo. Exploratory microbiome analyses indicated an increase in the relative abundance of Lactobacillus, suggesting potential modulation of the gut-adipose axis. CKDB-322 was well tolerated, with no clinically significant adverse events or laboratory abnormalities.

CONCLUSIONS: Collectively, CKDB-322 demonstrated a favorable safety profile and produced statistically significant improvements in multiple adiposity-related outcomes, including reductions in body fat mass, abdominal adiposity, and key anthropometric measures, supporting its potential as a functional ingredient for body fat reduction and metabolic health.},
}

Humans
Female
Male
Adult
Middle Aged
Double-Blind Method
*Probiotics/administration & dosage/adverse effects/therapeutic use
*Overweight/therapy
*Lactiplantibacillus plantarum
*Adiposity
*Abdominal Fat
Aged
Young Adult
*Obesity, Abdominal/therapy
*Diatoms
Body Mass Index
Treatment Outcome
Adipose Tissue
Waist Circumference

@article {pmid41599842,
year = {2026},
author = {Adibi, S},
title = {A Conceptual Digital Health Framework for Longevity Optimization: Inflammation-Centered Approach Integrating Microbiome and Lifestyle Data-A Review and Proposed Platform.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020231},
pmid = {41599842},
issn = {2072-6643},
mesh = {Humans ; *Longevity ; *Inflammation ; Diet, Mediterranean ; *Life Style ; *Gastrointestinal Microbiome ; Biomarkers/blood ; Aged, 80 and over ; C-Reactive Protein/metabolism ; Male ; Artificial Intelligence ; Digital Health ; },
abstract = {Chronic low-grade inflammation, or "inflammaging," represents a central mechanism linking dietary patterns, gut microbiome composition, and biological aging. Evidence from Blue Zone populations and Mediterranean diet studies demonstrates that specific nutritional interventions are associated with up to 23% lower all-cause mortality, with analyses suggesting that part of this association may be mediated by measurable improvements in inflammatory biomarkers. This paper synthesizes published evidence from Mediterranean diet trials, centenarian microbiome studies, and digital health platforms to propose a comprehensive digital health framework that integrates quarterly inflammation and microbiome monitoring with continuous lifestyle tracking to deliver personalized longevity interventions. This paper introduces the Longevity-Inflammation Index (L-II), a composite score combining high-sensitivity C-reactive protein, interleukin-6, tumor necrosis factor-alpha, and microbiome-derived markers, with scoring algorithms derived from centenarian population studies. The proposed platform leverages artificial intelligence to generate evidence-based recommendations adapted from centenarian and Mediterranean dietary patterns. Published evidence from multiple randomized controlled trials demonstrates that Mediterranean dietary interventions reduce hs-CRP by 18-32%, increase microbiome diversity by 6-28%, and improve metabolic markers including HOMA-IR and TG/HDL ratios. Digital health platforms demonstrate sustained engagement rates of 58-84% at 12 months, with dietary logging frequencies of 4-6 days per week. Cost-effectiveness analyses of dietary interventions show incremental cost-effectiveness ratios of USD 2100-4800 per quality-adjusted life year gained. This inflammation-centered digital health framework offers a scalable approach for translating longevity research into practical interventions for healthy aging, with validation studies needed to confirm the integrated platform's efficacy and real-world implementation feasibility.},
}

Humans
*Longevity
*Inflammation
Diet, Mediterranean
*Life Style
*Gastrointestinal Microbiome
Biomarkers/blood
Aged, 80 and over
C-Reactive Protein/metabolism
Male
Artificial Intelligence
Digital Health

@article {pmid41599822,
year = {2026},
author = {De Beul, E and Heyse, J and Jurgelewicz, M and Baudot, A and Vu, LD and Van den Abbeele, P},
title = {N-Acetylglucosamine and Immunoglobulin Strengthen Gut Barrier Integrity via Complementary Microbiome Modulation.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020210},
pmid = {41599822},
issn = {2072-6643},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Acetylglucosamine/pharmacology ; Adult ; Animals ; Caco-2 Cells ; *Immunoglobulins/pharmacology ; Fatty Acids, Volatile/metabolism ; *Intestinal Mucosa/drug effects/microbiology/metabolism ; Cattle ; Male ; Female ; Coculture Techniques ; },
abstract = {Background: Gut barrier dysfunction and altered gut microbial metabolism are emerging signatures of chronic gut disorders. Considering growing interest in combining structurally and mechanistically distinct bioactives, we investigated the individual and combined effects of serum-derived bovine immunoglobulin (SBI) and N-acetylglucosamine (NAG) on the gut microbiome and barrier integrity. Methods: The validated ex vivo SIFR[®] (Systemic Intestinal Fermentation Research) technology, using microbiota from healthy adults (n = 6), was combined with a co-culture of epithelial/immune (Caco-2/THP-1) cells. Results: While SBI and NAG already significantly improved gut barrier integrity (TEER, transepithelial electrical resistance, +21% and +29%, respectively), the strongest effect was observed for SBI_NAG (+36%). This potent combined effect related to the observation that SBI and NAG each induced distinct, complementary shifts in microbial composition and metabolite output. SBI most selectively increased propionate (~Bacteroidota families) and health-associated indole derivatives (e.g., indole-3-propionic acid), while NAG most specifically boosted acetate and butyrate (~Bifidobacteriaceae, Ruminococcaceae, and Lachnospiraceae). The combination of SBI_NAG displayed effects of the individual ingredients, thus, for instance, enhancing all three short-chain fatty acids (SCFA) and elevating microbial diversity (CMS, community modulation score). Conclusions: Overall, SBI and NAG exert complementary, metabolically balanced effects on the gut microbiota, supporting combined use, particularly in individuals with gut barrier impairment or dysbiosis linked to lifestyle or early-stage gastrointestinal disorders.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Acetylglucosamine/pharmacology
Adult
Animals
Caco-2 Cells
*Immunoglobulins/pharmacology
Fatty Acids, Volatile/metabolism
*Intestinal Mucosa/drug effects/microbiology/metabolism
Cattle
Male
Female
Coculture Techniques

@article {pmid41599794,
year = {2026},
author = {Al Hazaimeh, R and Shackelford, L and Boateng, J},
title = {Effects of Mixed Fruits and Berries on Ameliorating Gut Microbiota and Hepatic Alterations Induced by Cafeteria Diet.},
journal = {Nutrients},
volume = {18},
number = {2},
pages = {},
doi = {10.3390/nu18020181},
pmid = {41599794},
issn = {2072-6643},
support = {ALAX-012-0918//USDA/NIFA Capacity-Building Grant/ ; ALAX-12-2017//USDA/NIFA Evans-Allen/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome ; Male ; Rats, Sprague-Dawley ; *Fruit ; *Liver/pathology/metabolism ; Rats ; Dysbiosis ; *Fatty Liver/etiology/prevention & control ; Disease Models, Animal ; Metabolic Syndrome/etiology ; *Diet/adverse effects ; },
abstract = {Background/Objectives: The study investigated the potential of mixed fruits and berries (MFB) as a dietary intervention to mitigate cafeteria (CAF) diet-induced gut microbiome dysbiosis and hepatic dysfunction associated with metabolic syndrome and steatohepatitis (MASH) in an adolescent rat model. Methods: Forty-eight adolescent male Sprague-Dawley rats (n = 3 cages per group (two rats per cage)) were divided into eight experimental groups, where NC received the normal AIN-93G basal diet, PC received the CAF diet and normal AIN-93G basal diet, T1 and T2 received MFB supplementation (3% and 6% levels) without CAF exposure, P1 and P2 received a MFB (3% and 6% levels) supplementation initiated at the onset of CAF feeding, and I1 and I2 received MFB supplementation initiated 2 weeks after CAF feeding. After 6 weeks, cecal 16S rRNA, hepatic histopathology, Oil Red O staining, and metabolic dysfunction-associated steatotic liver disease (MASLD)-related biomarkers (liver enzymes, alanine aminotransferase (ALT), and aspartate aminotransferase (AST)) were analyzed. Results: AST: ALT ratio was the highest in the PC group (3.63, p < 0.05) compared to the MFB groups. Oil Red O staining showed lower hepatic lipid accumulation, and histological analysis demonstrated a marked reduction in portal inflammatory cell infiltration in MFB. Alpha diversity (Simpson Index) decreased in PC (Kruskal-Wallis, p = 0.043). CAF increased Lactobacillus johnsonii (+75%, p < 0.05), while reducing L. murinus and L. intestinalis (~90%, p < 0.05). MFB supplementation restored Bifidobacterium Pseudolongum and increased Akkermansia muciniphila levels in the P2, I1, and I2 groups (~20-fold, p < 0.05). Bacteroides dorei was present in all groups except the PC group. These bacteria presented a positive correlation with key SCFAs. Conclusions: The results from this study indicated that MFB supplementation modulated gut microbiota composition and enhanced SCFA production, thereby strengthening intestinal barrier integrity and reducing gut-derived inflammation. Collectively, these effects attenuated hepatic lipid accumulation and inflammation, highlighting the potential of MFB to restore gut-liver axis homeostasis disrupted by CAF-induced dysbiosis in adolescent rats.},
}

Animals
*Gastrointestinal Microbiome
Male
Rats, Sprague-Dawley
*Fruit
*Liver/pathology/metabolism
Rats
Dysbiosis
*Fatty Liver/etiology/prevention & control
Disease Models, Animal
Metabolic Syndrome/etiology
*Diet/adverse effects

@article {pmid41599773,
year = {2026},
author = {Mucci, B and Palazzolo, E and Ruberti, F and Ientile, L and Natale, M and Esposito, S},
title = {Advances in the Management of Pediatric Inflammatory Bowel Disease: From Biologics to Small Molecules.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010176},
pmid = {41599773},
issn = {1424-8247},
abstract = {Background: The management of pediatric inflammatory bowel disease (PIBD) has evolved significantly over the past two decades, transitioning from corticosteroids and immunomodulators to biologic and small-molecule therapies. These advances have aimed not only to control inflammation but also to promote mucosal healing, improve growth, and enhance long-term quality of life. Objectives: This narrative review summarizes current evidence on the efficacy, safety, and clinical applications of biologic and novel small-molecule therapies in PIBD, highlighting emerging trends in personalized and precision-based management. Methods: A literature search was performed across PubMed, Embase, and the Cochrane Library, focusing on studies published within the last five years. Additional data were retrieved from key guidelines and position papers issued by ECCO-ESPGHAN, SIGENP, the FDA, and the EMA. Results: Anti-tumor necrosis factor (TNF) agents such as infliximab and adalimumab remain first-line biologics with proven efficacy in remission induction and maintenance. Newer biologics-vedolizumab, ustekinumab, risankizumab, and mirikizumab-offer alternatives for anti-TNF-refractory cases, showing encouraging short-term results and favorable safety profiles. Although many are approved only for adults with limited pediatric evidence, emerging small molecules-including Janus kinase (JAK) inhibitors (tofacitinib, upadacitinib) and sphingosine-1-phosphate (S1P) modulators (etrasimod)-provide oral, rapidly acting, and non-immunogenic treatment options for refractory disease. Furthermore, the gut microbiome is increasingly recognized as an emerging therapeutic target in PIBD, with growing evidence that host-microbiome interactions can influence both the efficacy and safety of biologics and small-molecule therapies. Conclusions: While biologics and small molecules have transformed PIBD management, challenges remain, including high treatment costs, limited pediatric trial data, and variable access worldwide. Future directions include multicenter pediatric studies, integration of pharmacogenomics, and biomarker-guided precision medicine to optimize early, individualized treatment and improve long-term outcomes.},
}

@article {pmid41599753,
year = {2026},
author = {Jin, Y and Wang, L and Lin, R and He, J and Liu, D and Liu, Y and Deng, Y},
title = {Synergistic Effects of Plant Polysaccharides and Probiotics: A Novel Dietary Approach for Parkinson's Disease Intervention.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010157},
pmid = {41599753},
issn = {1424-8247},
support = {Grant Nos. 82003985, 81973712, and 82004030//the National Natural Science Foundation of China/ ; Grant No. 20230204019YY//the Jilin Province Science and Technology Development Plant/ ; Grant No. 2023C027-3//the Jilin Provincial Development and Reform Commission Project/ ; Grant Nos, S202410199012, S202410199095X, andS202510199023//the Undergraduate Innovation and Entrepreneurship Proiects/ ; },
abstract = {Parkinson's disease (PD), the second most common neurodegenerative disorder globally, relies primarily on dopamine replacement therapy for conventional treatment. This approach fails to reverse core pathological processes and is associated with long-term side effects. Recent research on the microbiota-gut-brain axis (MGBA) has revealed that PD pathology may originate in the gut, forming a vicious cycle from the gut to brain through α-synuclein propagation, gut dysbiosis, intestinal barrier disruption, and neuroinflammation. This offers a novel perspective for managing PD through dietary interventions that modulate the gut microbiome. However, single probiotic or prebiotic interventions show limited efficacy. This review systematically introduces the novel concept of "synbiotics combining medicinal plant polysaccharides with probiotics," aiming to integrate traditional "medicinal food" wisdom with modern microbiome science. The article systematically elucidates the pathological mechanisms of MGBA dysfunction in PD and the intervention mechanisms of probiotics and emphasizes the structural and functional advantages of medicinal plant polysaccharide as superior prebiotics. The core section delves into the multifaceted synergistic mechanisms between these two components: enhancing probiotic colonization and vitality, optimizing microbial metabolic output, synergistically reinforcing the intestinal and blood-brain barriers, and jointly regulating immune and neuroinflammation. This approach targets the MGBA to achieve multi-level intervention for PD.},
}

@article {pmid41599684,
year = {2026},
author = {Bangeppagari, M and Jagadish, P and Srinivasa, A and Choi, W and Tiwari, P},
title = {Natamycin in Food and Ophthalmology: Knowledge Gaps and Emerging Insights from Zebrafish Models.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010086},
pmid = {41599684},
issn = {1424-8247},
abstract = {Natamycin, a polyene macrolide antifungal, has long been used as a food preservative and is the only Food and Drug Administration (FDA)-approved topical treatment for fungal keratitis. While its safety is supported by specific ergosterol interaction and minimal systemic absorption, current research mainly focuses on short-term effects, often overlooking long-term, developmental, and microbiome-related impacts. In food applications, questions remain about cumulative exposure and potential disruptions to gut microbiota. For ophthalmology, advanced delivery methods like nanocarriers and hydrogels enhance drug penetration but may alter pharmacokinetics and pose formulation challenges. Regulatory approvals have historically depended on established safe use and limited toxicological data, emphasizing the need for more systematic evaluations. Zebrafish (Danio rerio) represent a promising yet underutilized model for addressing significant gaps in research, particularly in the realms of microbiome studies, ocular health, developmental processes, and multigenerational effects. When paired with omics technologies, zebrafish facilitate comprehensive system-level mapping of drug-induced outcomes. This review consolidates existing evidence and positions zebrafish as a vital translational link between in vitro assays, mammalian models, and clinical practice. Additionally, it proposes a framework to ensure the effective and scientifically supported use of natamycin in both food and medicinal applications.},
}

@article {pmid41599664,
year = {2025},
author = {Hwang, JH and Choi, YK},
title = {Herbal and Natural Products for Antibiotic-Associated Diarrhea: A Systematic Review of Animal Studies Focusing on Molecular Microbiome and Barrier Outcomes.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010064},
pmid = {41599664},
issn = {1424-8247},
support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; },
abstract = {Background/Objectives: Antibiotic-associated diarrhea (AAD) arises from antibiotic-induced disruption of microbial diversity, metabolic activity, epithelial integrity, and mucosal immunity. Probiotics are widely used but often show limited efficacy under antibiotic pressure. Herbal and natural products (HNPs) may provide multi-target benefits by modulating microbiota-dependent and host-directed pathways. This review synthesized animal studies evaluating HNP or HNP-probiotic combination (HNP-C) therapies using molecular microbiome endpoints. Methods: Following PRISMA 2020 guidelines, controlled in vivo studies assessing HNP or HNP-C interventions for AAD were searched in Pubmed, EMBASE, Web of Science, Scopus, and CNKI through November 2025. Eligible studies reported microbial diversity, taxonomic shifts, short-chain fatty acids (SCFAs), barrier markers, or immune responses. Risk of bias was assessed using the SYRCLE tool. Due to heterogeneity, findings were narratively synthesized. Results: Twenty-seven studies met inclusion criteria (21 HNP, 6 HNP-C). HNP monotherapies consistently improved α-diversity, shifted β-diversity toward healthy controls, restored SCFA-producing taxa, and increased SCFA levels. They also enhanced tight junction proteins and reduced inflammatory cytokines. HNP-C interventions demonstrated more comprehensive microbial, epithelial, and immune recovery; however, only two studies included direct comparisons among HNP-only, probiotic-only, and combination groups. In these, HNP-C showed greater improvements than individual components, suggesting complementary or potentially complementary or additive effects. Other HNP-C studies were limited by absent comparator arms. Conclusions: HNPs appear to support recovery of microbial diversity, metabolic function, epithelial barrier integrity, and immune regulation by engaging microbiota-dependent and host-mediated mechanisms. HNP-C strategies may offer complementary benefits, although rigorously controlled comparative studies and clinical validation remain needed.},
}

@article {pmid41599644,
year = {2025},
author = {Machado, EP and Junkert, AM and Lazo, REL and Fernandes, IDC and Tonin, FS and Ferreira, LM and Borba, HHL and Pontarolo, R},
title = {Mapping the Vaginal Metabolic Profile in Dysbiosis, Persistent Human Papillomavirus Infection, and Cervical Intraepithelial Neoplasia: A Scoping Review.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {1},
pages = {},
doi = {10.3390/ph19010042},
pmid = {41599644},
issn = {1424-8247},
abstract = {Background/Objectives: This scoping review aimed to map evidence on metabolic alterations in the vaginal environment associated with dysbiosis, transient and persistent human papillomavirus (HPV) infection, and cervical dysplasia, highlighting potential metabolic and protein biomarkers for early detection of cervical cancer. Methods: Systematic searches were conducted in PubMed, Scopus, and Web of Science, following the JBI methodology and PRISMA-ScR guidelines. Studies jointly evaluating vaginal metabolites and proteins in women with HPV and cervical intraepithelial neoplasia (CIN) in the context of dysbiosis were included. Results: After duplicate removal, 196 records were screened, and 41 studies were selected-mostly cross-sectional observational designs-published between 2006 and 2025, predominantly by Chinese research groups. Lactobacillus spp. predominated in HPV-negative women, while HPV infection was associated with a dysbiotic environment enriched with anaerobes such as Gardnerella vaginalis, Atopobium vaginae, Prevotella, and Sneathia. Of 389 metabolic and protein markers associated with HPV infection and CIN, 44 underwent ROC analysis, with prolineaminopeptidase, 5'-O-methylmelledonal, and calonectin showing high diagnostic performance (AUC > 0.90). Conclusions: These results suggest vaginal microbiome and metabolic profiles may represent promising biomarkers for persistent HPV infection. Further, longitudinal studies with larger samples are needed for clinical validation.},
}

@article {pmid41599414,
year = {2026},
author = {Buendia-Corona, RE and Velasco Dey, MF and Valencia Robles, L and Hernández-Biviano, HJ and Hermosillo-Abundis, C and Castro-Pastrana, LI},
title = {Computational Identification of Blood-Brain Barrier-Permeant Microbiome Metabolites with Binding Affinity to Neurotransmitter Receptors in Neurodevelopmental Disorders.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {2},
pages = {},
doi = {10.3390/molecules31020366},
pmid = {41599414},
issn = {1420-3049},
support = {CVU 921738//SECIHTI/ ; },
mesh = {*Blood-Brain Barrier/metabolism ; Humans ; *Neurodevelopmental Disorders/metabolism/microbiology ; Molecular Docking Simulation ; *Receptors, Neurotransmitter/metabolism/chemistry ; *Gastrointestinal Microbiome ; },
abstract = {The gut microbiome produces thousands of metabolites with potential to modulate central nervous system function through peripheral or direct neural mechanisms. Tourette syndrome, attention-deficit/hyperactivity disorder, and autism spectrum disorder exhibit shared neurotransmitter dysregulation and microbiome alterations, yet mechanistic links between microbial metabolites and receptor-mediated neuromodulation remain unclear. We screened 27,642 microbiome SMILES metabolites for blood-brain barrier permeability using rule-based SwissADME classification and a PyTorch 2.0 neural network trained on 7807 experimental compounds (test accuracy 86.2%, AUC 0.912). SwissADME identified 1696 BBB-crossing metabolites following Lipinski's criteria, while PyTorch classified 2484 metabolites with expanded physicochemical diversity. Following 3D conformational optimization (from SMILES) and curation based on ≤32 rotatable bonds, molecular docking was performed against five neurotransmitter receptors representing ionotropic (GABRA2, GRIA2, GRIN2B) and metabotropic (DRD4, HTR1A) receptor classes. The top 50 ligands across five receptors demonstrated method-specific BBB classification (44% SwissADME-only, 44% PyTorch-only, 12% overlap), validating complementary prediction approaches. Fungal metabolites from Ascomycota dominated high-affinity top ligands (66%) and menaquinone MK-7 showed broad phylogenetic conservation (71.4% of phylum). Our results establish detailed receptor-metabolite interaction maps, with fungal metabolites dominating high-affinity ligands, challenging the prevailing bacterial focus of the microbiome and providing a foundation for precision medicine and a framework for developing microbiome-targeted therapeutics to address clinical needs in neurodevelopmental disorders.},
}

*Blood-Brain Barrier/metabolism
Humans
*Neurodevelopmental Disorders/metabolism/microbiology
Molecular Docking Simulation
*Receptors, Neurotransmitter/metabolism/chemistry
*Gastrointestinal Microbiome

@article {pmid41599407,
year = {2026},
author = {Cevallos-Fernández, E and Beltrán-Sinchiguano, E and Jácome, B and Quintana, T and Rivera, N},
title = {Fermented Plant-Based Foods and Postbiotics for Glycemic Control-Microbial Biotransformation of Phytochemicals.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {2},
pages = {},
doi = {10.3390/molecules31020360},
pmid = {41599407},
issn = {1420-3049},
mesh = {Humans ; *Phytochemicals/metabolism/pharmacology ; Animals ; *Fermented Foods ; *Glycemic Control ; Biotransformation ; Fermentation ; Gastrointestinal Microbiome ; },
abstract = {Plant-based fermented foods are increasingly promoted for glycemic control, yet their mechanisms and clinical impact remain incompletely defined. This narrative review synthesizes mechanistic, preclinical, and human data for key matrices-kimchi and other fermented vegetables, tempeh/miso/natto, and related legume ferments, kombucha and fermented teas, plant-based kefir, and cereal/pulse sourdoughs. Across these systems, microbial β-glucosidases, esterases, tannases, and phenolic-acid decarboxylases remodel polyphenols toward more bioaccessible aglycones and phenolic acids, while lactic and acetic fermentations generate organic acids, exopolysaccharides, bacterial cellulose, γ-polyglutamic acid, γ-aminobutyric acid, and bioactive peptides. We map these postbiotic signatures onto proximal mechanisms-α-amylase/α-glucosidase inhibition, viscosity-driven slowing of starch digestion, gastric emptying and incretin signaling, intestinal-barrier reinforcement, and microbiota-dependent short-chain-fatty-acid and bile-acid pathways-and their downstream effects on AMPK/Nrf2 signaling and the gut-liver axis. Animal models consistently show improved glucose tolerance, insulin sensitivity, and hepatic steatosis under fermented vs. non-fermented diets. In humans, however, glycemic effects are modest and highly context-dependent: The most robust signal is early postprandial attenuation with γ-PGA-rich natto, strongly acidified or low-glycemic sourdough breads, and selected kombucha formulations, particularly in individuals with impaired glucose regulation. We identify major sources of heterogeneity (starters, process parameters, substrates, background diet) and safety considerations (sodium, ethanol, gastrointestinal symptoms) and propose minimum reporting standards and trial designs integrating metabolomics, microbiome, and host-omics. Overall, plant-based ferments appear best positioned as adjuncts within cardiometabolic dietary patterns and as candidates for "purpose-built" postbiotic products targeting early glycemic excursions and broader metabolic risk.},
}

Humans
*Phytochemicals/metabolism/pharmacology
Animals
*Fermented Foods
*Glycemic Control
Biotransformation
Fermentation
Gastrointestinal Microbiome

@article {pmid41599227,
year = {2026},
author = {Cordero, C and Caballero-Román, A and Martínez-Ruiz, S and Olivo-Martínez, Y and Baldoma, L and Badia, J},
title = {Extracellular Vesicles from Probiotic and Beneficial Escherichia coli Strains Exert Multifaceted Protective Effects Against Rotavirus Infection in Intestinal Epithelial Cells.},
journal = {Pharmaceutics},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/pharmaceutics18010120},
pmid = {41599227},
issn = {1999-4923},
support = {PID2019-107327RB-100//MCIU(MICCIN)/AEI/ ; PID2022-137192OB-I00//MICIU/AEI/10.13039/501100011033/ ; },
abstract = {Background/Objectives: Rotavirus remains a major cause of severe acute gastroenteritis in infants worldwide. The suboptimal efficacy of current vaccines underscores the need for alternative microbiome-based interventions, including postbiotics. Extracellular vesicles (EVs) from probiotic and commensal E. coli strains have been shown to mitigate diarrhea and enhance immune responses in a suckling-rat model of rotavirus infection. Here, we investigate the regulatory mechanisms activated by EVs in rotavirus-infected enterocytes. Methods: Polarized Caco-2 monolayers were used as a model of mature enterocytes. Cells were pre-incubated with EVs from the probiotic E. coli Nissle 1917 (EcN) or the commensal EcoR12 strain before rotavirus infection. Intracellular Ca[2+] concentration, ROS levels, and the expression of immune- and barrier-related genes and proteins were assessed at multiple time points post-infection. Results: EVs from both strains exerted broad protective effects against rotavirus-induced cellular dysregulation, with several responses being strain-specific. EVs interfered with viral replication by counteracting host cellular processes essential for rotavirus propagation. Specifically, EV treatment significantly reduced rotavirus-induced intracellular Ca[2+] mobilization, ROS production, and COX-2 expression. In addition, both EV types reduced virus-induced mucin secretion and preserved tight junction organization, thereby limiting viral access to basolateral coreceptors. Additionally, EVs enhanced innate antiviral defenses via distinct, strain-dependent pathways: EcN EVs amplified IL-8-mediated responses, whereas EcoR12 EVs preserved the expression of interferon-related signaling genes. Conclusions: EVs from EcN and EcoR12 act through multiple complementary mechanisms to restrict rotavirus replication, spread, and immune evasion. These findings support their potential as effective postbiotic candidates for preventing or treating rotavirus infection.},
}

@article {pmid41599184,
year = {2026},
author = {Caturano, A and Nilo, D and Nilo, R and Sircana, MC and Erul, E and Zielińska, K and Russo, V and Santonastaso, E and Sasso, FC},
title = {Old Drug, New Science: Metformin and the Future of Pharmaceutics.},
journal = {Pharmaceutics},
volume = {18},
number = {1},
pages = {},
doi = {10.3390/pharmaceutics18010077},
pmid = {41599184},
issn = {1999-4923},
abstract = {Metformin, a 60-year-old biguanide and cornerstone of type 2 diabetes therapy, continues to challenge and inspire modern pharmaceutical science. Despite its chemical simplicity, metformin displays highly complex pharmacokinetic and pharmacodynamic behavior driven by transporter dependence, luminal activity, and formulation-sensitive exposure. Originally regarded as limited by low permeability and incomplete absorption, metformin has emerged as a paradigm for gut-targeted therapy, controlled- and delayed-release systems, and personalized pharmaceutics. Growing evidence has repositioned the intestine, rather than systemic plasma exposure, as a major site of action, highlighting the central role of organic cation transporters and multidrug efflux systems in determining efficacy, variability, and gastrointestinal tolerability. Beyond metabolic control, insights into transporter regulation, pharmacogenetics, microbiome interactions, and manufacturing quality have expanded metformin's relevance as a model compound for contemporary drug development. Advances in formulation design, quality-by-design manufacturing, and regulatory control have further reinforced its clinical robustness, while repurposing efforts in oncology, immunometabolism, and regenerative medicine underscore its translational potential. This review integrates mechanistic pharmacology, formulation science, and clinical translation to position metformin not merely as an antidiabetic agent, but as a didactic model illustrating the evolution of pharmaceutics from molecule-centered design to system-oriented, precision-driven therapy.},
}

@article {pmid41599092,
year = {2026},
author = {Sinhalage, K and Polizel, GHG and Karrow, NA and Schenkel, FS and Cánovas, Á},
title = {Sheep Genetic Resistance to Gastrointestinal Nematode Infections: Current Insights from Transcriptomics and Other OMICs Technologies-A Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010106},
pmid = {41599092},
issn = {2076-0817},
support = {0//Ontario Ministry of Agriculture, Food and Agribusiness (OMAFA), the Ontario Agri-Food Innovation Alliance/ ; 0//Agricultural Research and Innovation Ontario (ARIO)/ ; 0//Ontario Sheep Farmers/ ; 0//the Natural Sciences and Engineering Research Council of Canada (NSERC; Ottawa, Ontario, Canada) and the NSERC - Discovery Grant Established Researchers/ ; 0//Food from Thought, University of Guelph/ ; },
mesh = {Animals ; Sheep ; *Sheep Diseases/parasitology/genetics/immunology ; *Nematode Infections/veterinary/genetics/parasitology/immunology ; *Disease Resistance/genetics ; Transcriptome ; Nematoda ; Genomics/methods ; *Gastrointestinal Diseases/veterinary/genetics/parasitology/immunology ; Host-Parasite Interactions/genetics ; Proteomics ; Gene Expression Profiling ; },
abstract = {Gastrointestinal nematode (GIN) infections are the most prevalent parasitic diseases in grazing sheep worldwide, causing significant productivity losses, high mortality and, as a result, economic losses and emerging animal welfare concerns. Conventional control strategies, primarily relying on anthelmintic treatments, face limitations due to rising drug resistance and environmental concerns, underscoring the need for sustainable alternatives. Selective breeding for host genetic resistance has emerged as a promising strategy, while recent advances in transcriptomics and integrative omics research are providing deeper insights into the immune pathways and molecular and genetic mechanisms that underpin host-parasite interactions. This review summarizes current evidence on transcriptomic signatures associated with resistance and susceptibility to H. contortus and T. circumcincta GIN infections, highlighting candidate genes, functional genetic markers, key immune pathways, and regulatory networks. Furthermore, we discuss how other omics approaches, including genomics, proteomics, metabolomics, microbiome, and multi-omics integrations, provide perspectives that enhance the understanding of the complexity of the GIN resistance trait. Transcriptomic studies, particularly using RNA-Sequencing technology, have revealed differential gene expression, functional genetic variants, such as SNPs and INDELs, in expressed regions and splice junctions, and regulatory long non-coding RNAs that distinguish resistance from susceptible sheep, highlighting pathways related to Th2 immunity, antigen presentation, tissue repair, and stress signaling. Genomic analyses have identified SNPs, QTL, and candidate genes linked to immune regulation and parasite resistance. Proteomic and metabolomic profiling further elucidates breed- and tissue-specific alterations in protein abundance and metabolic pathways, while microbiome studies demonstrate distinct microbial signatures in resistant sheep, suggesting a role in modulating host immunity. In conclusion, emerging multi-omics approaches and their integration strategies provide a comprehensive framework for understanding the complex host-parasite interactions that govern GIN resistance, offering potential candidate biomarkers for genomic selection and breeding programs aimed at developing sustainable, parasite-resistant sheep populations.},
}

Animals
Sheep
*Sheep Diseases/parasitology/genetics/immunology
*Nematode Infections/veterinary/genetics/parasitology/immunology
*Disease Resistance/genetics
Transcriptome
Nematoda
Genomics/methods
*Gastrointestinal Diseases/veterinary/genetics/parasitology/immunology
Host-Parasite Interactions/genetics
Proteomics
Gene Expression Profiling

@article {pmid41599047,
year = {2026},
author = {Gioula, G and Exindari, M},
title = {The Airway Microbiome as a Modulator of Influenza Virus Infection: Mechanistic Insights and Translational Perspectives-Review.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010063},
pmid = {41599047},
issn = {2076-0817},
mesh = {Humans ; *Influenza, Human/microbiology/virology/immunology ; *Microbiota ; Animals ; *Orthomyxoviridae ; *Respiratory System/microbiology ; },
abstract = {Outcomes of influenza virus infection vary widely across individuals, reflecting not only viral genetics and host factors but also the composition and function of the airway microbiome. Over the past few years, mechanistic work has clarified how specific commensals (for example, Staphylococcus epidermidis and Streptococcus oralis) restrict influenza replication by priming epithelial interferon-λ programs, reshaping intracellular metabolite pools (notably polyamines), dampening host protease activity, and maintaining barrier integrity; meanwhile, pathobionts (notably Staphylococcus aureus and Streptococcus pneumoniae) can enhance viral fitness via secreted proteases and neuraminidases that activate hemagglutinin and remodel sialylated glycoconjugates and mucus, setting the stage for secondary bacterial disease. Recent studies also highlight the gut-lung axis: gut microbiota-derived short-chain fatty acids (SCFAs), especially acetate, protect tight junctions and modulate antiviral immunity in influenza models. Together, these insights motivate translational strategies-from intranasal live biotherapeutics (LBPs) to metabolite sprays and decoy/dual neuraminidase approaches-that complement vaccines and antivirals. We synthesize recent evidence and outline a framework for leveraging the airway microbiome to prevent infection, blunt severity, and reduce transmission. Key priorities include strain-level resolution of commensal effects, timing/dosing windows for metabolites and LBPs, and microbiome-aware clinical pathways for anticipating and averting bacterial coinfection. Overall, the airway microbiome emerges as a tractable lever for influenza control at the site of viral entry, with several candidates moving toward clinical testing.},
}

Humans
*Influenza, Human/microbiology/virology/immunology
*Microbiota
Animals
*Orthomyxoviridae
*Respiratory System/microbiology

@article {pmid41599046,
year = {2026},
author = {Plewa, P and Graczyk, P and Figiel, K and Dach, A and Pawlik, A},
title = {Gut and Joint Microbiome and Dysbiosis: A New Perspective on the Pathogenesis and Treatment of Osteoarthritis.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010062},
pmid = {41599046},
issn = {2076-0817},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Osteoarthritis/therapy/microbiology/pathology/etiology ; *Dysbiosis/microbiology/therapy ; Probiotics/therapeutic use ; Animals ; *Joints/microbiology/pathology ; },
abstract = {Osteoarthritis (OA) is one of the most common and burdensome musculoskeletal disorders and a major cause of pain, disability, and reduced quality of life worldwide. In recent years, increasing attention has been paid to extra-articular factors influencing its development and progression, opening new avenues of research into pathophysiological mechanisms and potential therapies. One of the most promising areas concerns the role of the gut-joint axis and related alterations in the gut microbiome. Numerous studies indicate that an imbalance of gut bacteria, increased intestinal permeability, and low-grade inflammation may contribute to the progression of degenerative joint processes. The mechanisms through which the microbiota influences the immune system and host metabolism are becoming increasingly well understood, including pathways involving short-chain fatty acids, tryptophan metabolites, and bile acids. Despite growing evidence linking dysbiosis to the pathogenesis of OA, effective therapeutic strategies based on microbiome modulation remain under active investigation. Among the most frequently studied approaches are probiotics, dietary interventions, and more advanced strategies such as gut microbiota transplantation and targeted modulation of microbial metabolites. However, before these methods can become part of routine treatment, extensive clinical trials and a clearer understanding of causal relationships between the microbiome and joint degeneration are required. This article summarises the current state of knowledge regarding the role of the gut microbiome in osteoarthritis, outlines key research findings, and highlights current and potential therapeutic directions.},
}

Humans
*Gastrointestinal Microbiome
*Osteoarthritis/therapy/microbiology/pathology/etiology
*Dysbiosis/microbiology/therapy
Probiotics/therapeutic use
Animals
*Joints/microbiology/pathology

@article {pmid41599039,
year = {2026},
author = {Wang, Z and Chen, G and Yang, M and Wang, S and Fang, J and Shi, C and Gu, Y and Ning, Z},
title = {Host-Filtered Blood Nucleic Acids for Pathogen Detection: Shared Background, Sparse Signal, and Methodological Limits.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010055},
pmid = {41599039},
issn = {2076-0817},
support = {2024-PWXZ-04//New Quality Clinical Specialty Program of High-end Medical Disciplinary Construction in Shanghai Pudong New Area/ ; 2024ZDXK0019//Shanghai Municipal Health Commission, Key Discipline of Shanghai Health System, Cardiology/ ; PW2025D-01//The Scientific Research Program of Shanghai Pudong New Area Health Commission (the Joint Research and Development Program)/ ; },
mesh = {Humans ; *Metagenomics/methods ; *Tuberculosis/microbiology/diagnosis/blood ; Microbiota/genetics ; *Cell-Free Nucleic Acids/blood/genetics ; *Coronary Artery Disease/microbiology/diagnosis/blood ; Mycobacterium tuberculosis/genetics/isolation & purification ; Male ; Female ; Cohort Studies ; },
abstract = {Plasma cell-free RNA (cfRNA) metagenomics is increasingly explored for blood-based pathogen detection, but the structure of the shared background "blood microbiome", the reproducibility of reported signals, and the practical limits of this approach remain unclear. We performed a critical re-analysis and benchmarking ("stress test") of host-filtered blood RNA sequencing data from two cohorts: a bacteriologically confirmed tuberculosis (TB) cohort (n = 51) previously used only to derive host cfRNA signatures, and a coronary artery disease (CAD) cohort (n = 16) previously reported to show a CAD-shifted "blood microbiome" enriched for periodontal taxa. Both datasets were processed with a unified pipeline combining stringent human read removal and taxonomic profiling using the latest versions of specialized tools Kraken2 and MetaPhlAn4. Across both cohorts, only a minority of non-host reads were classifiable; under strict host filtering, classified non-host reads comprised 7.3% (5.0-12.0%) in CAD and 21.8% (5.4-31.5%) in TB, still representing only a small fraction of total cfRNA. Classified non-host communities were dominated by recurrent, low-abundance taxa from skin, oral, and environmental lineages, forming a largely shared, low-complexity background in both TB and CAD. Background-derived bacterial signatures showed only modest separation between disease and control groups, with wide intra-group variability. Mycobacterium tuberculosis-assigned reads were detectable in many TB-positive samples but accounted for ≤0.001% of total cfRNA and occurred at similar orders of magnitude in a subset of TB-negative samples, precluding robust discrimination. Phylogeny-aware visualization confirmed that visually "enriched" taxa in TB-positive plasma arose mainly from background-associated clades rather than a distinct pathogen-specific cluster. Collectively, these findings provide a quantitative benchmark of the background-dominated regime and practical limits of plasma cfRNA metagenomics for pathogen detection, highlighting that practical performance is constrained more by a shared, low-complexity background and sparse pathogen-derived fragments than by large disease-specific shifts, underscoring the need for transparent host filtering, explicit background modeling, and integration with targeted or orthogonal assays.},
}

Humans
*Metagenomics/methods
*Tuberculosis/microbiology/diagnosis/blood
Microbiota/genetics
*Cell-Free Nucleic Acids/blood/genetics
*Coronary Artery Disease/microbiology/diagnosis/blood
Mycobacterium tuberculosis/genetics/isolation & purification
Male
Female
Cohort Studies

@article {pmid41599006,
year = {2025},
author = {Kaminska, D and Ratajczak, M and Nowicka, W and Dlugaszewska, J and Gajecka, M},
title = {New Strategies for Preventing Perinatal Group B Streptococcus (GBS) Infections.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010022},
pmid = {41599006},
issn = {2076-0817},
mesh = {Humans ; *Streptococcal Infections/prevention & control/microbiology ; *Streptococcus agalactiae/drug effects/immunology ; Pregnancy ; Female ; Infant, Newborn ; *Infectious Disease Transmission, Vertical/prevention & control ; *Pregnancy Complications, Infectious/prevention & control/microbiology ; Anti-Bacterial Agents/therapeutic use ; Antibiotic Prophylaxis/methods ; Streptococcal Vaccines/immunology ; Vagina/microbiology ; },
abstract = {Group B Streptococcus (GBS) is a component of the natural human microbiota, colonizing the genitourinary tract and the distal gastrointestinal tract. Due to its production of numerous virulence factors, GBS can cause infections in pregnant women, newborns, and immunocompromised individuals. In newborns, GBS infection may present as severe pneumonia, meningitis, or sepsis. Screening for maternal GBS colonization, combined with intrapartum antibiotic prophylaxis for colonized women, is currently regarded as the most effective strategy for preventing neonatal GBS infections. However, growing concerns regarding antibiotic resistance and the negative impact of antibiotics on the neonatal microbiome have intensified the search for alternative approaches. These include the development of a vaccine and methods to reduce vaginal colonization in pregnant women.},
}

Humans
*Streptococcal Infections/prevention & control/microbiology
*Streptococcus agalactiae/drug effects/immunology
Pregnancy
Female
Infant, Newborn
*Infectious Disease Transmission, Vertical/prevention & control
*Pregnancy Complications, Infectious/prevention & control/microbiology
Anti-Bacterial Agents/therapeutic use
Antibiotic Prophylaxis/methods
Streptococcal Vaccines/immunology
Vagina/microbiology

@article {pmid41598993,
year = {2025},
author = {Wu, X and Zhang, X and Liang, Y and Chen, X and Guo, Y and Zhao, W},
title = {Causal Relationships Between the Oral Microbiome and Autoimmune Diseases: A Mendelian Randomization Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/pathogens15010009},
pmid = {41598993},
issn = {2076-0817},
support = {82270965//National Natural Science Foundation of China/ ; 2023B03J1253//Science and Technology Program in Guangzhou/ ; PY2024032//Science Research Cultivation Program of Stomatological Hospital, Southern Medical University/ ; },
mesh = {Humans ; Mendelian Randomization Analysis ; *Autoimmune Diseases/microbiology/etiology/genetics ; *Microbiota ; Genome-Wide Association Study ; *Mouth/microbiology ; Saliva/microbiology ; },
abstract = {The relationship between the oral microbiome and autoimmune diseases (ADs) has attracted considerable research interest. This study employed two-sample Mendelian randomization (MR) to investigate causal relationships between oral microbiota and six ADs, including rheumatoid arthritis (RA), type 1 diabetes (T1D), inflammatory bowel disease (IBD), multiple sclerosis (MS), systemic lupus erythematosus (SLE), and Sjögren's syndrome (SS). Using genome-wide association study data from oral microbiome features and ADs, we applied inverse-variance weighted estimation complemented by sensitivity analyses and reverse MR to assess robustness and reverse causation. Analysis of 309 tongue dorsum and 285 salivary microbial features identified four tongue dorsum and five salivary taxa with genome-wide significant causal effects. Specific microbial taxa from both oral niches demonstrated protective or risk-enhancing effects for RA, T1D, IBD, and MS, while no causal associations were found for SLE or SS. These findings establish the causal role of specific oral microbiota in autoimmune pathogenesis and highlight priority candidates for further investigation as potential microbial biomarkers.},
}

Humans
Mendelian Randomization Analysis
*Autoimmune Diseases/microbiology/etiology/genetics
*Microbiota
Genome-Wide Association Study
*Mouth/microbiology
Saliva/microbiology

@article {pmid41598945,
year = {2026},
author = {Hirata, K and Suzuki, T and Yura, K and Asahi, T and Kataoka, K},
title = {Gut Microbiome Differences Across Mixed-Sex and Female-Only Social Rearing Regimes in Female Field Crickets Teleogryllus occipitalis (Orthoptera: Gryllidae).},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010091},
pmid = {41598945},
issn = {2075-4450},
support = {24KJ2101//Japan Society for the Promotion of Science/ ; JPJ009237//Cabinet Office/ ; },
abstract = {The insect gut microbiome contributes to various host physiological processes and behaviors, such as digestion, nutrient absorption, immunity, mate choice, and fecundity. The social environment can shape gut microbial communities. Mixed-sex vs. female-only rearing is an important social context because it differs in exposure to the opposite sex and mating opportunities, which may in turn affect female physiology that may influence their gut microbiome. Despite the growing recognition of these social-microbial interactions, most studies have relied on 16S rRNA amplicon sequencing or qPCR, which provide only coarse taxonomic resolution and limited functional insight. In this study, we used whole-genome shotgun metagenomics to examine changes in microbial diversity and functional gene composition in the female field cricket Teleogryllus occipitalis (Serville) (Orthoptera: Gryllidae) reared under two social conditions: mixed-sex rearing and female-only rearing. Species richness and diversity analyses revealed that community composition separated between females from mixed-sex and female-only rearing. Functional profiling indicated higher relative abundances of genes annotated to nutrient processing and inter-bacterial competition in females from mixed-sex rearing, whereas females from female-only rearing showed relative enrichment of genes annotated to stress resistance and nitrogen fixation. These findings provide a genome-resolved foundation for testing how social rearing conditions covary with gut microbiome composition and functional potential in female crickets.},
}

@article {pmid41598908,
year = {2026},
author = {González-Peña, R and Hidalgo-Martínez, DO and Laredo-Tiscareño, SV and Huerta, H and de Luna-Santillana, EJ and Adame-Gallegos, JR and Rodríguez-Alarcón, CA and Rubio-Tabares, E and García-Rejón, JE and Muñoz-Ramírez, ZY and Tangudu, C and Garza-Hernández, JA},
title = {Characterization of the Bacteriome of Culicoides reevesi from Chihuahua, Northern Mexico: Symbiotic and Pathogenic Associations.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010052},
pmid = {41598908},
issn = {2075-4450},
support = {419- 395 24-23//Secretaría de Ciencia, Humanidades, Tecnología e Innovación (SECIHTI)/ ; SIP20250075//Secretaría de Investigación y Posgrado from Instituto Politécnico Nacional/ ; },
abstract = {Culicoides biting midges are vectors of veterinary and zoonotic pathogens, yet the bacteriome of several species remains unexplored. Culicoides reevesi, a poorly studied species in northern Mexico, represents an opportunity to investigate microbial associations that may influence vector biology. Adults of C. reevesi were analyzed using 16S rRNA amplicon sequencing, followed by functional prediction with PICRUSt2. Heatmaps and pathway summaries were generated to highlight dominant taxa and functions. The bacteriome was dominated by Pseudomonadota, followed by Actinomycetota, Bacillota, and Bacteroidota. Symbiotic taxa such as Asaia and Cardinium were identified alongside potentially pathogenic bacteria, including Escherichia coli, Mycobacterium avium, Vibrio parahaemolyticus, and Enterococcus faecalis. Functional predictions indicated metabolic versatility, with abundant pathways related to aerobic respiration, the TCA cycle, amino acid biosynthesis, and quorum sensing. Despite all samples being collected from the same site and date, apparent differences in bacterial composition were observed across pools, suggesting microhabitat or host-related variability. This study provides the first taxonomic and functional baseline of the C. reevesi bacteriome. The detection of both symbiotic and pathogenic bacteria highlights the dual ecological role of the microbiome in host fitness and pathogen transmission potential. In conclusion, we suggest that these microbial associations influence vector physiology and competence, providing a basis for future microbiome-based control strategies. These findings emphasize the importance of integrating microbiome analyses into entomological surveillance and vector control strategies in endemic regions.},
}

@article {pmid41598906,
year = {2026},
author = {Guo, B and Yi, X and Sun, Q and Sun, K and Guo, L and Guo, Y},
title = {The Honey Bee Body Surface as a Microbial Hub: Connectivity Shaped by Monoculture vs. Polyculture Farming.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010053},
pmid = {41598906},
issn = {2075-4450},
abstract = {Honey bees, as vital pollinators and essential contributors to terrestrial ecosystems, play a critical role in maintaining biodiversity and ecological stability. Beyond their role as pollinators, honey bees are increasingly recognized as bioindicators of environmental health, with their microbiomes reflecting habitat quality, agricultural practices, and broader ecological conditions. This study examines the impact of monoculture and polyculture systems on bee-associated microbiomes, focusing on microbial diversity, composition, and functional roles. Microbial communities from floral surfaces, pollen, nectar, foraging bees, hive matrices, and bioaerosols were analyzed across three agricultural plots: a rape monoculture, a pear monoculture, and a polyculture plot. Using 16S rRNA amplicon sequencing, network co-occurrence analysis, and microbial source tracking, the findings reveal that plant species and cultivation methods significantly shape microbial dynamics (Adonis = 0.67 ***). Floral microbiomes exhibit host specificity (Adonis = 0.73 ***), while the honey bee body surface functions as a microbial hub linking environmental, floral, and hive microbial networks (average degree pear: 21.86; rape: 21.96). The polyculture system improves microbial diversity due to the diversity of nectar plants, enhancing ecosystem connectivity and potentially benefiting honey bee health. These results highlight the ecological importance of optimizing agricultural practices to preserve microbial diversity, enhance honey bee health, and maintain ecological stability.},
}

@article {pmid41598897,
year = {2025},
author = {Nie, Y and Yu, G and Hu, H},
title = {Niche Differentiation and Predicted Functions of Microbiomes in a Tri-Trophic Willow-Gall (Euura viminalis)-Parasitoid Wasp System.},
journal = {Insects},
volume = {17},
number = {1},
pages = {},
doi = {10.3390/insects17010043},
pmid = {41598897},
issn = {2075-4450},
support = {32560120//National Natural Science Foundation of China/ ; },
abstract = {Chalcidoids (Hymenoptera: Chalcidoidea), the most important natural enemies of parasitoids, serve as a pivotal factor in the regulation and management of pest populations. Microbiotas mediate interactions among plants, herbivores, and natural enemies and shape host immunity, parasitoid development, and gall formation; however, the niche-specific diversity and functions of tritrophic parasitoid-host-gall systems remain unclear. Focusing on leaf galls induced on twisted willow (Salix matsudana f. tortuosa) by the willow-galling sawfly Euura viminalis and on two chalcidoids, Eurytoma aethiops and Aprostocetus sp., we profiled bacterial and fungal microbiomes across plant surfaces, gall lumen, host larval tissues, and parasitoids using HTAS. Fungal diversity peaked on parasitoids but was depleted in the gall lumen and host tissues; bacterial richness showed the opposite trend, peaking in the gall lumen and decreasing on parasitoids. In networks contrasted by kingdom, fungi showed positive interface-hub connectivity (Cladosporium, Alternaria), whereas bacteria showed negative hub-mediated associations (Pseudomonas, Acinetobacter), indicating habitat-specific replacements: exposed niches favored transport, two-component, secretion-motility and energy functions, whereas the gall lumen reduced transport/motility but selectively retained N/S metabolism; and in host tissues, information processing and nitrogen respiration were highlighted. These results inform microbiome-guided parasitoid biocontrol.},
}

@article {pmid41598765,
year = {2026},
author = {Khan, ZE and Dulai, AS and O'Neill, A and Min, M and Lee, J and Dion, C and Afzal, N and Chaudhuri, RK and Lee, A and Sivamani, RK},
title = {Impact of Isosorbide Diesters from Coconut and Sunflower Fatty Acids on Pediatric Atopic Dermatitis and the Skin Microbiome: A Randomized, Double-Blind, Vehicle-Controlled Trial.},
journal = {Journal of clinical medicine},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/jcm15020829},
pmid = {41598765},
issn = {2077-0383},
support = {N/A//Sytheon/ ; },
abstract = {Background/Objectives: Topical application of isosorbide diesters (IDEAS) derived from coconut and sunflower seed oil improve atopic dermatitis (AD) and reduce topical steroid use in adults. This randomized, double-blind, vehicle-controlled trial evaluates topical IDEAS (isosorbide diesters) with colloidal oatmeal for pediatric AD. Methods: Subjects aged 2-17 with mild to moderate AD applied either colloidal oatmeal cream or colloidal oatmeal cream with IDEAS daily. Hydrocortisone 2.5% was used as needed. AD severity, itch, sleep, steroid use, and microbiome data were collected at baseline, week 4, and week 8. Results: More participants in the IDEAS group compared to the control group achieved EASI 50 (81.0% vs. 56.3%, p = 0.10) and EASI 75 (42.9% vs. 18.8%, p = 0.12) and achieved a 4-point reduction in subjective itch at week 4 (45.5% vs. 6.3%, p = 0.0085) and week 8 (42.9% vs. 12.5%, p = 0.045). Use of topical steroids was lower in the IDEAS group (3.4 g vs. 13.3 g, p = 0.012) and the relative abundance of Staphylococcus aureus was reduced after 8 weeks. Conclusions: The addition of IDEAS to colloidal lotion improved AD, improved itch, reduced the use of topical steroids, and reduced the relative abundance of S. aureus in the skin microbiome.},
}

@article {pmid41598409,
year = {2026},
author = {Passali, GC and Santantonio, M and Passali, D and Passali, FM},
title = {The Diabetic Nose: A Narrative Review of Rhinologic Involvement in Diabetes (1973-2025).},
journal = {Journal of clinical medicine},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/jcm15020472},
pmid = {41598409},
issn = {2077-0383},
abstract = {Background: Although diabetes mellitus is traditionally viewed as a systemic metabolic disorder, growing evidence indicates that it also affects the upper airways through vascular, inflammatory, and neuro-sensory mechanisms. The sinonasal mucosa, highly vascularized and immunologically active, may represent an early target of diabetic microangiopathy and immune-metabolic imbalance. Objectives: Our objectives are to synthesize current evidence on the rhinologic manifestations of DM, with a focus on chronic rhinosinusitis, olfactory dysfunction, and other nasal disorders, and to identify the main pathophysiologic and clinical patterns linking diabetes to sinonasal disease. Results: Evidence suggests that DM, particularly type 2 DM, increases susceptibility to CRSwNP and modulates the sinonasal microbiome toward Gram-negative predominance. Surgical outcomes after endoscopic sinus surgery are generally comparable between diabetics and non-diabetics when perioperative care is optimized. Olfactory dysfunction occurs more frequently and severely in diabetic patients, likely reflecting the combined effects of chronic inflammation, vascular compromise, and insulin resistance. Additional manifestations include recurrent epistaxis, delayed mucociliary clearance, and chronic cough. Allergic rhinitis appears to not be increased, and maybe even inversely related, especially among users of DPP-4 inhibitors. Conclusions: Diabetes intersects with rhinologic health through immune-metabolic, vascular, and epithelial pathways that may shape susceptibility, disease phenotype, and neurosensory decline. Future research should focus on disentangling type-specific mechanisms, metabolic biomarkers, and longitudinal outcomes, with the aim of developing precision-based approaches to rhinologic assessment and management in diabetic patients.},
}

@article {pmid41598336,
year = {2026},
author = {Faggiani, I and Villaseca, IL and D'Amico, F and Furfaro, F and Zilli, A and Massironi, S and Parigi, TL and Solitano, V and Cicerone, C and Peyrin-Biroulet, L and Danese, S and Allocca, M},
title = {Perianal Crohn's Disease in Inflammatory Bowel Disease: Diagnosis, Assessment and Treatment.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010182},
pmid = {41598336},
issn = {2075-1729},
abstract = {Perianal fistulizing Crohn's disease (pfCD) represents one of the most challenging manifestations of CD, often associated with severe phenotypes, refractory luminal inflammation, and a substantial reduction in quality of life. Its pathogenesis is multifactorial and incompletely understood, involving genetic susceptibility, epithelial and stromal dysfunction, and microbiome-related mechanisms. Diagnosis and monitoring rely on advanced imaging, while management requires coordinated medical-surgical strategies. Significant unmet needs persist regarding standardized treatment targets, optimal imaging follow-up, and personalized therapeutic pathways. In this review, we aim to summarise and provide a comprehensive overview of the most recent evidence across pathogenesis, diagnosis, classification systems, and therapeutic approaches in pfCD. We highlight key advances in understanding epithelial-mesenchymal transition, immune-microbiome interactions, and genetic determinants of disease behaviour. Improvements in diagnostic modalities-including MRI-based scores, ultrasound technologies, volumetric assessment, and AI-enhanced imaging-are discussed alongside modern classification systems such as TOPClass. Evidence guiding medical therapy, seton management, and surgical decision-making is reviewed, emphasising integrated, goal-oriented care. Despite substantial progress, pfCD remains a difficult-to-treat condition with persistent gaps in early diagnosis, objective monitoring, and individualized management. Emerging imaging technologies, standardized treatment targets, and structured classification frameworks offer promising strategies to overcome current limitations and improve long-term outcomes.},
}

@article {pmid41598246,
year = {2026},
author = {Guo, Y and Zhang, Y and Hui, Q and Zhu, S and Wang, J and Song, L},
title = {Scalp Microbiome Composition in Young Women: Associations with Scalp Type, Sensitivity, and Lifestyle Factors.},
journal = {Life (Basel, Switzerland)},
volume = {16},
number = {1},
pages = {},
doi = {10.3390/life16010091},
pmid = {41598246},
issn = {2075-1729},
abstract = {BACKGROUND: The scalp represents a distinct ecological niche within the skin, and the structure of its microbiota, together with the factors shaping it, is considered important for the maintenance of scalp health.

METHODS: This study systematically analyzed the bacterial and fungal community structures on the scalps of 63 healthy Chinese women aged 18-25, and examined their associations with scalp type, sensitivity, and lifestyle factors. Scalp samples were collected, questionnaire surveys were administered, scalp physiological parameters were measured, and high-throughput sequencing of 16S rRNA and ITS genes was performed.

RESULTS: The results showed that, in this unique scalp skin niche, the dominant bacterial phylum was Actinobacteria, while the dominant fungal phylum was Ascomycota. The predominant bacterial genera were Cutibacterium and Staphylococcus, and the fungal community was dominated by Malassezia. When scalp types were categorized according to sebum content, dry scalps showed enrichment of Micrococcus, Streptococcus, Delftia, Staphylococcus aureus, and Staphylococcus hominis, whereas oily scalps, on the other hand, are primarily colonized by Cutibacterium and Staphylococcus species. In addition, we observed microbial interactions under different physiological conditions. The relative abundance of Cutibacterium decreased with increasing scalp sensitivity. Higher psychological stress, insufficient sleep, and high-sugar/high-fat dietary patterns tended to coincide with shifts in the relative abundance of Malassezia, implying that these influences may act through fungal rather than bacterial components of the scalp microbiota. Scalp sensitivity showed the strongest association with β-diversity among the variables examined, although the effect size was modest and did not reach conventional significance in the multivariable PERMANOVA.

CONCLUSIONS: In young women, the scalp constitutes a distinct cutaneous niche whose microbiota is jointly shaped by sebum level, barrier sensitivity, and lifestyle factors, with sensitivity emerging as one of the more influential dimensions of community variation. These findings provide guidance for future in-depth research on the scalp microbiome network and offer a foundational reference for preventing suboptimal and pathological scalp conditions.},
}

@article {pmid41597776,
year = {2026},
author = {Zeng, M and Zhou, H and Wu, Q and Wang, K and Liu, H and Yang, Y and Peng, W and Chen, A and Deng, X and Ji, C and Zhang, X and Han, J},
title = {Diversity Analysis of Fecal Microbiota in Goats Driven by White Blood Cell Count.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010259},
pmid = {41597776},
issn = {2076-2607},
abstract = {The Leizhou goat is a vital indigenous breed, yet its disease resilience can complicate early health monitoring. The white blood cell (WBC) count is a key indicator of immune status, but its relationship with the gut microbiota remains uncharacterized in this breed. This study aimed to characterize the fecal microbiota of Hainan black goats stratified based on their WBC counts. The goats were stratified into Lower, Middle, and High WBC groups based on peripheral WBC counts to compare their fecal microbiota and identify potential associations with systemic immunity. Significant differences in microbial alpha- and be-ta-diversity were observed among the groups, with the High WBC group showing the greatest richness. The microbiota was dominated by Bacillota and Bacteroidota at the phylum level. Linear discriminant analysis Effect Size (LEfSe) identified specific taxa en-riched in each group, such as Ruminococcusin the High WBC group. Critically, Spearman correlation analysis demonstrated significant positive correlations between WBC counts and the relative abundance of genera like unclassified_f_Oscillospiraceae and unclassi-fied_c_Clostridia. These findings demonstrate that WBC counts are significantly associated with distinct shifts in the gut microbial community structure of Hainan black goats. The identified WBC-associated microbial biomarkers suggest a link between the gut microbi-ome and host immune regulation, providing a foundation for future research on microbi-ota-mediated health assessment in goats.},
}

@article {pmid41597766,
year = {2026},
author = {Raber, J and O'Niel, A and Kasschau, KD and Pederson, A and Robinson, N and Guidarelli, C and Chalmers, C and Winters-Stone, K and Sharpton, TJ},
title = {Diet-Microbiome Relationships in Prostate-Cancer Survivors with Prior Androgen Deprivation-Therapy Exposure and Previous Exercise Intervention Enrollment.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010251},
pmid = {41597766},
issn = {2076-2607},
support = {5T32AG055378//OHSU Knight Cancer Institute; NIA T32/ ; 5T32AG055378//NIA T32/ ; },
abstract = {The gut microbiome is a modifiable factor in cancer survivorship. Diet represents the most practical intervention for modulating the gut microbiome. However, diet-microbiome relationships in prostate-cancer survivors remain poorly characterized. We conducted a comprehensive analysis of diet-microbiome associations in 79 prostate-cancer survivors (ages 62-81) enrolled in a randomized exercise intervention trial, 59.5% of whom still have active metastatic disease. Dietary intake was assessed using the Diet History Questionnaire (201 variables) and analyzed using three validated dietary pattern scores: Mediterranean Diet Adherence Score (MEDAS), Healthy Eating Index-2015 (HEI-2015), and the Mediterranean-Dash Intervention for Neurodegenerative Delay (MIND) diet score. Gut microbiome composition was characterized via 16S rRNA sequencing. Dimensionality reduction strategies, including theory-driven diet scores and data-driven machine learning (Random Forest, and Least Absolute Shrinkage and Selection Operator (LASSO)), were used. Statistical analyses included beta regression for alpha diversity, Permutational Multivariate Analysis of Variance (PERMANOVA) for beta diversity (both Bray-Curtis and Sørensen metrics), and Microbiome Multivariable Associations with Linear Models (MaAsLin2) with negative binomial regression for taxa-level associations. All models tested interactions with exercise intervention, APOLIPOPROTEIN E (APOE) genotype, and testosterone levels. There was an interaction between MEDAS and exercise type on gut alpha diversity (Shannon: p = 0.0022), with stronger diet-diversity associations in strength training and Tai Chi groups than flexibility controls. All three diet-quality scores predicted beta diversity (HEI p = 0.002; MIND p = 0.025; MEDAS p = 0.034) but not Bray-Curtis (abundance-weighted) distance, suggesting diet shapes community membership rather than relative abundances. Taxa-level analysis revealed 129 genera with diet associations or diet × host factor interactions. Among 297 dietary variables tested for cognitive outcomes, only caffeine significantly predicted Montreal Cognitive Assessment (MoCA) scores after False Discovery Rate (FDR) correction (p = 0.0009, q = 0.014) through direct pathways beneficial to cognitive performance without notable gut microbiome modulation. In cancer survivors, dietary recommendations should be tailored to exercise habits, genetic background, and hormonal status.},
}

@article {pmid41597765,
year = {2026},
author = {Alkaff, AH and Malik, A and Situmeang, PA and Heng, NCK},
title = {Genetic Characteristics Associated with Probiotic Functions in Four Indonesian Skin Microbiome-Derived Bacterial Strains.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010248},
pmid = {41597765},
issn = {2076-2607},
abstract = {The human skin microbiome has gained considerable attention as a resource for the development of innovative probiotics for cosmetic purposes or promoting skin health. However, the evaluation of new probiotic strains to ensure their "generally recognized as safe" (GRAS) status remains challenging. Here, we have subjected the annotated draft genome sequences of four human skin-derived bacterial strains, namely Bacillus subtilis MBF10-19J, Micrococcus luteus MBF05-19J, Staphylococcus hominis MBF12-19J, and Staphylococcus warneri MBF02-19J, to bioinformatic analyses to detect the genes associated with important probiotic traits, as well as undesirable characteristics such as antibiotic resistance, virulence factors, and toxic metabolites. Each bacterium harbors at least one type of adhesin-encoding gene, while only S. hominis MBF12-19J and S. warneri MBF02-19J contain the putative genes encoding enzymes for metabolism improvement. In vitro assays, including antibiotic susceptibility and antimicrobial activity testing, revealed strain-specific safety characteristics that complement the genomic findings. With regard to antibiotic resistance determinants, S. hominis MBF12-19J showed the most favorable profile, S. warneri MBF02-19J and M. luteus MBF05-19J appeared suitable when used with appropriate caution, and B. subtilis MBF10-19J exhibited amoxicillin resistance, i.e., warrants careful evaluation. Further in vivo validation is needed to determine whether these strains do indeed comply with GRAS evaluation frameworks.},
}

@article {pmid41597762,
year = {2026},
author = {Xiong, Y and Dai, Z and He, F and Liu, R and Wang, J and Zhan, Z and Jia, H and Chen, S and Cai, L},
title = {Effect of Hantavirus Infection on the Rodent Lung Microbiome: Specific Regulatory Roles of Host Species and Virus Types.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010244},
pmid = {41597762},
issn = {2076-2607},
support = {2024JJ9472//The natural science foundation of Hunan provincial/ ; },
abstract = {The lung-targeting characteristic of Hantavirus infection and the unclear mechanism underlying its interaction with the lung microbiome hampers the development of effective prevention and control strategies. In this study, lung tissues from Apodemus agrarius and Rattus norvegicus were collected at Hantavirus surveillance sites in Hunan Province. Metagenomic sequencing was subsequently applied to compare microbiome diversity, community structure, and function between infected and uninfected groups. Then the linear discriminant analysis effect size (LEfSe) was employed to identify key biomarkers. The results indicated that after infection with Hantaan virus (HTNV), Apodemus agrarius exhibited significantly increased evenness but markedly decreased richness of lung microbial communities, as reflected by consistent reductions in the number of observed species, Abundance-based Coverage Estimator (ACE) index, and Chao1 index. In contrast, Rattus norvegicus infected with Seoul virus (SEOV) showed no significant difference in microbial richness compared with uninfected controls, and even a slight increase was observed. These findings suggest that host species and virus type may play an important role in shaping microbial community responses. Furthermore, β-diversity analysis showed that the community structure was clearly separated by the host rodent species, as well as by their virus infection status. LEfSe analysis identified taxa with discriminatory power associated with infection status. Streptococcus agalactiae and Streptococcus were associated with SEOV-infected Rattus norvegicus, while Chlamydia and Chlamydia abortus were relatively enriched in uninfected Apodemus agrarius. This exploratory study reveals preliminary association between specific host-Hantavirus pairings (HTNV-Apodemus agrarius and SEOV-Rattus norvegicus) and the rodent lung microbiome, offering potential insights for future research into viral pathogenesis.},
}

@article {pmid41597752,
year = {2026},
author = {Mukhtar, F and Guarnieri, A and Naro, MD and Nicolosi, D and Brancazio, N and Varricchio, A and Varricchio, A and Zubair, M and Didbaridze, T and Petronio Petronio, G and Di Marco, R},
title = {Clinical and Immunological Perspectives on the Nasal Microbiome's Role in Olfactory Function and Dysfunction.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010234},
pmid = {41597752},
issn = {2076-2607},
abstract = {The nasal microbiome represents a complex and dynamic microbial ecosystem that contributes to mucosal defense, epithelial homeostasis, immune regulation, and olfactory function. Increasing evidence indicates that this microbial community actively interacts with host physiology, while alterations in its composition are associated with chronic inflammation, oxidative stress, and olfactory impairment. Such changes have been reported in conditions including chronic rhinosinusitis, allergic rhinitis, and post-viral anosmia. Beyond local effects, chronic nasal inflammation has been hypothesized to influence neuroinflammatory processes and protein aggregation pathways involving α-synuclein and tau, potentially linking nasal microbial imbalance to neurodegenerative mechanisms. However, current evidence remains largely indirect and does not support a causal relationship. This narrative review summarizes current clinical and immunological evidence on the role of the nasal microbiome in olfactory function and dysfunction, highlighting limitations of existing studies and outlining future research directions.},
}

@article {pmid41597750,
year = {2026},
author = {Aljuaid, RS and Alshareef, SA and Jamal, BT and Dhafeer, FH and Alnahari, AA and Ashy, RA},
title = {Spatial and Vertical Stratification of Groundwater Microbial Communities Reveals Proteobacterial Dominance and Redox-Driven Ecological Transitions.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010232},
pmid = {41597750},
issn = {2076-2607},
abstract = {Groundwater microbial communities exhibit pronounced vertical and spatial structuring driven by physicochemical gradients. Here, we investigated microbial assemblages across surface and subsurface layers of three groundwater wells distributed along a 1.26 km transect in the Wadi Awja aquifer system (Jeddah, Saudi Arabia) using high-throughput 16S rRNA gene amplicon sequencing. Across all samples, Pseudomonadota (Proteobacteria) dominated community composition, accounting for ~50-65% of surface assemblages and increasing to ~90% in deeper strata, indicating strong vertical selection. This depth-associated enrichment coincided with reduced community evenness and the prevalence of metabolically versatile, facultatively anaerobic taxa. Although Actinomycetota, Bacteroidota, and Planctomycetota contributed substantially to overall diversity, their relative abundances declined with depth, reinforcing the dominance of Proteobacteria under suboxic conditions. Notably, members of Enterobacteriaceae, particularly Escherichia spp., were consistently enriched in deeper layers, coinciding with simplified community structures. Collectively, these results demonstrate that groundwater microbial communities undergo sharp redox-associated ecological transitions over short spatial scales, emphasizing the role of localized hydrogeochemical heterogeneity in shaping subsurface microbial assemblages.},
}

@article {pmid41597728,
year = {2026},
author = {de Groen, P and Gouw, SC and Hanssen, NMJ and Nieuwdorp, M and Rampanelli, E},
title = {Early-Life Gut Microbiota: Education of the Immune System and Links to Autoimmune Diseases.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010210},
pmid = {41597728},
issn = {2076-2607},
support = {09150182010020//NWO-VICI grant 2020/ ; 101141346//ERC Advanced grant/ ; 4-SRA-2025-1766-M-B//BREAKTHROUGH T1D Grant/ ; 09150172210050//ZonMw-VIDI grant 2023/ ; },
abstract = {Early life is a critical window for immune system development, during which the gut microbiome shapes innate immunity, antigen presentation, and adaptive immune maturation. Disruptions in microbial colonization-driven by factors such as cesarean delivery, antibiotic exposure, and formula feeding-deplete beneficial early-life taxa (e.g., Bifidobacterium, Bacteroides, and Enterococcus) and impair key microbial functions, including short-chain fatty acid (SCFA) production by these keystone species, alongside regulatory T cell induction. These dysbiosis patterns are associated with an increased risk of pediatric autoimmune diseases, notably type 1 diabetes, inflammatory bowel disease, celiac disease, and juvenile idiopathic arthritis. This review synthesizes current evidence on how the early-life microbiota influences immune maturation, with potential effects on the development of autoimmune diseases later in life. We specifically focus on human observational and intervention studies, where treatments with probiotics, synbiotics, vaginal microbial transfer, or maternal fecal microbiota transplantations have been shown to partially restore a disrupted microbiome. While restoration of the gut microbiome composition and function is the main reported outcome of these studies, to date, no reports have disclosed direct prevention of autoimmune disease development by targeting the early-life gut microbiome. In this regard, a better understanding of the early-life microbiome-immune axis is essential for developing targeted preventive strategies. Future research must prioritize longitudinal evaluation of autoimmune outcomes after microbiome modulation to reduce the burden of chronic immune-mediated diseases.},
}

@article {pmid41597727,
year = {2026},
author = {Song, H and Oh, SW and Oh, JH and Unno, T},
title = {Characterization of the Oral and Stomach Microbial Community Structure in Patients with Intestinal Metaplasia, Dysplasia, and Gastric Cancer Through High-Throughput Sequencing.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010209},
pmid = {41597727},
issn = {2076-2607},
support = {EMBRF-2022-07//the Research Institute of Medical Science, The Catholic University of Korea/ ; RS-2023-00285353//the Ministry of Education/ ; },
abstract = {Gastric cancer (GC) is the fifth most common cancer worldwide, with the highest incidence in East Asia. Although H. pylori is a well-known risk factor, carcinogenesis can occur independently of H. pylori infection, and approximately 43% of adults carry H. pylori as part of their native microbiota. This study aimed to identify potential oral and gastric microbial markers across different histological stages of GC in both H. pylori-positive and -negative patients. Buccal swabs and gastric mucosa samples were collected from patients with intestinal metaplasia, low-grade dysplasia, high-grade dysplasia, early GC, or advanced GC. Total DNA was extracted, and 16S rRNA gene amplicon sequencing was performed. Microbiome diversity generally remained stable across histological stages, with no directional shifts in community structure. Differential abundance analysis revealed higher relative abundances of Anaerostipes, Phocaeicola, and Collinsella in the gastric antrum of cancerous samples. Anaerostipes and Phocaeicola are typically enriched in the intestinal microbiota but are rarely observed in the stomach, suggesting their potential ecological and pathological relevance in gastric carcinogenesis. In H. pylori-negative patients, however, a different stage-associated abundance pattern was observed, in which Faecalibacterium, a genus predominantly associated with the intestinal environment, was less abundant in advanced gastric cancer samples than in earlier histological stages within the gastric body. These findings suggest that microbial changes during gastric cancer progression may follow different trajectories depending on H. pylori infection status. In oral samples, Haemophilus and Prevotella were more abundant in intestinal metaplasia than in low-grade dysplasia, and network analysis indicated links between Neisseria and Filifactor at oral and gastric sites. However, as the study population was limited to a single country and ethnicity, the applicability of these microbial markers should be carefully considered.},
}

@article {pmid41597726,
year = {2026},
author = {Lee, HJ and Park, SH and Han, SY and Lee, JH and Kim, DU and Seo, HI},
title = {Differences in the Biliary Microbiome Between Biliary Tract Cancer and Benign Biliary Disease.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010208},
pmid = {41597726},
issn = {2076-2607},
support = {202100350001//Biomedical Research Institute, Pusan National University Hospital/ ; },
abstract = {Bile contains many bacteria that can contribute to various diseases. Therefore, identifying bile microbiome differences between benign and malignant conditions is essential. In this study, bile samples were collected aseptically from 141 patients with biliary tract cancer (BTC) or benign biliary diseases (BBDs) who underwent endoscopic retrograde cholangiopancreatography or biliary tract surgery. Quality control PCR was performed to amplify the V3-V4 region of the bacterial 16S rRNA gene. Metagenomic sequencing of bile was successfully performed in 35 of 56 samples collected from patients with BTC and 24 of 85 samples from patients with BBD. The mean alpha diversity values comprised 2.788 ± 2.833 and 2.319 ± 1.355 in the BBD and BTC groups, respectively (p = 0.399). The bacterial species (4.7%) were shared between groups, whereas 12.3% and 83% were indicated to patients with BTC and BBD, respectively. Bacteroides coprocola, Prevotella copri, and Bacteroides plebeius were more frequently identified in the bile of patients with BTC, whereas Bacteroides vulgatus and Bacteroides uniformis were more abundant in the bile of patients with BBD. Distinct patterns of microorganism abundance between the two groups of patients suggest association of bile microbiome with disease status, so its diagnostic potential should be validated in further studies.},
}

@article {pmid41597719,
year = {2026},
author = {van Oppen, MJH and Doering, T and Martins Fernandes, L},
title = {Can Bacterial Manipulation Deliver Reef-Scale Thermal Enhancement of Corals?.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010202},
pmid = {41597719},
issn = {2076-2607},
abstract = {A rapid decline of coral reefs is taking place around the world, with climate warming being the biggest driver behind this deterioration. Efforts to increase coral climate resilience via bioengineering methods have thus become urgent, and there is hope that such interventions can help corals and coral reefs survive until a time when no further climate warming occurs and perhaps a future of climate cooling is imaginable. The manipulation of coral-associated bacterial communities is among the less advanced interventions currently being explored. Nevertheless, early findings provide confidence that some level of thermal enhancement can be achieved via the inoculation of corals with beneficial bacteria. The small number of studies available, however, is limited in terms of the traits used to select candidate bacteria and their ability to ascribe host enhancement to specific bacterial taxa and functions. Further, findings to date are unable to decipher whether candidate bacteria integrate stably within the coral microbiome. These shortcomings prevent assessment of the efficacy of bacterial manipulation to enhance the long-term thermal resilience of corals on the reef. Here we summarise the state-of-play of the field and provide recommendations to fast-track this approach via fine-tuning experimental designs and methods.},
}

@article {pmid41597715,
year = {2026},
author = {Ruzaini Abdullah, MH and Zainudin, MHM and Aljaberi, MA and Binti Abdul Mutalib, NA and Neoh, HM and Hamat, RA},
title = {First Report of fusF Gene in Staphylococcus kloosii from Virgin Tropical Soil: Expanding the Ecological Reservoirs of Fusidic Acid Resistance.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010197},
pmid = {41597715},
issn = {2076-2607},
support = {FRGS/1/2020/SKK0/UPM/01/2//Ministry of Higher Education (Malaysia)/ ; },
abstract = {Fusidic acid resistance in Staphylococcus spp. has historically been confined to Staphylococcus ureilyticus, with limited data on its environmental distribution. This study presents the first detection of the fusidic acid resistance gene fusF in Staphylococcus kloosii recovered from virgin soil at Kampung Batu 16, Dusun Tua, Hulu Langat, Malaysia. A total of ten Staphylococcus isolates were identified using the VITEK[®]2 system with high confidence (97-99%), comprising seven S. kloosii and three S. ureilyticus. Sequencing of representative isolates further corroborated the species identification. All isolates displayed phenotypic resistance to fusidic acid, while all S. ureilyticus (3/3) exhibited multi-drug resistant (MDR) traits and S. kloosii (7/7) exhibited non-MDR traits. PCR and sequencing confirmed the presence of fusF gene in S. ureilyticus (3/3) and S. kloosii (3/7). In addition, fusB and fusC genes were not detected in both species. The phylogenetic analysis (Maximum Likelihood, Tamura-Nei model) revealed high sequence conservation and clustering between fusF-positive S. kloosii and S. ureilyticus soil isolates, suggesting recent horizontal gene transfer between these two related species. The first detection of fusF gene in S. kloosii from virgin soil signifies the expansion of the ecological and host range beyond S. ureilyticus, establishes virgin soil as a potential antimicrobial resistance (AMR) reservoir, and underscores the One Health risks of resistance dissemination from environmental staphylococci. This baseline study highlights the importance of early AMR surveillance in tropical environments prior to agricultural development.},
}

@article {pmid41597703,
year = {2026},
author = {Sánchez-Becerra, AE and Peña-Rodríguez, M and Vega-Magaña, AN and García-Arellano, S and Romo-Rubio, HA and Flores-Navarro, S and Escobedo-Melendez, G and Aranda-Romo, S and Zepeda-Nuño, JS},
title = {Oral Microbiome Dynamics in Patients with Acute Lymphoblastic Leukemia and Oral Mucositis.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010185},
pmid = {41597703},
issn = {2076-2607},
abstract = {The oral microbiome of patients with acute lymphoblastic leukemia (ALL) undergoes changes caused by the neoplasia as well as the antimicrobial activity of chemotherapy (CTX), which promotes the development of oral mucositis (OM). This study aimed to analyze the oral microbiome dynamics and salivary cytokine production in pediatric ALL patients before and during CTX, comparing children who did and did not develop OM. We conducted a longitudinal, observational, and analytical study including 32 newly diagnosed pediatric ALL patients (ages 2-16 years) undergoing CTX. Oral rinse and non-stimulated saliva samples were collected at baseline (day 0), day 14, and day 21 of induction of CTX, with an additional sample taken during OM episodes when possible. Microbiome analysis was performed using 16S rRNA sequencing on an Illumina MiSeq platform, and salivary cytokines were measured using a Luminex multiplex assay. The most pronounced microbiome changes occurred on day 14, particularly in patients who developed OM, characterized by higher α diversity, increased abundance of opportunistic taxa, and elevated IL-6 concentrations. In contrast, patients who did not develop OM exhibited a more stable microbial composition. Overall, these findings indicate that temporal oral dysbiosis and increased IL-6 may serve as early markers and potential predictors of OM development during chemotherapy in pediatric ALL patients.},
}

@article {pmid41597701,
year = {2026},
author = {Mollova, D and Baev, V and Borisova, T and Rusinova, M and Iliev, I},
title = {A Metagenomic Comparison of the Colostrum Microbiome in Bulgarian Mothers by Delivery Mode: A Pilot Study.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010184},
pmid = {41597701},
issn = {2076-2607},
support = {KP-06-M81/6//Bulgarian Science Fund/ ; },
abstract = {Colostrum harbors a highly diverse microbial community, predominantly composed of genera such as Staphylococcus, Streptococcus, Lactobacillus, Bifidobacterium, and Enterococcus. The composition and diversity of this microbiota are influenced by maternal factors-including age, body mass index, lactation activity, stress levels, and gestational diabetes-as well as external factors such as mode of delivery, antibiotic exposure, diet, and geographic location. This microbial community plays a critical role in maternal and neonatal health by contributing to early gut colonization, supporting digestion, promoting immune system development, and protecting against pathogenic microorganisms through mechanisms such as antimicrobial peptide production by lactic acid bacteria. The primary aim of this study was to evaluate the impact of mode of delivery on colostrum microbiota by comparing mothers who delivered vaginally with those who underwent cesarean section. Colostrum samples from 15 mothers were subjected to DNA extraction, high-throughput sequencing, and bioinformatic analyses to characterize microbial composition and predicted functional profiles. Although substantial inter-individual variability was observed, no statistically significant differences were detected in overall microbial diversity or community structure between the two delivery groups. However, distinct bacterial taxa and functional characteristics were identified that were specific to each mode of delivery, suggesting subtle delivery-related influences on colostrum microbiota composition.},
}

@article {pmid41597671,
year = {2026},
author = {Mihu, ML and Nadăş, GC and Bouari, CM and Fiț, NI and Răpuntean, S},
title = {Klebsiella pneumoniae Infections in Dogs: A One Health Review of Antimicrobial Resistance, Virulence Factors, Zoonotic Risk, and Emerging Alternatives.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010149},
pmid = {41597671},
issn = {2076-2607},
abstract = {Klebsiella pneumoniae is increasingly reported in canine medicine, with growing attention to multidrug-resistant (MDR) and hypervirulent strains. Although its overall prevalence in dogs appears relatively low, published studies indicate that affected animals may harbor clinically important resistance determinants, including extended-spectrum β-lactamases and, less frequently, carbapenemases. Canine isolates described in the literature also carry virulence-associated traits such as hypermucoviscosity and enhanced iron-acquisition systems, which overlap with features of high-risk human lineages and suggest potential, but largely inferred, interspecies links. These observations highlight the relevance of a One Health perspective and the importance of coordinated surveillance that includes companion animals. This narrative review synthesizes available literature on the epidemiology, clinical presentations, antimicrobial resistance, virulence traits, and molecular characteristics of K. pneumoniae in dogs. We critically evaluate evidence suggesting that dogs may function as reservoirs, sentinels, or amplifiers of MDR strains, particularly in clinical settings or following antimicrobial exposure. In addition, we summarize emerging alternative and adjunctive strategies-such as bacteriophage therapy, antimicrobial peptides, anti-virulence approaches, microbiome-based interventions, as well as strengthened antimicrobial stewardship and infection-control practices-that are under investigation as complements to conventional antibiotics. Overall, published evidence indicates that K. pneumoniae infections in dogs represent an under recognized but potentially important clinical and One Health concern. Continued surveillance, responsible antimicrobial use, and rigorous evaluation of non-antibiotic strategies will be essential to inform future veterinary practice and public health policy.},
}

@article {pmid41597670,
year = {2026},
author = {Soyfoo, M and Sarrand, J},
title = {Plasmablast Storms: Microbial Drivers of Acute and Chronic Autoimmune Flares.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010152},
pmid = {41597670},
issn = {2076-2607},
abstract = {Autoimmune flares are often accompanied by abrupt surges of circulating plasmablasts-short-lived, high-output antibody-secreting cells generated through extrafollicular B-cell activation in response to microbial cues. Three categories of microbial input appear to repeatedly trigger these "plasmablast storms": latent herpesvirus reactivations (Epstein-Barr virus, cytomegalovirus, human herpesvirus-6, varicella-zoster virus), acute respiratory or gastrointestinal infections including SARS-CoV-2, and chronic oral or gut dysbiosis. Although biologically distinct, these stimuli converge on innate sensing pathways driven by pathogen-associated molecular patterns such as unmethylated CpG DNA, single-stranded RNA, lipopolysaccharide, and bacterial lipoglycans. Through Toll-like receptors and type I interferon signalling, microbial signatures accelerate class switching, amplify inflammatory cytokine milieus, and lower B-cell activation thresholds, enabling rapid plasmablast mobilisation. Dysbiosis further maintains B cells in a hyper-responsive state by disrupting mucosal homeostasis and altering microbial metabolite profiles, thereby reducing the stimulus required to trigger plasmablast bursts. Once generated, these waves of oligoclonal plasmablasts home to inflamed tissues, where chemokine and adhesion landscapes shape their retention during flares. Emerging evidence suggests that such episodic plasmablast expansions promote autoantibody diversification, somatic hypermutation, and epitope spreading, progressively eroding tolerance. This review synthesizes these insights into a unified model in which infections and dysbiosis promote microbe-licensed plasmablast storms that influence the tempo and severity of autoimmune disease.},
}

@article {pmid41597661,
year = {2026},
author = {Zavala-Medina, LC and Salas-Leiva, JS and Villegas-Mercado, CE and Arreguín-Cano, JA and Soto-Barreras, U and Santana-Delgado, SA and Larrinua-Pacheco, AD and García-Vega, MF and Bermúdez, M},
title = {Oral Dysbiosis and Neuroinflammation: Implications for Alzheimer's, Parkinson's and Mood Disorders.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010143},
pmid = {41597661},
issn = {2076-2607},
abstract = {BACKGROUND: Growing evidence indicates that oral microbiome dysbiosis contributes to systemic inflammation, immune activation, and neural dysfunction. These processes may influence the onset and progression of major neuropsychiatric and neurodegenerative disorders. This review integrates clinical, epidemiological, and mechanistic findings linking periodontal pathogens and oral microbial imbalance to Alzheimer's disease (AD), Parkinson's disease (PD), depression, and anxiety.

METHODS: A narrative review was conducted using PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar to identify recent studies examining alterations in the oral microbiota, microbial translocation, systemic inflammatory responses, blood-brain barrier disruption, cytokine signaling, and neural pathways implicated in brain disorders.

RESULTS: Evidence from human and experimental models demonstrates that oral pathogens, particularly Porphyromonas gingivalis, Fusobacterium nucleatum, and Treponema denticola, can disseminate systemically, alter immune tone, and affect neural tissues. Their virulence factors promote microglial activation, cytokine release (IL-1β, IL-6, TNF-α), amyloid-β aggregation, and α-synuclein misfolding. Epidemiological studies show associations between oral dysbiosis and cognitive impairment, motor symptoms in PD, and alterations in mood-related taxa linked to stress hormone profiles. Immunometabolic pathways, HPA-axis activation, and the oral-gut-brain axis further integrate these findings into a shared neuroinflammatory framework.

CONCLUSIONS: Oral dysbiosis emerges as a modifiable contributor to neuroinflammation and brain health. Periodontal therapy, probiotics, prebiotics, synbiotics, and targeted inhibitors of bacterial virulence factors represent promising strategies to reduce systemic and neural inflammation. Longitudinal human studies and standardized microbiome methodologies are still needed to clarify causality and evaluate whether restoring oral microbial balance can modify the course of neuropsychiatric and neurodegenerative disorders.},
}

@article {pmid41597651,
year = {2026},
author = {Colangeli, L and Teofani, A and Desideri, A and Biocca, S and Pacifico, T and Parrotta, ME and Fertitta, V and Fortini, P and Ceccarini, G and Magno, S and Pelosini, C and Santini, F and Novelli, G and Sbraccia, P and Guglielmi, V},
title = {Gut Microbiota in Lipodystrophies and Obesity: A Common Signature?.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010132},
pmid = {41597651},
issn = {2076-2607},
abstract = {Lipodystrophies are rare syndromes characterized by partial or complete loss of subcutaneous adipose tissue leading to ectopic lipid deposition, insulin resistance, and the same metabolic derangements observed in obesity. Given the role of gut microbiota in metabolic disorders, we investigated whether its signature in obesity may be mirrored by that found in lipodystrophies, possibly contributing to their overlapping metabolic abnormalities. In this cross-sectional study, we included 8 individuals with lipodystrophy (LD), 16 individuals with obesity (Ob)-further categorized into 8 metabolically healthy (MHO) and 8 metabolically unhealthy (MUHO)-and 16 normal-weight controls (N). We assessed clinical and metabolic characteristics and performed 16S rRNA sequencing and bioinformatic analyses on fecal samples to characterize the gut microbiome. LD presented significantly lower body mass index (BMI) and waist circumference than Ob, but, from a metabolic perspective, LD showed similarity with MUHO and presented significantly lower levels of HDL-C and higher triglycerides compared to both N and MHO. Gut microbiota analysis revealed reduced α-diversity in LD, MHO and MUHO compared to N, whilst β-diversity and Firmicutes/Bacteroidetes ratio differences were not significant. At the phylum level, differential abundance analysis revealed that LD individuals exhibit similar microbial characteristics to MUHO and higher Verrucomicrobiota levels compared to MHO. The shared gut microbiota signature suggests another potential unexplored link between the pathogenesis of metabolic complications in lipodystrophies and obesity, providing novel insights into the complex interplay between dysbiosis and adiposopathy. Larger longitudinal studies are needed to explore the role of specific taxa and for a more precise characterization of different lipodystrophy subtypes.},
}

@article {pmid41597646,
year = {2026},
author = {Ali, A and Keelan, JA and Penova-Veselinovic, B and Allentoft, ME and Bunce, M and Christophersen, CT},
title = {Optimising Vaginal Microbiome Profiling for Clinical Translation: A Comparative Assessment of Sample Storage Methods and a Vagina-Specific 16S rRNA Gene Database.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010128},
pmid = {41597646},
issn = {2076-2607},
support = {H1017003370//Telethon-Perth Children's Hospital Research Fund and Western Australia Department of Health/ ; },
abstract = {Vaginal microbiome composition has been linked to risk of preterm birth (PTB), a persistent global health challenge. 16S rRNA microbial profiling has identified specific vaginal community state types (CSTs) that have been associated with PTB risk. Diagnostic profiling requires standardised pre-analytical protocols. We evaluated two storage methods and validated a curated, vagina-specific 16S rRNA gene database (VagDB) to enhance annotation. Paired Copan FLOQ swabs from 22 women at high PTB risk were processed for either (a) dry/immediate freezing or (b) Amies-stabilisation/refrigeration. Amplicon sequence variants were generated via 16S rRNA gene (V4) PCR and Illumina sequencing. We assessed diversity, composition, and community state type (CST) allocation. Amies-stabilised samples yielded significantly higher DNA (p = 0.003), but this did not alter species richness, evenness, or community structure. VagDB enhanced species-level resolution. PCoA showed robust clustering by participant and CST (p < 0.001), irrespective of storage; CST concordance exceeded 90%. Routinely collected vaginal swabs in stabilisation medium with an 8-72 h refrigeration window yield reliable data, supporting the integration of vaginal microbiome profiling into clinical PTB risk assessment.},
}

@article {pmid41597613,
year = {2026},
author = {Jarrín-V, P and Carrión-Olmedo, JC and Loján, P and Reyes-Barriga, D and Lara, M and Oña, A and Quiroz-Moreno, C and Castillejo, P and Tenea, GN and Díaz, M and Monfort-Lanzas, P and Molina, CA},
title = {Predicted Bacterial Metabolic Landscapes of the Sumaco Volcano: A Picrust2 Analysis of 16S rRNA Data from Amazonian Ecuador.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010094},
pmid = {41597613},
issn = {2076-2607},
support = {NA//National Institute of Biological Resources (NIBR) and the Korea International Cooperation Agency (KOICA) of the Republic of Korea/ ; },
abstract = {The Sumaco volcano in Ecuador, which has a distinct geological origin from the Andes and is located in the Amazon basin, offers an opportunity to study untouched microbiomes. We explored comparative patterns of abundance from predicted functional profiling in soil samples collected along the elevation and sulfur gradients on its slopes. Using 16S rRNA gene metabarcoding, we inferred metagenome functional profiles, contrasting sample groups by altitude or soil sulfur concentration. We inferred that high-altitude communities may have higher predicted abundance for anaerobic metabolism (crotonate fermentation), coenzyme B12 synthesis, and degradation of diverse carbon sources (sugars and octane). High-sulfur soils were associated with an inferred enrichment of pathways for degrading complex organic compounds and nitrogen metabolism, reflecting adaptation to unique geochemical conditions. In contrast, low-sulfur soils are consistent with a higher predicted abundance of glycerol degradation. Within the limitation imposed by the potential weak associations of the applied predicted functional profiling to actual gene content, we propose that the inferred metabolic changes represent different ecological strategies for resource acquisition, energy generation, and stress tolerance, and they are optimized for varying conditions in this unique volcanic ecosystem. Our findings highlight how environmental gradients shape soil microbiome functional diversity and offer insights into microbial adaptation in Sumaco's exceptional geochemistry within the Amazon. Further efforts linking functional predictions back to specific taxa will offer a complete ecological perspective of the microbiome exploration in the Sumaco volcano.},
}

@article {pmid41597602,
year = {2025},
author = {Freixas-Coutin, JA and Seo, J and Su, L and Hood, S},
title = {Longitudinal Analysis of Vulvovaginal Bacteriome Following Use of Water- and Silicone-Based Personal Lubricants: Stability, Spatial Specificity, and Clinical Implications.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010082},
pmid = {41597602},
issn = {2076-2607},
support = {NA//Reckitt Benckiser (United Kingdom)/ ; },
abstract = {The vulvovaginal microbiome is a complex and dynamic ecosystem of microorganisms. The potential effects of common personal lubricants on its balance, which have implications for reproductive health, are still unknown. This study longitudinally assessed the impact of two commercially available lubricants on the composition and stability of the vaginal and vulvar bacteriome. Paired vaginal and vulvar swabs were collected at baseline and after repeated lubricant use, and the bacteriome was assessed using 16S rRNA gene amplicon sequencing. Alpha and beta diversity were assessed using Shannon entropy and Bray-Curtis dissimilarity, respectively. The results showed that the vaginal bacteriome was dominated by Lactobacillus and Firmicutes, while vulvar communities were more diverse and had higher abundances of Prevotella, Finegoldia, and Peptoniphilus. Both alpha and beta diversity measures indicated that the vaginal and vulvar bacteriome remained largely stable even after repeated lubricant use. Minor and non-significant changes in genus-level composition were observed, particularly in the vulvar samples. A moderate but significant correlation (Mantel r = 0.274, p = 0.001) was also observed between the vaginal and vulvar bacteriome. Overall, this study shows that short-term, repeated use of the water-based lubricant and the silicone-based lubricant tested in this study does not significantly disrupt the vaginal or vulvar bacteriome.},
}

@article {pmid41597601,
year = {2025},
author = {Wang, H and Ma, W and Malik, MI and Shah, AM and Liu, A and Hu, G and Jing, J and Li, H and Huang, Y and Zhang, Q and Zhou, J and Bai, B and Yang, Y and Wang, Z and Zhang, J and Hao, L},
title = {Effects of Different Feeding Methods on Growth Performance, Enzyme Activity, Rumen Microbial Diversity and Metabolomic Profiles in Yak Calves.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010081},
pmid = {41597601},
issn = {2076-2607},
support = {2024-ZJ-905; 2025KTST04; QHKLYC-GDCXCY-2023-086//Qinghai Provincial Natural Science Fund for Distinguished Young Scholars; Qinghai University Research Ability Enhancement Project; Qinghai University Graduate Supervisor Innovation Team, Leading talent of "Kunlun Talents High-level Innovation and Entrepre/ ; },
abstract = {Yaks are important for the ecology and economy of the Qinghai-Tibetan Plateau. The growth of the yak industry depends on sustainable and accelerated growth of calves, sustaining herd reproduction and production systems. Yak calves born in the summer months of June and July are faced with a heightened risk of winter mortality. Exclusive traditional, natural feeding prolongs the suckling period, and this leads to a series of problems due to the harsh high-altitude environment, such as inadequate nutrition leading to retarded growth and an imbalanced herd structure. To enhance growth performance and breeding efficiency, 12 male calves of similar weights (68.53 ± 6.41 kg) were randomly assigned to a control group (suckle the dam (SU)) or an experimental group (early weaning with full feeding, concentrate and oat hay at a 7:3 ratio (CO)). The results showed that compared with suckling, early weaning with full feeding significantly improved the growth performance, volatile fatty acids and digestive enzyme activity. The abundance of the Firmicutes was reduced, but there was an increased abundance of Bacteroidetes, which affected the rumen metabolome. In conclusion, early weaning with full feeding improves growth performance, promotes rumen fermentation and carbohydrate degradation, reduces the diversity and richness of rumen microbial flora and alters the content and pathways of metabolites in yak calves. These factors contribute to the growth and market readiness of yak calves born in June and July, accelerate herd turnover and enhance the production efficiency of grazing yaks.},
}

@article {pmid41597595,
year = {2025},
author = {Wang, J and Xu, D and Hu, S and Zheng, B and Chen, Y and Pan, T},
title = {The Impact of Microbiome on Breast Cancer and Regulatory Strategies.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010075},
pmid = {41597595},
issn = {2076-2607},
support = {Grant No. 81602716//National Natural Science Foundation of China/ ; },
abstract = {Breast cancer, the most prevalent malignant tumor in women, is closely linked to the human microbiota. The microbiome participates throughout breast cancer pathogenesis, including its occurrence, progression, response to anti-tumor therapies, and treatment-related complications. This review examines the central hypothesis that microbiome-driven inflammatory and immune mechanisms shape breast cancer progression through two key pathways: systemic immune-inflammatory regulation and local tumor microenvironment remodeling. Furthermore, microorganisms and their metabolites modulate systemic treatments by interfering with drug metabolism and altering systemic or local immune-inflammatory environments. Targeting the microbiota represents a promising strategy for enhancing anticancer efficacy and reducing treatment-related complications. This review aims to advance the understanding of the etiology and disease progression of breast cancer from the perspective of microbial-regulated inflammation and immunity, offering new insights for its prevention and treatment.},
}

@article {pmid41597583,
year = {2025},
author = {Ashkanani, A and Ashkanani, G and Yousef, M and Rob, M and Al-Marri, M and Naseem, N and Laws, S and Chaari, A},
title = {Microbiome and Skin Health: A Systematic Review of Nutraceutical Interventions, Disease Severity, Inflammation, and Gut Microbiota.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010063},
pmid = {41597583},
issn = {2076-2607},
abstract = {Skin disorders are a major global cause of morbidities, and increasing evidence links several to gut microbiome dysregulation. Because of this the bidirectional gut-skin axis, nutraceuticals have been proposed as therapeutic adjuncts, but their clinical effects across skin conditions remain unclear. To understand how pro/pre/synbiotics can affect health, we conducted a systematic review to investigate disease severity indices, inflammatory and immunological markers, quality of life, and changes in gut microbiota composition. PubMed, Embase, and Web of Science were utilized to identify relevant randomized clinical trials. Selected articles were pre-piloted for in-depth analysis and data extraction. We included 60 randomized controlled trials involving human participants with 5 dermatological conditions, including atopic dermatitis, psoriasis, acne vulgaris, chronic urticaria, and melasma, treated with probiotics, prebiotics, or synbiotics. Risk of bias was generally low across trials, with some having concerns. The SCORAD of the treated group was substantially lower than that of the placebo group in 30 of the 47 trials on atopic dermatitis. Inflammatory markers showed a range of results; some showed significant changes, while others produced contradictory results. Five trials that examined atopic dermatitis and psoriasis independently showed a significant improvement in Quality of Life. The PASI score was considerably lower in psoriasis in three of the five RCTs. Acne vulgaris, melasma, and chronic urticaria were not well documented. Major limitations included heterogeneity in interventions and outcomes, small sample sizes, and inconsistent reporting of microbiome analyses. Nutraceuticals show potential as additional treatments, but further, large scale studies are required.},
}

@article {pmid41597581,
year = {2025},
author = {Ferreira, FR and Rouvier, GA and Hassib, L and de Andrade Morraye, R and da Silva, YSP and da Gama, LFS and Pereira, IS and Oliveira Gomes, A and Rosa, MJG and de Morais-Scussel, AC and de Molfetta, GA and Silva, WA},
title = {Prebiotic Treatment During Pregnancy Prevents Social Deficits Associated with Autism Spectrum Disorder-like Behavior Induced by Maternal Immune Activation.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010060},
pmid = {41597581},
issn = {2076-2607},
support = {403318/2023-8//CNPq/ ; E-26/SEI-260003/012160/2021//Fundação de Amparo a Pesquisa do Estado do Rio de Janeiro/ ; 88887.923410/2023-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 2023/16731-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; },
abstract = {Maternal exposure to infectious agents has been associated with an increased risk of mental disorders in offspring, such as autism spectrum disorder. Evidence suggests that maternal immune responses during infection can significantly impact the neurodevelopment of the offspring, potentially affecting central nervous system functions in the future. Inulin is an indigestible soluble fiber that acts as a prebiotic. It promotes the production of short-chain fatty acids, such as butyrate, which can help inhibit the production of pro-inflammatory cytokines. Thus, this study aims to investigate whether inulin treatment during pregnancy can mitigate or reduce the impact of maternal immune activation (MIA) on the neurodevelopment of the offspring. Swiss mice were used in a dose-response study to evaluate the protective effects of inulin against maternal exposure to soluble Toxoplasma gondii antigen. Adult offspring of both sexes underwent behavioral assessments, and their gut microbiota was characterized. Both males and females in the soluble T. gondii antigen (STAg) group exhibited reduced sociability, as evidenced by the three-chamber social interaction test. Moreover, co-treatment with inulin mitigated this effect. Additionally, anhedonia was observed only in female offspring from the MIA group, but treatment with 1% and 3% inulin also mitigated this effect. The analysis of fecal microbiota showed significant differences between the STAg and inulin treatments at both the family and genus levels. Therefore, inulin appears to have a potential protective effect on the neurodevelopment of the offspring exposed to maternal antigenic challenges during pregnancy mediated by offspring microbiome modulations.},
}

@article {pmid41597577,
year = {2025},
author = {Zhang, Y and Zhang, M and Zhao, Z and Peng, Y and Deng, F and Jiang, H and Zhang, M and Song, B and Kim, JK and Pan, JH and Chai, J and Li, Y},
title = {High-Altitude Extreme Environments Drive Convergent Evolution of Skin Microbiota in Humans and Horses.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010057},
pmid = {41597577},
issn = {2076-2607},
support = {32170430//the National Natural Science Foundation of China/ ; },
abstract = {Unique skin microbial communities have been shaped by the harsh climatic conditions in high-altitude areas, such as intense ultraviolet radiation and low oxygen concentration. However, it is unknown whether high altitude contributes to shaping common microbiota inhabiting the skin across different mammals. The skin microbial communities of humans and horses living in high-altitude (Tibetan) and low-altitude areas were analyzed using full-length 16S rRNA sequencing technology. Alpha diversity differed between high- and low-altitude groups (p < 0.01). Skin microbial community composition also differed between high- and low-altitude areas (p < 0.05). Some of the common taxa present in the skin of humans and horses in high-altitude areas were identified as extreme microorganisms capable of adapting to the harsh high-altitude environment. Five bacterial taxa, including the genera Sphingomonas, Brevundimonas, and Kocuria, as well as the species Acinetobacter guillouiae and Arboricoccus pini, were significantly enriched (p < 0.01) on the skin of both humans and horses in high-altitude areas. Meanwhile, some taxa enriched on the skin surface at the same altitude showed preferences for mammalian species. Acinetobacter johnsonii, Anaerococcus nagyae, and Anaerococcus octavius were significantly enriched (p < 0.05) in the skin of humans at both high and low altitudes, whereas Acinetobacter pseudolwoffii and Armatimonas rosea, Archangium gephyra and Acinetobacter lwoffii were significantly enriched (p < 0.05) in the skin of horses at both high and low altitudes. In the network analyses, a positive correlation (p < 0.01) was shown between the skin taxa enriched in high-altitude areas and each other, while a negative correlation (p < 0.01) was found between the skin microorganisms enriched in high-altitude areas and those enriched in low-altitude areas. Overall, our findings indicate that high-altitude extreme environments drive convergent evolution of skin microbiota across mammals, reflecting the joint effects of environmental selection and host-related filtering on community assembly. This cross-species comparison provides a framework for understanding skin microbiome responses to extreme environments in plateau mammals.},
}

@article {pmid41597572,
year = {2025},
author = {Li, J and Qi, M and Zhang, J and Zuo, Y},
title = {Plant-Mediated Soil Sickness: Steering the Rhizosphere into a Pathogenic Niche.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010052},
pmid = {41597572},
issn = {2076-2607},
support = {31760360//National Natural Science Foundation of China/ ; 202301AT070007//Natural Science Foundation of Yunnan Province of China/ ; 202101BD070001-078//Natural Science Agricultural Joint Foundation of Yunnan Province of China/ ; },
abstract = {Continuous monoculture of Panax notoginseng leads to severe replant disease, yet the mechanisms by which root exudates mediate rhizosphere microbiome assembly and pathogen enrichment remain poorly understood. Here, we demonstrate that long-term root exudate accumulation acts as an ecological filter, driving the fungal community toward a phylogenetically impoverished, pathogen-dominated state. Specifically, exudates enriched the soil-borne pathogen Fusarium while reducing the abundance of potentially antagonistic fungi. In contrast, bacterial communities exhibited higher resilience, with exudates selectively enriching oligotrophic taxa such as Terrimonas and MND1, but suppressing nitrifying bacteria (e.g., Nitrospira) and plant-growth-promoting rhizobacteria (PGPR). Microbial functional profiling revealed a shift in nitrogen cycling, characterized by suppressed nitrification and enhanced nitrate reduction. Crucially, co-occurrence network analysis identified bacterial taxa strongly negatively correlated with Fusarium, providing a synthetic community blueprint for biocontrol strategies. Our study establishes a mechanistic link between root exudate accumulation and negative plant-soil feedback in monoculture systems, highlighting microbiome reprogramming as a key driver of replant disease. These insights offer novel avenues for manipulating rhizosphere microbiomes to sustain crop productivity in intensive agricultural systems.},
}

@article {pmid41597571,
year = {2025},
author = {Amirkhanzadeh Barandouzi, Z and Bruner, DW and Lin, Y and Choi, H and Zeki, LR and Akangbe, T and Epari, A and Li, H},
title = {Probiotics for Anxiety and Depressive Symptoms in Cancer: A Systematic Review of Animal and Human Studies with Mechanistic Insights.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010051},
pmid = {41597571},
issn = {2076-2607},
support = {UL1TR002378//National Center for Advancing Translational Sciences of the National Institutes of Health/ ; 5K12ES033593-04//Pediatric and Reproductive Environmental Health Scholars Southeastern Environmental Exposures and Disparities (PREHS SEED) Program/ ; },
abstract = {Probiotics have been increasingly evaluated for their potential effect on anxiety and depression through the modulation of the gut-brain axis. Individuals with cancer experience a high prevalence of these symptoms. However, the effects of probiotics and their underlying mechanisms in this population have not been systematically evaluated. This review synthesizes current evidence regarding probiotic interventions for anxiety and depression in cancer and examines the associated mechanistic pathways. A systematic search for original trials in PubMed, Embase, CINAHL, Web of Science, and PsycINFO was conducted in May 2025. Eligible studies included animal models or adults with cancer who received probiotics alone or in combination with other treatments, with outcomes related to anxiety, depressive symptoms, or depression. Search terms included animal model, cancer, probiotics, anxiety, depressive symptoms, depression, gastrointestinal microbiome, gut microbiome, and microbiota. The review followed PRISMA guidelines. Risk of bias in trials was assessed using the SYRCLE and Cochrane RoB2 tool. Nine studies met the inclusion criteria, including seven human studies, one animal study, and one mixed human-animal study, with human sample sizes ranging from 24 to 266. The animal study reported reductions in depressive and anxiety-like behaviors, paralleled by modulation of the hypothalamic-pituitary-adrenal (HPA) axis, reduced inflammation, rebalancing of the gut microbiota, and improvements in neurotransmitter pathways. Findings from human studies were more variable. Some trials reported improvements in anxiety, and depressive symptoms, while others showed no significant differences compared with control groups. Studies that combined probiotics with antidepressants or exercise demonstrated the most pronounced reductions in anxiety and depression. Mechanistic insights from human studies partially aligned with animal evidence, with several trials showing reductions in inflammatory markers (IL-6, TNF-α), improvements in neuroendocrine measures (serotonin, dopamine, cortisol), stabilization of metabolic markers, and favorable shifts in gut microbiota, although these effects were not consistent across all studies. Probiotics appear to be safe within the intervention periods of the reviewed studies (<24 weeks), as no serious adverse effects were reported. Substantial heterogeneity across studies, including variations in cancer type, intervention duration, probiotic strains, formulations, dosages, and study design combined with small sample sizes, restricts the ability to draw definitive conclusions. Rigorously designed randomized controlled trials with larger sample sizes and mechanistic biomarkers are required to confirm the efficacy of probiotics for relieving anxiety and depression in the cancer population.},
}

@article {pmid41597570,
year = {2025},
author = {Cesanelli, F and Scarvaglieri, I and De Francesco, MA and Alberti, M and Salvi, M and Tiecco, G and Castelli, F and Quiros-Roldan, E},
title = {The Human Virome in Health and Its Remodeling During HIV Infection and Antiretroviral Therapy: A Narrative Review.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010050},
pmid = {41597570},
issn = {2076-2607},
abstract = {The human virome represents a fundamental yet understudied component of the microbiome, influencing immune regulation and disease. Given the profound immune dysregulation and microbial imbalance associated with HIV infection, understanding virome alterations during HIV and antiretroviral therapy is essential. This narrative review seeks to integrate and discuss the latest evidence regarding the structure and behavior of the human virome in healthy individuals, in the context of HIV infection, and under antiretroviral therapy. A comprehensive literature search was performed in MEDLINE and Google Scholar for peer-reviewed English-language articles published up to November 2025. Studies describing virome composition, diversity, and interactions in people living with HIV, as well as antiretroviral-induced changes, were included. Reference lists of relevant papers were screened to identify additional sources. Data were extracted and synthesized narratively, emphasizing human studies and supported by evidence from primate models where applicable. HIV infection induces profound alterations in the human virome, notably an expansion of eukaryotic viruses such as Anelloviridae, Adenoviridae, and Parvoviridae, accompanied by reduced bacteriophage diversity. Antiretroviral therapy partially restores virome balance but fails to fully re-establish pre-infection diversity, with persistent enrichment of Anelloviridae reflecting incomplete immune reconstitution. Virome perturbations correlate with immune activation, microbial translocation, and inflammation, contributing to comorbidities despite virological suppression. Emerging evidence suggests regimen-specific effects, with integrase inhibitor-based therapies showing more favorable viromic recovery. HIV and antiretroviral therapy profoundly remodel the human virome, with lasting implications for immune homeostasis and chronic inflammation. The ongoing disruption of the virome highlights its promise as both a biomarker and a potential therapeutic target in the management of HIV. Longitudinal, multi-omic studies are needed to clarify the causal role of virome alterations and guide future interventions.},
}

@article {pmid41597565,
year = {2025},
author = {Li, X and Huang, T and Li, Y and Pang, Z and Zhang, Y},
title = {Multi-Regional Study on the Microbial Community Structure, Core Microbiome and Functional Characteristics in Deep Fracture Waters.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010045},
pmid = {41597565},
issn = {2076-2607},
support = {42502251//National Natural Science Foundation of China/ ; SKL-K202303//the State Key Laboratory of Lithospheric and Environmental Coevolution/ ; },
abstract = {The deep terrestrial subsurface is the largest reservoir of Earth's freshwater resources as well as the largest habitat for prokaryotic life. However, the deep-subsurface microbiome, especially its spatial distribution across countries/continents, is still poorly understood. In this study, we compiled and compared 30 16S rRNA gene amplicon libraries from three deep fractured aquifers in different parts of the world (depth range of tens of meters to 2.4 km below surface) to understand the spatial distribution and functions of deep-subsurface microbial community, and to test for the presence of core taxa. The results revealed spatially heterogenous microbial community composition at both the local and the global scales, even at the phylum level. Environmental filtering was identified as an important driver of the microbial community structure of deep groundwaters. Despite the spatial heterogeneity, the three aquifers share a core microbiome at the genus level. Only one family, Comamonadaceae, was present in all the 30 samples analyzed. Several other families were also prevalent, including Hydrogenophilaceae, Omnitrophaceae, BSV26 (Candidatus Kryptonia), and an unclassified Thermodesulfovibrionia. FAPROTAX functional prediction indicated that chemoheterotrophic functions predominate, and the core microbial genera, together with the dominant genera, collectively govern the functional characteristics. Taken together, our findings provide new insights into the spatial heterogeneity and functional potential of deep-subsurface ecosystems across the globe.},
}

@article {pmid41597557,
year = {2025},
author = {Domingues, VDSP and Sousa, MP and Waldow, V and Akamine, R and Seldin, L and Jurelevicius, D},
title = {Sulfide Production and Microbial Dynamics in the Water Reinjection System from an Offshore Oil-Producing Platform.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010038},
pmid = {41597557},
issn = {2076-2607},
support = {001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; },
abstract = {In addition to seawater in the injection header (IH) to enhance oil recovery, oil companies reuse produced water (PW), a byproduct of oil extraction, and implement produced water reinjection systems (PWRI). Although the microorganisms in IH are controlled by biocides, PW is generally treated by flotation to remove oil residues before PWRI. However, IH, PW, and PWRI can be sources of sulfate-reducing bacteria (SRB) related to oil reservoir souring. Here, we evaluated hydrogen sulfide (H2S) production in IH, PW, and PWRI, as well as the microbial dynamics (most probable number-MPN, quantitative PCR, and amplicon sequencing), of a Brazilian oil reservoir. Results revealed that the highest average H2S concentration occurred in PW samples. However, the dissolved H2S threshold concentration of 2 mg L[-1] was exceeded in 18% of PW and ~16% of PWRI samples, respectively. Although MPN showed no correlation between H2S and the number of SRB or total anaerobic heterotrophic bacteria (TAHB), qPCR and microbiome data revealed that the SRB Desulfobacterota was the most abundant in PW and PWRI. Overall, flotation was associated with (i) low microbial control in PW; and (ii) the enrichment of SRB (mainly Desulfobacterota), Thermotogota, and Proteobacteria groups in PWRI.},
}

@article {pmid41597554,
year = {2025},
author = {Dai, X and Yang, P and Zhou, C and Chen, Z and Li, S and Zhu, T},
title = {Bacillus mojavensis dxk33 Modulates Rhizosphere Microbiome and Suppresses Root Rot in Cunninghamia lanceolata.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010034},
pmid = {41597554},
issn = {2076-2607},
support = {2024NSFSC1193//Natural Science Foundation of Sichuan/ ; },
abstract = {Soil-borne pathogens cause devastating root rot diseases in forest ecosystems, often by inducing dysbiosis in the rhizosphere microbiome. While antagonistic bacteria can suppress disease, their effects frequently extend beyond direct inhibition to include ecological restructuring of resident microbial communities. However, the causal relationships between such microbiome restructuring and disease suppression in tree species remain poorly understood. Here, we show that the antagonistic bacterium B. mojavensis dxk33 effectively suppresses F. solani-induced root rot in C. lanceolata, and that this disease suppression coincides with a partial reversal of pathogen-associated dysbiosis in the rhizosphere. Inoculation with dxk33 significantly promoted plant growth and reduced the disease index by 72.19%, while concurrently enhancing soil nutrient availability and key C-, N- and P-cycling enzyme activities. High-throughput sequencing revealed that dxk33 inoculation substantially reshaped the rhizosphere microbiome, counteracting the pathogen's negative impact on microbial diversity and coinciding with a shift toward a more stable community structure. Under pathogen stress, dxk33 enriched beneficial bacterial taxa such as Pseudomonas and Sphingomonas and suppressed pathogenic fungi while promoting beneficial fungi such as Mortierella. Linear discriminant analysis and functional prediction further indicated that dxk33 remodeled ecological guilds enriched for mycorrhizal and saprotrophic fungi, and reactivated bacterial metabolic pathways and signaling networks that were suppressed by the pathogen. Taken together, our findings are consistent with a multi-tiered mode of action in which direct antagonism by B. mojavensis dxk33 operates alongside associated changes in the rhizosphere microbiome that resemble a disease-suppressive state, although the present experimental design does not allow a strictly causal role for microbiome reconfiguration in disease suppression to be established. This study provides a mechanistic framework for understanding how microbiome engineering may mitigate soil-borne diseases in perennial trees and highlights the potential of targeted microbial interventions for sustainable forest management.},
}

@article {pmid41597549,
year = {2025},
author = {Komatsu, Y and Furuichi, M and Kokubo, T},
title = {Gastrointestinal Journey of Human Milk Oligosaccharides: From Breastfeeding Origins to Functional Roles in Adults.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010029},
pmid = {41597549},
issn = {2076-2607},
abstract = {Human milk oligosaccharides (HMOs) are the third most abundant solid component in human milk and play crucial roles in shaping the gut microbiome and promoting infant health. Although their functions during infancy are well established, emerging evidence suggests that HMOs exert region-specific effects throughout the gastrointestinal tract, extending their benefits beyond early life. This review summarizes current findings on HMO activity in the oral cavity, stomach, small intestine, and large intestine, focusing on their microbiota-modulating, barrier-enhancing, and immunoregulatory effects. In the oral cavity, HMOs inhibit pathogen adhesion and biofilm formation, maintaining oral homeostasis. In the stomach, fucosylated and sialylated HMOs act as soluble decoy receptors, preventing Helicobacter pylori infection. In the small intestine, HMOs strengthen epithelial integrity, regulate inflammation, and promote nutrient absorption. In the large intestine, they serve as selective prebiotics for beneficial microbes, enhancing short-chain fatty acid production and improving barrier function. Although preclinical and clinical studies demonstrate their safety and efficacy, further research is required to elucidate their mechanisms in adults. Overall, HMOs represent multifunctional bioactive glycans with promising applications for gastrointestinal health across all ages.},
}

@article {pmid41597540,
year = {2025},
author = {Yu, J and Ao, Y and Chen, H and Liu, C and Deng, T and Wang, D and Xiang, M and Wan, P and Cheng, L},
title = {Effects of Dietary Supplementation with Dihydromyricetin on Hindgut Microbiota and Metabolite Profiles in Dairy Cows.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010020},
pmid = {41597540},
issn = {2076-2607},
support = {No.2023BBB058//Key Research and Development Program of Hubei Province/ ; No.D20220056//Science and Technology Program of Enshi Tujia and Miao Autonomous Pre-fecture/ ; },
abstract = {High-yielding dairy cows suffer from a high metabolic load and oxidative stress, which lead to systemic inflammation and metabolic disorders, increasing the susceptibility of these cows to various production diseases. Dihydromyricetin (DMY) has demonstrated potent antioxidant and anti-inflammatory physiological functions; however, research into its application in ruminants remains limited. This study investigated whether DMY supplementation is associated with the maintenance of metabolic homeostasis through the regulation of gut microbiota and metabolite profiles. A total of 14 mid-lactation Holstein dairy cows were randomly divided into two groups (n = 7 per group) and supplemented with DMY at 0 or 0.05% in their basal diet for 60 consecutive days. The effects of DMY on the blood biochemical indicators and the antioxidant capacity of the dairy cows were then determined. Alterations to the gut microbiome and the fecal and plasma metabolome were analyzed through 16S rDNA sequencing and untargeted metabolomics. The results showed that DMY significantly improved the activity of serum glutathione peroxidase (GSH-Px) and presented a trend of increasing the total antioxidant capacity (T-AOC). The abundance of multiple fiber-degrading and beneficial commensal bacteria in the gut, including Fibrobacter_succinogenes, Ruminococcus_albus, and Turicibacter, was significantly elevated by the DMY intervention, accompanied by the upregulation of 8,11,14-eicosatrienoic acid, myricetin, dihydro-3-coumaric acid, PGE1, L-leucine, nicotinuric acid, pantothenic acid, and pyruvate in the feces and plasma. Moreover, DMY supplementation notably reduced the abundance of potential pathogenic microbes, such as Chloroflexi, Deltaproteobacteria, RFP12, and Succinivibrio, and downregulated the levels of 12-hydroxydodecanoic acid, 12,13-DHOME (12,13-dihydroxy-9Z-octadecenoic acid), 16-hydroxyhexadecanoic acid, niacin, and glycerol 3-phosphate. These differential metabolites were principally enriched in the mTOR signaling pathway; pantothenate, nicotinate, and thiamine metabolism; glutathione metabolism; and glycolysis/gluconeogenesis. In summary, dietary supplementation with DMY increased the abundance of intestinal fiber-degrading bacteria and multiple metabolites with known anti-inflammatory and antioxidant properties in the feces and plasma, and was associated with alterations in metabolic pathways involving B-vitamins, amino acids, and glutathione. This suggests a potential role for DMY in supporting metabolic homeostasis in dairy cows.},
}

@article {pmid41597522,
year = {2025},
author = {Tamahara, T and Kouketsu, A and Fukase, S and Sripodok, P and Saito, T and Ito, A and Li, B and Kumada, K and Shimada, M and Iikubo, M and Shimizu, R and Yamauchi, K and Sugiura, T},
title = {Ecological and Functional Landscape of the Oral Microbiome: A Multi-Site Analysis of Saliva, Dental Plaque and Tongue Coating.},
journal = {Microorganisms},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/microorganisms14010002},
pmid = {41597522},
issn = {2076-2607},
support = {JP24K1310 and JP22K17150//JSPS KAKENHI/ ; },
abstract = {The oral cavity contains several microbial niches, including saliva, dental plaque and tongue coating, each shaped by distinct local environments and host factors. This study compared the ecological and functional characteristics of the microbiomes of these three oral sites within the same individuals and examined host conditions associated with their variation. Saliva, supragingival plaque and tongue coating samples were collected simultaneously from 31 adults without clinical oral lesions. The bacterial 16S rRNA gene (V3-V4 region) was sequenced using the Illumina MiSeq platform, and analyses included α and β diversity, Mantel correlations, differential abundance tests, network analysis and functional prediction. The three sites displayed a clear ecological gradient. Saliva and tongue coating were taxonomically similar but were influenced by different host factors, whereas plaque maintained a distinct, biofilm-like structure with limited systemic influence. Functional divergence was most pronounced on the tongue coating despite its taxonomic similarity to saliva, whereas functional differences between saliva and plaque were modest despite larger taxonomic separation. These findings indicate that microbial composition and function vary independently across oral niches and support the need for multi-site sampling to more accurately characterize oral microbial ecology.},
}

@article {pmid41597510,
year = {2026},
author = {Boccuzzi, M and Aiuto, R and Lombardo, L and Piasente, M and Bianchi, AE and Clivio, A},
title = {Oral Microbiome and Metabolome Changes During Orthodontic Treatments: A Systematic Review of Limited Clinical Evidence.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {1},
pages = {},
doi = {10.3390/medicina62010224},
pmid = {41597510},
issn = {1648-9144},
mesh = {Humans ; *Microbiota/physiology ; *Metabolome/physiology ; *Mouth/microbiology ; *Orthodontic Appliances/adverse effects ; *Orthodontics/methods ; },
abstract = {Background and Objectives: Recent advances in dentistry include microbiological and metabolomic analyses, which have the potential to improve the understanding of oral microbiome-host imbalances during orthodontic treatment. Fixed appliances, functional devices and, more recently, clear aligners have been associated with several oral health conditions, including enamel demineralization, dental caries, gingivitis, periodontitis and root and bone resorption. In this context, metabolomic approaches may enable the identification of metabolites in biological samples that could potentially serve as biomarkers and reflect functional biological changes within the oral ecosystem. Investigating orthodontic appliances and associated metabolomic alterations may therefore contribute to advancing current knowledge in orthodontics. This systematic review aimed to describe the available evidence on oral metabolomic changes during orthodontic treatment. Materials and Methods: A systematic literature search was conducted in PubMed, Web of Science, Scopus and the Cochrane Library. A total of 1632 records were identified. After duplicate removal and screening, 18 full-text articles were assessed for eligibility. Of these, 15 studies were excluded, and three studies met the inclusion criteria. Risk of bias was assessed using the ROBINS-I and RoB 2 tools, and the GRADE approach was applied to evaluate the certainty of evidence. The review protocol was registered in PROSPERO (CRD420251141544). Results: Three studies met the inclusion criteria. Overall, the available evidence was limited and heterogeneous. The included studies suggested potential differences in oral microbiome composition and metabolomic profiles between patients treated with fixed appliances and those treated with clear aligners. Reported metabolomic findings were exploratory and involved amino acid-related, immune-associated, and acidic metabolic pathways. Limitations: Only three studies were included, all conducted in a single country. The small sample size and methodological heterogeneity limit the generalizability of the findings. In addition, potential confounding variables highlight the need for further standardized longitudinal studies.},
}

Humans
*Microbiota/physiology
*Metabolome/physiology
*Mouth/microbiology
*Orthodontic Appliances/adverse effects
*Orthodontics/methods

@article {pmid41597500,
year = {2026},
author = {Hendem, E and Koçak, MZ and Çetinkaya, AM and Dinç, G and Çağlayan, M and Uğraklı, M and Çağlayan, D and Araz, M and Eryılmaz, MK and Sakin, A and Eren, OÖ and Tatlı, AM and Geredeli, Ç and Artaç, M},
title = {The Impact of Concurrent Proton Pump Inhibitors on Nivolumab Response in Metastatic Non-Small Cell Lung Cancer: A Multicenter Real-Life Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {1},
pages = {},
doi = {10.3390/medicina62010214},
pmid = {41597500},
issn = {1648-9144},
mesh = {Humans ; *Proton Pump Inhibitors/therapeutic use/pharmacology ; *Carcinoma, Non-Small-Cell Lung/drug therapy/mortality ; Male ; *Nivolumab/therapeutic use/pharmacology ; Female ; Retrospective Studies ; Middle Aged ; Aged ; *Lung Neoplasms/drug therapy/mortality ; Immune Checkpoint Inhibitors/therapeutic use ; Kaplan-Meier Estimate ; Aged, 80 and over ; Antineoplastic Agents, Immunological/therapeutic use ; Drug Interactions ; },
abstract = {Background and Objectives: Clinically meaningful drug-drug interactions may be overlooked in oncology. Proton pump inhibitors (PPIs) may modulate outcomes with immune checkpoint inhibitors (ICIs) by altering the gut microbiome, altering the immune milieu, and affecting transporter interactions. We evaluated whether concomitant PPI use affects survival among patients with metastatic non-small cell lung cancer (NSCLC) treated with nivolumab. Materials and Methods: We retrospectively included patients with metastatic NSCLC who received second-line nivolumab across five oncology centers (January 2020-June 2023). Patients were grouped as concomitant PPI users vs. non-users. Overall survival (OS) and progression-free survival (PFS) were estimated by the Kaplan-Meier method and compared with the log-rank test; multivariable Cox models assessed independent associations. Results: A total of 194 patients were screened, of whom 30 were excluded according to predefined criteria. The final analysis included 164 patients-85 PPI users and 79 non-users. Median OS was 26.1 months (95% CI 15.5-36.7) in PPI users and 29.3 months (22.2-36.4) in non-users; this difference was not statistically significant (p = 0.54). Median PFS was 6.2 months (3.7-8.6) in PPI users vs. 10.2 months (7.1-13.2) in non-users (p = 0.04). In multivariable analysis, absence of concomitant PPI use (No vs. Yes) was independently associated with longer PFS (HR = 0.52, 95% CI 0.24-0.89, p = 0.03), whereas PPI use was not associated with OS (HR = 0.96, 95% CI 0.67-1.61, p = 0.83). Conclusions: Concomitant PPI use during nivolumab therapy was associated with significantly shorter PFS and a numerical reduction in OS in real-world metastatic NSCLC. Where clinically feasible, the need for PPIs should be re-evaluated before and during ICI therapy.},
}

Humans
*Proton Pump Inhibitors/therapeutic use/pharmacology
*Carcinoma, Non-Small-Cell Lung/drug therapy/mortality
Male
*Nivolumab/therapeutic use/pharmacology
Female
Retrospective Studies
Middle Aged
Aged
*Lung Neoplasms/drug therapy/mortality
Immune Checkpoint Inhibitors/therapeutic use
Kaplan-Meier Estimate
Aged, 80 and over
Antineoplastic Agents, Immunological/therapeutic use
Drug Interactions

@article {pmid41597231,
year = {2026},
author = {Feng, Y and Geng, Y and Liu, S and Huang, X and Mou, C and Zhao, H and Zhou, J and Li, Q and Deng, Y},
title = {Overwinter Syndrome in Grass Carp (Ctenopharyngodon idellus) Links Enteric Viral Proliferation to Mucosal Disruption via Multiomics Investigation.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020157},
pmid = {41597231},
issn = {2073-4409},
support = {2024YFD2401102//National Key R&D ProgramNational Key R&D Program/ ; 2025ZNSFSC1081//Sichuan Provincial Natural Science Foundation/ ; NKYRCZX2025031//Research Initiation Funding from the Sichuan Academy of Agricultural Sciences/ ; SCCXTD-2025-15//Sichuan Freshwater Fish Innovation Team of the National Modern Agricultural Industrial Technology System/ ; },
mesh = {Animals ; *Carps/virology/microbiology ; *Fish Diseases/virology/microbiology/genetics ; *Intestinal Mucosa/virology/pathology/microbiology ; Gastrointestinal Microbiome ; Metagenomics ; Transcriptome ; Multiomics ; },
abstract = {Overwinter Syndrome (OWS) affects grass carp (Ctenopharyngodon idellus) aquaculture in China, causing high mortality and economic losses under low temperatures. Failure of antibiotic therapies shows limits of the 'low-temperature-pathogen' model and shifts focus to mucosal barrier dysfunction and host-microbiome interactions in OWS. We compared healthy and diseased grass carp collected from the same pond using histopathology, transcriptomics, proteomics, and metagenomics. This integrated approach was used to characterize intestinal structure, microbial composition, and host molecular responses at both taxonomic and functional levels. Results revealed a three-layer barrier failure in OWS fish: the physical barrier was compromised, with structural damage and reduced mucosal index; microbial dysbiosis featured increased richness without changes in diversity or evenness, and expansion of the virobiota, notably uncultured Caudovirales phage; and mucosal immune dysregulation indicated loss of local immune balance. Multi-omics integration identified downregulation of lysosome-related and glycosphingolipid biosynthesis pathways at transcript and protein levels, with disrupted nucleotide metabolism. Overall gut microbial richness, rather than individual taxa abundance, correlated most strongly with host gene changes linked to immunity, metabolism, and epithelial integrity. Although biological replicates were limited by natural outbreak sampling, matched high-depth multi-omics datasets provide exploratory insights into OWS-associated intestinal dysfunction. In summary, OWS entails a cold-triggered breakdown of intestinal barrier integrity and immune homeostasis. This breakdown is driven by a global restructuring of the gut microbiome, which is marked by increased richness, viral expansion, and functional shifts, ultimately resulting in altered host-microbe crosstalk. This ecological perspective informs future mechanistic and applied studies for disease prevention.},
}

Animals
*Carps/virology/microbiology
*Fish Diseases/virology/microbiology/genetics
*Intestinal Mucosa/virology/pathology/microbiology
Gastrointestinal Microbiome
Metagenomics
Transcriptome
Multiomics

@article {pmid41597223,
year = {2026},
author = {Chagas, J and Gilmer, G and Sowa, G and Vo, N},
title = {Impact of Menopause and Associated Hormonal Changes on Spine Health in Older Females: A Review.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020148},
pmid = {41597223},
issn = {2073-4409},
mesh = {Humans ; *Menopause/physiology/metabolism ; Female ; *Low Back Pain/physiopathology/metabolism ; *Spine ; *Hormones/metabolism ; Animals ; },
abstract = {Low back pain (LBP) represents a major societal and economic burden, with annual costs in the United States estimated at $90-134.5 billion. LBP disproportionately impacts postmenopausal women relative to age-matched men, suggesting a role for sex-specific biological factors. Although the mechanisms underlying this disparity are not fully understood, hormonal imbalance during menopause may contribute to LBP pathophysiology. This narrative review aimed to elucidate the impact of menopause on LBP, with emphasis on hormonal effects on spinal tissues and systemic processes. A literature search was conducted, followed by screening of titles, abstracts, and full texts of original clinical studies, preclinical research using human or animal samples, and relevant reviews. Rigour and reproducibility were evaluated using the ARRIVE Guidelines and the Modified Downs & Black Checklist. Evidence indicates that menopause is associated with changes in intervertebral discs, facet joint, ligamentum flavum, skeletal muscle, sympathetic innervation, and systemic systems such as the gut microbiome. However, most findings are correlational rather than causal. Evidence supporting hormone replacement therapy for LBP remains inconclusive, whereas exercise and other treatments, including parathyroid hormones, show more consistent benefits. Future studies should focus on causal mechanisms and adhere to rigour guidelines to improve translational potential.},
}

Humans
*Menopause/physiology/metabolism
Female
*Low Back Pain/physiopathology/metabolism
*Spine
*Hormones/metabolism
Animals

@article {pmid41597211,
year = {2026},
author = {Böckels, L and Alexa, D and Antal, DC and Gațcan, C and Alecu, C and Kacani, K and Crețu, RA and Piseru, EA and Bîlcu, RV and Cuciureanu, DI},
title = {The Microbiome-Neurodegeneration Interface: Mechanisms, Evidence, and Future Directions.},
journal = {Cells},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/cells15020135},
pmid = {41597211},
issn = {2073-4409},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Neurodegenerative Diseases/microbiology/metabolism ; Animals ; Dysbiosis ; Blood-Brain Barrier/metabolism ; },
abstract = {The gut microbiota has emerged as a central regulator of the gut-brain axis, profoundly influencing neural, immune, and metabolic homeostasis. Increasing evidence indicates that disturbances in microbial composition and function contribute to the onset and progression of neurodegenerative diseases (NDs) through mechanisms involving neuroinflammation, oxidative stress, and impaired neurotransmission. Gut dysbiosis is characterized by a loss of microbial diversity, a reduction in beneficial commensals, and an enrichment of pro-inflammatory taxa. These shifts alter intestinal permeability and systemic immune tone, allowing microbial metabolites and immune mediators to affect central nervous system (CNS) integrity. Metabolites such as short-chain fatty acids (SCFAs), tryptophan derivatives, lipopolysaccharides (LPS), and trimethylamine N-oxide (TMAO) modulate blood-brain barrier (BBB) function, microglial activation, and neurotransmitter synthesis, linking intestinal imbalance to neuronal dysfunction and cognitive decline. Disruption of this gut-brain communication network promotes chronic inflammation and metabolic dysregulation, key features of neurodegenerative pathology. SCFA-producing and tryptophan-metabolizing bacteria appear to exert neuroprotective effects by modulating immune responses, epigenetic regulation, and neuronal resilience. The aim of this work was to comprehensively explore the current evidence on the bidirectional communication between the gut microbiota and the CNS, with a focus on identifying the principal molecular, immune, and metabolic mechanisms supported by the strongest and most consistent data. By integrating findings from recent human studies, this review sought to clarify how microbial composition and function influence neurochemical balance, immune activation, and BBB integrity, ultimately contributing to the onset and progression of neurodegenerative processes. Collectively, these findings position the gut microbiota as a dynamic interface between the enteric and CNS, capable of influencing neurodegenerative processes through immune and metabolic signaling.},
}

Humans
*Gastrointestinal Microbiome/physiology
*Neurodegenerative Diseases/microbiology/metabolism
Animals
Dysbiosis
Blood-Brain Barrier/metabolism

@article {pmid41596956,
year = {2026},
author = {Angane, M and Paturi, G and Butts, CA and Quek, SY},
title = {Synergistic Effects of Plant Essential Oils and Extracts on Gut Microbiota in Rats.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020358},
pmid = {41596956},
issn = {2304-8158},
support = {4200-UOA-48422-A8AN//University of Auckland/ ; },
abstract = {The application of essential oils and plant extracts as natural food preservatives has gained increasing interest; however, their potential impacts on gut health and host physiology remain unknown. This study evaluated the effects of synergistic combinations of peppermint essential oil (EO) + thyme EO and peppermint EO + feijoa peel extract on gut microbiota composition and colonic morphology in a rat model. Sprague-Dawley rats were orally given the synergistic combinations daily for 28 days, and their effects were assessed using 16S rRNA gene sequencing of the caecum microbiota and histological analysis of proximal colon tissues. Alpha diversity metrics showed no significant differences (p > 0.05) between treatment and control groups, and beta diversity indicated no treatment-related shift in the bacterial communities. Taxonomic profiling at the phylum, family, and genus levels showed comparable relative abundances of dominant microbial taxa across all treatments, with no evidence of dysbiosis. Histological examination of proximal colon tissues revealed no significant changes in crypt depth between treated and control groups, confirming the absence of adverse morphological effects on the intestinal epithelium. The results of this study indicate that synergistic combinations of peppermint EO, thyme EO, and feijoa peel extract do not adversely affect the gut microbiota composition and colonic morphology in rats, thereby supporting their application as preservatives in foods.},
}

@article {pmid41596857,
year = {2026},
author = {Tsouggou, N and Korozi, E and Pemaj, V and Drosinos, EH and Kapolos, J and Papadelli, M and Skandamis, PN and Papadimitriou, K},
title = {Advances in Shotgun Metagenomics for Cheese Microbiology: From Microbial Dynamics to Functional Insights.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {2},
pages = {},
doi = {10.3390/foods15020259},
pmid = {41596857},
issn = {2304-8158},
abstract = {The cheese microbiome is a complex ecosystem strongly influenced by both technological practices and the processing environment. Moving beyond traditional cultured-based methods, the integration of shotgun metagenomics into cheese microbiology has enabled in-depth resolution of microbial communities at the species and strain levels. The aim of the present study was to review recent applications of shotgun metagenomics in cheese research, underscoring its role in tracking microbial dynamics during production and in discovering genes of technological importance. In addition, the review highlights how shotgun metagenomics enables the identification of key metabolic pathways, including amino acid catabolism, lipid metabolism, and citrate degradation, among others, which are central to flavor formation and ripening. Results of the discussed literature demonstrate how microbial composition, functional traits, and overall quality of cheese are determined by factors such as raw materials, the cheesemaking environment, and artisanal practices. Moreover, it highlights the analytical potentials of shotgun metagenomics, including metagenome-assembled genomes (MAGs) reconstruction, characterization of various genes contributing to flavor-related biosynthetic pathways, bacteriocin production, antimicrobial resistance, and virulence, as well as the identification of phages and CRISPR-Cas systems. These insights obtained are crucial for ensuring product's authenticity, enabling traceability, and improving the assessment of safety and quality. Despite shotgun metagenomics' advantages, there are still analytical restrictions concerning data handling and interpretation, which need to be addressed by importing standardization steps and moving towards integrating multi-omics approaches. Such strategies will lead to more accurate and reproducible results across studies and improved resolution of active ecosystems. Ultimately, shotgun metagenomics has shifted the field from descriptive surveys to a more detailed understanding of the underlying mechanisms shaping the overall quality and safety of cheese, thus bringing innovation in modern dairy microbiology.},
}

@article {pmid41596745,
year = {2026},
author = {Lee, JH and Han, KI and Jeong, E and Moon, J and Kim, MA and Koo, BS and Lee, Y and Baek, S and Kim, HS and Kim, TJ},
title = {Effects and Molecular Mechanisms of Heat-Killed Postbiotic Enterococcus faecalis EF-2001 on Muscle Volume and Grip Strength in Dexamethasone-Induced Muscle Atrophy in SD Rats.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021105},
pmid = {41596745},
issn = {1422-0067},
support = {RS-2022-00167156//the Ministry of SMEs and Startups (MSS, Republic of Korea)/ ; },
mesh = {Animals ; *Dexamethasone/adverse effects ; *Muscular Atrophy/chemically induced/pathology/metabolism/drug therapy ; *Enterococcus faecalis ; Rats, Sprague-Dawley ; Male ; Rats ; Mice ; *Probiotics/pharmacology ; Muscle Fibers, Skeletal/drug effects/metabolism ; *Hand Strength ; Cell Line ; Muscle, Skeletal/drug effects/pathology ; Hot Temperature ; Proto-Oncogene Proteins c-akt/metabolism ; },
abstract = {The interaction between the gut microbiota and human health has gained increasing recognition, accelerating advances in microbiome research. While early studies have emphasized probiotics, concerns regarding antibiotic resistance and adverse effects, such as sepsis, have shifted research interest towards heat-treated microbial cells or postbiotics. This study investigated the therapeutic potential of heat-killed postbiotic Enterococcus faecalis EF-2001-one of the most widely used postbiotics worldwide-for the prevention and treatment of muscle atrophy. In vitro, mouse C2C12 myotubes were pretreated with heat-killed postbiotic EF-2001 (50-500 μg/mL) for 48 h and then treated with dexamethasone (100 μM) to induce muscle atrophy. In vivo, male Sprague Dawley rats were treated with low-dose (3 mg/kg) and high-dose (30 mg/kg) EF-2001 for efficacy studies. Heat-killed postbiotic EF-2001 attenuated cellular and DNA damage in dexamethasone-induced C2C12 myotubes. Specifically, heat-killed postbiotic EF-2001 increased AKT phosphorylation while suppressing Atrogin-1 expression, thereby alleviating muscle atrophy. In a Sprague Dawley rat model, heat-killed postbiotic EF-2001 significantly reduced dexamethasone-induced muscle loss by regulating muscle atrophy-associated signaling pathways, including Atrogin-1 expression. Collectively, these findings demonstrate that heat-killed EF-2001 alleviates dexamethasone-induced muscle atrophy and support its potential as a postbiotic. This study provides a solid foundation for future human clinical studies by establishing preclinical evidence for the biological activity of heat-killed EF-2001.},
}

Animals
*Dexamethasone/adverse effects
*Muscular Atrophy/chemically induced/pathology/metabolism/drug therapy
*Enterococcus faecalis
Rats, Sprague-Dawley
Male
Rats
Mice
*Probiotics/pharmacology
Muscle Fibers, Skeletal/drug effects/metabolism
*Hand Strength
Cell Line
Muscle, Skeletal/drug effects/pathology
Hot Temperature
Proto-Oncogene Proteins c-akt/metabolism

@article {pmid41596739,
year = {2026},
author = {Ottria, R and Mirmajidi, S and Ciuffreda, P},
title = {Gut Microbiota-Derived Short-Chain Fatty Acids in Inflammatory Bowel Disease: Mechanistic Insights into Gut Inflammation, Barrier Function, and Therapeutic Potential.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021095},
pmid = {41596739},
issn = {1422-0067},
mesh = {Humans ; *Gastrointestinal Microbiome ; *Fatty Acids, Volatile/metabolism/therapeutic use ; *Inflammatory Bowel Diseases/microbiology/metabolism/drug therapy ; Animals ; Intestinal Mucosa/metabolism/microbiology/immunology ; Butyrates/metabolism ; Inflammation/metabolism ; },
abstract = {This review delves into the complex relationship between short-chain fatty acids (SCFAs) produced by the gut microbiota and inflammatory bowel disease (IBD). IBD, which includes Crohn's disease and ulcerative colitis, is a group of chronic gastrointestinal disorders with an increasing global incidence. Despite extensive research, the exact etiopathogenesis remains elusive, although a complex interplay involving genetic predisposition, environmental influences, and abnormal immune responses against commensal gut microbes is widely recognized. SCFAs, primarily acetate and butyrate, emerge as key microbial metabolites derived from the fermentation of dietary fiber. They exert profound effects on gut homeostasis, notably with butyrate serving as an essential energy source for colonocytes, strengthening epithelial integrity, actively modulating local and systemic immune functions, suppressing the expression of pro-inflammatory cytokines, and enhancing mucosal defense mechanisms. However, clinical trials exploring SCFA administration have frequently yielded variable and inconsistent results due to differences in study design and patient characteristics. This review thoroughly analyzes the diverse roles of SCFAs in the large intestine, focusing on the intestinal barrier, immune modulation, and microbiota. It critically examines the therapeutic potential of SCFAs, including acetate and propionate, in addition to the well-known butyrate, in IBD management.},
}

Humans
*Gastrointestinal Microbiome
*Fatty Acids, Volatile/metabolism/therapeutic use
*Inflammatory Bowel Diseases/microbiology/metabolism/drug therapy
Animals
Intestinal Mucosa/metabolism/microbiology/immunology
Butyrates/metabolism
Inflammation/metabolism

@article {pmid41596659,
year = {2026},
author = {Sánchez-Recillas, E and Almanza-Aguilera, E and Bars-Cortina, D and Zamora-Ros, R and Godínez-Santillán, RI and Sánchez-Tusié, AA and Vergara-Castañeda, HA},
title = {Effect of Garambullo (Myrtillocactus geometrizans) Consumption on the Intestinal Microbiota Profile in an Early-Phase Rat Model of Colon Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27021014},
pmid = {41596659},
issn = {1422-0067},
support = {1560335//Secretaría de Ciencia, Humanidades, Tecnología e Innovación/ ; FME202404//Autonomous University of Queretaro - FONFIVE/ ; },
mesh = {Animals ; *Gastrointestinal Microbiome/drug effects ; *Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy ; Male ; Rats ; Rats, Sprague-Dawley ; Disease Models, Animal ; Azoxymethane ; Feces/microbiology ; RNA, Ribosomal, 16S/genetics ; Dextran Sulfate ; *Plant Extracts/pharmacology ; Bacteria/genetics/classification ; },
abstract = {Bioactive compounds in food contribute to reducing the risk of developing colon cancer by modulating the gut microbiota. We have recently demonstrated that garambullo (Myrtillocactus geometrizans), an endemic fruit of Mexico rich in bioactive compounds, attenuates aberrant crypt foci in an animal model. However, its potential to modulate the gut microbiota is unknown. The main objective of this study was to evaluate whether its consumption modulates colon carcinogenesis by altering the microbiota in an in vivo model induced by azoxymethane and dextran sulfate sodium (AOM/DSS). Fecal samples were collected from twelve male Sprague-Dawley rats and analyzed for microbiota composition after 0, 8, and 16 weeks of treatment with saline (control), AOM/DSS, garambullo (G), or residue of garambullo (RG) with AOM/DSS (G+AOM/DSS and RG+AOM/DSS, respectively). Characterization of the microbiome was based on the conserved region of the 16S rRNA V3-V4 gene, and analyzed by the ZymoBIOMICS' Targeted Metagenomics Sequencing (Zymo Research) service. In an animal model induced with AOM/DSS for 8 weeks, consumption of G and its residue increased the bacterial genera Shuttleworthiia, Subdoligranulum, Lactobacillus, Faecalibacterium, and Alloprevotella (p < 0.05). Consumption of G and its residue allowed the proliferation of bacteria that produce short-chain fatty acids and are associated with protective mechanisms of the colon.},
}

Animals
*Gastrointestinal Microbiome/drug effects
*Colonic Neoplasms/microbiology/chemically induced/pathology/drug therapy
Male
Rats
Rats, Sprague-Dawley
Disease Models, Animal
Azoxymethane
Feces/microbiology
RNA, Ribosomal, 16S/genetics
Dextran Sulfate
*Plant Extracts/pharmacology
Bacteria/genetics/classification

@article {pmid41596563,
year = {2026},
author = {Jäger, E and Peeva, V and Gnad, T and Haange, SB and Rolle-Kampczyk, U and Stäubert, C and Krumbholz, P and Heiker, JT and Gebhardt, C and Krügel, U and Sen, P and Harazin, M and Stab, V and Münzker, J and Hamdani, N and Pfeifer, A and von Bergen, M and Till, A and Fenske, WK},
title = {Antibiotic-Mediated Modulation of the Gut Microbiome Identifies Taurine as a Modulator of Adipocyte Function Through TGR5 Signaling.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020917},
pmid = {41596563},
issn = {1422-0067},
support = {01EO1501//BMBF/ ; AOBJ: 450149205//DFG/ ; AOBJ: 624808//DFG/ ; AOBJ: 432325352//DFG/ ; AOBJ: 335447717//DFG/ ; AOBJ: 624810//DFG/ ; AOBJ: 209933838//DFG/ ; },
mesh = {*Taurine/pharmacology/metabolism ; *Gastrointestinal Microbiome/drug effects ; Animals ; *Receptors, G-Protein-Coupled/metabolism/genetics ; Mice ; *Adipocytes/metabolism/drug effects ; Lipolysis/drug effects ; Male ; *Signal Transduction/drug effects ; Humans ; *Anti-Bacterial Agents/pharmacology ; Rats ; Thermogenesis/drug effects ; Diet, High-Fat/adverse effects ; Adipose Tissue, Brown/metabolism/drug effects ; Obesity/metabolism ; Mice, Inbred C57BL ; },
abstract = {Gut microbiota has emerged as a modulator of host metabolism and energy balance. However, the precise microbial metabolites mediating thermogenic activation in obesity remain largely undefined. We investigated the effect of antibiotic treatment under a high-fat diet on metabolites and its contribution to lipolysis and thermogenesis. Antibiotic treatment in high-fat diet-fed rats reduced adiposity and enhanced adaptive thermogenesis. Metabolomics revealed elevated taurine levels in the cecum content and plasma of antibiotic-treated animals, correlating with increased expressions of UCP1 and TGR5 in brown adipose tissue. Taurine enhanced lipolysis and oxygen consumption in mouse adipose tissue and human adipocytes. Thereby, taurine modulated lipolysis dependent on TGR5 signaling in adipose tissue. Human data confirmed that taurine promotes browning of white adipocytes and that acute cold exposure leads to a marked drop in circulating taurine, suggesting its rapid recruitment into thermogenic tissues. Besides its synthesis in the liver and dietary uptake, taurine can be a microbiota-derived metabolite that activates adipose thermogenesis and lipolysis through TGR5 and possibly taurine transporter-dependent mechanisms. These findings uncover a gut-adipose axis with therapeutic potential for metabolic disease.},
}

*Taurine/pharmacology/metabolism
*Gastrointestinal Microbiome/drug effects
Animals
*Receptors, G-Protein-Coupled/metabolism/genetics
Mice
*Adipocytes/metabolism/drug effects
Lipolysis/drug effects
Male
*Signal Transduction/drug effects
Humans
*Anti-Bacterial Agents/pharmacology
Rats
Thermogenesis/drug effects
Diet, High-Fat/adverse effects
Adipose Tissue, Brown/metabolism/drug effects
Obesity/metabolism
Mice, Inbred C57BL

@article {pmid41596486,
year = {2026},
author = {Sá, L and Machado, E and Ginani, V and Timbó, R and Romiti, R and Kurizky, P and Gomes, C},
title = {Species-Level Comparative Metagenomic Analysis of the Bacterial Abundance of the Gut Microbiome in Psoriasis, Hidradenitis Suppurativa, and Pemphigus Foliaceous Patients Using Shotgun Next-Generation Sequencing.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020838},
pmid = {41596486},
issn = {1422-0067},
support = {00193-00000279/2023-70//Fundação de Apoio à Pesquisa do Distrito Federal (FAP-DF)/ ; 445040/2023-8//National Council for Scientific and Technological Development/ ; 21/2023//Departamento de Ciência e Tecnologia, da Secretaria de Ciência, Tecnologia, Inovação e Com-plexo da Saúde, do Ministério da Saúde (Decit/SECTICS/MS)/ ; },
mesh = {Humans ; *Psoriasis/microbiology ; *Pemphigus/microbiology ; Female ; Male ; *Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenomics/methods ; Middle Aged ; Adult ; *Hidradenitis Suppurativa/microbiology ; Feces/microbiology ; *Bacteria/genetics/classification ; Aged ; },
abstract = {Recent studies have revealed a specific relationship between gut bacteria and inflammatory skin profiles. We aimed to perform a species-level comparative metagenomic analysis of the gut microbiome in patients with psoriasis, hidradenitis suppurativa (HS), and pemphigus foliaceus (PF). We included omnivorous nonsmokers and nondrinkers with psoriasis (n = 24), HS (n = 10), and PF (n = 11), as well as healthy controls (n = 10). We collected faecal samples from all patients for classic parasitological analysis. Gut microbiome analysis was conducted using shotgun next-generation sequencing. We used the Deseq2, Limma_voom, LinDA, and MaAMaAsLin 2 bioinformatics tools to evaluate concordance and differential abundance between patients. Thirteen patients (23.64%) were diagnosed with active intestinal parasitosis. The presence of intestinal parasitosis was significantly related to immunosuppression (p = 0.009). The most abundant microorganism species found in the faeces of the patients evaluated was Escherichia coli. Psoriasis patients presented a greater abundance of bacteria from the Veillonellaceae family, whereas PF patients presented a greater abundance of Firmicutes bacteria. Patients with PF showed increased E. coli virulence and antibiotic resistance functional markers. Immunosuppression significantly influenced the presence of intestinal parasitosis as well as increased the virulence of functional markers in patients with PF receiving systemic corticosteroid therapy.},
}

Humans
*Psoriasis/microbiology
*Pemphigus/microbiology
Female
Male
*Gastrointestinal Microbiome/genetics
High-Throughput Nucleotide Sequencing/methods
*Metagenomics/methods
Middle Aged
Adult
*Hidradenitis Suppurativa/microbiology
Feces/microbiology
*Bacteria/genetics/classification
Aged

@article {pmid41596463,
year = {2026},
author = {Sankararaman, S and Liu, R and Sun, X and Retuerto, M and Schindler, T and Roesch, E and Sferra, TJ and Drumm, M and Ghannoum, M and Zhang, L},
title = {Comparison of Stool Microbiome in Children with Cystic Fibrosis Treated with and Without Elexacaftor-Tezacaftor-Ivacaftor-A Pilot Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020814},
pmid = {41596463},
issn = {1422-0067},
support = {Pilot Faculty Award - P0598//Rainbow Babies & Children's Hospital/ ; },
mesh = {Humans ; *Cystic Fibrosis/drug therapy/microbiology ; Child ; Male ; Female ; Adolescent ; *Aminophenols/therapeutic use/pharmacology ; Pilot Projects ; Child, Preschool ; *Quinolones/therapeutic use/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Feces/microbiology ; Drug Combinations ; *Benzodioxoles/therapeutic use ; *Pyridines/therapeutic use ; *Indoles/therapeutic use ; Prospective Studies ; *Pyrazoles/therapeutic use ; Quinolines ; },
abstract = {Prior studies in people with cystic fibrosis (CF) demonstrated a positive impact of ivacaftor on the stool microbiome. However, studies evaluating the impact of elexacaftor-tezacaftor-ivacaftor (ETI) on gut dysbiosis are limited. In this prospective, observational study, we evaluated the differences in stool microbiome in children (aged 2-17 years) with CF who were treated with ETI for at least two months and compared with children with CF who did not receive ETI. We also included healthy siblings as controls. There were no significant differences in the demographics between the groups. There were no significant differences in alpha diversity between the groups for both bacteriome and mycobiome. Alpha diversity showed a negative trend with the duration of ETI therapy for both bacteriome and mycobiome. Firmicutes and Proteobacteria were the most abundant phyla and core members across all samples, regardless of disease status or treatment. Ascomycota and Basidiomycota were the most abundant and core members across all samples, regardless of disease status or treatment. Alpha diversity showed a negative trend with the duration of ETI therapy for both bacteriome and mycobiome in children with CF treated with ETI. Future studies are needed to confirm or refute our preliminary findings.},
}

Humans
*Cystic Fibrosis/drug therapy/microbiology
Child
Male
Female
Adolescent
*Aminophenols/therapeutic use/pharmacology
Pilot Projects
Child, Preschool
*Quinolones/therapeutic use/pharmacology
*Gastrointestinal Microbiome/drug effects
*Feces/microbiology
Drug Combinations
*Benzodioxoles/therapeutic use
*Pyridines/therapeutic use
*Indoles/therapeutic use
Prospective Studies
*Pyrazoles/therapeutic use
Quinolines

@article {pmid41596452,
year = {2026},
author = {Jandosov, J and Chenchik, D and Baimenov, A and Silvestre-Albero, J and Bernardo, M and Azat, S and Doszhanov, Y and Sabitov, A and Busquets, R and Howell, C and Mikhalovsky, S and Mansurov, Z},
title = {Assessment of Phenolic and Indolic Compounds Removal from Aqueous Media Using Lignocellulose-Derived Surface-Modified Nanoporous Carbon Adsorbents: A Comparative Study.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020804},
pmid = {41596452},
issn = {1422-0067},
support = {AP23485436//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
mesh = {Adsorption ; *Carbon/chemistry ; *Lignin/chemistry ; *Indoles/chemistry/isolation & purification ; *Nanopores/ultrastructure ; *Phenols/chemistry/isolation & purification ; Cresols/chemistry ; Water Purification/methods ; *Water Pollutants, Chemical/chemistry ; Indoleacetic Acids/chemistry/isolation & purification ; Uremic Toxins/chemistry ; },
abstract = {P-cresol, indole and indole-3-acetic acid (IAA) are catabolites of amino acids, formed by the gut microbiome. Most of these aromatic hydrocarbon derivatives are excreted by the colon before reentering the body to form "exogenous" protein-bound uremic toxins (PBUTs), which aggravate chronic kidney disease (CKD). Removal efficiencies of these PBUT precursors from model phosphate-buffered saline solutions by three different surface-modified nanoporous carbon adsorbents (PCs) were studied. PCs were produced by physicochemical and/or acid base activation of carbonized rice husk waste. Removal rates achieved values of 32-96% within a 3 h contact time. High micro/mesoporosity and surface chemistry of the N- and P-doped biochars were established by N2 adsorption studies, SEM/EDS analysis, XPS and FT-IR-spectroscopy. The ammoxidized PC-N1 had the highest adsorption capacity (1.97 mmol/g for IAA, 2.43 mmol/g for p-cresol and 2.42 mmol/g for indole), followed by "urea-nitrified" PC-N2, whilst the phosphorylated PC-P demonstrated the lowest adsorption capacity for these solutes. These results do not correlate with the total pore volume values for PC-N2 (0.91 cm[3]/g) < PC-P (1.56 cm[3]/g) < PC-N1 (1.84 cm[3]/g), suggesting that other parameters such as the micropore volume (PC-N1 > PC-N2 > PC-P) and the interaction of surface chemical functional groups with the solutes play key roles in the adsorption mechanism. N-doped PC-N1 and PC-N2 have basic functional groups with higher affinity with acidic IAA and p-cresol. The ion-exchange mechanism of phenolic and indolic compound chemisorption by nanoporous carbon adsorbents, modified with surface N- and P-containing functional groups, has been proposed.},
}

Adsorption
*Carbon/chemistry
*Lignin/chemistry
*Indoles/chemistry/isolation & purification
*Nanopores/ultrastructure
*Phenols/chemistry/isolation & purification
Cresols/chemistry
Water Purification/methods
*Water Pollutants, Chemical/chemistry
Indoleacetic Acids/chemistry/isolation & purification
Uremic Toxins/chemistry

@article {pmid41596418,
year = {2026},
author = {Wang, J and Zeng, NK and Zhang, X},
title = {Tuber Inoculation Drives Rhizosphere Microbiome Assembly and Metabolic Reprogramming in Corylus.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020768},
pmid = {41596418},
issn = {1422-0067},
support = {2019RC185 and 320RC597//Natural Science Foundation of HainanProvince/ ; (2024)171//Project of Science and Technology Programs of Guizhou Province/ ; Gui(2024)TG12//Project of Central Government Financial Fund for Forest Reform and Development/ ; },
mesh = {*Rhizosphere ; *Microbiota ; Mycorrhizae/physiology ; Symbiosis ; Plant Roots/microbiology/metabolism ; Metabolomics/methods ; *Plant Tubers/microbiology/metabolism ; Soil Microbiology ; Metabolic Reprogramming ; },
abstract = {To elucidate the potential of integrated multi-omics approaches for studying systemic mechanisms of mycorrhizal fungi in mediating plant-microbe interactions, this study employed the Tuber-inoculated Corylus system as a model to demonstrate how high-throughput profiling can investigate how fungal inoculation reshapes the rhizosphere microbial community and correlates with host metabolism. A pot experiment was conducted comparing inoculated (CTG) and non-inoculated (CK) plants, followed by integrated multi-omics analysis involving high-throughput sequencing (16S/ITS), functional prediction (PICRUSt2/FUNGuild), and metabolomics (UPLC-MS/MS). The results demonstrated that inoculation significantly restructured the fungal community, establishing Tuber as a dominant symbiotic guild and effectively suppressing pathogenic fungi. Although bacterial alpha diversity remained stable, the functional profile shifted markedly toward symbiotic support, including antibiotic biosynthesis and environmental adaptation. Concurrently, root metabolic reprogramming occurred, characterized by upregulation of strigolactones and downregulation of gibberellin A5, suggesting a potential "symbiosis-priority" strategy wherein carbon allocation shifted from structural growth to energy storage, and plant defense transitioned from broad-spectrum resistance to targeted regulation. Multi-omics correlation analysis further revealed notable associations between microbial communities and root metabolites, proposing a model in which Tuber acts as a core regulator that collaborates with the host to assemble a complementary micro-ecosystem. In summary, the integrated approach successfully captured multi-level changes, suggesting that Tuber-Corylus symbiosis constitutes a fungus-driven process that transforms the rhizosphere from a competitive state into a mutualistic state, thereby illustrating the role of mycorrhizal fungi as "ecosystem engineers" and providing a methodological framework for green agriculture research.},
}

*Rhizosphere
*Microbiota
Mycorrhizae/physiology
Symbiosis
Plant Roots/microbiology/metabolism
Metabolomics/methods
*Plant Tubers/microbiology/metabolism
Soil Microbiology
Metabolic Reprogramming

@article {pmid41596401,
year = {2026},
author = {Zhu, Z and Liu, Z and He, Y and He, X and Zheng, W and Jiang, M},
title = {G Protein-Coupled Receptors in Irritable Bowel Syndrome: Mechanisms and Therapeutic Opportunities.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020752},
pmid = {41596401},
issn = {1422-0067},
support = {2023YFC2706500 and 2023YFC2706504//The National Key Research and Development Program of China/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/metabolism/therapy/microbiology/immunology/drug therapy ; *Receptors, G-Protein-Coupled/metabolism ; Animals ; Gastrointestinal Microbiome ; Signal Transduction ; },
abstract = {Irritable bowel syndrome (IBS) is a functional gastrointestinal disorder characterized by abdominal pain, altered motility, and visceral hypersensitivity. Emerging evidence implicates G protein-coupled receptors (GPCRs) as key integrators of microbial, immune, endocrine, and neural signals in IBS pathophysiology. This review summarizes recent advances in understanding how GPCRs mediate gut immune regulation, microbiota-host crosstalk, metabolic signaling, and pain processing in IBS. Recent studies show that microbial metabolites (e.g., short-chain fatty acids, biogenic amines, and lipid mediators) signal through GPCRs on immune cells, epithelia, and neurons to influence intestinal homeostasis. On immune cells and neurons, GPCRs also mediate signals from external substances (such as fats, sugars, histamine, etc.) to regulate immune and neural functions. And there are challenges and future directions in targeting GPCRs for IBS, including patient heterogeneity and the complexity of host-microbiome interactions. This review provides a mechanistic framework for GPCR-based therapies in IBS.},
}

Humans
*Irritable Bowel Syndrome/metabolism/therapy/microbiology/immunology/drug therapy
*Receptors, G-Protein-Coupled/metabolism
Animals
Gastrointestinal Microbiome
Signal Transduction

@article {pmid41596399,
year = {2026},
author = {Tian, X and Chen, Q and He, Y and Cheng, Y and Zhao, M and Li, Y and Yu, M and Jiang, J and Wang, L},
title = {Berberine: A Negentropic Modulator for Multi-System Coordination.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020747},
pmid = {41596399},
issn = {1422-0067},
mesh = {*Berberine/pharmacology/therapeutic use ; Humans ; Animals ; AMP-Activated Protein Kinases/metabolism ; Lipid Metabolism/drug effects ; Signal Transduction/drug effects ; },
abstract = {Berberine (BBR), a protoberberine alkaloid with a long history of medicinal use, has consistently demonstrated benefits in glucose-lipid metabolism and inflammatory balance across both preclinical and human studies. These diverse effects are not mediated by a single molecular target but by BBR's capacity to restore network coordination among metabolic, immune, and microbial systems. At the core of this regulation is an AMP-activated Protein Kinase (AMPK)-centered mechanistic hub, integrating signals from insulin and nutrient sensing, Sirtuin 1/3 (SIRT1/3)-mediated mitochondrial adaptation, and inflammatory pathways such as nuclear Factor Kappa-light-chain-enhancer of Activated B cells (NF-κB) and NOD-, LRR- and Pyrin Domain-containing Protein 3 (NLRP3). This hub is dynamically regulated by system-level inputs from the gut, mitochondria, and epigenome, which in turn strengthen intestinal barrier function, reshape microbial and bile-acid metabolites, improve redox balance, and potentially reverse the epigenetic imprint of metabolic stress. These interactions propagate through multi-organ axes, linking the gut, liver, adipose, and vascular systems, thus aligning local metabolic adjustments with systemic homeostasis. Within this framework, BBR functions as a negentropic modulator, reducing metabolic entropy by fostering a coordinated balance among these interconnected systems, thereby restoring physiological order. Combination strategies, such as pairing BBR with metformin, Sodium-Glucose Cotransporter 2 (SGLT2) inhibitors, and agents targeting the microbiome or inflammation, have shown enhanced efficacy and substantial translational potential. Berberine ursodeoxycholate (HTD1801), an ionic-salt derivative of BBR currently in Phase III trials and directly compared with dapagliflozin, exemplifies the therapeutic promise of such approaches. Within the hub-axis paradigm, BBR emerges as a systems-level modulator that recouples energy, immune, and microbial circuits to drive multi-organ remodeling.},
}

*Berberine/pharmacology/therapeutic use
Humans
Animals
AMP-Activated Protein Kinases/metabolism
Lipid Metabolism/drug effects
Signal Transduction/drug effects

@article {pmid41596382,
year = {2026},
author = {Han, L and Yang, Y and Zhang, B and Wang, Y and Ji, Y and Du, S and Zou, Y},
title = {Seed Oil of Lycium barbarum L. from Qaidam Basin Prevents and Treats UV-Induced Photodamage in BABL/c Mice Skin by Modulating Skin Microbiome and Amino Acid Metabolism.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020731},
pmid = {41596382},
issn = {1422-0067},
support = {2025ZY011//Central Government-Guided Local Science and Technology Development Fund Project in Qinghai Province/ ; },
mesh = {Animals ; *Ultraviolet Rays/adverse effects ; Mice ; *Microbiota/drug effects/radiation effects ; *Skin/drug effects/radiation effects/microbiology/metabolism/pathology ; *Amino Acids/metabolism ; *Lycium/chemistry ; Mice, Inbred BALB C ; *Plant Oils/pharmacology/chemistry ; *Seeds/chemistry ; Metabolomics ; *Skin Aging/drug effects/radiation effects ; Cytokines/metabolism ; Skin Microbiome ; },
abstract = {Ultraviolet (UV) radiation is a primary environmental factor responsible for skin photodamage, and exposure to UV rays is strongly linked to a variety of skin diseases. This study examined the prophylactic and therapeutic effects of Seed Oil of Lycium barbarum L. from the Qaidam basin (QLBSO) in a UV-induced skin photodamage model in BALB/c mice, exploring potential mechanisms by analyzing the skin microbiota and metabolites using 16S rDNA sequencing and metabolomics. The results showed that QLBSO effectively alleviated UV-induced histopathological changes in mouse skin. It also significantly increased the activity of superoxide dismutase (SOD) and catalase (CAT) in UV-damaged skin tissue, while reducing levels of inflammatory cytokines, including interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), and interleukin-1β (IL-1β), as well as matrix metalloproteinases-1 (MMP-1) and MMP-3. Omics analysis revealed that QLBSO successfully restored the balance of the skin microbiota and corrected disruptions in amino acid metabolism caused by UV exposure. Notably, Firmicutes_A and Kineothrix, along with cysteine, cystine, glycine, arginine, proline, and choline, were identified as key microbial species and metabolites responsive to QLBSO's prophylactic and therapeutic effects. In conclusion, QLBSO likely protects against UV-induced skin photodamage by modulating the skin microbiota and amino acid metabolism, providing a scientific foundation for its potential use in skin health protection.},
}

Animals
*Ultraviolet Rays/adverse effects
Mice
*Microbiota/drug effects/radiation effects
*Skin/drug effects/radiation effects/microbiology/metabolism/pathology
*Amino Acids/metabolism
*Lycium/chemistry
Mice, Inbred BALB C
*Plant Oils/pharmacology/chemistry
*Seeds/chemistry
Metabolomics
*Skin Aging/drug effects/radiation effects
Cytokines/metabolism
Skin Microbiome

@article {pmid41596292,
year = {2026},
author = {Lagunas-Cruz, MDC and Valle-Mendiola, A and Soto-Cruz, I},
title = {The Vaginal Microbiome and Host Health: Implications for Cervical Cancer Progression.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020640},
pmid = {41596292},
issn = {1422-0067},
support = {CBF-2023-2024-1208//Secretaría de Ciencia Tecnología e Innovación/ ; },
mesh = {Humans ; Female ; *Vagina/microbiology/virology ; *Microbiota ; *Uterine Cervical Neoplasms/microbiology/pathology/virology ; Papillomavirus Infections/microbiology/complications/virology ; Lactobacillus ; Disease Progression ; Dysbiosis/microbiology ; },
abstract = {The vaginal microbiome plays a crucial role in maintaining host health by preserving a balanced microenvironment. Nevertheless, the definition of a "normal" vaginal microbiome remains controversial, as its composition varies depending on factors such as ethnicity and geographical origin. In most cases, members of the genus Lactobacillus predominate in healthy vaginal microbiomes, protecting against potential pathogens through specific mechanisms such as the secretion of lactic acid and bacteriocins, among others. A reduction in Lactobacillus abundance, accompanied by an increase in anaerobic organisms, predisposes the host to the development of various pathologies. Among these pathologies is infection with human papillomavirus (HPV) and the subsequent development of cervical cancer. A progressive decline in Lactobacillus has been observed as the lesion advances in different populations worldwide. In the case of the Mexican population, several Lactobacillus have been reported in healthy microbiomes: L. gasseri, L. fermentum, L. rhamnosus, L. jensenii, L. crispatus, L. delbrueckii, L. acidophilus, and L. brevis. In contrast, genera reported in dysbiosis include Sneathia, while Brevibacterium aureum and Brachybacterium conglomeratum have been associated with HPV16 infection and/or SIL. The mere presence of some bacteria is not sufficient to modulate the cellular activity of host cells; therefore, the expression, production and activity of different proteins could be affected by the vaginal microbiome. The impact of the microbiome on host cell function is the result of different metabolites produced by the bacteria, which suppress or activate different signaling and metabolic pathways. The molecular interactions between the host and microbiome, as well as their role in cervical carcinogenesis, are still unknown. In this review, we focus on the vaginal microbiome, HPV, and the impact that the interaction of the microbiome with HPV has in cervical cancer development.},
}

Humans
Female
*Vagina/microbiology/virology
*Microbiota
*Uterine Cervical Neoplasms/microbiology/pathology/virology
Papillomavirus Infections/microbiology/complications/virology
Lactobacillus
Disease Progression
Dysbiosis/microbiology

@article {pmid41596275,
year = {2026},
author = {Paprocka, P and Spałek, J and Daniluk, T and Kaliniak, S and Durnaś, B and Okła, S and Bucki, R},
title = {The Importance of Ear Canal Microbiota and Earwax in the Prevention of Outer Ear Infections.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020622},
pmid = {41596275},
issn = {1422-0067},
support = {SUPB.RN.24.043//This work was supported by Jan Kochanowski University in Kielce, Poland (SUPB.RN.24.043 to B.D.)/ ; },
mesh = {Humans ; *Microbiota ; *Ear Canal/microbiology ; Cerumen ; Animals ; *Otitis Externa/prevention & control/microbiology ; Biofilms ; },
abstract = {This article describes the microbiome of the outer ear and the earwax in the ear canal, which performs various protective functions against bacterial infections. This article is based on an analysis of literature gathered from databases including PubMed, Google Scholar, Web of Science, and Scopus, primarily from the last 15 years. The search strategy included MeSH terms: ear canal, microbiome, earwax, cerumen, antibacterial peptides, ear infections, biofilm. Only peer-reviewed articles were included. The natural ear canal microbiota provides so-called colonization resistance, which protects against invasion by pathogenic microorganisms. Earwax is composed primarily of keratin secreted by epithelial cells and substances secreted by sweat and apocrine glands. It plays a key role in the physiology of the ear canal, maintaining a low pH, limiting moisture, and exhibiting antimicrobial properties. Both an excess and a deficiency of earwax can lead to dysbiosis of the outer ear, and consequently to the development of various infections. In an era of increasing antibiotic resistance and the search for new solutions in the fight against pathogenic microorganisms, understanding the natural properties of earwax is becoming increasingly important.},
}

Humans
*Microbiota
*Ear Canal/microbiology
Cerumen
Animals
*Otitis Externa/prevention & control/microbiology
Biofilms

@article {pmid41596220,
year = {2026},
author = {Hussain, SA and Sarker, MI and Liu, Y and Jin, TZ},
title = {DNA Methylation and Its Role in Personalized Nutrition: Mechanisms, Clinical Insights, and Future Perspectives.},
journal = {International journal of molecular sciences},
volume = {27},
number = {2},
pages = {},
doi = {10.3390/ijms27020566},
pmid = {41596220},
issn = {1422-0067},
mesh = {Humans ; *DNA Methylation ; *Precision Medicine/methods ; *Epigenesis, Genetic ; Diet ; Animals ; },
abstract = {DNA methylation is a central epigenetic mechanism that mediates the interaction between nutritional exposures and gene regulation. Emerging evidence demonstrates that diet, bioactive compounds, genetic background, and lifestyle factors collectively shape the human methylome, influencing metabolic function, disease susceptibility, and biological aging. This review synthesizes current knowledge on the molecular and biochemical mechanisms of DNA methylation, the role of nutrients and dietary patterns in modulating methylation dynamics, and findings from human clinical trials evaluating nutritional interventions. Genotype-specific responses, including polymorphisms in one-carbon metabolism and metabolic pathways, are discussed as key determinants of interindividual variation in methylation outcomes. The review further highlights the advances in epigenetic clocks, systems biology, and multi-omics integration that support the development of precision nutrition frameworks. Ethical considerations and future challenges related to data interpretation, accessibility, and the regulation of epigenetic testing are also examined. Collectively, this review provides an integrative perspective on how DNA methylation serves as a dynamic interface between diet and health and outlines opportunities for implementing personalized nutrition strategies to improve metabolic resilience and promote healthy aging.},
}

Humans
*DNA Methylation
*Precision Medicine/methods
*Epigenesis, Genetic
Diet
Animals

@article {pmid41596178,
year = {2026},
author = {Feix, JB and Cheng, G and Hardy, M and Kalyanaraman, B},
title = {Microbial Metabolism of Levodopa as an Adjunct Therapeutic Target in Parkinson's Disease.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antiox15010120},
pmid = {41596178},
issn = {2076-3921},
support = {1R21NS137244-01A1/NH/NIH HHS/United States ; },
abstract = {Parkinson's disease is the second leading neurodegenerative disease of aging. For over five decades, oral levodopa has been used to manage the progressive motor deficits that are the hallmark of the disease. However, individual dose requirements are highly variable, and patients typically require increased levodopa dosage as the disease progresses, which can cause undesirable side effects. It has become increasingly apparent that the gut microbiome can have a major impact on the metabolism and efficacy of therapeutic drugs. In this Perspective, we examine recent studies highlighting the impact of metabolism by Enterococcus faecalis, a common commensal gut bacterium, on levodopa bioavailability. E. faecalis expresses a highly conserved tyrosine decarboxylase that promiscuously converts levodopa to dopamine in the gut, resulting in decreased neuronal uptake of levodopa and reduced dopamine formation in the brain. Mitochondria-targeted antioxidants conjugated to a triphenylphosphonium moiety have shown promise in transiently suppressing the growth of E. faecalis and decreasing microbial levodopa metabolism, providing an approach to modulating the microbiome that is less perturbing than conventional antibiotics. Thus, mitigating metabolism by the gut microbiota is an attractive therapeutic target to preserve and potentiate the efficacy of oral levodopa therapy in Parkinson's disease.},
}

@article {pmid41596119,
year = {2026},
author = {Patanè, GT and Moreira, RJ and Almeida-Santos, M and Putaggio, S and Barreca, D and Oliveira, PF and Alves, MG},
title = {Anthocyanins and Metabolic Disease: A New Frontier in Precision Nutrition.},
journal = {Antioxidants (Basel, Switzerland)},
volume = {15},
number = {1},
pages = {},
doi = {10.3390/antiox15010061},
pmid = {41596119},
issn = {2076-3921},
support = {2024.03012.BD//Fundação para a Ciência e Tecnologia/ ; UIDB/50006/2020//Laboratório Associado para a Química Verde/ ; CEECINST/00026/2018//Fundação para a Ciência e Tecnologia/ ; CDL-CTTRI-267-SGRH/2022//Fundação para a Ciência e Tecnologia/ ; UIDB/04501/2020-DOI 10.54499/UIDB/04501/2020 and UIDP/04501/2020-DOI 10.54499/UIDP/04501/2020//iBiMED/ ; },
abstract = {Metabolic syndrome (MetS) represents a global health challenge mainly driven by chronic low-grade inflammation and persistent oxidative stress (OS). Current therapeutic and nutritional strategies often fail to resolve these interconnected core pathologies due to the multifactorial nature of MetS. Anthocyanins (ACNs), a class of potent dietary flavonoids, offer significant promise due to their established pleiotropic effects, including robust antioxidant activity through modulation of the Nrf2/ARE pathway, anti-inflammatory effects via NF-κB suppression, and overall support for glucose and lipid homeostasis. However, the therapeutic efficacy of ACNs is characterized by interindividual variability, which is intrinsically linked to their low systemic bioavailability. This heterogeneity in the response is due to the complex interplay between genetic polymorphisms affecting absorption, distribution, metabolism, and excretion (ADME), as well as the specific biotransformation capacity of the gut microbiome. This review proposes that achieving the full clinical potential of ACNs requires moving beyond conventional nutritional advice. We propose that precision nutrition, which integrates multi-omics data (e.g., genomics, metagenomics, and metabolomics), can determine the individual phenotype, predict functional metabolic response, and tailor safer and effective ACN-rich interventions. This integrated, multifactorial approach is essential for optimizing the antioxidant and metabolic benefits of ACNs for the prevention and management of MetS and its associated pathologies.},
}

@article {pmid41595645,
year = {2026},
author = {Rusu, M and Ichim, C and Anderco, P and Pălăștea, A and Boicean, A},
title = {Gut-Kidney Axis: Unraveling the Role of the Microbiome in Chronic Kidney Disease.},
journal = {Biomedicines},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biomedicines14010109},
pmid = {41595645},
issn = {2227-9059},
abstract = {Chronic kidney disease (CKD), which affects over 850 million individuals globally, is increasingly regarded as a systemic condition in which the gut microbiota represents a key pathogenic node. This review provides an integrated overview of mechanistic, translational and clinical data implicating the gut-kidney axis in CKD. The CKD-associated microbiota displays a characteristic dysbiosis, marked by depletion of short-chain fatty acid-producing commensals, overgrowth of proteolytic and urease-expressing taxa and disruption of epithelial barrier integrity. These disturbances favor the generation and systemic accumulation of gut-derived uremic toxins, most notably indoxyl sulfate, p-cresyl sulfate, indole-3-acetic acid and trimethylamine-N-oxide, which promote endothelial dysfunction, vascular calcification, fibrosis and chronic inflammation, thereby hastening renal function loss and heightening cardiovascular risk. Microbiome-directed interventions, including dietary modification, prebiotics, probiotics, synbiotics, intestinal dialysis, fecal microbiota transplantation, gut-acting sorbents and nephroprotective phytochemicals, are summarized with emphasis on their effects on uremic toxin burden and clinical surrogates. System-level implications of the gut-kidney axis for cardiovascular disease, immunosenescence and sarcopenia are discussed, together with future priorities for integrating multi-omics profiling and precision microbiome-based strategies into nephrology practice.},
}

@article {pmid41595609,
year = {2025},
author = {Zimbru, EL and Zimbru, RI and Bojin, FM and Chiriac, SD and Haidar, L and Andor, M and Tănasie, G and Tatu, C and Georgescu, M and Uța, C and Bănărescu, CF and Groza, S and Panaitescu, C},
title = {Microbiota-Driven Immune Dysregulation Along the Gut-Lung-Vascular Axis in Asthma and Atherosclerosis.},
journal = {Biomedicines},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biomedicines14010073},
pmid = {41595609},
issn = {2227-9059},
abstract = {Background: Asthma and atherosclerosis frequently coexist in clinical populations and share convergent immunometabolic pathways amplified by gut microbial dysbiosis. We propose the gut-lung-vascular axis as a unifying mechanistic framework connecting epithelial and endothelial inflammation providing a foundation for understanding shared inflammatory mechanisms beyond tissue-specific disease boundaries. Methods: A targeted narrative review systematically appraised clinical, experimental and multi-omics studies published over the last five years to delineate microbiota-driven pathways relevant to asthma and atherosclerosis. Particular emphasis was placed on specific microbial taxa, metabolite profiles and immunometabolic networks that connect gut dysbiosis with respiratory and cardiovascular dysfunction. Results: Across human and experimental cohorts, dysbiosis marked by depletion of short-chain fatty acids (SCFAs) producing taxa (Faecalibacterium, Roseburia, Bacteroides) and enrichment of pathobionts (Proteobacteria, Haemophilus, Moraxella, Streptococcus) promotes epithelial and endothelial barrier dysfunction, amplifying Th2/Th17-skewed inflammation and endothelial injury. Key metabolites, including SCFAs, trimethylamine N-oxide (TMAO), secondary bile acids (BA), indole/tryptophan derivatives and lipopolysaccharides (LPS), serve as molecular connectors linking gut, airway and vascular inflammation. Microbial signatures and metabolomic patterns hold emerging diagnostic and therapeutic potential, and several drug classes (e.g., statins, corticosteroids, proton-pump inhibitors (PPIs)) further modulate host-microbiota interactions. Conclusions: Shared microbial taxa and metabolite signatures in asthma and atherosclerosis support microbiota-mediated immune dysregulation along the gut-lung-vascular axis as a common pathogenic framework. Microbial and metabolite profiling may enable improved risk stratification and precise, microbiota-targeted therapies. Integrating microbiome-informed diagnostics and personalized interventions could help reduce systemic inflammation and the burden of these overlapping inflammatory diseases.},
}

@article {pmid41595585,
year = {2025},
author = {Pasitka, LP and Molnár, T and Urbán, E and Csécsei, P and Hetesi, Z and Mód, J and Bán, Á},
title = {Periodontal Bacteria and Outcomes Following Aneurysmal Subarachnoid Hemorrhage: A Prospective Observational Analysis.},
journal = {Biomedicines},
volume = {14},
number = {1},
pages = {},
doi = {10.3390/biomedicines14010048},
pmid = {41595585},
issn = {2227-9059},
abstract = {Background: Periodontitis has been associated with systemic diseases such as cerebrovascular events. Emerging research highlights the potential role of the microbiome in intracranial aneurysm formation and rupture. Aims: We aimed to explore the associations among periodontal pathogens and the outcomes in patients with aneurysmal subarachnoid hemorrhage (aSAH). Materials and Methods: A total of 43 aSAH patients were enrolled. Clinical probing depth measurement and microbiological culture were performed for all participants. The markers of systemic immune response (IL-6, hsCRP) and brain injury (NSE, S100B) were measured between 24 and 48 h after admission. Development of delayed cerebral ischemia (DCI) as the primary and clinical outcome, based on modified Rankin Scale as secondary endpoints, comprised the chosen metrics. Results: A significant association was observed between patients with periodontal pocket depth PPD ≥ 5 mm (n = 28) and DCI, which developed in 19 patients (p = 0.007). In the subgroup of patients with PPD ≥ 5 mm significant associations were found between certain periodontal pathogens and DCI. Higher hsCRP (p = 0.05), IL-6 (p = 0.037) levels were observed in cases with periodontal pathogens, independent of the depth of the pocket, suggesting systemic inflammation. Conclusions: Elevated hsCRP and IL-6 levels, periodontal pocket depth ≥ 5 mm, and red-complex periodontal pathogens are associated with an increased risk of DCI after aSAH, suggesting a role for periodontal disease-related systemic inflammation in DCI risk stratification.},
}