@article {pmid42355923,
year = {2026},
author = {Mammadov, RA and Roest, HP and Fuhler, GM and Su, J and Visseren, T and Janssen, HLA and Porte, RJ and Murad, SD and Hansen, BE and van der Laan, LJW and Peppelenbosch, MP},
title = {Association of FUT2 rs601338 Genotype with Colonic Mucosal Microbiome Composition, Post-Transplant Bacteremia, and All-Cause Mortality After Liver Transplantation for Primary Sclerosing Cholangitis: A Retrospective Cohort Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
pmid = {42355923},
issn = {2077-0383},
abstract = {Background/Objectives: Primary sclerosing cholangitis (PSC) is a chronic cholestatic liver disease frequently requiring liver transplantation (LTx). The gut-liver axis, host genetics, and microbial dysbiosis are thought to contribute to disease progression and post-transplant outcomes. The FUT2 rs601338 polymorphism influences mucosal fucosylation, host-microbial interactions, and susceptibility to infection. This study aimed to investigate the association between FUT2 genotype, colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in a retrospective single-center PSC cohort. Methods: This retrospective cohort study included PSC patients who underwent LTx at Erasmus MC University Medical Center (Rotterdam, The Netherlands) between 1987 and 2015. Pre-transplant archival formalin-fixed paraffin-embedded (FFPE) colonic biopsy specimens were available for microbiome analysis. Of 169 transplanted patients, FFPE tissue was available for 98 individuals, and FUT2 rs601338 genotyping was successfully performed in 87 patients. Patients were classified as FUT2 non-secretors (AA, n = 28) and secretors (GA/GG, n = 59). Post-transplant bacteremia was assessed based on clinically indicated blood cultures during follow-up. Colonic mucosal microbiome composition was analyzed using 16S rRNA gene sequencing. Results: FUT2 non-secretors showed a distinct colonic mucosal microbiome profile compared with secretors, characterized by differential abundance of selected taxa within Proteobacteria, Firmicutes, and Bacteroidetes. Post-transplant bacteremia occurred in 30 patients and was more frequent among non-secretors (43%) compared with secretors (15%). Both FUT2 non-secretor status and post-transplant bacteremia were associated with reduced all-cause post-transplant survival in Kaplan-Meier analysis and remained associated with mortality in multivariable regression models. Specific microbial taxa were also showed associations with bacteremia, mortality, and established prognostic scores, including the Amsterdam-Oxford Model and Mayo Risk Score. Conclusions: FUT2 genotype is associated with alterations in colonic mucosal microbiome composition, post-transplant bacteremia, and all-cause mortality in PSC patients undergoing liver transplantation. These findings suggest a potential interplay between host genetics, intestinal microbiota, and infectious complications after transplantation. Given the retrospective design, limited sample size, and use of archival FFPE tissue, all findings should be interpreted as exploratory and hypothesis-generating. Prospective multicenter studies using standardized sampling and high-resolution metagenomic approaches are warranted for validation.},
}

@article {pmid42356004,
year = {2026},
author = {Greța-Oanță, AL and Roman, A and Berindan-Neagoe, I and Strilciuc, Ș and Vesa, ȘC and Pop, LA and Trombitaș, VE and Albu, S},
title = {Direct Maxillary Sinus Tissue Analysis for TAS2R38 Polymorphisms: Establishing a Tissue-Based Translational Framework in Odontogenic Rhinosinusitis.},
journal = {Journal of clinical medicine},
volume = {15},
number = {12},
pages = {},
pmid = {42356004},
issn = {2077-0383},
support = {882//Iuliu Hațieganu University of Medicine and Pharmacy/ ; },
abstract = {Background/Objectives: Bitter taste receptors (T2Rs), specifically T2R38, are present in the respiratory epithelium and react with bacterial quorum-sensing molecules to induce an innate immunity response. Although TAS2R38 polymorphisms have been correlated with susceptibility to chronic rhinosinusitis (CRS), they have not yet been explored in odontogenic rhinosinusitis (ORS), a distinct form of CRS with particular microbial and inflammatory features. We aim to establish a proof-of-concept methodology for investigating TAS2R38 genetic variants in ORS using direct maxillary sinus tissue analysis and demonstrate the feasibility of this translational approach. Methods: We conducted a prospective pilot case-control study of 36 ORS patients and 37 controls undergoing septoplasty without sinonasal disease. Maxillary sinus mucosal biopsies were obtained intraoperatively with informed consent. Genomic DNA was extracted using the PureLink Genomic DNA Mini Kit and quantified via NanoDrop spectrophotometry. TAS2R38 haplotypes were determined and classified as taster (PAV/PAV), non-taster (AVI/AVI), or intermediate (PAV/AVI) phenotype. Results: Among fully classifiable canonical TAS2R38 phenotypes (32 ORS patients, 28 controls), distributions were: tasters 12.5% vs. 25.0%, non-tasters 31.3% vs. 25.0%, and intermediate 56.3% vs. 50.0%. AVI/AVI non-taster status was not significantly associated with ORS susceptibility (OR = 1.36, 95% CI: 0.44-4.25; Fisher's exact p = 0.775). Conclusions: This proof-of-concept study demonstrates that genotyping-grade genomic DNA can be recovered from acutely inflamed maxillary sinus mucosa, validating this substrate for future tissue-based expression, functional, and microbiome analyses not obtainable from peripheral samples; germline genotyping itself does not require sinus tissue. The observed difference in non-taster prevalence (31.3% vs. 25.0%) did not reach statistical significance and is reported descriptively. This directional trend is hypothesis-generating only and, given the limited statistical power, does not constitute evidence for an association. The demonstrated feasibility, together with the established biological rationale, supports an adequately powered confirmatory study and lays the foundation for future investigation of taste receptor genetics in ORS pathogenesis, and potentially personalized therapeutic strategies.},
}

@article {pmid42356063,
year = {2026},
author = {Kyrochristou, I and Fousekis, F and Kyrochristou, GD and Schizas, D and Pappas-Gogos, G and Raptis, D and Ioannidis, O and Vlachos, K and Lianos, GD},
title = {Impact of Gut Microbiota on the Clinical Course and Treatment Outcomes of Colorectal Cancer-A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356063},
issn = {1648-9144},
mesh = {Humans ; *Colorectal Neoplasms/microbiology/therapy/diagnosis ; *Gastrointestinal Microbiome/physiology ; Treatment Outcome ; Prognosis ; Feces/microbiology ; },
abstract = {Background and Perspectives: As colorectal cancer research focuses on improving screening policies and treatment strategies, the gut microbiome is emerging as a novel diagnostic and prognostic biomarker. This systematic review aims to present the available data on the role of gut microbiota in colorectal cancer diagnosis, prognosis, and treatment response. Materials and Methods: A systematic search under the PRISMA recommendation was conducted in PubMed database, until February 2026. Original human studies evaluating associations between gut microbiome composition and CRC diagnosis, survival outcomes, or therapeutic response were included. Both stool- and tissue-based analyses were considered. A qualitative synthesis of the data was performed. Results: Thirty-six studies met the inclusion criteria, encompassing case-control cohorts, prospective survival analyses, and early-phase translational trials. Across populations and sequencing methodologies, gut microbiome alterations were consistently identified, with enrichment of oral-derived anaerobes, particularly Fusobacterium nucleatum, and depletion of beneficial commensal taxa in CRC patients compared with controls. Beta-diversity analyses frequently showed distinct clustering of microbial communities between the CRC and control groups, whereas alpha-diversity findings were heterogeneous. Several stool-based multi-species classifiers demonstrated good to excellent diagnostic performance, particularly when combined with established screening modalities. Tumor-associated microbial signatures were further associated with adverse survival outcomes and, in exploratory cohorts, with differential treatment response. Emerging evidence suggests that the microbiome may represent a modifiable environmental factor, particularly relevant in early-onset CRC. Conclusions: The gut microbiome represents a promising adjunctive biomarker for CRC diagnosis and prognostic stratification, with potential implications for precision oncology. However, methodological heterogeneity and the need for prospective validation currently limit its routine clinical implementation.},
}

Humans
*Colorectal Neoplasms/microbiology/therapy/diagnosis
*Gastrointestinal Microbiome/physiology
Treatment Outcome
Prognosis
Feces/microbiology

@article {pmid42356119,
year = {2026},
author = {Persely, A and Piroska, M and Zoldi, L and Beszedics, B and Juhasz, J and Makra, N and Dunai, ZA and Szabo, D and Tarnoki, DL and Tarnoki, AD},
title = {The Role of Gut Microbiome in Mild Cognitive Impairment: A Twin Study.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356119},
issn = {1648-9144},
mesh = {Humans ; Male ; *Cognitive Dysfunction/microbiology/physiopathology ; *Gastrointestinal Microbiome/physiology ; Aged ; Female ; RNA, Ribosomal, 16S/analysis ; Feces/microbiology ; Aged, 80 and over ; Twins, Monozygotic ; },
abstract = {Background and Objectives: Recent studies have revealed the potential roles of gut microbiota and microbial metabolites in influencing mild cognitive impairment (MCI) and Alzheimer's disease via the gut-brain axis. This relationship has not yet been investigated in monozygotic twin pairs, which represent an ideal model for minimizing genetic confounding. Materials and Methods: Seven twin pairs discordant for ACE and 15 for MoCA were enrolled. Stool samples were subjected to 16S ribosomal RNA-based microbiome analysis. Results: No significant differences in alpha or beta diversity were observed between MCI-discordant twin pairs at the genus or family level. The most robust finding was a significantly lower abundance of Lachnospiraceae in MCI-affected twins, identified independently by ANCOM-BC and LEfSe. Additional exploratory findings included higher abundances of Sutterella, Succinivibrio, Odoribacter, and Ruminococcus. However, several taxa showed opposing patterns between ACE- and MoCA-derived cohorts, highlighting the methodological impact of cognitive instrument selection. Conclusions: The convergent reduction of Lachnospiraceae across two independent analytical methods represents the most substantive finding. The remaining results are exploratory, limited by small sample size, restricted statistical power, and lack of availability to fully control for dietary habits, physical activity, and medication use. Validation in larger longitudinal twin cohorts with a standardized cognitive assessment is warranted.},
}

Humans
Male
*Cognitive Dysfunction/microbiology/physiopathology
*Gastrointestinal Microbiome/physiology
Aged
Female
RNA, Ribosomal, 16S/analysis
Feces/microbiology
Aged, 80 and over
Twins, Monozygotic

@article {pmid42356129,
year = {2026},
author = {Pilateris, I and Bostanjopoulou, S},
title = {"Brain-First" vs. "Body-First" PD: Definitions and Implications in Everyday Clinical Practice: A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356129},
issn = {1648-9144},
mesh = {Humans ; *Parkinson Disease/physiopathology/diagnosis/classification ; Disease Progression ; Biomarkers ; *Brain/physiopathology ; },
abstract = {(1) Background and Objectives: Parkinson's disease's (PD) underlying pathophysiology still remains incompletely understood, with Braak's hypothesis of ASyn pathology propagation being the most widely accepted. Recently, a novel model has been introduced, proposing two distinct ASyn propagation pathways: a bottom-up trajectory termed Body-first PD, and a central nervous system (CNS)-initiated pathway termed Brain-first PD. This distinction introduces new perspectives in the PD literature landscape regarding diagnosis, prognostic factors and patient management. This study set out to systematically synthesize the current literature comparing Brain-first and Body-first PD, with a focus on clinical characteristics and disease progression, diagnostic biomarkers, and management approaches. (2) Materials and Methods: A systematic literature search was conducted in March 2025 using PubMed, Cochrane Library, DOAJ and Google Scholar. Human observational, diagnostic, and interventional studies published between 2019 and March 2025, including patients with de novo or early PD, were eligible. Pre-motor REM sleep behavioral disorder (RBD) was used as the primary differentiation criterion. Risk of bias was evaluated using the Joanna Briggs Institute (JBI) critical appraisal checklists. Results were synthesized using a narrative approach. (3) Results: Sixteen studies comprising 2107 PD patients met the inclusion criteria. Body-first PD was associated with a higher non-motor symptom (NMS) burden, faster disease progression, and a higher prevalence of cognitive impairment. Additionally, Body-first PD patients exhibited more widespread and symmetrical neurodegeneration, along with electrophysiological and metabolic differences. Distinct biomarker and microbiome profiles were also observed between subtypes. No eligible studies addressing management approaches were identified. (4) Conclusions: In conclusion, the available evidence suggests that Brain-first and Body-first PD may represent two distinct pathophysiological entities, a proposal with great significance for the diagnosis, prognosis and management of PD patients. However, the predominantly cross-sectional nature of the current literature limits causal inference. Future longitudinal and interventional studies are required to clarify the potential clinical implications of this subtype classification theory.},
}

Humans
*Parkinson Disease/physiopathology/diagnosis/classification
Disease Progression
Biomarkers
*Brain/physiopathology

@article {pmid42356145,
year = {2026},
author = {Anton, D and Băciuț, M and Almășan, O},
title = {The Oral-Gut Microbiome Connection in Patients with Periodontitis: A Systematic Review.},
journal = {Medicina (Kaunas, Lithuania)},
volume = {62},
number = {6},
pages = {},
pmid = {42356145},
issn = {1648-9144},
support = {100418/29.08.2025, SMIS code 350525//Ministry of Investments and European Projects/ ; },
mesh = {Humans ; *Periodontitis/microbiology/physiopathology/complications ; *Gastrointestinal Microbiome/physiology ; Inflammation ; *Mouth/microbiology ; *Microbiota ; },
abstract = {Background and Objectives: This study aims to evaluate the recent literature on the oral-gut connection in the context of periodontal disease, emphasizing the significance of systemic risk associated with chronic inflammation. This review explores whether chronic inflammation resulting from periodontal disease can induce systemic conditions through alterations in the gut microbiome and whether periodontal treatment may contribute to overall health improvement. Materials and Methods: A systematic database search was performed using pre-established search strategies. Searches were conducted in three databases between 1 and 20 October 2025. A total of 578 articles were screened for eligibility based on inclusion and exclusion criteria. Two authors agreed on the selection process used. The methodological quality of the included studies was assessed using the Newcastle-Ottawa scale and the Risk of Bias 2 Tool. Results: Eleven studies were considered eligible for inclusion in the review. The gut microbiome is similar to the oral microbiome in patients with periodontitis. Gut microbial shifts may drive systemic inflammation and metabolic dysfunction. Tooth loss and gum disease are linked to alterations in the gut bacteria, potentially compromising the intestinal barrier permeability. In contrast, the presence of natural teeth may prevent oral-gut bacterial transmission. Changes in the gut microbiota are correlated with improvements in periodontal status after non-surgical periodontal therapy. Conclusions: The evidence presented in this review supports an association between periodontitis, oral-gut microbial alterations, and systemic inflammatory conditions. However, most available studies are observational, limiting causal inference. Targeted modulation of the gut microbiome may represent a promising area for future research, but its clinical applicability remains inconclusive.},
}

Humans
*Periodontitis/microbiology/physiopathology/complications
*Gastrointestinal Microbiome/physiology
Inflammation
*Mouth/microbiology
*Microbiota

@article {pmid42356224,
year = {2026},
author = {Barbazza, S and van der Hoeven, M and Ponce, MC and Weber, AM and Fauzi, MD and Soekarjo, DD and Ryan, EP and Fortin, S and Wieringa, FT},
title = {Addition of Prebiotic Rice Bran to Ready-to-Use Therapeutic Food Modulated Changes in Body Composition Only of 6-23-Month-Old Children During Treatment for Uncomplicated Acute Malnutrition: The Solutions to Enhance Health with Alternative Treatment (SEHAT) Study.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356224},
issn = {2072-6643},
support = {NA//Thrasher Research Fund/ ; },
mesh = {Humans ; *Oryza ; Double-Blind Method ; *Body Composition ; Female ; Male ; Infant ; *Prebiotics/administration & dosage ; Weight Gain ; Food, Processed ; Treatment Outcome ; *Severe Acute Malnutrition/diet therapy ; },
abstract = {Background: Ready-to-use therapeutic foods (RUTFs) have been developed to treat severe acute malnutrition (SAM) in children by promoting rapid weight gain, but the long-term effects have been overlooked. Incorporating prebiotic rice bran into RUTF can enhance balanced weight gain. We hypothesized that children receiving RUTF + rice bran would exhibit increased fat-free mass (FFM) and reduced body fat percentage and abdominal adiposity. Methods: A double-blinded randomized controlled trial (ClinicalTrials.gov:NCT05319717) involving 200 children with different degrees of acute malnutrition compared the effectiveness of RUTF with or without rice bran. Children received treatment for 8 weeks, with another 8 weeks of follow-up. Anthropometry, including skinfolds, was collected every 4 weeks. Results: Compliance was similar in both groups (~21%). Children aged 6 to 23 months receiving RUTF + rice bran gained more FFM than those receiving RUTF alone (p = 0.05 at week 8). Over the 8-week treatment, the fat mass index increased in children receiving RUTF (p = 0.02), but not in those receiving RUTF + rice bran (p = 0.48), although the increase in body fat percentage was similar (p = 0.23). The ratio of abdominal to peripheral skinfolds decreased in both groups during treatment but increased during follow-up, though the difference was not statistically significant. In children aged 24 to 59 months, no significant differences in body composition were observed. The fat-free mass index increased in both groups during treatment but declined afterwards, with significant changes noted in the RUTF + rice bran group. Conclusions: The addition of rice bran to RUTF affected body composition changes during treatment only in younger children, where more lean mass was gained and fat mass gain was limited. Differences in intestinal microbiome maturity might underlie this age difference.},
}

Humans
*Oryza
Double-Blind Method
*Body Composition
Female
Male
Infant
*Prebiotics/administration & dosage
Weight Gain
Food, Processed
Treatment Outcome
*Severe Acute Malnutrition/diet therapy

@article {pmid42356234,
year = {2026},
author = {Eftekhar, MS and Singh, D and Katz, J and Nguyen, V and Menghini, P and Rodriguez-Palacios, A and Cominelli, F and Raffner Basson, A},
title = {Effect of Short-Term Grape Powder Supplementation in Patients with Crohn's Disease: A Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356234},
issn = {2072-6643},
support = {n/a//California Grape Commission/ ; K01DK127008, DK055812, DK091222, DK097948, and P01DK091222//NIH/NIDDK/ ; 1P01DK091222-24/NH/NIH HHS/United States ; 1R21DK118373-24/NH/NIH HHS/United States ; },
mesh = {Humans ; *Crohn Disease/microbiology/diet therapy ; Pilot Projects ; *Vitis ; Adult ; Female ; *Dietary Supplements ; Male ; Feces/microbiology/enzymology ; Powders ; *Gastrointestinal Microbiome/drug effects ; Middle Aged ; Peroxidase/analysis ; C-Reactive Protein/metabolism/analysis ; },
abstract = {Background: The overall objective of this pilot diet intervention study was to determine the effect of grape powder (GP) supplementation on gut microbiota composition and inflammatory markers in individuals with Crohn's disease (CD). Methods: Adult CD participants were recruited from the Digestive Health Institute at University Hospitals Medical Center, Cleveland. All participants were supplemented with 45 g/day of freeze-dried grape powder (equivalent to ~1.5 cups of fresh grapes) daily for 21 days. The primary outcome was the change in fecal microbiome profiles. Secondary outcomes included the absolute difference (day 21-day 0) in Harvey Bradshaw Index (HBI) score, fecal myeloperoxidase (MPO), and high-sensitivity C-reactive protein (hsCRP). Results: A total of 21 CD participants were included in the final analysis. After 21 days of GP supplementation, more than half of the participants (13, 61.9%) experienced a reduction in fecal MPO, while 80% (17) experienced either a reduction or no change in HBI score. Microbiome analysis revealed modest but directional shifts, including enrichment of Akkermansiaceae, Bacteroidaceae, Tannerellaceae, Rikenellaceae, and Monoglobaceae. While overall community structure did not significantly change at the cohort level, individualized microbiome responses as well as functional pathway shifts were observed following the intervention. Conclusions: Daily supplementation with freeze-dried grape powder for 21 days was safe and well-tolerated in adults with CD and was associated with modest shifts in gut microbiome composition. This study was registered on clinicaltrials.gov (NCT05972694; 5 February 2024).},
}

Humans
*Crohn Disease/microbiology/diet therapy
Pilot Projects
*Vitis
Adult
Female
*Dietary Supplements
Male
Feces/microbiology/enzymology
Powders
*Gastrointestinal Microbiome/drug effects
Middle Aged
Peroxidase/analysis
C-Reactive Protein/metabolism/analysis

@article {pmid42356238,
year = {2026},
author = {Wang, J and Ma, F and Wang, PF and Hung, CH and Wu, KT and Liao, LA and Guo, JY and Hou, CW},
title = {Effects of Probiotic and Dietary Fiber Supplementation on Metabolic Syndrome-Related Features, Mood, and Sleep in Adults with Obesity.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356238},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage ; *Dietary Fiber/administration & dosage ; *Obesity/psychology/complications ; Female ; *Metabolic Syndrome ; Male ; Adult ; Double-Blind Method ; Middle Aged ; *Dietary Supplements ; *Affect/drug effects ; *Sleep/drug effects ; Cholesterol, HDL/blood ; Treatment Outcome ; Sleep Quality ; },
abstract = {Background: Obesity is associated with metabolic dysregulation, mood disturbance, and poor sleep quality. Although dietary fiber and probiotic supplementation have both been proposed as microbiome-targeted strategies for obesity management, their independent and combined effects remain unclear. Methods: In this double-blind, randomized, placebo-controlled 2 × 2 factorial trial, 56 adults with obesity were randomized to placebo, dietary fiber, probiotic, or combined supplementation for 8 weeks. One withdrew during baseline assessment, and 55 participants were included in the intention-to-treat analysis. Outcomes included metabolic syndrome-related indicators, mood assessed by the Profile of Mood State, and sleep quality assessed by the Pittsburgh Sleep Quality Index. Intervention effects were evaluated using factorial ANCOVA with baseline adjustment. Results: No significant dietary fiber × probiotic interactions were detected. Dietary fiber supplementation showed selective favorable effects, mainly on HDL cholesterol and mood-related outcomes. Probiotic supplementation showed a significant main effect primarily on HDL cholesterol but did not remain significant after FDR correction. Sleep-related improvements were observed only in within-group analyses and were not supported by significant factorial ANCOVA effects. Combined supplementation did not provide additional benefits over single-component interventions. Conclusions: Dietary fiber supplementation may have selective favorable effects in adults with obesity, particularly on HDL cholesterol and mood-related outcomes. The absence of additional benefit from combined supplementation suggests that the effectiveness of synbiotic strategies may depend on the compatibility between the selected dietary fiber and probiotic strains.},
}

Humans
*Probiotics/administration & dosage
*Dietary Fiber/administration & dosage
*Obesity/psychology/complications
Female
*Metabolic Syndrome
Male
Adult
Double-Blind Method
Middle Aged
*Dietary Supplements
*Affect/drug effects
*Sleep/drug effects
Cholesterol, HDL/blood
Treatment Outcome
Sleep Quality

@article {pmid42356276,
year = {2026},
author = {Scrivin, R and Martinez, I and Henningsen, K and Slater, G and Henry, R and Anderson, D and Costa, RJS},
title = {Faecal Bacterial and Short-Chain Fatty Acid Profiles in Response to 48 h FODMAP Intervention Prior to Endurance Exercise.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356276},
issn = {2072-6643},
mesh = {Humans ; *Fatty Acids, Volatile/metabolism/analysis ; *Feces/microbiology/chemistry ; *FODMAP Diet ; Male ; *Gastrointestinal Microbiome ; Biomarkers/blood ; *Physical Endurance/physiology ; Young Adult ; Adult ; },
abstract = {Background/Objectives: Short-term low-fermentable oligo-, di-, and monosaccharide and polyol (FODMAP) diets can reduce exercise-associated gastrointestinal symptoms (Ex-GIS); however, their effects on the gut microbiome, short-chain fatty acids (SCFAs), and gastrointestinal biomarkers remain unclear. This study explored the effects of 48 h dietary FODMAP manipulation within a high-carbohydrate diet on faecal bacterial and SCFA profiles, and their relationships with exercise-induced gastrointestinal syndrome (EIGS) biomarkers, Ex-GIS, and performance. Methods: Twelve endurance athletes experiencing Ex-GIS were randomly allocated to a 48 h high-carbohydrate (mean ± SD: 12.1 ± 1.8 g∙d[-1])-high-FODMAP (HC-HFOD) (54.8 ± 10.5 g∙d[-1]) and a 48 h high-carbohydrate-low-FODMAP (HC-LFOD) (3.0 ± 0.2 g∙d[-1]) diet before 2 h of running at 60% V˙O2max, followed by a 1 h distance test (22.9 ± 1.2 °C, 46 ± 8% RH). Baseline faecal samples were collected before exercise trials to determine faecal bacterial and SCFA profiles. Blood samples were collected pre- and post-exercise to determine plasma I-FABP, sCD14, and CRP concentrations. Ex-GIS were recorded every 15 min throughout exercise. Results: Faecal bacterial α-diversity and relative abundance (RA%) at the phylum level were unchanged following both diets, while several family- and genus-level taxa RA% values were changed (p < 0.05), with greater shifts after HC-HFOD. HC-HFOD significantly increased faecal total-SCFA (p = 0.004), acetic (p = 0.002), and butyric (p = 0.028) acid concentrations. Strong positive and negative correlations between bacterial RA% and EIGS biomarkers and Ex-GIS were observed. Strong negative correlations with bacterial RA% and performance were observed. Conclusions: The 48 h HC-HFOD resulted in greater increases in bacterial RA% and SCFA concentrations compared with baseline. Bacterial RA% correlated bidirectionally with EIGS biomarkers and Ex-GIS, alongside strong negative associations with performance.},
}

Humans
*Fatty Acids, Volatile/metabolism/analysis
*Feces/microbiology/chemistry
*FODMAP Diet
Male
*Gastrointestinal Microbiome
Biomarkers/blood
*Physical Endurance/physiology
Young Adult
Adult

@article {pmid42356291,
year = {2026},
author = {Lupu, A and Anton, E and Sasaran, MO and Tarnita, I and Ioniuc, I and Rusu, TE and Moisa, S and Tarca, E and Butnariu, LI and Mitrofan, EC and Nedelcu, AH and Anton, SC and Knieling, A and Morariu, ID and Lupu, VV},
title = {The Role of Microbiota in Type 1 Diabetes: Insights into Dysbiosis and Immune Interactions.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356291},
issn = {2072-6643},
mesh = {Humans ; *Diabetes Mellitus, Type 1/immunology/microbiology ; *Dysbiosis/immunology/microbiology ; *Gastrointestinal Microbiome/immunology ; Animals ; },
abstract = {Type 1 Diabetes (T1D) is a complex autoimmune disorder characterized by immune-mediated destruction of pancreatic β cells, driven by genetic susceptibility and modulated by environmental factors, notably the gut microbiome. Dysbiosis, manifested as reduced microbial diversity, perturbations in the Firmicutes/Bacteroidetes ratio, and compromised short-chain fatty acid production, contributes to T1D pathogenesis through mechanisms involving immune system dysregulation and heightened intestinal permeability. Emerging evidence indicates a relationship between the gut and oral microbiomes, as well as the potential influence of the virome and mycobiome. This narrative review synthesizes the current literature on the intricate interplay between the gut microbial ecosystem, the host immune response, and the development of T1D, highlighting the potential for targeted microbiome-based interventions to ameliorate disease progression. A more nuanced understanding of these multi-kingdom interactions is essential for developing precise therapeutic strategies to prevent or delay T1D onset and to improve patient outcomes through restoration of immune tolerance and gut homeostasis.},
}

Humans
*Diabetes Mellitus, Type 1/immunology/microbiology
*Dysbiosis/immunology/microbiology
*Gastrointestinal Microbiome/immunology
Animals

@article {pmid42356304,
year = {2026},
author = {Thomas, KL and Wahlquist, AE and Clark, WA},
title = {Maternal Pre-Pregnancy Body Mass Index and Its Impact on Short- and Long-Chain Fatty Acid and Microbiome Profiles of Human Breast Milk in Caucasian Women of Northeast Tennessee.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356304},
issn = {2072-6643},
mesh = {Humans ; Female ; *Body Mass Index ; *Milk, Human/microbiology/chemistry ; Adult ; *Microbiota ; Pregnancy ; *Fatty Acids/analysis ; White People ; Maternal Nutritional Physiological Phenomena ; Cohort Studies ; *Fatty Acids, Volatile/analysis ; Lactation ; Young Adult ; },
abstract = {Background: Increasing evidence suggests that breast milk and its bioactive components, including short-chain fatty acids and the milk microbiome, are influenced by maternal nutrition and body mass index (BMI). Bioactive components transferred to the infant through breast milk play a pivotal role in infant growth and development and have indications in the child's future short- and long-term health outcomes. This study aimed to assess the impact of maternal pre-pregnancy BMI (PP-BMI) on human breast milk macronutrient composition, short- and long-chain fatty acid profiles, and breast milk microbiome profiles. Approach: This was an exploratory cohort study of forty-four lactating Caucasian women, two to fourteen weeks postpartum, divided into groups based on pre-pregnancy body mass index (BMI). Study participants signed informed consent, completed health and nutritional surveys, and provided a breast milk sample. Breast milk samples were subjected to proximate analysis, microbiome identification and short- and long-chain fatty acid extraction and analysis. Results: Maternal age, maternal physical activity, infant birth weight, and time of lactation at sample collection were not significantly different between the maternal PP-BMI groups. PP-BMI was significantly different between the two maternal groups. No significant differences were found between the maternal BMI groups concerning nutritional intake. No differences in breast milk microbiomes were observed in alpha diversity and beta diversity between the maternal PP-BMI groups. For long-chain fatty analysis in breast milk samples, myristic acid was significantly higher in the PP-BMI overweight/obese group while stearic acid was significantly higher in the PP-BMI normal-weight group. Butyric, valeric, and isocaproic acid concentrations in HBM were significantly higher in the PP-BMI normal-weight group and lower or undetectable in the PP-BMI overweight/obese group. Conclusions: Data from this exploratory cohort study indicate that maternal diet and pre-pregnancy BMI may be associated with differences in selected HBM fatty acids. There were no significant differences in microbiomes for alpha and beta diversity in breast milk between maternal PP-BMI groups; however, lower relative abundance was observed in the breast milk of the PP-BMI overweight/obese group. These findings should be interpreted in the context of the study's limitations, including convenience recruitment from a Facebook group, the modest sample size, and restriction to Caucasian women from a single geographic region.},
}

Humans
Female
*Body Mass Index
*Milk, Human/microbiology/chemistry
Adult
*Microbiota
Pregnancy
*Fatty Acids/analysis
White People
Maternal Nutritional Physiological Phenomena
Cohort Studies
*Fatty Acids, Volatile/analysis
Lactation
Young Adult

@article {pmid42356326,
year = {2026},
author = {Gong, X and Wang, Y and Chu, W and Zhao, Y and Liu, J and Zou, Q},
title = {Integrated Metabolomic and Microbiome Profiling Reveals Divergent Effects of No- and High-Fat Coffee in Mice.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356326},
issn = {2072-6643},
support = {RX-ZD202510//peking University Health Science Center Luckin Coffee Health Innovation Base/ ; },
mesh = {Animals ; Male ; *Coffee/chemistry ; Mice, Inbred C57BL ; *Metabolomics/methods ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Metabolome ; Multiomics ; Diet, High-Fat ; Chlorogenic Acid/metabolism ; Bacteria/classification/genetics ; *Dietary Fats/administration & dosage ; RNA, Ribosomal, 16S ; },
abstract = {Background/Objectives Coffee is widely consumed worldwide and is rich in bioactive compounds with potential metabolic benefits. Recently, lipid-enriched coffee formulations have gained popularity; however, their biological effects and underlying mechanisms remain poorly understood. Methods In this study, we employed an integrated multi-omics approach to investigate the impact of coffee and high-fat coffee on the plasma metabolome and gut microbiota of C57BL/6J mice. Eighteen male mice were randomly assigned to three groups (n = 6) and received water, coffee, or high-fat coffee by oral gavage daily for 14 days. The plasma metabolome was analyzed via UHPLC-MS/MS, and the gut microbiota was profiled u 16S rRNA gene sequencing. Results Metabolomic analysis revealed distinct clustering patterns among groups. A total of 200 metabolites were significantly altered in the coffee group compared with the water group, while 86 metabolites were altered in the high-fat coffee group compared with the coffee group, with 56 overlapping metabolites suggesting a core metabolic response. Microbiome analysis showed that coffee consumption increased the abundances of Akkermansia and Bifidobacterium and decreased the levels of Ligilactobacillus and Muribaculum. Coriobacteriaceae UCG-002 and Turicibacter were significantly enriched in the high-fat coffee group, whereas Lachnospiraceae NK4A136 group, Mucispirillum and unclassified Lactobacillaceae were reduced. Association analysis highlighted the top 20 metabolites with the highest degree of connection to gut microbial genera, two of which belong to the chlorogenic acid pathway. Conclusions Reduced levels of ferulic acid and 3-hydroxybenzoic acid, two metabolites potentially involved in antioxidant and anti-inflammatory activities, were observed in the high-fat coffee group, suggesting that dietary cream influences microbiota-associated chlorogenic acid metabolism.},
}

Animals
Male
*Coffee/chemistry
Mice, Inbred C57BL
*Metabolomics/methods
*Gastrointestinal Microbiome/drug effects
Mice
*Metabolome
Multiomics
Diet, High-Fat
Chlorogenic Acid/metabolism
Bacteria/classification/genetics
*Dietary Fats/administration & dosage
RNA, Ribosomal, 16S

@article {pmid42356333,
year = {2026},
author = {Bragazzi, NL and Ceylan, Hİ and Rosi, A and Scazzina, F and de Giorgio, A and Dergaa, I and Scoditti, E and Garbarino, S},
title = {The Co-Evolution of Sleep and Diet: Toward an Emerging Framework of Evolutionary Chrononutrition in Circadian-Metabolic Health.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356333},
issn = {2072-6643},
mesh = {Humans ; *Sleep/physiology ; *Biological Evolution ; *Circadian Rhythm/physiology ; *Diet ; *Feeding Behavior/physiology ; Animals ; Energy Metabolism ; },
abstract = {Sleep and dietary behavior are deeply conserved biological processes that co-evolved under ecological pressures shaping human anatomy, metabolism, immunity, cognition, and life history strategies. Major transitions in human dietary ecology, including plant-dominant hominin foraging, increased meat consumption, control of fire and cooking, agricultural domestication, industrialization, and postindustrial globalization, restructured nutrient intake, pathogen exposure, microbial ecology, metabolic demands, and temporal organization of behavior. Emerging evidence from evolutionary genomics, chronobiology, neuroendocrinology, and microbiome science indicates that sleep-feeding interactions represent a conserved adaptive regulatory module optimized for fluctuating energy availability and strong photoperiodic entrainment. Modern environments characterized by widespread availability of highly palatable, energy-dense foods rich in refined carbohydrates, added sugars, and multiple industrial additives, together with artificial light at night, continuous caloric access, sedentary behavior, and psychosocial stress produce a profound evolutionary mismatch destabilizing circadian-metabolic homeostasis. This mismatch is characterized by circadian disruption, temporal misalignment of feeding and sleep behaviors, and, in many populations, insufficient sleep duration. Within this conceptual landscape, the emerging framework of "evolutionary chrononutrition" proposes that metabolic health and sleep integrity depend not only on what humans eat, but critically on when food is consumed in relation to endogenous circadian architecture shaped across deep evolutionary time. This review synthesizes anthropological, physiological, and molecular evidence to develop an integrative evolutionary framework linking sleep and diet to contemporary cardiometabolic, neurodegenerative, inflammatory, and psychiatric disorders, with particular emphasis on how each major dietary transition plausibly altered sleep duration, architecture, circadian timing, neuroendocrine regulation, and the temporal alignment between feeding behavior and biological rhythms.},
}

Humans
*Sleep/physiology
*Biological Evolution
*Circadian Rhythm/physiology
*Diet
*Feeding Behavior/physiology
Animals
Energy Metabolism

@article {pmid42356344,
year = {2026},
author = {Ciurea, NA and Mahdi, L and Graziani, A and Di Ciaula, A and Portincasa, P and Khalil, M},
title = {Targeting the Human Gut Microbiota-Between Conventional Therapy and Precision Genetic Engineering.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356344},
issn = {2072-6643},
support = {CUP H93C22000950001; HORIZON-HLTH-2022-STAYHLTH-01-05; Project 101080329//PRIMA Programme (Partnership for Research and Innovation in the Mediterranean Area/ ; },
mesh = {Humans ; *Gastrointestinal Microbiome/physiology/genetics ; Fecal Microbiota Transplantation ; Probiotics/therapeutic use ; *Genetic Engineering/methods ; *Precision Medicine/methods ; Prebiotics ; },
abstract = {The gut microbiota is increasingly examined as a therapeutic target because it contributes to epithelial barrier integrity, microbial metabolite production, bile acid transformation, immune regulation, and communication between the gut and distant organs. This structured narrative review synthesizes evidence on microbiota involvement in metabolic, gastrointestinal, hepatic, cancer, and neuroimmune conditions, including MASLD/MASH, inflammatory bowel disease, irritable bowel syndrome, obesity, type 2 diabetes, hypertension, colorectal cancer, Parkinson's disease, and autism spectrum disorder. Across these conditions, microbiome findings are biologically plausible but heterogeneous. Many associations are shaped by diet, geography, medication exposure, host genetics, disease stage, sampling methods, and analytical pipelines. Microbial alterations should therefore be interpreted as context-dependent signals and candidate modifiers rather than universal causal markers. Conventional microbiota targeted strategies include diet, physical activity, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation. These approaches are clinically familiar, but their effects are often broad, host specific, strain dependent, and difficult to assign to one mechanism. Fecal microbiota transplantation has the clearest clinical role in recurrent Clostridioides difficile infection, while evidence for most other indications remains inconsistent. Engineered microbial therapeutics offer greater experimental precision through signal sensing, payload delivery, metabolic modulation, and genetic circuit design. However, most evidence remains preclinical or early translational. Progress requires stronger human trials, standardized methods, mechanistic validation, safety monitoring, ecological containment, transparent reporting, and proportionate regulation.},
}

Humans
*Gastrointestinal Microbiome/physiology/genetics
Fecal Microbiota Transplantation
Probiotics/therapeutic use
*Genetic Engineering/methods
*Precision Medicine/methods
Prebiotics

@article {pmid42356358,
year = {2026},
author = {Calabrese, FM and Bianco, A and Chiarini, M and Prospero, L and Franco, I and Bernardi, M and Celano, G and Calasso, M and Riezzo, G and Verrelli, N and D'Attoma, B and Ignazzi, A and Apa, CA and Giannelli, G and De Angelis, M and Russo, F},
title = {GPCS Stratification of Exercise-Induced Gut Microbiota and Metabolome Remodeling in IBS: An Exploratory Multi-Omics Study.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356358},
issn = {2072-6643},
support = {This research was funded by the Italian Ministry of Health (Ricerca Corrente 2026). The funder had no role in the study design, data collection, data analysis, interpretation of results, manuscript writing, or the decision to submit for publication.//Ministry of Health/ ; },
mesh = {Humans ; *Irritable Bowel Syndrome/microbiology/metabolism/therapy ; Multiomics ; *Metabolome ; *Gastrointestinal Microbiome/physiology ; *Exercise/physiology ; Female ; Metabolomics ; Prospective Studies ; Male ; Middle Aged ; Biomarkers ; Oxidative Stress ; Fatty Acids, Volatile/metabolism ; Volatile Organic Compounds/metabolism ; },
abstract = {BACKGROUND/OBJECTIVES: Exercise is increasingly recognized as a modulator of host-microbiome interactions, yet its role in irritable bowel syndrome (IBS) remains poorly characterized.

METHODS: In this prospective, single-arm, before-and-after interventional study, we used an integrated multi-omics approach based on metataxonomics and metabolomics to assess the effects of a structured 12-week moderate aerobic exercise program in 80 patients with mild-to-moderate IBS, stratified by Global Physical Capacity Score (GPCS). Biochemical and inflammatory markers have been gathered.

RESULTS: Exercise did not alter overall microbial diversity but selectively enriched short-chain fatty acid (SCFA)-producing taxa and remodeled the volatile organic compound (VOC) profile toward a more efficient metabolic state. Notably, conventional biochemical and inflammatory markers failed to distinguish response subgroups, whereas GPCS stratification revealed distinct microbial and metabolomic trajectories. Individuals with higher baseline physical capacity had higher acetate levels and lower levels of VOCs associated with dysbiosis and oxidative stress.

CONCLUSIONS: Our results suggest that baseline physical capacity is a primary determinant of the microbiome's responsiveness to exercise, challenging the reliance on static biochemical profiling. Despite the lack of a control group and the exploratory nature of some metabolomic signals, this study provides a framework for precision exercise interventions in IBS. Our work identifies GPCS as a clinically relevant stratification tool. The full trial protocol is registered on ClinicalTrials.gov under the identifier NCT05453084.},
}

Humans
*Irritable Bowel Syndrome/microbiology/metabolism/therapy
Multiomics
*Metabolome
*Gastrointestinal Microbiome/physiology
*Exercise/physiology
Female
Metabolomics
Prospective Studies
Male
Middle Aged
Biomarkers
Oxidative Stress
Fatty Acids, Volatile/metabolism
Volatile Organic Compounds/metabolism

@article {pmid42356389,
year = {2026},
author = {Scott, C and Stamataki, N and McLaughlin, J},
title = {Stevia Rebaudiosides Usage as a Sugar Reduction Tool: A Narrative Review of Their Metabolic, Gut Microbiome and Weight Management Effects in Human Clinical Studies.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356389},
issn = {2072-6643},
support = {None//Cargill (United States)/ ; },
mesh = {Humans ; *Stevia/chemistry ; *Diterpenes, Kaurane/pharmacology ; *Gastrointestinal Microbiome/drug effects ; *Sweetening Agents/pharmacology ; *Weight Loss/drug effects ; *Non-Nutritive Sweeteners/pharmacology ; Obesity ; },
abstract = {Background/Objectives: Stevia rebaudiosides represent a class of compounds extracted from the Stevia rebaudiana Bertoni plant or produced via yeast fermentation, which provide a sweet taste with little to no calories. These compounds are commercially referred to as stevia and are used in the food industry to reduce sugar in foods and beverages. Stevia is a non-nutritive sweetener (NNS), which is a class of ingredients which represent both artificial and plant-based sweeteners. NNSs are widely used and have been well studied. However, their effects on efficacy for weight management as a sugar reduction tool and overall metabolic effects are inconsistent. Of the approved NNSs for use, stevia is relatively new and one of the least studied. However, recent human clinical research has provided insights into stevia's metabolic effects, effects on the gut microbiome and effects on weight management when used to replace sugar. The objective of this narrative review of human clinical studies is to provide an overview of the effects of stevia rebaudiosides (largely rebaudioside A) on glucoregulatory and cardiometabolic functions, as well as their effects on gut microbiome and weight management. These studies were typically short term (acute to three months) and heterogeneous by design, and they contained stevia rebaudiosides as lone sweeteners and as part of a binary blend with other NNSs. The majority of metabolic studies on stevia rebaudiosides have evaluated the effects on glucose homeostasis and, to a lesser extent, the effects on cardiometabolic function, the gut microbiome, and weight management. These studies suggest that stevia rebaudiosides have no statistically significant effects on glycemia, insulinemia, blood lipids, appetite hormones, or the gut microbiome. Limited studies suggest that, particularly when compared to sucrose, stevia produces very modest body weight and BMI changes, while studies on subjective appetite and food intake have had inconsistent results. Conclusions: Longer-term studies are needed, with more consistent and rigorous design protocols across various populations. However, current human clinical studies suggest that stevia rebaudiosides have a limited impact on metabolic functions, and the observed effects on gut microbiome and changes in body weight, particularly when used to replace sugar, warrant further study.},
}

Humans
*Stevia/chemistry
*Diterpenes, Kaurane/pharmacology
*Gastrointestinal Microbiome/drug effects
*Sweetening Agents/pharmacology
*Weight Loss/drug effects
*Non-Nutritive Sweeteners/pharmacology
Obesity

@article {pmid42356397,
year = {2026},
author = {Wang, C and Liu, Z},
title = {Nutrition Across the Life Course and Risk of Young-Onset Breast Cancer: Mechanisms, Evidence, and Prevention Opportunities.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356397},
issn = {2072-6643},
support = {2025-67017-45104, ZL//United States Department of Agriculture/ ; MAS00586, ZL//National Institute of Food and Agriculture/ ; },
mesh = {Humans ; Female ; *Breast Neoplasms/prevention & control/epidemiology/etiology ; Risk Factors ; *Diet/adverse effects ; Developmental Origins of Health and Disease ; Age of Onset ; *Nutritional Status ; Adolescent ; Pregnancy ; Epigenesis, Genetic ; Young Adult ; Child ; },
abstract = {The incidence of cancer in young adults has risen worldwide. Women comprise a disproportionate share of young-onset cases, among whom breast cancer predominates. This shift parallels globalization and urbanization, including the wider adoption of Western-pattern diets. Although hereditary syndromes explain a minority of cases, the secular rise underscores the impact of modifiable exposures, particularly diet. Prenatal life, neonatal life, childhood, adolescence, and early adulthood are critical periods during which dietary exposures may shape long-term mammary development. Mammary tissue undergoes rapid proliferation and differentiation during development, creating windows of heightened susceptibility to carcinogenic insults. However, most existing studies emphasize dietary exposures during a single developmental period; the entire span of critical developmental windows plays a formative role in shaping young-onset breast cancer (YoBC) risk, and the mechanisms underlying this life-course shaping remain insufficiently characterized. This review comprehensively synthesizes evidence on how nutrition across sensitive developmental windows shapes the risk of YoBC. We evaluate protective and adverse dietary factors within these stages and examine mechanistic pathways linking early-life nutrition to carcinogenesis, focusing on hormonal regulation, epigenetic programming, chronic inflammation, and the gut microbiome. A structured literature search was conducted in PubMed, Embase, and Web of Science for English-language articles published from 1990 through May 2026, supplemented by hand-searching of relevant reviews and key primary studies. By framing nutrition and breast cancer through a life-course lens, this review provides an integrated foundation for stage-specific prevention strategies and identifies priority directions for future research on early-life dietary determinants of YoBC.},
}

Humans
Female
*Breast Neoplasms/prevention & control/epidemiology/etiology
Risk Factors
*Diet/adverse effects
Developmental Origins of Health and Disease
Age of Onset
*Nutritional Status
Adolescent
Pregnancy
Epigenesis, Genetic
Young Adult
Child

@article {pmid42356418,
year = {2026},
author = {Posta, E and Gyarmati, E and Majoros, L and Fekete, I and Varkonyi, I and Zold, E and Barta, Z},
title = {Across Kingdoms: The Bacteriome, Mycobiome, and Virome in Autoimmune Diseases: Mechanistic Insights, Therapeutic Perspectives, and the Emerging Role of COVID-19.},
journal = {Nutrients},
volume = {18},
number = {12},
pages = {},
pmid = {42356418},
issn = {2072-6643},
mesh = {Humans ; *COVID-19/immunology ; *Autoimmune Diseases/microbiology/immunology/virology/therapy ; SARS-CoV-2 ; *Virome ; Dysbiosis/immunology ; *Gastrointestinal Microbiome/immunology ; },
abstract = {Autoimmune and immune-mediated inflammatory diseases (IMIDs) develop when genetically and environmentally susceptible hosts lose stable immune tolerance. The gut ecosystem is increasingly recognized as a biologically active interface in this process. Its bacterial, fungal, and viral components may shape mucosal and systemic immunity through antigenic stimulation, barrier regulation, and metabolite-dependent signaling, although the strength of evidence is uneven: bacteriome data are currently the most mature, whereas mycobiome, virome, and phageome findings remain more disease-specific and emerging. Dysbiosis may influence autoimmunity through overlapping routes, including epithelial barrier failure, altered short-chain fatty acid, bile acid, and tryptophan metabolism, molecular mimicry, and cross-kingdom microbial interactions. Nutrition is central to this network because dietary substrates determine microbial growth, metabolic output, epithelial integrity, and immune-cell differentiation. In this narrative review, we integrate evidence on disease-associated bacteriome, mycobiome, and virome patterns in systemic autoimmune diseases, with emphasis on rheumatoid arthritis, systemic lupus erythematosus, Sjögren's syndrome, systemic sclerosis, spondyloarthritis, vasculitides, and idiopathic inflammatory myopathies. COVID-19 is considered not as a proven causal driver of autoimmunity, but as an example of an environmental and infectious insult capable of perturbing microbiome-barrier-immune communication. Finally, we discuss diet-based and microbiome-targeted approaches, including probiotics, prebiotics, synbiotics, and postbiotics, as adjunctive strategies that may help restore microbial resilience and immune balance. A better understanding of the diet-microbiome-host immunity axis may support more personalized preventive and therapeutic concepts in autoimmune disease.},
}

Humans
*COVID-19/immunology
*Autoimmune Diseases/microbiology/immunology/virology/therapy
SARS-CoV-2
*Virome
Dysbiosis/immunology
*Gastrointestinal Microbiome/immunology

@article {pmid42356450,
year = {2026},
author = {Chen, Y and Lei, S and Chen, Z and Gao, W and Liu, G and Wang, Y and Wang, L and Zhang, X and Xiao, X and Long, Q},
title = {Gut Microbiota and Metabolite Remodeling Underlies the Anxiolytic Effect of Anshen Bunao Oral Liquid.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {6},
pages = {},
pmid = {42356450},
issn = {1424-8247},
support = {A2024378//Research Foundation of Medical Science and Technology of Guangdong Province/ ; 20254092//Research Project of Chinese Medicine in TCM Bureau of Guangdong Province/ ; 2025KTSCX056//Guangdong University Featured Innovation Program Project/ ; },
abstract = {Background/Objectives: Anshen Bunao Oral Liquid (ABOL) is a traditional medicinal formula comprising Cornu Cervi Pantotrichum, Radix Polygoni Multiflori Preparata and other ingredients. It replenishes essence, nourishes qi and blood, and soothes the spirit. It is used in clinical practice to treat neurasthenia and insomnia (emotion-related symptoms), and its key component, glycyrrhizin, exhibits anxiolytic properties. This aligns with the holistic approach of traditional Chinese medicine (TCM) to regulating neuropsychiatric disorders. The aim of this study is to evaluate the anxiolytic efficacy of ABOL in rats with anxiety induced by chronic restraint stress (CRS), and to clarify its mechanism by focusing on modulation of the gut-brain axis (microbiota and metabolism). Methods: Sprague-Dawley rats underwent three hours of restraint per day for 28 days to induce anxiety. ABOL was administered intragastrically in three doses. Anxiety-like behaviours were assessed using OFT, EPM and SPT. Serum, tissue and faecal samples were analysed using ELISA, histopathology, immunohistochemistry, non-targeted metabolomics, 16S rRNA sequencing and RT-qPCR. Results: CRS induced anxiety-like behaviours, impaired weight gain and perturbed the balance of neurotransmitters (decreasing 5-HT, GABA, NE and DA, while increasing CORT), inducing inflammation/oxidative stress, hippocampal neuronal injury, intestinal barrier dysfunction and gut microbiota/metabolic dysregulation. ABOL effectively reversed these abnormalities by restoring the balance of neurotransmitters and the HPA axis, suppressing inflammation and oxidation, protecting neurons and the intestinal barrier, remodelling the gut microbiota (enriching Akkermansia and balancing Firmicutes/Bacteroidota) and regulating sphingolipid and glycerophospholipid pathways. The interaction between the gut microbiota and metabolites may contribute to this pharmacological effect. Conclusions: ABOL exerts anxiolytic effects by modulating the gut-brain axis at multiple targets, involving microbiota remodelling, regulation of lipid metabolism and improvement of pathology. This validates its ethnopharmacological value, linking traditional Chinese medicine to the development of modern anxiolytics.},
}

@article {pmid42356488,
year = {2026},
author = {Pereira, AMPT and Domingues, E and Silva, LJG and Freitas, A and Morais, PV and Domingues, S and Lima, T and da Silva, GJ and Chung, AP and Gomes, J},
title = {Biofiltration of Emerging Contaminants as a Sustainable Pest Management Strategy and Its Impact on Corbicula fluminea.},
journal = {Pharmaceuticals (Basel, Switzerland)},
volume = {19},
number = {6},
pages = {},
pmid = {42356488},
issn = {1424-8247},
support = {CEECIND/01207/2018//Fundação para a Ciência e Tecnologia/ ; UIDB/00102/2025//Fundação para a Ciência e Tecnologia/ ; UID/04539/2025//Fundação para a Ciência e Tecnologia/ ; LA/P/0058/2020//Fundação para a Ciência e Tecnologia/ ; UID/00285//Fundação para a Ciência e Tecnologia/ ; LA/P/0112/2020//Fundação para a Ciência e Tecnologia/ ; C644866475-00000012//Fundação para a Ciência e Tecnologia/ ; },
abstract = {Background/Objectives: Water scarcity is driving the development of strategies for treating municipal wastewater (MW) to enable its safe reuse. Nonetheless, MW contains contaminants of emerging concern (CECs), such as pharmaceuticals and antimicrobial-resistant (AMR) bacteria, which require innovative treatment technologies. In this context, Corbicula fluminea, an invasive freshwater clam, presents a high biofiltration capacity, and its environmental impact could be mitigated by assigning it a beneficial role in wastewater treatment. Methods: The ability of C. fluminea to remove chemical and biological CECs from real MW secondary-treated effluents was assessed. The effects of real wastewater on the clams' microbiome and on colony-forming unit (CFU) counts in their soft tissues were also assessed. Results: Under real conditions, the clams achieved over 73% removal for 3 chemical CECs after 24 h, with an average removal of approximately 39%. The clams showed recovery of both CFU counts and microbial community composition, dominated by opportunistic and stress-tolerant groups in the presence of pharmaceuticals. The removal of multidrug-resistant bacteria was evaluated; despite real wastewater reducing clearance rates, the clams significantly reduced these bacteria within 24 h. Conclusions: These results demonstrate that C. fluminea can serve as an effective polishing treatment, improving effluent quality, supporting control of this invasive species.},
}

@article {pmid42357147,
year = {2026},
author = {Chen, X and Hou, C and Yu, H and Xie, J},
title = {Enhanced Yield of GmJAG1-Edited Soybeans Accompanied by Improved Function of the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {42357147},
issn = {2223-7747},
support = {2023YFF1001600//National Key R&D Program of China/ ; },
abstract = {In the present study, we investigated how soybean yield is enhanced upon editing of the gene GmJAG1 and the consequent influence on the structure and function of the rhizosphere microbiome. Field trials revealed that gene-edited (GE) soybeans had a 55.22% increase in yield without concomitant changes in root length. Metagenomic sequencing of the rhizosphere soil microbiome showed that, compared with the corresponding non-edited line (CK), the alpha diversity of the GE groups remained unaltered, whereas beta diversity differed significantly at the soybean reproductive (R2) stage. Notably, the rhizosphere microbiome of GE soybeans at the R2 stage exhibited enrichment of functional pathways related to transport, amino acid biosynthesis, and central metabolism. These findings suggest that GmJAG1 editing may shape the functional profile of the rhizosphere microbiome, which could potentially contribute to yield gains. This work offers a novel microbiological perspective for understanding the mechanisms by which yield may be improved in GE crops.},
}

@article {pmid42357156,
year = {2026},
author = {Yang, S and Niu, Z and Miao, Y and Chen, Y and Lyu, G and Ma, W and Wang, Y and Lyu, L and Tian, X},
title = {Targeted Recruitment of Cross-Kingdom Phosphate-Solubilizing Microbes Drives Asymmetric Rhizosphere Responses Between Solanum rostratum and Cenchrus pauciflorus Benth. in Sandy Habitats.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {42357156},
issn = {2223-7747},
support = {32360267//National Natural Science Foundation of China/ ; 32260683//National Natural Science Foundation of China/ ; 2025MS03103//Natural Science Foundation of Inner Mongolia Autonomous Region/ ; GXKY26Z004//Fundamental Research Funds for the Universities directly under Inner Mongolia Autonomous Region/ ; 2026ZD025//Key Project of the Natural Science Foundation of Inner Mongolia Autonomous Region/ ; },
abstract = {In resource-poor sandy habitats, alien plant co-invasion often triggers intense belowground competition mediated by rhizosphere microorganisms. However, the mechanisms by which these plants overcome nutrient limitations remain unclear. Here, we conducted an eight-month in situ monitoring of single- and co-invasion plots of Solanum rostratum and Cenchrus pauciflorus Benth. in the Horqin Sandy Land. By integrating soil enzyme assays with 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing, we characterized their rhizosphere microbial community assembly. Co-invasion exposed both species to convergent biotic stress, characterized by the significant enrichment of the pathogenic fungi Didymella and Pseudogymnoascus (linear discriminant analysis (LDA) > 4.0). To mitigate these pressures, the dominant competitor, S. rostratum, specifically recruited a cross-kingdom phosphate-solubilizing consortium comprising Bacillus and Penicillium (LDA > 4.0). This targeted recruitment significantly enhanced rhizosphere activities, increasing phosphatase and sucrase to 86.10 U/g and 2.17 U/g, respectively, thereby maintaining available phosphorus at a high level (35.55 mg/kg). Conversely, the subordinate competitor, C. pauciflorus, lost key native stress-resistant bacteria such as Rubrobacter (relative abundance dropping from 5.39% to 3.27%) and failed to recruit effective microbes, leading to the rapid depletion of available phosphorus (dropping to 21.38 mg/kg). Ultimately, under dual nutrient and pathogenic stress, the precise recruitment and functional integration of cross-kingdom phosphate-solubilizing microbes are strongly linked to the divergent belowground competitive outcomes between these co-invading plants.},
}

@article {pmid42357188,
year = {2026},
author = {Song, Y and Yamashita, H and Ikka, T},
title = {Abiotic Stress Reshapes Rhizosphere Community Assembly and Tea Quality: Root Exudates, Plant-Soil Interactions and Microbial Management.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {42357188},
issn = {2223-7747},
abstract = {Abiotic stresses affect the growth of tea plants (Camellia sinensis) and reduce their yield and quality. The tea plant is a perennial crop. Its adaptability to abiotic stresses and the formation of quality depend not only on internal physiological regulation, but also on long-term interactions with the surrounding soil environment. However, how abiotic stresses reshape the tea rhizosphere community structure, and the knowledge of how these changes shape tea quality remains limited. This review summarizes current knowledge on the tea rhizosphere microbiome under abiotic stress. First, we examine how stress reshapes microbial communities, including their composition, metabolic functions, interaction networks, and the recruitment driven by root exudates. Second, we explore the mechanism of rhizosphere microorganisms affecting tea plants, including participation in nutrient cycling, interaction mediated by exudates, and the regulation of secondary metabolic pathways related to the quality of tea. Finally, we discuss several nutrient-based and microbiome-based management strategies, such as the use of combined fertilizer, intercropping, PGPR, AMF, and SynComs. This review connects stress physiology, rhizosphere ecology, and tea quality regulation within a microbiome-centered framework, providing a basis for strategies that enhance stress tolerance and tea quality stability in the tea plant.},
}

@article {pmid42357236,
year = {2026},
author = {Wang, S and He, T and Liu, Q and Fu, M and Zhang, N and Bao, L},
title = {Recent Advances in Physiological and Biochemical Responses of Grapevines to Downy Mildew Infection.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {12},
pages = {},
pmid = {42357236},
issn = {2223-7747},
support = {202404BI090011//Yunnan Provincial Science and Technology Department/ ; },
abstract = {Grapevine downy mildew, caused by the oomycete pathogen Plasmopara viticola (P. viticola), is one of the most devastating diseases threatening the global grape industry. The pathogen invades host plants through stomata, triggering a series of highly coordinated physiological disorders and biochemical defense events. This review systematically summarizes the dynamic changes in morphological structures (stomatal characteristics), physiological functions (photosynthesis, membrane system integrity, and carbon metabolism), and multi-level biochemical defense systems (reactive oxygen species (ROS) scavenging enzyme system, phenylpropanoid metabolic pathway, pathogenesis-related proteins, and phenolic compounds) in grapevines following infection. It focuses on analyzing the differences in the timing, intensity, and metabolic reprogramming of defense responses between resistant and susceptible cultivars, pointing out that the essence of disease resistance lies in early pathogen recognition and rapid defense induction. The conflicting conclusions regarding indicators such as soluble sugars, peroxidase (POD), and superoxide dismutase (SOD) are discussed from the perspectives of experimental systems, cultivar genetic backgrounds, and pathogen physiological race differences. Furthermore, the known physiological and biochemical alterations are linked to upstream signaling pathways, including salicylic acid and jasmonic acid (SA/JA), calcium signaling, and mitogen-activated protein kinase (MAPK) cascades. Recent advances in revealing resistance mechanisms in the omics era are also introduced. Finally, future research directions are proposed, including constructing multi-indicator dynamic evaluation models, verifying key gene functions using gene editing, exploring the potential of epigenetic regulation, and developing integrated control strategies combined with microbiome research. This review aims to provide theoretical support for grapevine downy mildew resistance breeding and sustainable disease management.},
}

@article {pmid42357267,
year = {2026},
author = {Dumitru, CN and Dumitru, AO and Goroftei, L and Niculet, E and Ignat, MD and Baroiu, L and Nechita, A and Balan, G},
title = {Pharmacomicrobiomics of Non-Antibiotic Drugs: Mechanisms and Clinical Consequences of Gut Microbiota Alterations.},
journal = {Pharmaceutics},
volume = {18},
number = {6},
pages = {},
pmid = {42357267},
issn = {1999-4923},
support = {NA//"Dunarea de Jos" University of Galati/ ; },
abstract = {Background: The gut microbiota constitutes a metabolically active "second genome" that profoundly modulates drug pharmacokinetics, pharmacodynamics, and adverse reaction profiles. Beyond antibiotics, widely prescribed non-antibiotic pharmacotherapies exert clinically relevant pharmacomicrobiomic effects with implications for therapeutic optimisation and pharmacovigilance. Methods: This narrative review, conducted following PRISMA 2020 reporting principles (without PROSPERO pre-registration), searched PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library (January 2015-December 2024) for evidence on proton pump inhibitors (PPIs), metformin, NSAIDs, statins, SGLT2 inhibitors, and oral iron. Evidence tables included clinical human studies with molecular microbiota characterisation (16S rRNA or shotgun metagenomics), ≥20 participants, and a control arm; preclinical data informed mechanistic synthesis. Results: Of 68 eligible studies, 20 met criteria for the evidence tables. PPIs significantly remodelled gut microbiota composition with enrichment of oral-origin taxa ("oralisation of the gut"), associating with Clostridioides difficile infection and SIBO. Metformin enriched Akkermansia muciniphila and butyrate producers, contributing causally to glycaemic efficacy. NSAIDs compromised barrier integrity, with synergistic dysbiosis under PPI co-prescription. Statins correlated with reduced prevalence of the dysbiotic Bact2 enterotype. SGLT2 inhibitor data remained discordant. Oral iron consistently enriched Enterobacteriaceae at the expense of beneficial commensals.},
}

@article {pmid42357332,
year = {2026},
author = {Elbehiry, A and Abalkhail, A and Alhumaydhi, FA and Marzouk, E},
title = {Phenotype-Guided Nanotherapeutic Strategies for Carbapenem-Resistant Acinetobacter baumannii: Toward Precision Antimicrobial Intervention.},
journal = {Pharmaceutics},
volume = {18},
number = {6},
pages = {},
pmid = {42357332},
issn = {1999-4923},
abstract = {Carbapenem-resistant Acinetobacter baumannii (CRAB) is considered a persistent clinical problem characterized by high mortality and restricted therapeutic options. The current antimicrobial regimen focuses on active bacteria without taking into account physiological states that influence the treatment response. Biofilm formation, metabolic changes, efflux activity, and membrane remodeling reduce antibiotic activity at infection sites and help bacteria survive despite in vitro susceptibility. Clinical performance is also compromised by inadequate tissue penetration, toxicity, and inconsistent pharmacokinetics, which reduce the ability to maintain effective antimicrobial activity at the target site. Therefore, a new strategy is needed that considers how bacteria behave during infection. Nanotherapeutic systems can optimize antimicrobial delivery by changing drug distribution and enabling sustained antimicrobial release within infected tissues. These properties can improve antimicrobial distribution within biofilms and structurally restricted infection sites. This review proposes a phenotype-guided approach linking dominant bacterial phenotypes with targeted nanotherapeutic intervention. Advances in nanoscale diagnostics and computational analysis allow earlier identification and more precise characterization of resistance features, so treatment decisions reflect the current state of infection. When integrated with nanotechnology, this information supports treatment approaches that adapt to changes in bacterial behavior over time. Extending this concept to host-directed and microbiome-informed interventions provides additional control by addressing factors that sustain infection beyond the pathogen. These elements create an integrated system that connects detection, analysis, and treatment, allowing therapy to match the biological conditions of infection for more precise CRAB management.},
}

@article {pmid42357491,
year = {2026},
author = {Deng, L and Ling, X and Li, L and He, Y and Guo, M},
title = {Advances in Scalp Microbiome Research: Molecular Insights into the Metabolism-Inflammation-Barrier Axis and Dandruff Pathogenesis.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {12},
pages = {},
pmid = {42357491},
issn = {1420-3049},
mesh = {Humans ; Filaggrin Proteins ; *Dandruff/microbiology/metabolism/etiology/pathology ; Skin Microbiome ; *Scalp/microbiology/metabolism ; *Inflammation/microbiology/metabolism ; Malassezia ; *Microbiota ; },
abstract = {Dandruff (DF) is a prevalent, recurrent inflammatory scalp disorder increasingly recognized as a complex state of functional dysbiosis rather than a simple Malassezia overcolonization. The scalp microbiome is predominantly shaped by Malassezia species (M. restricta and M. globosa), Cutibacterium, and Staphylococcus species. Recent multi-omics evidence indicates that DF pathogenesis is driven by the destabilization of microbial interaction networks and strain-level functional heterogeneity, characterized by the disruption of the C. acnes/S. epidermidis balance and the opportunistic expansion of Staphylococcus aureus. Mechanistically, Malassezia utilizes its lipolytic repertoire to hydrolyze host sebum into irritant free fatty acids and peroxides. Concurrently, oxidative metabolites like squalene peroxide (SQOOH) penetrate the stratum corneum to activate the NF-κB and aryl hydrocarbon receptor (AhR) pathways, triggering a pro-inflammatory cascade that overexpresses keratins (K6/16/17) and downregulates filaggrin. This molecular cascade drives abnormal keratinocyte turnover and lipidomic remodeling, establishing a self-perpetuating "metabolism-inflammation-barrier disruption" pathological cycle. This review systematically elucidates the molecular etiology of DF as an ecological disorder driven by a tripartite imbalance among the microbiome, host physiology, and the environmental niche. We propose that next-generation therapeutic paradigms must transcend traditional antifungal eradication, focusing instead on targeted molecular intervention and microecological restoration to recalibrate overall scalp homeostasis.},
}

Humans
Filaggrin Proteins
*Dandruff/microbiology/metabolism/etiology/pathology
Skin Microbiome
*Scalp/microbiology/metabolism
*Inflammation/microbiology/metabolism
Malassezia
*Microbiota

@article {pmid42357585,
year = {2026},
author = {Mitea, G and Schröder, V and Radu, MD and Mireșan, H and Iancu, IM},
title = {Plant-Derived Foods and Medicines as Modulators of the Gut Microbiome: Molecular Interactions and Implications for Disease and Therapy.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {12},
pages = {},
pmid = {42357585},
issn = {1420-3049},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Animals ; },
abstract = {The digestive system is one of the most complex systems in the body, integrating multiple functions, closely linked to and influenced by chemosensory mechanisms, as well as by the presence, composition, and dynamics of the microbiome. Increasing attention has been directed toward plant-derived foods and medicines, which interact with gut microbiota and modulate host physiological responses through microbial metabolism, leading to the formation of bioactive metabolites that influence host signaling pathways and therapeutic response. The review, based on relevant articles from major international databases using specific terms with a focus on microbiome-mediated interactions and molecular mechanisms, highlights the role of microbiome and diagnostic methods through the analysis of specific composition and changes in microbiota, as well as the importance of microbiomes in relation to the treatment of chronic diseases, given their complex influence on drug metabolism. The microbiome influences the response to medications and resistance to therapy, being also involved in the metabolism of plant-derived foods and medicines through complex microbial interactions, while the importance of modern diagnostic approaches supports the use of microbiome analysis to improve diagnosis, monitoring, and personalized medical strategies.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Animals

@article {pmid42357732,
year = {2026},
author = {Klinsoda, J and Limsuwan, S and Sornard, W and Thamsatit, P and Tansakul, N},
title = {Longitudinal Assessment of the Canine Fecal Microbiota in Response to Dietary Hempseed By-Product and Oil: A 90-Day Nutritional Intervention Study.},
journal = {Veterinary sciences},
volume = {13},
number = {6},
pages = {},
pmid = {42357732},
issn = {2306-7381},
support = {Grant FF (KU-SRIU) 17.67//Kasetsart University Research and Development Institute (KURDI/ ; },
abstract = {Industrial hemp (Cannabis sativa L.) derivatives are emerging as functional ingredients in companion animal nutrition; however, their long-term effects on the canine gut microbiome remain unclear. This exploratory study investigated the impact of dietary supplementation with two hempseed-based formulations (fiber-rich by-product vs. fat-rich oil coating) on the fecal microbiota of healthy adult dogs over 90 days. Twenty-four dogs were randomly assigned to control, hempseed by-product (11% inclusion), or hempseed oil (2% coating) diet groups. Fecal samples collected on days 0, 30, and 90 were analyzed using 16S rRNA gene sequencing to assess microbial composition and diversity. The hempseed oil group showed a distinguishable increase in species richness. Both hempseed-based diets were associated with compositional shifts in formulation-specific ways: the oil coating with a higher relative abundance of Lactobacillaceae (notably Ligilactobacillus), and the by-product with a higher relative abundance of Actinobacteriota (particularly Collinsella). Both treatments preserved several microbiota genera. Beta diversity analysis revealed significant temporal restructuring, with convergence toward a stabilized ecosystem by day 90. These findings demonstrate that hempseed fractions modulate the canine microbiome in a formulation-specific manner without disrupting ecological stability, supporting beneficial health effects in canine nutrition.},
}

@article {pmid42343158,
year = {2026},
author = {Aryal, S and Mell, B and Tummala, R and Manandhar, I and Kumariya, S and Kondapalli, N and Yeoh, BS and Ahlidja, W and Mautin Akinola, O and Pachhain, S and Bardhan, P and Saha, P and Zeydabadinejad, S and Osman, I and Thodeti, C and Yang, T and Vijay-Kumar, M and Reddivari, L and Joe, B},
title = {Gut microbiome drives glycodeoxycholic acid-mediated attenuation of hypertension.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2691346},
doi = {10.1080/19490976.2026.2691346},
pmid = {42343158},
issn = {1949-0984},
mesh = {Animals ; *Hypertension/microbiology/metabolism/physiopathology/drug therapy ; Receptors, G-Protein-Coupled/genetics/metabolism ; *Gastrointestinal Microbiome ; Rats, Inbred Dahl ; Blood Pressure/drug effects ; Rats ; Male ; *Glycodeoxycholic Acid/metabolism ; Bile Acids and Salts/metabolism ; Cecum/microbiology ; Fecal Microbiota Transplantation ; },
abstract = {Gut microbiota and bile acids are increasingly recognized to regulate blood pressure, but the mechanisms remain unclear. Takeda G-protein coupled receptor 5 (TGR5) is a major receptor for secondary bile acids. We hypothesized that loss of TGR5 function remodels gut microbiota and influences blood pressure. Using CRISPR/Cas9, TGR5 knockout (Tgr5KO) rats on the Dahl Salt-Sensitive (S) background were generated and characterized. Compared to the control S rats, Tgr5KO rats demonstrated significantly lower blood pressure, a distinct shift in gut microbiota composition, and an increase in the secondary bile acid, particularly, glycodeoxycholic acid. Supplementation of glycodeoxycholic acid to the control S rats produced a similar gut microbial shift and lowered blood pressure. Furthermore, cecal microbiota transplantation from Tgr5KO to control S rats lowered blood pressure in the recipient rats. This first loss-of-function study demonstrates that deletion of TGR5 remodels gut microbiota, increases glycodeoxycholic acid, and lowers blood pressure regardless of TGR5 signaling status, identifying a promising gut-liver axis target for lowering hypertension.},
}

Animals
*Hypertension/microbiology/metabolism/physiopathology/drug therapy
Receptors, G-Protein-Coupled/genetics/metabolism
*Gastrointestinal Microbiome
Rats, Inbred Dahl
Blood Pressure/drug effects
Rats
Male
*Glycodeoxycholic Acid/metabolism
Bile Acids and Salts/metabolism
Cecum/microbiology
Fecal Microbiota Transplantation

@article {pmid42343209,
year = {2026},
author = {Jiang, M and Liu, R and Li, Z and Xu, H and Zeng, J and Qu, W and Hu, Z and Chen, Y and Feng, D and Wu, W},
title = {Aspergillus niger ZJ-17 enhances the yield and quality of Angelica dahurica var. formosana by modulating beneficial rhizobacteria: a sustainable strategy for plant production.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09252-9},
pmid = {42343209},
issn = {1471-2229},
support = {Grant No. 2021YFYZ0012//the Key R & D projects of the Sichuan Provincial Department of Science and Technology/ ; Grant No. 2021-16-4//the Key Discipline Construction Project of Traditional Chinese Medicine in Sichuan Province/ ; Grant No. 2024-55//the Sichuan Qihuang Scholar Capability Enhancement Project/ ; },
abstract = {BACKGROUND: Angelica dahurica var. formosana is a medicinal and edible plant. Higher abundance of Proteobacteria is an excellent characteristic of its rhizosphere bacterial community. Aspergillus niger ZJ-17 (AN17) significantly improved plant yield and quality while reducing fertilizer input application in both pot and field experiments. However, the impact of inoculants on resident soil bacteria directly determines their field application. Therefore, to systematically analyze how AN17 remodels host rhizosphere bacterial communities, we inoculated AN17 into the roots of A. dahurica var. formosana. The rhizosphere bacterial communities and root exudates were investigated at the harvest stage. Rhizosphere bacteria were isolated for in vitro experiments to elucidate the reasons for the changes in the rhizosphere bacterial community.

RESULTS: AN17 promoted nutrient utilization and absorption in rhizosphere soil and increased the accumulation of IAA and JA in plant roots. In the microbiome, the relative abundance of rhizosphere Proteobacteria increased after inoculation. A total of 832 bacterial strains were isolated from the rhizosphere of the host for in vitro experiments. In in vitro experiments, AN17 induced the enrichment of Proteobacteria through microbial interactions and the modulation of host root exudates. These root exudates promoted the proliferation of bacterial genera with higher abundance and diversity. In the metabolome, host root activity increased following AN17 inoculation. According to the KEGG analysis of root exudates, AN17 upregulated microbial metabolism in diverse environments, the biosynthesis of alkaloids derived from the shikimate pathway and tryptophan metabolism. Correlation analysis and in vitro tests revealed that AN17 regulated the secretion of phenolic acids (4-chlorophenol, 2-oxoadipic acid, pyrogallol, and vanillic acid) from roots, which serve as crucial components driving the enrichment of Proteobacteria. In both plate and pot experiments, these bacteria promoted the growth of A. dahurica var. formosana and activated nutrient availability.

CONCLUSIONS: We supplemented multiple growth-promoting strategies by which AN17 improves rhizosphere bacterial communities. Phenolic acids in root exudates were recognized during the stimulation of rhizosphere bacterial proliferation by AN17. The interaction relationships among plants, beneficial fungi and rhizobacteria were explored and revealed. This result provides a sustainable approach for rhizosphere bacterial optimization and chemical fertilizer reduction in agricultural production.},
}

@article {pmid42343255,
year = {2026},
author = {Grzyb, T and Szulc, J},
title = {Integrated functional genomics and safety assessment of plant-growth-promoting Caryophanales from post-maize-cultivation soils.},
journal = {BMC genomics},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12864-026-13058-2},
pmid = {42343255},
issn = {1471-2164},
support = {00077.DDD.6509.000167.2022.05//The Agency for Restructuring and Modernisation of Agriculture, Poland/ ; },
abstract = {This study aimed to evaluate six environmental bacterial strains isolated from post-maize cultivation soils as candidates for agricultural biopreparation development, using an integrated functional genomic and safety assessment framework. Building on experimental validation of plant-growth-promoting activities, the analysis included: plant-growth-promoting traits (PGPT-Pred) using PLABase; carbohydrate-active enzymes (CAZymes) relevant for lignocellulosic crop residue degradation (dbCAN3); secondary metabolite profiles (antiSMASH); and screening for virulence factors and antibiotic resistance genes (ABRicate, BTyper3).All analyzed strains possess 1,449-1,617 predicted PGPT-encoding genes (24.1-35.9% of total genes), which are strongly shaped by taxonomic relatedness, as confirmed by congruence testing against ANI-based genomic divergence. Paenibacillus amylolyticus 5mez and Priestia megaterium 7psych showed distinct functional profiles compared to Bacillus spp., while Bacillus subtilis sensu lato strains were most similar to each other. Genomic predictions suggest involvement in nutrient acquisition (N, P, K, Fe) and stress mitigation. Secondary metabolite analysis revealed high biosynthetic potential, with non-Bacillus species harbouring a large proportion of unknown gene clusters, indicating underexplored metabolite diversity. CAZyme profiling identified P. amylolyticus 5mez as the most enzyme-rich strain, while B. cereus s.s. zielonkawy showed ligninolytic potential despite low overall CAZyme abundance. The safety assessment identified B. cereus s.s. zielonkawy as toxigenic and unsuitable for use. Of the remaining strains, P. amylolyticus 5mez and Pr. megaterium 7psych demonstrated the most favourable safety profiles, exhibiting no detectable virulence factors or antibiotic resistance genes, justifying their priority use in agricultural biopreparations, pending phenotypic validation. Given the high-dimensional, low-sample-size nature of multi-trait datasets in applied microbial genomics, tailored statistical approaches, including noise-reduction-validated PCA and distance-based congruence testing, were applied; their rationale and limitations are discussed.},
}

@article {pmid42343426,
year = {2026},
author = {Mehta, V and Galletti, C and Mathur, A and Suresh, N and Nandi, D and Flores-Fraile, J},
title = {Efficacy of probiotics in the management of oral candidiasis: an umbrella review of systematic reviews and meta-analyses.},
journal = {Systematic reviews},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13643-026-03249-z},
pmid = {42343426},
issn = {2046-4053},
abstract = {BACKGROUND: Oral candidiasis (OC) is among the most prevalent oral infections, frequently associated with immunosuppression, denture wearing, advanced age, and excessive antibiotic use. Given the growing concerns about antifungal resistance, probiotics are being explored as potential adjuncts in the management of oral Candida overgrowth. Existing literature provides fragmented evidence; thus, an umbrella review was planned to synthesize the available evidence on the effectiveness of probiotic interventions in reducing oral Candida spp.

METHODS: A comprehensive, independent search was conducted in four databases (PubMed, Embase, Scopus, and Web of Science) covering literature from inception to 31st January 2026. Systematic reviews (SRs) with or without meta-analyses (MAs) assessing the effectiveness of probiotics in reducing oral Candida spp. count in terms of colony-forming units/mL (CFU/mL) were included. The quality assessment of the evidence was evaluated using A Measurement Tool to Assess Systematic Reviews 2 (AMSTAR 2) tool and the Grading of Recommendations Assessment, Development and Evaluation (GRADE) approach.

RESULTS: Out of the 157 retrieved records, 7 studies were included in this umbrella review, out of which 5 were SRMAs, and 2 were SRs. The interventions involved multi-strain probiotics delivered through various formulations, routes, and treatment durations. Across the 5 SRMAs, probiotic interventions demonstrated beneficial effects by reducing Candida spp. with effect estimates ranging from odds ratio (OR) 0.06 to 0.71; however, wide interstudy heterogeneity (I[2] = 0-78%) restricts the reliability and comparability of these findings. These effect estimates were derived from individual meta-analyses with heterogeneous study populations. Methodological assessment of the 7 included studies using the AMSTAR 2 tool identified 3 studies (42.8%) as having low confidence, while 4 studies (57.1%) were rated critically low. Similarly, the overall quality of evidence, as assessed by GRADE, ranged from low for the adult population to very low for the pediatric population, across three key clinical outcomes: reduction in oral Candida spp., clinical cure rate of OC, and recurrence rate.

CONCLUSIONS: Probiotics may have a potential role in the prevention and treatment of OC; however, the current evidence base cannot be generalized due to significant heterogeneity and methodological constraints. Probiotics can supplement conventional antifungal treatment, but their standalone use is not recommended yet. High-quality, standardized randomized controlled trials and comprehensive SRMAs are necessary to better understand the effectiveness of probiotics in OC management.

PROSPERO CRD420251117392.},
}

@article {pmid42343457,
year = {2026},
author = {Wang, C and Li, S and Liu, Y and Zhao, X and Wang, F and You, Y and Zhao, X},
title = {Temporal dynamics of rhizosphere microbiome assembly and carbon-phosphorus coupling in poplar-medicinal plant intercropping systems.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02453-2},
pmid = {42343457},
issn = {2049-2618},
abstract = {BACKGROUND: Intercropping can reshape the rhizosphere microbiome, but how specific companion plants influence nutrient cycling and host growth remains unclear. We proposed that intercropping poplar with medicinal plants creates distinct rhizosphere niches that select for microbial communities with distinct functional potential, thereby improving tree nutrition.

RESULTS: Intercropping significantly promoted poplar growth, with increases in diameter at breast height (DBH) of 15.33%, 14.3%, and 15.23% in systems with Anemarrhena asphodeloides, Belamcanda chinensis, and Saposhnikovia divaricata, respectively. Intercropping did not change microbial alpha diversity but led to plant-specific shifts in beta diversity with clear seasonal dynamics. Metagenomic analyses revealed corresponding shifts in the functional potential of microbial communities related to carbon (C) and phosphorus (P) cycling, including genes such as frdC, aldB, ppk2, and phnH. Intercropping, particularly with S. divaricata, was associated with an increased genetic potential for microbial C metabolism and​ a heightened potential for P solubilization. These co-occurring shifts in genetic potential were correlated with greater P accumulation in poplar leaves. Network analysis showed distinct temporal microbial co-occurrence patterns across intercropping treatments, with A. asphodeloides supporting the most interconnected community linked to P mobilization. Three bacterial genera (Priestia, Pseudomonas, Acinetobacter) were strongly associated with key soil nutrient pools. Re-inoculation experiments confirmed their functional roles: Priestia sp. increased N and P retention in the rhizosphere; Pseudomonas sp. promoted plant growth, suggesting a role in​ stimulating plant secondary metabolism; and Acinetobacter sp. enhanced organic C mineralization.

CONCLUSIONS: Intercropping with specific medicinal plants structures the rhizosphere microbiome through niche differentiation. This restructuring leads to distinct patterns of microbial functional potential, centered on C and P metabolism, which correlate with improved poplar nutrient acquisition and growth. Our findings, integrating metagenomic inference with experimental validation, provide a framework for selecting companion plants to steer the rhizosphere microbiome toward beneficial functional outcomes in agroforestry systems. Video Abstract.},
}

@article {pmid42343653,
year = {2026},
author = {Bruggeman, A and Vandenbroucke, RE and Santens, P},
title = {Rationale and current status of fecal microbiota transplantations for Parkinson's disease.},
journal = {Journal of Parkinson's disease},
volume = {},
number = {},
pages = {1877718X261455608},
doi = {10.1177/1877718X261455608},
pmid = {42343653},
issn = {1877-718X},
abstract = {Treating a neurological disorder through the gut may seem counterintuitive, yet multiple lines of evidence highlight the gut's important role in Parkinson's disease (PD). Prodromal gastrointestinal symptoms, the presence of aggregated α-synuclein in enteric neurons, increased intestinal inflammation, and impaired epithelial barrier integrity all point to gut-level involvement in PD pathophysiology. The gut microbiome, markedly altered in individuals with PD, may be a key driver of these changes. Fecal microbiota transplantation (FMT) is currently the most effective strategy for achieving broad and durable modifications of gut microbiota composition. However, FMT is a complex, multi-step procedure requiring stringent methodological control. Modulating gut bacteria has demonstrated therapeutic potential in preclinical models of PD, and recent clinical trials have begun evaluating FMT in patients, although outcomes have been variable. In this review, we examine potential explanations for these divergent results, with a particular focus on methodological differences across trials. We also outline future directions for optimizing FMT study design in PD and discuss how these insights may guide the development of next-generation microbiota-targeted therapies.},
}

@article {pmid42343855,
year = {2026},
author = {Baños-Quintana, AP and de Carvalho, ASP and Kaltenpoth, M},
title = {Symbiotic organs in insects: diversity, functional implications, and terminology.},
journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences},
volume = {381},
number = {1953},
pages = {},
doi = {10.1098/rstb.2024.0386},
pmid = {42343855},
issn = {1471-2970},
support = {//Deutsche Forschungsgemeinschaft/ ; //H2020 European Research Council/ ; //Max-Planck-Gesellschaft/ ; },
mesh = {Animals ; *Symbiosis ; *Insecta/microbiology/physiology/anatomy & histology ; Terminology as Topic ; *Fungi/physiology ; *Microbiota ; *Bacterial Physiological Phenomena ; },
abstract = {With over a million described species, insects represent the most successful group of animals on Earth. One of the drivers of insect diversity is their ability to engage in multifold beneficial symbioses with microorganisms, often involving specialized host organs to accommodate intra- or extracellular symbionts. The existence of such organs and their importance for sustaining and transmitting beneficial symbionts has been known for over a century, and specific terms have been established for categorizing organs harbouring intracellular bacteria (bacteriomes) or fungi (mycetomes), or cuticular crypts containing extracellular fungi (mycetangia). For others, however, general terms are lacking, e.g. organs containing extracellular bacteria associated with the cuticle or with the digestive tract. Furthermore, previously established terms have been misused in other contexts. Notably, 'bacteriome' has been increasingly employed in the microbiome field to refer to bacterial communities, instead of the term's original meaning of specialized organs housing intracellular bacterial symbionts. Here, we review and categorize the diversity of symbiotic organs in insects and propose a unified terminology. Our hope is that this common language will facilitate communication and thereby support the field of symbiosis research in unravelling commonalities and differences in the evolution, ecology, development, physiology and molecular basis across symbiotic interactions. This article is part of the theme issue 'Life in natural microcosms'.},
}

Animals
*Symbiosis
*Insecta/microbiology/physiology/anatomy & histology
Terminology as Topic
*Fungi/physiology
*Microbiota
*Bacterial Physiological Phenomena

@article {pmid42343916,
year = {2026},
author = {Liu, F and Xue, H and Jiang, Y and Chen, S and Zhang, Y and Yu, J and Qin, Y and Dong, X and Ou, Y and Qiu, R},
title = {Fluoride varnish application and the temporal evolution of supragingival microbiota in children with differential caries risk.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2682471},
pmid = {42343916},
issn = {2000-2297},
abstract = {BACKGROUND: Fluoride varnish is used to prevent early childhood caries, but its longitudinal ecological impact on the supragingival microbiome beyond enamel remineralization remains poorly understood, especially long-term.

OBJECTIVE: To characterize 24‑month supragingival plaque microbiome evolution in young children under biannual fluoride varnish, stratified by caries risk, and fluoride's ecological effect on microbial structure, interactions, and metabolism.

DESIGN: A total of 48 children were categorized into low‑, moderate‑, and high‑caries‑risk groups using the modified caries-risk assessment tool for preschool children (PSC-MCAT). All received fluoride varnish every six months. Supragingival plaque collected at five timepoints over 24 months. 16S rRNA sequencing assessed diversity, key taxa, co-occurrence networks, and PICRUSt2 metabolic pathways.

RESULTS: Baseline alpha‑ and beta‑diversity differed significantly across risk groups (p<0.05). After sustained fluoride, intergroup differences diminished. High‑risk group retained caries‑associated genera (e.g. Leptotrichia, Prevotella, Veillonella) with suppressed abundance. Fluoride increased network complexity and negative correlations in moderate‑/high‑risk groups. Glycolysis, TCA cycle, and starch/sucrose metabolism were inhibited in the high‑risk group post‑intervention.

CONCLUSIONS: Regular fluoride varnish reduces ecological disparities across risk groups, suppresses cariogenic taxa, and alters microbial interactions and carbohydrate metabolism, promoting homeostasis. High‑risk children may require more frequent interventions.},
}

@article {pmid42343917,
year = {2026},
author = {Krasaesin, A and Wongbanthit, Y and Chaiboonyarak, T and Wang, DH and Alinejad-Rokny, H and Samaranayake, L and Pongpanich, M and Porntaveetus, T},
title = {Shotgun metagenomic profiling reveals ecological and functional alterations of the oral microbiome in craniosynostosis.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2687219},
pmid = {42343917},
issn = {2000-2297},
abstract = {OBJECTIVE: To elucidate the microbial drivers underlying of craniosynostosis (CS) , which involves premature suture fusion and secondary dentofacial malformations likely to increase dental disease burden.

METHODS: Shotgun metagenomic sequencing of supragingival plaque from 44 participants (22 CS patients and 22 matched healthy controls, aged 6-17 years) were performed, following by bioinformatics evaluation.

RESULTS: Beta diversity demonstrated significant differences between groups (p < 0.01), whereas alpha diversity trended lower in the CS cohort. Taxonomic profiling revealed a dysbiotic signature in CS with high caries burden, defined by the enrichment of saccharolytic and anaerobic taxa (Scardovia, Actinomyces sp. oral taxon 448, Selenomonas sp. F0473, and Treponema lecithinolyticum)) alongside reduced health-associated genera like Haemophilus and Neisseria. Functional pathway analysis indicated metabolic remodeling, with upregulated fructan biosynthesis and starch degradation III pathways, consistent with caries-active biofilms.

CONCLUSION: These findings demonstrate that orofacial anomalies in CS favor the assembly of an acidogenic, virulent plaque biofilm. The first shotgun metagenomic profile of the oral microbiome in CS establishes a foundation for future investigations. Furthermore, clinical management of CS should extend beyond structural correction to incorporate microbiological monitoring and preventive strategies, reducing the elevated risk of dental disease in this vulnerable population.},
}

@article {pmid42343918,
year = {2026},
author = {J Rus, M and R Nieto, M and Oh, HJ and Yoo, H and Areal-Quecuty, V and Duarte Faria, F and Lendines-Cordero, D and Simon-Soro, A},
title = {Salivary estrone and estradiol are associated with oral microbiome profiles in aging women.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2690784},
pmid = {42343918},
issn = {2000-2297},
abstract = {OBJECTIVES: To explore whether salivary estrogens (estrone and estradiol) are associated with oral microbiome composition in aging women, and to assess the oral cavity as a potential sentinel of systemic hormonal changes during midlife.

MATERIALS AND METHODS: Cross-sectional study including 30 women aged 40-65 years. Saliva and microbial specimens were collected from four oral ecological niches (buccal mucosa, tongue dorsum, supragingival plaque, subgingival plaque). Microbiome composition and diversity were assessed by 16S rRNA gene sequencing, ecological indices, and co-occurrence network analysis. Salivary estrone and estradiol were quantified, and associations with oral health and microbial profiles were evaluated.

RESULTS: Estrone levels declined significantly with age and were associated with hyposalivation and lower oral health scores. Estrone was linked to increased microbial diversity on the tongue dorsum and enrichment of taxa such as Porphyromonas. In contrast, estradiol was positively associated with commensal genera (Streptococcus, Lactobacillus) and negatively with periodontal-associated taxa (Fusobacterium, Prevotella). Co-occurrence networks revealed niche-specific microbial shifts associated with estrogen levels.

CONCLUSIONS: Salivary estrogens, particularly estrone, shape oral microbial communities in aging women. The oral cavity may act as a window into systemic hormonal changes, supporting its role as a non-invasive sentinel of women's health during midlife.},
}

@article {pmid42343919,
year = {2026},
author = {Nicot, C},
title = {From Cold to Constrained: Why MSS Colorectal Cancer Resists Immunotherapy.},
journal = {Cancer biome and targeted therapy},
volume = {1},
number = {2},
pages = {320-327},
pmid = {42343919},
issn = {3070-9989},
}

@article {pmid42343926,
year = {2026},
author = {Kim, H and Zhou, M and Lin, L and Zhu, W and McAllister, TA and Guan, LL},
title = {PacBio full-length 16S rRNA gene sequencing processed with Emu and GTDB provides the highest taxonomic resolution for rumen bacteriome profiling.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag148},
pmid = {42343926},
issn = {2730-6151},
abstract = {Although full-length 16S rRNA gene sequencing has substantially improved taxonomic resolution compared to short-read approaches, a high proportion of unclassified taxa are reported in rumen microbiome studies. This limitation is largely driven by platform-specific analytical workflows and the insufficient representation of rumen-associated lineages in commonly used reference databases. Here, we identified the optimal combination of sequencing platform, analytical workflow, and reference database to improve rumen bacteriome classification. We analyzed short-read and full-length 16S rRNA gene sequences from rumen samples collected from two beef cattle populations. Short-read sequences were generated using Illumina NextSeq2000 and processed with QIIME2. Full-length sequences were generated using PacBio Revio (PacBio-16S) and Nanopore MinION (ONT-16S); PacBio-16S data were analyzed using QIIME2 and Emu, while Nanopore data were analyzed using EPI2ME and Emu. Five reference databases were evaluated across all analytical approaches: SILVA 138.2, SILVA 138.2 with Hungate1000 collection, NCBI, Greengenes2, and GTDB. The comparisons showed that PacBio-16S (Emu) achieved the highest proportion of classified reads among all platform-specific workflows, while GTDB consistently produced the highest number of non-redundant classified taxa. Prevotella, a dominant rumen genus, was abundant in Illumina and PacBio-16S datasets but was underrepresented in ONT-16S workflows. Species-level analyses further demonstrated that PacBio-16S (Emu) reliably provided more consistent and high-resolution identification of Prevotella species under GTDB across two beef populations. Overall, our results demonstrate that sequencing platform, workflow choice, and database selection strongly influence rumen bacteriome profiles. We recommend PacBio-16S (Emu) under GTDB as the most reliable workflow for achieving high-resolution taxonomic classification of rumen bacteriome.},
}

@article {pmid42343927,
year = {2026},
author = {González-Ramírez, IS and Song, MJ and Mehlferber, EC and Mishler, BD},
title = {Off-target metagenomics: Leveraging whole genome sequencing to study the bacteriome of the liverwort Calasterella californica.},
journal = {Applications in plant sciences},
volume = {14},
number = {3},
pages = {e70064},
pmid = {42343927},
issn = {2168-0450},
abstract = {PREMISE: The recovery of non-target organism reads, especially when whole organisms are sampled, constitutes a great opportunity for studying microbial communities. The increase in whole genome sequencing feasibility and the development of new marker-based pipelines enable the use of short reads to study bacterial communities associated with organisms.

METHODS: We utilized population genomic data of the liverwort Calasterella californica obtained through the California Conservation Genomics Project to characterize the composition of its associated bacterial communities and explore its variation across the geographic space.

RESULTS: The bacterial communities associated with C. californica were dominated by the methanotroph Methylobacterium and other Hyphomicrobiales, a group that includes well-known plant symbionts. While diversity metrics of bacteria composition were similar across localities, we found significant differences in the relative abundance of a few taxa across California regions, likely driven by differences in precipitation and temperature seasonality.

DISCUSSION: Our results support previous observations that liverwort bacterial communities are not randomly assembled, suggesting a potential role of the plant in determining community composition, an emerging pattern that deserves more attention. The novel off-target metagenomics approach can be applied to any population-level resequencing where whole organisms are sequenced, opening the door to exciting avenues of microbiome research using repurposed data from landscape genomics.},
}

@article {pmid42343970,
year = {2026},
author = {Das, R and Kumar, R and Tamang, B},
title = {Microbial community structure, functional potential, probiotic signatures, and MAG reconstruction of fermented bamboo shoots from Northeast India.},
journal = {FEMS microbes},
volume = {7},
number = {},
pages = {xtag032},
pmid = {42343970},
issn = {2633-6685},
abstract = {Fermented bamboo shoot (FBS) products are widely consumed traditional foods across the Northeast region (NER) of India, yet their microbiome structure, functional capacity, biosynthetic potential, and safety attributes remain insufficiently explored. Here, comparative shotgun metagenomics of ten traditional FBS products from six NER states was used to address these gaps integrating previously generated metagenomic data from Tripura with newly generated datasets from Manipur, Meghalaya, Arunachal Pradesh, Nagaland, and Sikkim thereby bringing the total number of samples to 24. Taxonomic profiling revealed a predominance of lactic acid bacteria, primarily members of Lactiplantibacillus, Levilactobacillus, Lactobacillus, Lactococcus, and Pediococcus, with pronounced product- and region-specific community signatures. Functional annotation demonstrated predominance of genes involved in carbohydrate metabolism, stress response, quorum sensing, ABC transporters, vitamin biosynthesis, and energy metabolism, supporting strong probiotic-associated functional potential across FBS types. AntiSMASH analysis enabled the identification of diverse biosynthetic gene clusters (BGCs) responsible for the production of various secondary metabolites, including bacteriocins, non-ribosomal peptides, terpenes, and siderophores, with higher biosynthetic diversity observed in Mesu (Sikkim), Tuaithar (Manipur), Lung-Seij (Meghalaya), and Bastenga (Nagaland). Antimicrobial resistance (AMR) profiling revealed a generally low resistome burden, dominated by intrinsic resistance determinants, with FBS Sikkim and Tripura exhibiting the lowest AMR prevalence among all products. High-quality metagenome-assembled genomes affiliated with Lactiplantibacillus plantarum, Lactobacillus acetotolerans, and Pediococcus pentosaceus exhibited conserved probiotic traits, carbohydrate-active enzymes, biosynthetic pathways, and a limited presence of mobile genetic elements. Overall, the microbiome-based comparative analysis provides a framework for understanding the microbial community structure and functional potential across the NER, demonstrating broad probiotic potential and biosynthetic richness, with mesu samples from Sikkim showed a comparatively consistent distribution of functional pathways, biosynthetic gene clusters, and AMR-related features relative to the other FBS samples analysed.},
}

@article {pmid42343982,
year = {2026},
author = {van Mourik, DJM and Balvers, M and Jansen, VLBI and de Jonge, PA and Coppens, M and Nieuwdorp, M and Middeldorp, S and Eikenboom, JCJ and Voorberg, J and van Mens, TE},
title = {Cross-Reactivity of Antiphospholipid Antibodies with Gut Commensal Proteins in Antiphospholipid Syndrome.},
journal = {TH open : companion journal to thrombosis and haemostasis},
volume = {10},
number = {},
pages = {a28685248},
pmid = {42343982},
issn = {2512-9465},
abstract = {BACKGROUND: Antiphospholipid syndrome (APS) is an autoimmune disease characterized by the persistent presence of antiphospholipid antibodies (aPL), mainly targeted against β2 glycoprotein 1 (β2GP1). The autoimmune response to β2GP1 is aimed at several B-cell and T-cell epitopes. Molecular mimicry of these epitopes by gut commensal proteins, so-called mimotopes, causing cross-immunization, might contribute to the formation of aPL.

OBJECTIVE: To study the potential role of gut microbiome cross-immunization in APS by examining cross-reactivity of aPL with gut commensal mimotope-containing proteins.

METHODS: Fecal microbial metagenome of APS patients was determined using shotgun sequencing. An in-house developed in silico pipeline was used to identify gut commensal proteins that show sequence homology with known β2GP1 B and T cell epitopes in the metagenomic data. An enzyme-linked immunosorbent assay was used to test the identified microbial proteins for IgG cross-reactivity, with plasma of 21 APS patients and 17 control participants.

RESULTS: The in silico pipeline resulted in the identification of six gut commensals with a B cell and T cell β2GP1 epitope homologue. Of these, YjjG family noncanonical pyrimidine nucleotidase, one of the candidate-β2GP1 B cell mimicking proteins, showed significantly increased IgG reactivity in APS patients compared to control participants, as well as higher binding of a specific anti-β2GP1 monoclonal antibody than a negative control.

CONCLUSION: Our study shows reactivity of IgG antibodies to YjjG family noncanonical pyrimidine nucleotidase from Roseburia amylophila in APS patients. Insights into the origins of antibody formation may yield new therapeutic targets for improvement of APS treatment.},
}

@article {pmid42344006,
year = {2026},
author = {Tepson, JA and Agyirifo, DS},
title = {Microbial Ecology at the Nexus of Food Safety and Biotechnology With Ecological Mechanisms, Risks, and Emerging Innovations.},
journal = {International journal of food science},
volume = {2026},
number = {},
pages = {6618960},
pmid = {42344006},
issn = {2314-5765},
abstract = {Food systems are complex microbial ecosystems in which microorganisms play dual and often contrasting roles as agents of foodborne contamination and as essential drivers of food production and biotechnological innovation. Microbial ecology provides an integrative framework for understanding how microbial interactions, environmental conditions, and human interventions shape food safety outcomes and technological processes. This narrative integrative review is aimed at synthesizing current literature on microbial ecology at the nexus of food safety and food biotechnology and at identifying key research gaps and future directions. In this study, peer-reviewed journal articles addressing microbial interactions, contamination pathways, and ecological mechanisms relevant to food safety and biotechnology published between 2015 and 2025 were retrieved from major scientific databases and were synthesized using a narrative integrative approach. The review highlights ecological factors including microbial competition, stress adaptation, and biofilm formation across pre- and postharvest environments. At the same time, these same ecological principles are harnessed in food biotechnology to drive controlled fermentations, enhance shelf life through biopreservation, develop functional probiotics and enzymes, and engineer microbial systems via synthetic biology. Advances in high-throughput sequencing technologies, including whole genome sequencing, metagenomics, and multiomics integration, are identified as transformative tools for linking food-associated microbial community structure to functional outcomes. Despite significant progress, challenges remain in translating ecological insights into reliable industrial and regulatory practices due to microbial complexity, data integration limitations, and safety considerations. The review positions microbial ecology as a strategic framework for advancing food safety, biotechnological innovation, and sustainable food systems.},
}

@article {pmid42344316,
year = {2026},
author = {Rachmatika, R and Prijono, SN and Sarwono, KA and Pakpahan, S and Sari, AP and Maharani, S and Saputra, S and Fitri, A and Ridwan, R and Widodo, W and Nugraha, RTP and Handayani, W and Sjahfirdi, L},
title = {Comparative characterization of oral and cloacal microbiomes in captive adult and juvenile coconut lorikeets (Trichoglossus haematodus) using full-length 16S rRNA sequencing.},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {2117-2132},
pmid = {42344316},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: The coconut lorikeet (Trichoglossus haematodus) is a nectarivorous parrot species of conservation concern in Indonesia, where captive breeding programs are increasingly implemented to reduce pressure on wild populations. Dietary modifications in captivity may influence host-associated microbiota, which play a critical role in health, nutrition, and adaptation. This study aimed to characterize and compare the oral and cloacal microbiomes of adult and juvenile T. haematodus using full-length 16S rRNA sequencing to elucidate age- and site-specific microbial patterns.

MATERIALS AND METHODS: Six clinically healthy captive T. haematodus (three adults and three juveniles) were maintained under standardized environmental and dietary conditions. Oral and cloacal swabs were collected, yielding twelve samples, which were subsequently pooled into four groups: adult oral (AO), adult cloaca (AC), juvenile oral (JO), and juvenile cloaca (JC). DNA was extracted and subjected to full-length 16S rRNA sequencing using Oxford Nanopore Technology. Bioinformatic analyses included taxonomic classification, alpha diversity (Observed operational taxonomic unit (OTU), abundance-based coverage estimator (ACE), Simpson, Fisher)), and beta diversity (Venn diagram and principal coordinates analysis).

RESULTS: A total of 1859 bacterial species were identified across all groups. Microbial composition differed markedly by age and anatomical site. Cloacal samples in both adults and juveniles were dominated by Rosenbergiella, with higher abundance in adults (~42%) than juveniles (~24%). Oral microbiota showed greater diversity, with Alcaligenes predominating in adults and Psittacicella in juveniles. Alpha diversity indices indicated higher richness in juvenile cloacal and AO samples, whereas adult cloacal samples exhibited lower diversity. Beta diversity analysis demonstrated clear separation among groups, indicating distinct microbial community structures influenced by both age and sampling site. Core microbiota shared across groups were limited, with substantial unique operational taxonomic units in each category.

CONCLUSION: This study provides the first comprehensive characterization of oral and cloacal microbiomes in captive T. haematodus. Microbial diversity and composition are strongly influenced by age and anatomical location, with cloacal microbiota showing greater stability and oral microbiota reflecting dietary and developmental differences. The dominance of nectar-associated bacteria such as Rosenbergiella highlights the ecological linkage between host diet and microbiome. These findings offer valuable insights for optimizing captive nutrition, improving health monitoring, and supporting conservation strategies for nectarivorous parrots.},
}

@article {pmid42344332,
year = {2026},
author = {Karalyan, Z and Sedrakyan, A and Arakelova, K and Zakharyan, M and Hakobyan, S and Hakobyan, S and Avetisyan, A and Bayramyan, N and Arzumanyan, H and Gevorgyan, V and Vardanyan, T and Baghdasaryan, B and Karalyan, A and Hakobyan, L and Poghosyan, A and Abroyan, L and Karalova, E and Voskanyan, H and Semerjyan, Z and Arakelova, E and Avagyan, H},
title = {African swine fever virus alters soil microbial biomass and biodiversity: Evidence from experimental soil systems.},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {1984-1998},
pmid = {42344332},
issn = {0972-8988},
abstract = {BACKGROUND AND AIM: African swine fever virus (ASFV) has expanded beyond its traditional ecological niches, raising concerns not only for animal health but also for environmental sustainability. While extensive research has focused on its persistence and transmission, little is known about its ecological effects in soil systems. This study aimed to investigate the influence of ASFV on soil microbial biomass, biodiversity, and associated ecological parameters.

MATERIALS AND METHODS: Eighteen anthrosol soil samples collected from agricultural regions of Armenia were subjected to controlled experimental conditions. Soil samples were treated with active ASFV (aASFV), inactivated ASFV (iASFV), and mock controls. Physicochemical properties, including pH and moisture content, were assessed. Microbial biomass was evaluated through soil protein quantification and viral nucleic acid (DNA and RNA) measurements. Microbial diversity was analyzed by enumerating culturable bacteria and fungi using selective media. Dissolved oxygen levels were measured to assess microbial activity. Quantitative real-time polymerase chain reaction was employed to evaluate viral genome dynamics and transcriptional activity. Statistical analyses were performed to determine correlations among measured variables.

RESULTS: ASFV exposure resulted in a general reduction in total microbial biomass, as evidenced by decreased soil protein content and viral nucleic acid concentrations in most samples. In contrast, microbial diversity, particularly among bacterial and fungal populations, showed an increasing trend, suggesting a restructuring of the microbial community. Active ASFV induced greater changes compared to the inactivated virus. A significant positive correlation was observed between protein content and microbial indicators, while a negative correlation was noted between oxygen levels and nucleic acid content. Viral transcriptional activity was detected in selected samples, with no evidence of complete viral replication. Limited detection of giant viruses suggested potential but inconclusive ecological interactions.

CONCLUSION: ASFV alters soil ecosystems through complex, multidirectional effects, characterized by reduced biomass and increased microbial diversity. These findings indicate that ASFV may indirectly influence soil ecological processes, even in the absence of active replication. The study highlights the importance of incorporating environmental perspectives into ASFV research and provides a foundation for future investigations on virus-soil-microbiome interactions.},
}

@article {pmid42344333,
year = {2026},
author = {Montayeva, N and Nurgaliyev, B and Kereyev, A and Nagimova, G and Kushmukhanov, Z},
title = {One Health perspective on mycotoxins in poultry production: Ecology, toxicological effects, occupational and environmental exposure, food safety risks, and mitigation strategies (2020-2025).},
journal = {Veterinary world},
volume = {19},
number = {5},
pages = {2172-2207},
pmid = {42344333},
issn = {0972-8988},
abstract = {Mycotoxins produced by toxigenic fungi remain a major challenge in poultry production and global food safety. Contamination of poultry feed with aflatoxins, ochratoxin A, fumonisins, deoxynivalenol, T-2 toxin, zearalenone, and other emerging mycotoxins is frequently reported worldwide, particularly under intensive production systems and changing climatic conditions. This review summarizes current evidence published between 2020 and 2025 on the occurrence, ecological drivers, toxicological effects, environmental and occupational exposure, food safety risks, analytical detection methods, and mitigation strategies of mycotoxins in poultry production within a One Health framework. Recent studies indicate that multi-mycotoxin contamination is common in poultry feeds, and emerging and masked mycotoxins may remain undetected by routine analytical approaches, thereby increasing the risk of underestimating exposure. Mycotoxins adversely affect poultry health through hepatotoxicity, nephrotoxicity, oxidative stress, immunosuppression, intestinal barrier disruption, microbiome dysbiosis, impaired reproductive performance, and reduced productivity. In addition, residues of several mycotoxins have been detected in meat and eggs, raising concerns regarding consumer safety. Airborne fungal spores and contaminated dust in poultry houses also represent important occupational hazards for poultry workers. Advances in analytical technologies, particularly Liquid Chromatography-Tandem Mass Spectrometry, biosensors, molecular diagnostics, and multiplex detection systems, have improved the sensitivity and reliability of mycotoxin monitoring. Various mitigation approaches, including feed hygiene management, adsorbents, probiotics, biological detoxification, and enzymatic degradation, have shown potential to reduce contamination and minimize toxic effects. However, the complete elimination of mycotoxins remains difficult due to the complexity of fungal ecology and the widespread occurrence of co-contamination. Overall, this review highlights the importance of integrated surveillance, improved feed management, advanced detection systems, and coordinated mitigation strategies within a One Health approach to reduce the impact of mycotoxins on poultry health, environmental safety, occupational exposure, and food security.},
}

@article {pmid42344551,
year = {2026},
author = {Martínez-Hernández, JI and Villegas-Mercado, CE and Santana-Delgado, SA and Orozco-Molina, GG and Arreguín-Cano, JA and Ordóñez-Torres, K and Luján-Aguilar, MA and Duarte-Chávez, LI and González-Acosta, A and Casavantes-Lazo, C and Bujanda-Ríos, CI and Bermúdez, M},
title = {Clear aligner therapy beyond esthetics: oral health, polymer materials, and the environmental cost of digital orthodontics.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1810940},
pmid = {42344551},
issn = {2673-4915},
abstract = {Clear aligner therapy (CAT) has become a popular orthodontic option, driven by advances in digital workflows, increasing aesthetic demands, and perceived benefits in comfort and oral hygiene. Although its clinical effectiveness has been well documented, a thorough review of its biological and environmental effects remains incomplete. This narrative review consolidates current evidence on CAT, exploring their history, material makeup, impact on oral health, and emerging environmental concerns. Recent clinical and microbiological research indicates that CAT may improve plaque control and periodontal health compared with fixed appliances; however, these benefits are heavily influenced by patient behavior, baseline caries risk, treatment duration, and adherence to hygiene and dietary guidelines. Evidence shows that aligner materials can support bacterial and fungal biofilm growth and, under certain conditions, may lead to enamel demineralization or erosion, emphasizing the need for personalized risk assessments and proper aligner maintenance. From a materials standpoint, modern aligners are primarily made from thermoplastic and polyurethane polymers, designed to exert controlled orthodontic forces and ensure durability. While beneficial clinically, these materials are poorly degradable and have limited recyclability. Life cycle analyses reveal that the environmental impact of CAT extends beyond disposal to include polymer production, energy-intensive manufacturing, packaging, and distribution. Additionally, emerging research suggests that aligners may release microplastics during use, adding to concerns about plastic pollution beyond solid waste. Given the rapid growth of the global clear aligner market, even small amounts of material per patient can result in a significant environmental impact. Overall, the evidence indicates that clear aligner therapy involves a complex interplay among biomechanics, patient care, materials science, and environmental sustainability. An integrated, life-cycle-based strategy is crucial to guiding clinicians, researchers, and manufacturers toward treatments that are both effective and environmentally responsible.},
}

@article {pmid42344668,
year = {2026},
author = {Huang, F and Zhang, Z and Zhao, Y and Ye, S and Gan, M and Li, X and Zhang, Y and Chen, L and Zhang, Y and Chen, L and Wang, T and Huang, J and Zhang, X},
title = {Altitude-Associated Divergence of the Gut Microbiome in Endangered Forest Musk Deer: Evidence From Integrated Metagenomics, Metabolomics, and Culturomics.},
journal = {Evolutionary applications},
volume = {19},
number = {6},
pages = {e70285},
pmid = {42344668},
issn = {1752-4571},
abstract = {High-altitude environments expose mammals and their gut symbionts to multifaceted stressors-hypoxia, cold, and intense UV radiation. Whether gut microbial communities undergo compositional restructuring in response to these stressors, and whether such restructuring carries translational value for captive conservation, remain unresolved questions. Here, we integrated deep shotgun metagenomics (≥ 15 Gb per sample), untargeted fecal metabolomics, and culturomics in 75 captive forest musk deer (Moschus berezovskii Flerov, 1929) housed at high altitude (~3900 m) and low altitude (~1450 m) facilities under uniform husbandry. Neutral community modeling showed a greater contribution of deterministic processes at high altitude (only 34.3% of species conformed to neutral expectations vs. 89.3% at low altitude), consistent with stronger environmental filtering. At high altitude, we observed enrichment of a functionally coherent guild of short-chain fatty acid (SCFA)-producing bacteria-centered on Flavonifractor plautii, Intestinimonas butyriciproducens, and Enterococcus faecium-that formed antagonistic co-occurrence networks with opportunistic pathogens including Clostridioides difficile and Campylobacter species, mirroring SCFA enrichment in phylogenetically diverse high-altitude mammals. Fecal metabolomics revealed coordinated shifts in urolithin biosynthesis, branch-specific regulation of the tryptophan-kynurenine pathway, and energy metabolism remodeling, all robustly predicted by microbiome composition via neural network modeling. Culturomics yielded seven safety-validated isolates with confirmed gastrointestinal stress tolerance and broad-spectrum pathogen-antagonistic activity in vitro. These findings provide an actionable framework for altitude-informed facility siting, fecal microbiota transplantation (FMT) donor selection, host-derived probiotic development, and non-invasive health surveillance in captive endangered species, and are broadly transferable to other taxa facing microbiome-associated disease pressure in captivity.},
}

@article {pmid42344726,
year = {2026},
author = {Khanna, V and Kumar, S and Kumar, S and Verma, S and Grigoriadis, A and Kumar, A},
title = {The gut microbiome in oral health and disease: evidence toward bidirectional oral-gut axis communication.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1817689},
pmid = {42344726},
issn = {1664-302X},
abstract = {The oral-gut microbiome axis has largely been seen as a unidirectional framework, in which dysbiotic oral flora is considered to contribute to gastrointestinal and systemic disease. However, recent evidence now challenges this view, indicating that gut microbial imbalance can act upstream to modulate oral immune homeostasis and disease susceptibility. Therefore, in the current perspective paper, we present a structured narrative review that synthesizes recent evidence from human microbiome, immunological, and genetic studies to propose a hypothetical mechanistic model in which gut dysbiosis may contribute to oral pathology. The literature discussed was identified through a targeted keyword-based search of major databases and complemented by manual screening of reference lists to capture relevant studies. Analyzing the evidence from human case-control and longitudinal cohort studies, as well as Mendelian randomization analysis, we identify convergent pathways linking gut dysbiosis to oral disease. These include systemic immune priming in autoimmune disorders with oral manifestations, depletion of gut-derived metabolites, such as short-chain fatty acids, that regulate epithelial barrier function and inflammation, and dysbiosis-associated barrier disruption that facilitates the systemic dissemination of microbial products and inflammatory mediators. Through these mechanisms, gut microbial imbalance contributes to chronic inflammatory conditions, altering host response and susceptibility to dental and mucosal diseases. In contrast, studies in healthy individuals show minimal oral-gut microbial overlap, supporting a model in which physiological compartmentalization is maintained in health and disrupted primarily under dysbiotic conditions. This synthesis reframes oral disease as host-microbiome dysregulation, highlighting gut microbiota as a driver of oral immune pathology.},
}

@article {pmid42344729,
year = {2026},
author = {Qian, X and Wu, Y and Wang, W and Shao, H and Xu, Z},
title = {The selection of matching donors for patients in fecal microbiota transplantation.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1859411},
pmid = {42344729},
issn = {1664-302X},
abstract = {Fecal microbiota transplantation (FMT) is an emerging therapeutic strategy with potential applications in the treatment of various diseases, particularly those associated with gut microbiome dysbiosis. However, clinical trials have demonstrated considerable variability in FMT efficacy-even among patients with the same disease. The heterogeneity of gut microbiota from donors is considered a key factor influencing patient outcomes. Consequently, the development of donor-recipient matching models has emerged as an advanced approach to enhance the effectiveness of FMT. As a practical clinical intervention, the therapeutic impact of FMT on specific diseases requires further investigation. This article reviews the development of donors and the matching patterns between donors and recipients, and summarizes the key factors influencing the transfer of the microbiota. It provides new insights for exploring novel and effective donor-recipient matching patterns.},
}

@article {pmid42344732,
year = {2026},
author = {Zapata-Contreras, D and Aldridge, J and González-Puelma, J and Navarrete, M and Urrea, C and Orellana, F and Iriarte, MJ and Delgado, C and Puente, M and Leiva, L and Godoy, L and Altamirano, A and Karelovic, S and Espinosa-Parrilla, Y},
title = {Microbial dynamics in gastric cancer: insights from full-length 16S rRNA nanopore sequencing in the MAGIC cohort.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841026},
pmid = {42344732},
issn = {1664-302X},
abstract = {Gastric dysbiosis, characterized by shifts in the microbial composition, has been increasingly associated with the development of gastric cancer, the fifth leading cause of cancer-related deaths worldwide and the second in Chile, yet its characterization through disease stages remains limited and its study in Latin American populations almost non-existent. While Helicobacter pylori is a well-established risk factor, recent evidence supports the involvement of non-Helicobacter pylori bacteria associated with disease progression, emphasizing the need to characterize the gastric microbiome in diverse populations and through cancer stages. In this study, 162 endoscopic biopsy tissues and gastrectomy tissues from 83 Chilean individuals enrolled in the Magellanic gastric cohort MAGIC and the BTUCH cohort were analyzed using high throughput full-length 16S rRNA sequencing based on Nanopore technology. Diversity analysis demonstrated significant differences among disease progression and histological subtypes. Spearman correlation identified 34 genera significantly associated with gastric cancer progression, including enrichment of Lactobacillus and Limosilactobacillus. Helicobacter stratification analysis revealed lower diversity and distinct community structure at early stages of disease. Declining Helicobacter abundance was associated with shifts toward degradation and biosynthetic/energy metabolism pathways suggesting potential metabolic adaptation in carcinogenesis. These findings reveal stage-specific restructuring of the gastric microbiota along disease progression and identify non-Helicobacter taxa as part of microbial signatures associated with different stages of gastric carcinogenesis.},
}

@article {pmid42344797,
year = {2026},
author = {Zhang, M and Lu, Y and Yuan, X},
title = {The tumor microenvironment: a dynamic ecosystem and therapeutic nexus in modern oncology.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1836055},
pmid = {42344797},
issn = {1663-9812},
abstract = {The tumor microenvironment (TME) has emerged as a central orchestrator of carcinogenesis, therapeutic resistance, and immune evasion, fundamentally reshaping the understanding of cancer as an ecosystem disease rather than a cell-autonomous genetic disorder. This review synthesizes contemporary advances in deconstructing the cellular and acellular architecture of the TME, encompassing cancer-associated fibroblasts, tumor-associated macrophages, aberrant vasculature, and a dynamically remodeled extracellular matrix. The molecular underpinnings of TME-mediated pathogenesis are critically evaluated, including metabolic reprogramming, epigenetic dysregulation, and systemic microbiome crosstalk, which collectively enforce immunosuppression and drive adaptive resistance. Building on this mechanistic framework, a new generation of therapeutic strategies designed to reprogram this malignant niche is highlighted: precision nanotechnologies for targeted and stimuli-responsive delivery; next-generation immunotherapies such as logic-gated CAR-T cells, bispecific engagers, and oncolytic viruses; metabolic and epigenetic modulators; stromal and vascular normalization approaches; and microbiome-based interventions, for instance fecal microbiota transplantation and defined bacterial consortia. Transformative tools, including patient-derived organoids, tumor-on-a-chip systems, 3D bioprinting, and artificial intelligence-powered multi-omics, are now enabling predictive modeling and personalized therapeutic forecasting. Despite persistent challenges posed by intratumoral heterogeneity, cellular plasticity, and the complexity of combination trial design, the convergence of these multidisciplinary approaches provides an unprecedented toolkit to durably reprogram the TME. Mastering this dynamic ecosystem is paramount to overcoming therapeutic roadblocks, and the strategic integration of these advances heralds a definitive paradigm shift toward TME-centric, adaptive, and personalized cancer therapy.},
}

@article {pmid42345017,
year = {2026},
author = {Bautista, J and Calderón-Cevallos, S and Salvador-Baquero, AM and Naranjo-Castillo, X and López-Cortés, A},
title = {Programming the tumor microenvironment through microbiome-driven mechanisms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1857151},
pmid = {42345017},
issn = {2235-2988},
mesh = {Humans ; *Tumor Microenvironment/immunology ; *Microbiota/immunology ; *Neoplasms/immunology/microbiology/pathology ; Animals ; Signal Transduction ; Toll-Like Receptors/metabolism ; Multiomics ; Fatty Acids, Volatile/metabolism ; Lipopolysaccharides/metabolism ; },
abstract = {The tumor microenvironment (TME) comprises interacting immune, stromal, and metabolic compartments that determine tumor behavior and treatment response. Microbial communities modulate host signaling within the TME through metabolite-driven and receptor-mediated mechanisms. Lipopolysaccharides (LPS), short-chain fatty acids (SCFAs), bile acids, and amino acid-derived metabolites engage host receptors, including Toll-like receptors, G protein-coupled receptors, and aryl hydrocarbon receptor pathways, to regulate immune cell differentiation, antigen presentation, and metabolic adaptation. These microbiome-derived signals promote context-dependent immune suppression or immune activation according to metabolite concentration, receptor engagement, and immune cell composition, thereby influencing tumor progression and immune evasion. Host-driven inflammation and metabolic constraints reshape microbial composition and function within tumor-associated niches. Microbiome-associated mechanisms contribute to tumor initiation, progression, and therapeutic response through modulation of immune checkpoint activity and drug metabolism. Major limitations include reliance on associative human data, methodological variability across sequencing approaches, contamination in low-biomass samples, and incomplete integration of multi-omics datasets. Clinical translation requires mechanistic validation, longitudinal study designs, and standardized analytical frameworks to define reproducible microbiome-associated signatures.},
}

Humans
*Tumor Microenvironment/immunology
*Microbiota/immunology
*Neoplasms/immunology/microbiology/pathology
Animals
Signal Transduction
Toll-Like Receptors/metabolism
Multiomics
Fatty Acids, Volatile/metabolism
Lipopolysaccharides/metabolism

@article {pmid42345020,
year = {2026},
author = {Ismaiel, A and Almonajjed, MB and Wardeh, M and Abdelghafar, A and Popa, SL and Sabo, C and Dumitrascu, DL},
title = {From dysbiosis to malignancy: decoding gut-driven pathways to clinical management in hepatocellular carcinoma.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1852380},
pmid = {42345020},
issn = {2235-2988},
mesh = {Humans ; *Dysbiosis/complications ; *Liver Neoplasms/therapy/etiology/pathology/microbiology ; *Carcinoma, Hepatocellular/therapy/etiology/pathology/microbiology ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Hepatocellular carcinoma (HCC) is undergoing a profound global epidemiological shift, transitioning from viral-driven etiologies to metabolic dysfunction-associated steatotic liver disease (MASLD). This transition challenges traditional cirrhosis-centric surveillance, as a significant proportion of MASLD-HCC develops in non-cirrhotic livers. Parallel to these metabolic shifts, the gut-liver axis has emerged as a central orchestrator of hepatocarcinogenesis. This review decodes the complex gut-driven pathways fueling HCC, highlighting the oncogenic consequences of structural and functional dysbiosis. Dietary patterns and etiology-specific microbial shifts compromise the intestinal and gut-vascular barriers, precipitating a structural "leaky gut". This disruption facilitates the robust translocation of pathogen-associated molecular patterns (PAMPs), particularly lipopolysaccharide (LPS), and toxic microbial metabolites like secondary bile acids, specifically deoxycholic acid, into the portal circulation. Consequently, hepatic innate immunity is chronically activated via Toll-like receptor 4 (TLR4) signaling on Kupffer and hepatic stellate cells, fostering metainflammation, cellular senescence, genomic instability, and a highly immunosuppressive, pro-tumorigenic microenvironment. Furthermore, the depletion of keystone commensals diminishes the protective reservoir of short-chain fatty acids (SCFAs), exacerbating oncogene activation. Translating these mechanistic insights into the clinic, we explore the utility of distinct microbial signatures and metabolomic profiles as non-invasive diagnostic biomarkers. Such tools are urgently needed to bridge the early-detection gap in the expanding MASLD demographic. Finally, we discuss the pivotal role of the microbiome in modulating responses to immune checkpoint inhibitors (ICIs), notably through immune-stimulating taxa like Akkermansia muciniphila, and outline emerging gut-targeted therapies, including next-generation probiotics and fecal microbiota transplantation, aimed at restoring host-microbiome homeostasis to prevent and manage HCC. By decoding these gut-driven pathways, this review provides a comprehensive framework for integrating the microbiome-onco axis into precision oncology, offering novel avenues to combat the rising global burden of hepatocellular carcinoma.},
}

Humans
*Dysbiosis/complications
*Liver Neoplasms/therapy/etiology/pathology/microbiology
*Carcinoma, Hepatocellular/therapy/etiology/pathology/microbiology
*Gastrointestinal Microbiome
Animals

@article {pmid42345222,
year = {2026},
author = {Yuan, J and Liu, M and He, Z and Li, H and Ma, L and Zhang, Q and Yin, Z and Guo, P and Yin, H},
title = {Fictibacillus tiangongensis sp. nov., isolated from the China Space Station.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {6},
pages = {},
doi = {10.1099/ijsem.0.007216},
pmid = {42345222},
issn = {1466-5034},
mesh = {China ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; Base Composition ; *Bacillaceae/classification/isolation & purification/genetics ; Nucleic Acid Hybridization ; *Spacecraft ; Peptidoglycan/chemistry ; Vitamin K 2/analogs & derivatives/chemistry/analysis ; Extreme Environments ; },
abstract = {The identification of novel microbial species in extreme environments significantly enhances our comprehension of Earth's biodiversity and concurrently offers invaluable resources and critical insights for scientific research, biotechnological innovation and environmental conservation. As part of the China Space Station Habitation Area Microbiome Program (CHAMP), a Gram-positive, facultatively anaerobic, motile, spore-forming, rod-shaped strain, designated JL2B1089[T], was isolated from the surface of hardware within the genus Fictibacillus. The strain grows optimally at 30-37 °C and pH 7-8 with 0-2.0% (w/v) NaCl. Phylogenetic analyses based on the genomic data revealed that JL2B1089[T] is closely related to Fictibacillus phosphorivorans Ca7[T], with average nucleotide identity and digital DNA-DNA hybridization values of 90.0 and 40.6%, respectively; both values are below the recommended thresholds for species delineation. Chemotaxonomic characteristics, including the major cellular fatty acids iso-C15:0 and anteiso-C15:0, the predominant menaquinone-7 and a cell-wall peptidoglycan containing meso-diaminopimelic acid, are consistent with those of the closely related taxa F. phosphorivorans Ca7[T] and Fictibacillus halophilus AS8[T]. Additionally, strain JL2B1089[T] shows specificity in utilizing certain substrates, such as amino acids and carboxylic acids. Pan-genome analysis and divergence analysis of the bacillithiol biosynthesis deacetylase (BshB1) protein suggest that this strain may adapt to the space environment through mechanisms involved in coping with cell morphological alterations, osmotic fluctuations and oxidative damage under microgravity conditions. Based on phenotypic, chemotaxonomic and genomic characteristics, strain JL2B1089[T] represents a novel species within the genus Fictibacillus, for which the name Fictibacillus tiangongensis sp. nov. is proposed. The type strain is JL2B1089[T] (=GDMCC 1.4870[T]=KCTC 43746[T]).},
}

China
*Phylogeny
RNA, Ribosomal, 16S/genetics
Fatty Acids/chemistry
DNA, Bacterial/genetics
Bacterial Typing Techniques
Sequence Analysis, DNA
Base Composition
*Bacillaceae/classification/isolation & purification/genetics
Nucleic Acid Hybridization
*Spacecraft
Peptidoglycan/chemistry
Vitamin K 2/analogs & derivatives/chemistry/analysis
Extreme Environments

@article {pmid42345379,
year = {2026},
author = {Goyal, M and Sandhu, NK},
title = {Lactase Deficiency in 2026: Understanding Pathophysiology, Global Persistence Trends, and Targeted Therapies for Lactose Intolerance.},
journal = {Journal of the American Nutrition Association},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/27697061.2026.2688511},
pmid = {42345379},
issn = {2769-707X},
abstract = {Lactose intolerance is a common digestive disorder found in many people around the world. It occurs when the body does not produce enough of the enzyme lactase needed to break down lactose, a type of sugar. Lactose is present in almost all mammal milk products, and for infants, this sugar is important for providing energy during their growth. There are many variations of adults with lactase persistence around the world; for example, in Nordic countries, more than 90% of adults produce lactase into adulthood, but in Southeast Asia, only around 10% of adults do so. Overall, about one-third of all adults can digest dairy products; however, many people believe that there will be negative side effects if they eat or drink dairy products. This leads to a restriction of dairy products that can hurt the body's ability to grow and get enough nutrients because dairy products contain many essential nutrient sources (protein, vitamins, minerals). About 68% of the world population is affected by lactose intolerance, but that figure has not changed much in the past decade. However, there are vast regional variations (5-28% in Europe and 70-98% in Asia and Africa). The therapeutic market, including enzyme supplements, probiotics, and dietary aids applicable in all of the severity stages of the condition, is estimated to be valued at $ 36.96 billion in 2026, which represents a 7.4% compound annual growth rate; to reach $ 49.13 billion in 2030 due to the creation of personalized interventions and dairy substitutes.},
}

@article {pmid42345435,
year = {2026},
author = {Low, WK},
title = {The Gut Microbiome May Play a Role in the Pathogenesis of Meniere's Disease.},
journal = {The journal of international advanced otology},
volume = {22},
number = {2},
pages = {1-8},
doi = {10.65717/iao.2026.262424},
pmid = {42345435},
issn = {2148-3817},
mesh = {Humans ; *Meniere Disease/microbiology/etiology/immunology/physiopathology ; *Gastrointestinal Microbiome/physiology/immunology ; Ear, Inner ; Animals ; Dysbiosis/complications ; },
abstract = {Meniere's disease (MD) was first described 650 years ago. It is now considered to be a multifactorial disorder involving immunological mechanisms, blood-labyrinth barrier breakdown, endolymphatic hydrops, vascular compromise, and genetic susceptibility. Chronic inflammation from both innate and adaptive immunity is evident in the inner ear, with autoimmunity and allergy possibly playing a role. Despite its long history, significant knowledge gaps in its pathogenesis remain. For example, there may be root causes from elsewhere that are contributing to these pathological processes occurring in the inner ear. In recent years, rapid progress has been made in research on the contributions of gut microbiome to human health and disease. In particular, changes in gut microbiome have been found to be associated with many disorders of the brain. The brain and the inner ear share similar vascular networks that create a physical barrier to limit paracellular diffusion. Emerging evidence shows gut dysbiosis can potentially result in sensori-neural hearing loss. Early evidence suggests changes in gut microbiome may be associated with MD, possibly via dysregulation of the arginine vasopressin/vasopressin type 2 receptor/aquaporin-2 (AVP-V2R-AQP2) signaling pathway in the inner ear from increased brain secretion of AVP. It remains to be seen if the belief that gut dysbiosis contributes to the pathogenesis of MD can be substantiated by future research. If so, addressing gut issues may prove to be an important strategy in the overall management of MD.},
}

Humans
*Meniere Disease/microbiology/etiology/immunology/physiopathology
*Gastrointestinal Microbiome/physiology/immunology
Ear, Inner
Animals
Dysbiosis/complications

@article {pmid42345569,
year = {2026},
author = {Guigard, L and Bal, V and Bintarti, AF and Buron, M and Chavan, E and Gonzalo, M and Liu, X and Zheng, W and Shade, A},
title = {From dividing to dormant: embracing the full activity spectrum for environmental microorganisms.},
journal = {Microbiology and molecular biology reviews : MMBR},
volume = {},
number = {},
pages = {e0035425},
doi = {10.1128/mmbr.00354-25},
pmid = {42345569},
issn = {1098-5557},
abstract = {SUMMARYMicroorganisms can cope with stress by entering dormancy, a viable state of reduced metabolic activity that enables persistence, dispersal, and long-term survival. However, microbial life in environmental systems is best understood as a spectrum of metabolic activity, spanning from highly active, dividing cells to deeply dormant phenotypes. This spectrum reflects dynamic survival strategies under fluctuating conditions, with critical implications for ecosystem stability, gene dissemination, and resilience to disturbances in natural and human-influenced systems. Yet, microbial activity is often treated as binary (active vs. dormant), oversimplifying a biological continuity that remains technically difficult to quantify. Here, we synthesize advances in microbial dormancy to reconceptualize activity as a spectrum. We review current and emerging methods to quantify environmental activity, linking each to the Central Dogma of molecular biology (DNA to RNA to protein) to guide interpretation along a generalizable continuum. Through a literature synthesis of terrestrial, aquatic, and wastewater treatment ecosystems, we compare how methods estimate active cells and populations. We recommend standardized reporting of total community size, active cell abundance, and proportional activity to enrich the interpretation of microbiome 'omics data, with activity intensity and active-inactive switching providing deeper insights. To achieve this, we advocate for increased accessibility and throughput of precise activity-discriminating technologies, alongside renewed use of reliable methods like direct cell counts and activity stains. Adopting this spectrum-based perspective will improve our ability to tackle key societal challenges, such as understanding microbial contributions to ecosystem function under climate change and gene dispersal at human-environment interfaces.},
}

@article {pmid42345642,
year = {2026},
author = {Ciesielska-Markowska, I and Mycroft-Rzeszotarska, K and Korczyński, P and Pulik, K and Górska, K},
title = {Characteristics of Respiratory Microbiome in COPD-A Literature Review.},
journal = {Advances in respiratory medicine},
volume = {94},
number = {3},
pages = {},
pmid = {42345642},
issn = {2543-6031},
support = {2019/35/B/NZ5/00694//National Science Centre/ ; },
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology ; *Microbiota ; *Respiratory System/microbiology ; },
abstract = {Chronic obstructive pulmonary disease (COPD) is a respiratory disease that progressively impairs airway function. Its aetiology and clinical presentation are very complex, resulting in an unpredictable course of the disease. The most important causes include smoking and environmental pollutants. However, upper airway microbiome dysbiosis has been linked with COPD severity. Through this review, we aim to compare the microbiome of the respiratory tract between its sites, and to see if there are any significant differences in the composition of the microbial flora of patients with COPD when compared to healthy individuals. While preparing this review, the PubMed database was searched using keywords such as bacteriome, COPD, exacerbation, and microbiome. Analysis of the airway microbiome shows that the three most abundant phyla are Firmicutes, Proteobacteria, and Bacteroidetes. The severity of the disease and the selected therapeutic methods influence the ratio of Proteobacteria and Firmicutes. It has been observed that a decrease in microbial diversity resulted in lower values of FEV1 in patients and could be related with COPD's progress and exacerbation events. While exacerbation cases need quick treatment, COPD's complex background makes it difficult to find a singular, microbial cause.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology
*Microbiota
*Respiratory System/microbiology

@article {pmid42345647,
year = {2026},
author = {Czyżak, B and Lasota, A and Majewski, S},
title = {Acute Exacerbation of Interstitial Lung Disease: A Case Series and a Narrative Literature Review.},
journal = {Advances in respiratory medicine},
volume = {94},
number = {3},
pages = {},
pmid = {42345647},
issn = {2543-6031},
mesh = {Humans ; *Lung Diseases, Interstitial/physiopathology/therapy/drug therapy ; Disease Progression ; Female ; Male ; Aged ; Middle Aged ; Idiopathic Pulmonary Fibrosis ; Risk Factors ; },
abstract = {Acute exacerbation of interstitial lung disease (AE-ILD) represents sudden, severe deterioration in patients with pre-existing ILD and is associated with high morbidity and mortality. Our work presents a case series of AE-ILD in patients with idiopathic pulmonary fibrosis (IPF), idiopathic non-specific interstitial pneumonia (iNSIP), and connective tissue disease-associated ILD (CTD-ILD) managed at our institution and provides a narrative review of AE-ILD. Across cases, AE-ILD manifested as rapid progression of dyspnea and extensive ground-glass opacities (GGOs) on imaging, often triggered by infections or immune-mediated processes. Despite treatment, all cases were fatal, confirming that mortality remains high in AE-ILD. In our literature review, we focus on dysregulated innate immunity, an altered microbiome, potential microaspiration, surgical procedures, and autoantibody-mediated inflammation as triggers, as well as the risk factors for and prevalence of AE-ILD. We also examine pharmacological and non-pharmacological interventions, with particular emphasis on the role of antifibrotic agents as a key protective factor. Evidence for and against corticosteroid use in AE-IPF and non-IPF AE-ILD is discussed, highlighting the radically different treatment approach for AE in melanoma differentiation-associated gene 5 (MDA5)-positive dermatomyositis (DM)-associated ILD compared to AE-IPF. Our findings underscore the heterogeneous presentation and poor prognosis of AE-ILD, emphasizing the urgent need for standardized diagnostic criteria, risk stratification, and prospective studies with larger cohorts to establish evidence-based therapeutic strategies.},
}

Humans
*Lung Diseases, Interstitial/physiopathology/therapy/drug therapy
Disease Progression
Female
Male
Aged
Middle Aged
Idiopathic Pulmonary Fibrosis
Risk Factors

@article {pmid42345774,
year = {2026},
author = {Giannoulis, T and Dovolou, E and Mamuris, Z and Amiridis, GS},
title = {Consequences of Heat Stress on Physiology, Microbiome Dynamics, and Multi-Omics in Dairy Cows: More than Meets the Eye.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345774},
issn = {2079-7737},
abstract = {Heat stress (HS) is at the top of the challenges facing modern dairy production, with annual losses according to global projections, under high-emission scenarios, reaching US$14.7-40.0 billion by the end of the century. This review emphasizes three interconnected topics that account for most of the proportion of the productive and reproductive losses during HS. First, the physiological consequences of HS are reviewed, with emphasis on the pair-fed thermal neutral (PFTN) paradigm, which established that reduced dry matter intake (DMI) accounts for only 35-50% of the observed milk yield decline, with the remainder arising from tissue-level effects of hyperthermia on mammary function, metabolism, and reproductive performance. Second, HS-induced microbiome disruption is examined as an active pathophysiological amplifier, whereby rumen dysbiosis compromises intestinal barrier integrity and drives systemic endotoxaemia, chronically amplifying the immune suppression already imposed by the thermal insult. Third, we focus on the integration of multi-omics platforms as a management approach, since single-omics analyses capture only a fraction of the biological complexity underlying the HS response. As the available datasets expand in coverage and scale, their integration through AI-driven analytical frameworks has the potential to substantially advance beyond the current fragmented picture, progressively building toward a systems-level model of thermal stress. Evidence-based mitigation strategies spanning environmental cooling, targeted nutritional supplementation, and genomic selection are critically evaluated within this framework, with emphasis on equity of access to evidence-based solutions across global dairy production systems.},
}

@article {pmid42345816,
year = {2026},
author = {Do, HT and Bhunyakarnjanarat, T and Dityen, K and Kaewopas, Y and Thammachareonrach, N and Paiboonkasarp, S and Jaroonwitchawan, T and Boonyasuppayakorn, S and Chancharoenthana, W and Leelahavanichkul, A},
title = {Abdominal Symptoms During the Febrile Phase Indicate Profound Innate Immune Responses in Dengue.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345816},
issn = {2079-7737},
support = {B48G6600112//the NSRF via the Program Management Unit for Human Resources & Institutional Development, Research and Innovation/ ; RA-MF-02/67//Rachadapisek Sompote Matching Fund/ ; RA-MF-01/68//Rachadapisek Sompote Matching Fund/ ; },
abstract = {Gastrointestinal symptoms (GI) (abdominal pain, vomiting, and diarrhea) during the febrile phase of dengue (less than 5 days from fever onset) might indicate prominent innate immune responses. Serum and feces samples from cases with GI symptoms versus those without GI symptoms (n = 20 per group) were analyzed. From these, only the neutrophil extracellular traps (NETs), serum fibroblast growth factor (FGF) 21, and fecal microbiome analyses, but not the routine parameters, endotoxemia, or serum cytokines, were higher in the GI cases than in the non-GI cases. From the in vitro experiments, both lipopolysaccharide (LPS) and the dengue virus (DENV) upregulated the FGF receptor 1 (FGFR1) and cytokines in hepatocytes (HepG2) and THP-1-differentiated macrophages. Meanwhile, LPS and DENV induced NETs in isolated neutrophils from healthy volunteers. Only the starvation protocol, but not LPS or DENV, enhanced supernatant FGF-21 from hepatocytes. Incubation of recombinant FGF-21 in LPS + DENV-activated cells (hepatocytes, macrophages, and neutrophils) attenuated inflammation, as determined by supernatant cytokines and NETs. Hence, abdominal symptoms in dengue during the febrile phase indicate prominent innate immune responses, as detected by NETs and FGF-21 (an acute-phase protein), implying significant hepatic stress with a possible counteracting anti-inflammation.},
}

@article {pmid42345817,
year = {2026},
author = {Stefan, G and Gurau, MR and Ciocîrlie, N and Tudor, L and Bărăităreanu, S and Tache-Codreanu, DL and Sporea, C and Gligor, A and Iancu, I and Herman, V},
title = {Horizontal Gene Transfer in Listeria monocytogenes: Evolution of Antimicrobial Resistance and Virulence in a One Health Context.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345817},
issn = {2079-7737},
abstract = {Listeria monocytogenes is a ubiquitous Gram-positive bacterium responsible for listeriosis, a foodborne zoonotic disease affecting humans and animals. Although infection in immunocompetent individuals is often asymptomatic or limited to mild self-limiting gastroenteritis, Listeria monocytogenes may cause severe invasive disease in vulnerable groups, including pregnant women, neonates, elderly individuals, and immunocompromised patients. Although the incidence of listeriosis is relatively low compared with many other foodborne pathogens, the high hospitalization and mortality rates associated with clinical cases make this bacterium a major concern for food safety and public health. The evolutionary success of L. monocytogenes reflects the interaction between a conserved core genome and a dynamic accessory genome shaped by horizontal gene transfer (HGT), ecological selection, and expansion of specific clones. Transient intestinal carriage in humans and animals, potentially influenced by gut microbiome composition, creates ecological interfaces where plasmids, transposons, prophages, and integrative conjugative elements contribute to the exchange of antimicrobial resistance determinants, virulence factors, and stress tolerance systems. Virulence diversification is further influenced by the differential distribution of pathogenicity islands such as LIPI-1, LIPI-3, and LIPI-4 across specific clonal lineages. These evolutionary processes occur across interconnected farm, food-production, environmental, and clinical ecosystems consistent with the One Health framework. Advances in whole-genome sequencing have clarified lineage-specific gene flow, expansion of specific clones, and the dynamics of the resistome and mobilome in L. monocytogenes populations. This narrative review aims to synthesize current knowledge on the mobile genetic elements and ecological interfaces that shape horizontal gene transfer in L. monocytogenes. Its novelty lies in integrating antimicrobial resistance, virulence-associated genomic islands, stress adaptation, and gut microbiome-mediated selection within a One Health and metapopulation framework. The main message of this review is that HGT should be interpreted as a context-dependent contributor to L. monocytogenes adaptation, acting together with clonal background, ecological selection, and mobile genetic elements.},
}

@article {pmid42345819,
year = {2026},
author = {Thingujam, D and Malacrinò, A and Pajerowska-Mukhtar, KM and Mukhtar, MS},
title = {Molecular, Microbial, and Ecological Drivers of Duckweed Phytoremediation in Aquatic Environments.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345819},
issn = {2079-7737},
support = {IOS-2038872//U.S. National Science Foundation/ ; OIA-2418230//U.S. National Science Foundation/ ; },
abstract = {Aquatic ecosystems are under severe stress from a diverse combination of contaminants, including heavy metals, pesticides, pharmaceuticals, and microplastics, driven by rapid industrialization, intensive agriculture, and urbanization. Globally, 80% of wastewater remains untreated, and conventional systems often fail to address emerging contaminants. Consequently, toxic heavy metals like lead and mercury can persist in water sources for decades. In response, phytoremediation has emerged as a scalable, eco-friendly, nature-based alternative. Among phytoremediation agents, duckweeds are increasingly recognized for their rapid growth, simple morphology, and continuous water-column contact. This review outlines the landscape of duckweed-based remediation, detailing molecular detoxification pathways and the synergistic role of associated microbiomes in enhancing environmental cleanup. Evidence indicates that contaminant removal is often supported by plant-microbe interactions. Despite extensive laboratory validation, field-scale implementation remains constrained by environmental complexity, pollutant mixtures, and variable climatic conditions. Furthermore, while duckweed systems hold promise within circular bioeconomy frameworks, converting wastewater into nutrient-rich biomass, contaminant accumulation in plant tissues raises concerns about biomass utilization and contaminant carryover. Addressing these challenges requires an integrative approach that links molecular detoxification, ecological interactions, and engineered system design to realize the full potential of duckweeds for sustainable aquatic pollution management.},
}

@article {pmid42345832,
year = {2026},
author = {Konwar, B and Kim, KS},
title = {The Programmable Microbiome: Integrative AI and Multi-Omics Frameworks for Precision T2DM Management.},
journal = {Biology},
volume = {15},
number = {12},
pages = {},
pmid = {42345832},
issn = {2079-7737},
abstract = {The gut microbiota is recognized as a programmable metabolic organ that governs systemic homeostasis. Recent advances (2023-2025) have pivoted Type 2 Diabetes Mellitus (T2DM) research from a host-centric perspective toward a failure of bidirectional host-microbe metabolic flux. This review evaluates the molecular mechanisms underpinning this shift, focusing on microbial metabolite signaling, virome-mediated modulation, and the emergence of drug-microbiome interactions as critical therapeutic variables. We highlight the transformative role of AI-guided mapping and digital twin simulations in modeling high-resolution metabolic flux and predicting the stability of engineered microbial consortia. By integrating meta-transcriptomics and epigenomics, we characterize the functional plasticity of the microbiome under therapeutic stress. We argue that framing the microbiota as a programmable infrastructure-integrated with AI analytics and metabolic engineering-enables adaptive, real-time interventions. This synthesis offers a blueprint for transitioning from correlative observations toward precision microbiome engineering to achieve sustained metabolic resilience.},
}

@article {pmid42345977,
year = {2026},
author = {Enax, J and Schulze Zur Wiesche, E and Epple, M},
title = {Tooth Enamel Demineralization: Caries and Erosion from the Viewpoint of Chemistry.},
journal = {Dentistry journal},
volume = {14},
number = {6},
pages = {},
pmid = {42345977},
issn = {2304-6767},
abstract = {The demineralization of tooth enamel is the primary consequence of dental caries, leading to cavities and finally tooth loss. Erosive tooth wear from acidic beverages and food is another factor that degrades enamel. In both cases, an acidic environment leads to etching and the final dissolution of tooth mineral, i.e., hydroxyapatite. Here, this process is discussed from a chemical perspective, taking into account the solubility of calcium phosphate and the presence of the pellicle (protein layer) and plaque (bacterial biofilms), which both affect the dissolution rate. While low pH is definitely decisive, calcium-binding ligands (e.g., acid anions, proteins) contribute to dissolution by removing calcium ions from the equilibrium. This is an important effect in the oral cavity where the concentration of biomolecules is high. The situation is complicated by the fact that the composition of saliva and the oral microbiome vary considerably between individuals. The state of current knowledge on the demineralization of enamel is summarized and discussed, also in the context of approaches to prevent dental caries and erosive tooth wear.},
}

@article {pmid42346015,
year = {2026},
author = {Habtemariam, S},
title = {The Gut Microbiome Dependency Continuum in Drug Discovery: A Unified Pharmacology Framework Linking Clinical Drugs, Natural Products, and Engineered Microbial Therapeutics.},
journal = {Biotech (Basel (Switzerland))},
volume = {15},
number = {2},
pages = {},
pmid = {42346015},
issn = {2673-6284},
abstract = {Highlighting its pivotal role in modern pharmacology, the gut microbiome is emerging as a key determinant of drug efficacy, toxicity, and bioavailability. This review proposes the Gut Microbiome Dependency Continuum, a four-layer framework describing progressively deeper levels of microbiome involvement in drug discovery and therapeutic function. The first layer, intact functional microbiome-dependent therapeutics and includes interventions such as faecal microbiota transplantation and defined microbial consortia. The second layer, microbiome-modulated approved drugs include widely used therapeutics whose pharmacokinetics or pharmacodynamics are strongly influenced by microbial metabolism. Examples include metformin, irinotecan, levodopa, and digoxin, where gut microbial interactions influence efficacy, toxicity, and inter-individual variability in treatment outcomes. The third layer, microbiota-transformable natural products, encompasses dietary and plant-derived compounds such as polyphenols, ginsenosides, alkaloids, fibres, isoflavones, lignans, and glucosinolates. Their biological activity depends on microbial biotransformation into bioactive metabolites. The fourth layer, engineered microbiome therapeutics, includes synthetic biology approaches such as programmable microbial systems, engineered probiotics, CRISPR-based microbiome editing, and microbiome-responsive drug delivery systems. It also includes synthetic microbial consortia, enabling targeted sensing, therapeutic delivery, and ecological reprogramming of gut microbial communities. Altogether, these layers define a continuum in which the gut microbiome evolves from a passive modulator to an essential metabolic organ and ultimately a programmable therapeutic platform. The article provides an integrated framework for microbiome-informed drug discovery. It also supports the development of precision, ecology-aware, and engineered microbial therapeutics.},
}

@article {pmid42346116,
year = {2026},
author = {Khan, SU and Chauhan, V and Chaudhary, AA and Khan, M},
title = {The Gut-Brain-Immune Axis: Multi-Omics Insights into Neurodegenerative and Metabolic Diseases.},
journal = {Cells},
volume = {15},
number = {12},
pages = {},
pmid = {42346116},
issn = {2073-4409},
support = {DDRSP-2601//Imam Mohammad ibn Saud Islamic University/ ; },
mesh = {Humans ; Multiomics ; *Neurodegenerative Diseases/immunology/metabolism ; Animals ; *Brain/immunology/metabolism ; *Metabolic Diseases/immunology/metabolism ; Gastrointestinal Microbiome ; Metabolomics ; },
abstract = {The axis linking the gut to the brain to the immune system connects all tissues involved-bacteria, immune cells, metabolism and the CNS-through a multidirectional communication network. Several studies have confirmed that when this axis is disrupted, it can be responsible for Alzheimer's disease, Parkinson's disease, obesity, type 2 diabetes, and NAFLD, and the main consequences come from increased systemic inflammation, altered regulation of immune cells, the production of microbial metabolites that alter signals to the immune cells and nervous system, increase in oxidative stress, breakdown of the gut barrier, and more. In recent years, advanced multi-omics technologies, such as metagenomics, transcriptomics, metabolomics, proteomics, and single-cell sequencing, have provided significant advancement in our understanding of all of the interacting nodes involved in the gut-brain-immune axis. These advanced sequencing technologies can characterize the microbial communities, host immune cells, metabolic profiles, and the degree of cell heterogeneity during a specific disease. Combining multi-omics information can reveal a few shared pathways between neurodegenerative and metabolic disorders, such as NF-κB, NLRP3 inflammasome activation, mitochondrial dysfunction, changes in SCFA metabolism, and the alteration of microbial populations in Alzheimer's and Parkinson's disease; metabolic dysbiosis and increased risk for Parkinson's disease; or changes in gut-to-brain-to-immune signaling contributing to diabetes complications and NAFLD. Artificial intelligence (AI) and machine learning are becoming promising tools for detecting biomarkers from these datasets, extracting knowledge, interpreting systems biology, and helping with developing precision medicine. In this review, we summarize current evidence that supports the role of the gut-brain-immune axis in neurodegenerative and metabolic diseases, highlighting results gained with the utilization of multi-omics approaches. We will describe the key microbial, immune, and metabolic pathways involved in pathogenesis and therapeutic approaches including psychobiotics, tailored nutrition, modulation of the microbiome, and metabolite interventions, discussing future perspectives of the translation of the gut-brain-immune axis knowledge into clinical practice.},
}

Humans
Multiomics
*Neurodegenerative Diseases/immunology/metabolism
Animals
*Brain/immunology/metabolism
*Metabolic Diseases/immunology/metabolism
Gastrointestinal Microbiome
Metabolomics

@article {pmid42346277,
year = {2026},
author = {Bodurska, T and Totev, T and Konova, E},
title = {Presence and Dominance of Lactobacillus in the Endometrial Microbiome and Age-Related Associations in Patients with Recurrent Reproductive Failure.},
journal = {Diseases (Basel, Switzerland)},
volume = {14},
number = {6},
pages = {},
pmid = {42346277},
issn = {2079-9721},
abstract = {OBJECTIVES: To evaluate the presence and dominance of Lactobacillus in the endometrial microbiome and their age-related associations in a large group of Bulgarian patients with recurrent implantation failure (RIF) and recurrent pregnancy loss (RPL) who attend our clinic.

METHODS: This retrospective study included 199 patients (mean age: 35.69 ± 5.16) with RIF (n = 103) and RPL (n = 96) who visited our fertility clinic between October 2019 and November 2022. Endometrial samples were analyzed using real-time PCR for target DNA sequences.

RESULTS: Overall, 62.8% (n = 125) exhibited an absence of Lactobacilli in their endometrial samples, with 63.1% (n = 65) of the RIF group and 62.5% (n = 60) of the RPL group showing a lack of Lactobacilli, with no statistically significant difference between the groups (p = 0.926). A Lactobacillus-dominant microbiome was found in 23.6% of the entire cohort (n = 47), 25.2% of the RIF group (n = 26) and 21.9% of the RPL group (n = 21). A reduced abundance of Lactobacilli was identified in 13.5% of the cohort (n = 27), though to differing degrees. There was no significant relationship between the abundance of Lactobacilli and belonging to the RIF or RPL group. A statistically significant difference was found in the mean age of two groups in cases with a Lactobacillus-dominant microbiome (mean age of 36.4 ± 4.8 years in the RIF group and 32.5 ± 3.5 years in the RPL group) (p = 0.004).

CONCLUSIONS: Our findings demonstrate a high prevalence of non-Lactobacillus-dominant microbiomes in a large group of Bulgarian patients with RIF and RPL and significant age-related Lactobacillus changes in the microbiome of patients with RPL. These results point to the potential role of the uterine microbiome and support the need for further prospective studies, especially in cases of advanced maternal age.},
}

@article {pmid42346347,
year = {2026},
author = {He, J and Qin, L and Sun, X},
title = {Bile Acids and the Gut-X Axis: TCM-Mediated Systemic Protection and Therapeutic Opportunities for Multi-Organ Diseases.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060366},
pmid = {42346347},
issn = {2218-1989},
support = {82405310//National Natural Science Foundation of China/ ; 1020241792//Natural Science Foundation of the Jiangsu Higher Education Institutions of China/ ; },
abstract = {The gut microbiota regulates host physiology and drives extraintestinal diseases through the gut-X axis. Bile acids (BAs) function as key mediators of this interorgan crosstalk by activating nuclear and membrane receptors (FXR, TGR5, PXR, VDR). Traditional Chinese Medicine (TCM) demonstrates efficacy across multiple organ systems through multi-component formulations. This narrative review synthesizes evidence from preclinical and clinical studies supporting that TCM exerts systemic protection via strategic modulation of the microbiota-BA-host receptor axis, which functions as a core regulatory circuit within a larger network of microbial metabolites. Mechanistically, representative TCM formulas remodel gut microbial ecology and reinforce intestinal barrier integrity, leading to optimized BA profiles. These favorable BA signatures engage tissue-specific receptor signaling to resolve inflammation, mitigate fibrosis, and restore metabolic homeostasis across the gut-heart, gut-kidney, gut-liver, gut-bone, and gut-endocrine axes. Support for this causal relationship is provided by microbiota depletion, fecal transplantation, and multi-omics studies, collectively suggesting that TCM's benefits are microbiota-dependent and at least partially BA-mediated. Moreover, context-dependent modulation of BA receptors, such as differential regulation of FXR, enables TCM to achieve pathology-specific outcomes. Current evidence is derived predominantly from preclinical models, and clinical data remain lacking. Nonetheless, the microbiota-BA-organ axis thus provides a potential framework for understanding TCM's systemic actions and establishes a molecular basis for developing microbiome-informed precision therapeutics. Future directions include patient stratification and precision intervention design inspired by TCM's ecological modulation strategies.},
}

@article {pmid42346351,
year = {2026},
author = {Ezzi, MY},
title = {Probiotics After Metabolic and Bariatric Surgery: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060371},
pmid = {42346351},
issn = {2218-1989},
abstract = {Background/Objectives: Patients undergoing metabolic and bariatric surgery (MBS) are at risk of micronutrient deficiencies and gut dysbiosis. Probiotics (such as Lactobacillus, Bifidobacterium) have been proposed as adjunct therapy to optimize postoperative outcomes. This review aimed to evaluate the effect of postoperative probiotic supplementation on anthropometric, metabolic, inflammatory, and micronutrient outcomes in MBS patients. Methods: Nine electronic databases were systematically searched, including PubMed, Web of Science, Cochrane Library, Google Scholar, Popline, Global Health Library, Virtual Health Library, New York Academy of Medicine, and OpenGrey, from inception through October 2024. Only randomized controlled trials (RCTs) were included. The Cochrane Collaboration risk-off-bias tool was used for quality assessment. Meta-analyses were performed using Comprehensive Meta-Analysis software version 2. Fixed-effects or random-effects models based on heterogeneity (I[2] threshold: 50%) were applied. Mean differences (MD) and 95% confidence intervals (CI) were calculated for all continuous variables. Results: Thirteen RCTs encompassing 666 patients (probiotics group: n = 344; control group: n = 322) were included. Incomplete outcome data represented the most prevalent high-risk domain (23%). Probiotic supplementation was associated with significantly improved serum vitamin D (MD: 25.32 nmol/L, 95% CI: 6.96-43.67, p = 0.007) and vitamin B12 levels (MD: 39.36 pg/mL, 95% CI: 1.88-76.84, p = 0.04). No statistically significant differences were observed in anthropometric outcomes (%EWL, BMI, weight, or waist circumference), lipid profile, glycemic indices, or inflammatory markers (TNF-α, IL-6, CRP). Conclusions: Postoperative probiotic supplementation may significantly improve vitamin D and B12 levels in patients undergoing MBS, suggesting a supportive role in mitigating micronutrient deficiencies. However, these findings should be interpreted with caution due to substantial heterogeneity across studies. Probiotics did not significantly affect weight loss, metabolic parameters, or inflammatory markers. Clinicians may consider probiotics as an adjunct strategy to support micronutrient status in at-risk postoperative patients. Large-scale, strain-specific trials incorporating standardized dietary control and microbiome profiling are warranted.},
}

@article {pmid42346365,
year = {2026},
author = {Xie, T and Ding, Q and Yang, L and Wang, J and Wei, J and Du, X and Jin, L},
title = {Screening of "Cry for Help" Signals from Angelica sinensis Induced by Fusarium solani and Their Potential for Biological Control.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060385},
pmid = {42346365},
issn = {2218-1989},
support = {Nos. 82160714 and 82560755//National Natural Science Foundation of China/ ; 2024QNTD36//Gansu Provincial Young Talent Project/ ; 23JRRA1711//Natural Science Foundation of Gansu Province/ ; 2025A-101//Gansu University Teacher Innovation Fund Project/ ; ZYZL-2024-04//Open Fund Project of the Gansu Provincial Key Laboratory of Traditional Chinese Medicine Quality and Standardization/ ; },
abstract = {BACKGROUND: Root rot caused by Fusarium solani is a devastating disease in Angelica sinensis (danggui), leading to severe yield and quality losses. Sustainable control strategies are urgently needed. According to the plant "cry for help" theory, plants under pathogen attack may recruit beneficial microbes via root exudates. However, whether A. sinensis employs this strategy against F. solani remains unknown. This study aimed to identify potential "cry for help" metabolites and evaluate their biocontrol potential.

METHODS: LC-MS analysis revealed that F. solani infection significantly altered the metabolic profiles of both A. sinensis roots and rhizosphere soil.

RESULTS: Comparative analysis identified seven metabolites specifically upregulated in infected plants but not detected in the pathogen, including taurine, oxoadipic acid, quinolinic acid, 6-phosphogluconic acid, methyl cinnamate, 2-phenylethanol, and (R)-3-hydroxybutyric acid. Exogenous application of these seven metabolites revealed that taurine and methyl cinnamate significantly alleviated disease symptoms, improved plant growth (root length, biomass), and enhanced the activities of key defense enzymes (peroxidase, POD, phenylalanine ammonia-lyase, PAL, lipoxygenase, LOX, polyphenol oxidase, PPO). Furthermore, taurine and methyl cinnamate reshaped the rhizosphere microbiome. The incidence of root rot was reduced by 51.3% and 50.8%, respectively. Taurine enriched actinobacteria (e.g., Paeniglutamicibacter) and reduced the relative abundance of pathogenic Ascomycota fungi, while methyl cinnamate markedly enriched the nitrogen-fixing bacterium Azotobacter and the saprophytic fungus Schizothecium. Crucially, both treatments significantly suppressed the proliferation of F. solani in the rhizosphere.

CONCLUSIONS: Our findings demonstrate for the first time that A. sinensis activates a "cry for help" response upon attack by F. solani, with taurine and methyl cinnamate preliminarily identified as key signaling metabolites that can directly or indirectly inhibit the development of A. sinensis root rot. These compounds enhance plant resistance and recruit beneficial microorganisms, offering a novel and promising ecological strategy for the green control of A. sinensis root rot.},
}

@article {pmid42346385,
year = {2026},
author = {Li, J and Xu, X and Wang, H and Gao, R and Li, B and You, X},
title = {Relationship Between Calcium and Gut Microbial Composition and Metabolic Pathways in Children with Autism.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060405},
pmid = {42346385},
issn = {2218-1989},
support = {531100006787540685//Chinese Academy of Medical Sciences & Peking Union Medical College/ ; },
abstract = {Background/Objectives: Trace elements may influence autism spectrum disorder (ASD) severity through interactions with the gut microbiota and microbial metabolic functions, but calcium-related evidence remains limited. This cross-sectional study examined associations among hair calcium, gut microbial taxa, metabolic pathways, and behavioral phenotypes in children with ASD. Methods: We analyzed 183 children with ASD who had behavioral assessments, hair calcium measurements, and fecal shotgun metagenomic sequencing data. Participants in the lowest and highest calcium quartiles were first compared to characterize group-level microbiome differences. Full-sample analyses then tested associations among continuous hair calcium, microbial taxa, metabolic pathways, and behavioral measures after covariate adjustment. Benjamini-Hochberg false discovery rate correction was applied for multiple testing. Results: Hair calcium was positively associated with CARS, ATEC-Total, ATEC-1, and ATEC-3 scores, with the strongest associations involving ATEC-1 and ATEC-3. Alpha and beta diversity did not differ significantly between calcium quartile groups, but group-based microbiome analyses identified 63 differential species and 22 differential MetaCyc pathways. Full-sample integrated analyses connected calcium-associated microbial taxa, metabolic pathways, and ASD behavioral measures. Conclusions: Hair calcium was associated with ASD behavioral severity, selected gut microbial species, and microbial metabolic pathways. These findings support an association framework connecting longer-term calcium-related mineral profiles, gut microbial functional potential, and behavioral phenotypes, providing a basis for future longitudinal and multi-omics studies.},
}

@article {pmid42346391,
year = {2026},
author = {Cheng, F and Lv, C and Yi, Y and Wang, D and Wang, W and Li, T and Zhou, R and Li, Q and Qin, S},
title = {Multi-Targeted Intervention of Eucommia ulmoides and Its Bioactive Constituents Against Metabolic Syndrome: From Molecular Mechanisms and Gut Microbiota Modulation to Clinical Translation.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060411},
pmid = {42346391},
issn = {2218-1989},
support = {82305009//National Natural Science Foundation of China/ ; 2024JJ5225//Department of Science and Technology of Hunan Province/ ; },
abstract = {Background/Objectives: Metabolic syndrome (MetS) is a pressing global health challenge comprising obesity, hyperglycemia, hypertension, and hyperlipidemia. Conventional polypharmacy often presents long-term compliance issues and side effects. Eucommia ulmoides Oliv., a traditional medicinal and edible plant rich in iridoids, lignans, flavonoids, and polysaccharides, has emerged as a promising natural intervention. This review aims to systematically summarize the bioavailability and multifaceted pharmacological mechanisms of E. ulmoides and its bioactive components in alleviating MetS. Methods: We comprehensively reviewed the recent in vitro and in vivo literature to map the functional evidence, specific signaling pathways, and gut microbiota-host interactions associated with E. ulmoides extracts and its key phytochemicals (e.g., asperuloside) against various metabolic dysfunctions. Results: Current evidence indicates that E. ulmoides operates through a "multi-component, multi-target, and multi-pathway" paradigm. For hyperlipidemia and obesity, it activates hepatic lipid metabolism (PPARα/CPT1A, FXR/CYP7A1) and mitigates oxidative stress (Nrf2/ARE). Furthermore, it dose-dependently reshapes the gut microbiota by enriching beneficial bacteria like Akkermansia and increasing butyrate production, exerting profound gut-liver axis regulation. It also ameliorates hypertension by activating the ACE2-Ang-(1-7)-Mas axis, improves insulin resistance via the AMPK/PI3K/Akt cascade, and manages hyperuricemia by modulating XOD and renal transporters. Notably, the low oral bioavailability of its glycosides highlights the crucial role of gut microbial hydrolysis in its efficacy. Conclusions: E. ulmoides holds substantial therapeutic potential as a multi-target natural supplement for MetS. However, future translational applications necessitate large-scale randomized clinical trials, multi-omics studies to further clarify host-microbiome interactions, and the development of standardized formulations to ensure clinical efficacy.},
}

@article {pmid42346411,
year = {2026},
author = {Vankayala, USA and Sohail, A and George, B and Singh, M and Khayat, O and Kreidieh, M and Hasham, A and Quiel, L},
title = {The Gut Microbiome in Heart Failure: Pathways to Inflammation and Therapeutic Targets.},
journal = {Metabolites},
volume = {16},
number = {6},
pages = {},
doi = {10.3390/metabo16060431},
pmid = {42346411},
issn = {2218-1989},
abstract = {Heart failure (HF) continues to be a major global health burden, with persistent morbidity and mortality despite guideline-directed and device-based therapies. Evidence suggests the gut-heart axis is a critical and underrecognized contributor to HF progression. Alterations in cardiac output and systemic venous congestion in HF lead to intestinal hypoperfusion, mucosal edema, and loss of barrier integrity, increasing intestinal permeability, gut dysbiosis, and translocation of microbial products. This systemic translocation is associated with chronic low-grade inflammation that activates innate immune pathways that correlate with endothelial dysfunction, oxidative stress, fibroblast activation, and adverse cardiac remodeling. Gut-derived metabolites derived by microbial metabolism modulate cardiovascular health by altering the metabolic profiles. Dysbiosis results in loss of protective short-chain fatty acid (SCFA)-producing bacteria and enriches pro-inflammatory taxa such as trimethylamine N-oxide (TMAO)-producing bacteria. Elevated TMAO is associated with increased mortality and hospitalization in HF, whereas SCFAs enhance barrier integrity and immune tolerance. Secondary bile acids and uremic toxins such as indoxyl sulfate and p-cresyl sulfate further link dysbiosis to fibrosis and vascular stiffness. Circulating markers such as TMAO, lipopolysaccharide-binding protein (LBP), and soluble CD14 carry prognostic value beyond traditional cardiac biomarkers. This review highlights current experimental, translational, and clinical evidence describing gut dysbiosis and its molecular links to HF progression. Targeting the gut-heart axis represents a novel therapeutic approach in HF. Dietary modulation, probiotics/prebiotics, fecal microbiota transplantation, and inhibitors of microbial metabolic pathways show promise. Future research should emphasize microbiota-based interventions in HF management.},
}

@article {pmid42346510,
year = {2026},
author = {Borrego-Ruiz, A and Borrego, JJ},
title = {The Gut Microbiome in Early Ontogeny: Implications for Brain and Immune System Development.},
journal = {Journal of developmental biology},
volume = {14},
number = {2},
pages = {},
pmid = {42346510},
issn = {2221-3759},
abstract = {The gut microbiome plays a pivotal role in modulating multiple physiological processes from the earliest stages of life. However, the complete scope of its effects during childhood is yet to be fully elucidated, which underscores the importance of enhancing the understanding of this emerging area of research. This narrative review provides an overview of the influence of the gut microbiome in early human ontogeny by examining its role in brain and immune development, as well as its involvement in neurodevelopmental disorders and early-life mental health. The gut microbiome contributes to shaping the development and function of both the brain and the immune system. Its influence appears to be primarily mediated through the synthesis of neurotransmitters and microbial metabolites, as well as through the activation of specific pathways within the hypothalamic-pituitary-adrenal axis. Nevertheless, the exact mechanisms through which the gut microbiome exerts these effects, and the full extent of its impact on neurodevelopmental and immune health, remain incompletely understood and continue to be active areas of research and scientific debate. Ultimately, advances revealing how the gut microbiome shapes early brain and immune system development will create new opportunities for innovative interventions and predictive strategies aimed at transforming pediatric health outcomes.},
}

@article {pmid42346523,
year = {2026},
author = {Morales-Mora, LA and Maldonado-Mendoza, IE and Nava-Galicia, SB and Romero-Arenas, O and Arroyo-Becerra, A and Villalobos-López, MA and Cortés-Espinosa, DV and Bibbins-Martínez, MD},
title = {Trichoderma spp. Associated with Teosinte (Zea mays spp. mexicana) Rhizosphere Exhibit Potential Plant Growth-Promoting and Antagonistic Functional Traits.},
journal = {Journal of fungi (Basel, Switzerland)},
volume = {12},
number = {6},
pages = {},
pmid = {42346523},
issn = {2309-608X},
support = {Research project grant SIP20251091//Instituto Politécnico Nacional/ ; },
abstract = {Wild maize (teosinte) has been reported to be less susceptible to biotic and abiotic stresses than its modern relative, corn. The composition of the teosinte root microbiome may be linked to traits such as drought tolerance and pest resistance. Trichoderma spp. are ubiquitous saprotrophic fungi found in the plant rhizosphere, enhancing host plant growth and crop productivity while alleviating biotic and abiotic stresses. The present study identified ten Trichoderma fungal isolates associated with the rhizosphere microbiome of teosinte (Zea mays spp. mexicana) and performed in vitro screening to assess both their multi-trait plant growth-promoting activities and their biological control potential against the phytopathogens Aspergillus flavus and Fusarium verticillioides. Additionally, interaction tests were conducted to evaluate the phytostimulant effect of Trichoderma spp. on maize (Zea mays) seed germination. Taxonomic and phylogenetic analysis identified five different Trichoderma species: T. rifaii (TA and TH); T. azevedoi (TB and TI); T. afroharzianum (TE); T. hamatum (TF and TG); and Trichoderma sp. (aff. bannaense) (TC, TD, and TJ). Partial least squares discriminant analysis revealed the isolates TF, TG, and TJ to have the highest potential for use as biocontrol and biostimulant agents. The present study is the first to examine Trichoderma species associated with the teosinte microbiome, and the results suggest that Trichoderma isolates are a potential sustainable alternative for improving maize cultivation.},
}

@article {pmid42346610,
year = {2026},
author = {Zagorianakou, N and Makrydimas, S and Moustakli, E and Oikonomou, ED and Mitrogiannis, I and Sintou, E and Makrydimas, G},
title = {Epigenetics, Oxidative Stress, and the Microbiome in Endometriosis: Toward an Integrated Mechanistic Framework for Precision Medicine.},
journal = {Journal of personalized medicine},
volume = {16},
number = {6},
pages = {},
pmid = {42346610},
issn = {2075-4426},
abstract = {Endometriosis (EM) is a chronic, estrogen-dependent inflammatory disorder affecting approximately 6-10% of women of reproductive age in the general population and remains a major cause of chronic pelvic pain and infertility. High recurrence rates and enduring symptoms despite current treatments underscore the need for a more thorough understanding of its intricate biology. There is growing evidence that the interaction among oxidative stress (OS), microbiome dysbiosis, and epigenetic dysregulation contributes to immunological activation, hormonal imbalance, and the persistence of ectopic lesions. Important disease mechanisms, such as progesterone resistance, inflammatory signaling, and aberrant cellular proliferation, are influenced by epigenetic changes, which include aberrant DNA methylation, histone modifications, and dysregulated non-coding RNAs. Simultaneously, high levels of reactive oxygen species (ROS) reinforce lesion survival and chronic inflammation by promoting angiogenesis, fibrosis, and tissue damage. Changes in the microbiome also affect immunological responses, oxidative balance, estrogen metabolism, and epigenetic control, indicating the existence of interrelated pathogenic loops. This narrative review presents an integrated mechanistic framework for endometriosis, summarizing the available data that connect these pathways. Furthermore, the growing implications of non-invasive biomarkers and precision medicine techniques highlight the potential for improved diagnosis, disease classification, and targeted treatment approaches.},
}

@article {pmid42346643,
year = {2026},
author = {Lee, H and Sajid, K and Lee, D},
title = {Bridging Ancestry-Stratified Bias in Pharmacogenomics AI: Toward Metabolomics-Inclusive Multi-Omics Precision Medicine.},
journal = {Journal of personalized medicine},
volume = {16},
number = {6},
pages = {},
pmid = {42346643},
issn = {2075-4426},
abstract = {Pharmacogenomics AI offers significant potential for individualized drug therapy; however, its clinical benefits remain unevenly distributed. Models trained predominantly on European-ancestry data consistently underperform in non-European populations, with polygenic risk scores (PRS) showing an estimated 39-73% reduction in predictive accuracy in African-ancestry cohorts across complex traits. These disparities have driven increased interest in moving beyond single-layer genomic approaches. Multi-omics frameworks integrating genomic, transcriptomic, proteomic, and metabolomic data have emerged as a promising strategy to improve prediction across heterogeneous clinical populations, as each molecular layer provides distinct and complementary biological information. Among these layers, metabolomics may represent a particularly transferable component across populations. Metabolite profiles capture the downstream functional output of biological systems influenced by genetic, environmental, dietary, and microbiome-related factors, and may therefore be less reliant on ancestry-stratified allele frequency structures that underlie performance disparities in genomic models. This review synthesizes evidence regarding the mechanistic basis of genomic bias in pharmacogenomics AI, the emerging role of multi-omics integration, especially metabolomics, in improving predictive performance, and the current landscape of computational strategies for bias mitigation, including federated learning, transfer learning, domain adaptation, and synthetic data generation. Collectively, current evidence supports metabolomics-inclusive multi-omics frameworks as a biologically plausible, hypothesis-generating strategy to reduce reliance on ancestry-linked genomic features. However, direct evidence that such frameworks reduce ancestry-related bias in clinical AI outputs remains limited, underscoring the need for globally diverse datasets and prospective multi-population validation.},
}

@article {pmid42346798,
year = {2026},
author = {Mizuno, S and Espinoza, JL and Vu, LQ and Banno, H and Iida, Y and Shinohara, S and Dac, DT and Nakagami, Y and Uchino, K and Horio, T and Hanamura, I and Asai, N and Enomoto, M and Tani, H and Nakayama, T and Suzuki, S and Takami, A},
title = {Ascophyllan Supplementation Is Safe and Associated with Exploratory Modulation of Innate Immune Phenotypes, Biochemical Parameters, and the Gut Microbiome in a Randomized Pilot Trial.},
journal = {Marine drugs},
volume = {24},
number = {6},
pages = {},
pmid = {42346798},
issn = {1660-3397},
support = {#21K08427//Ministry of Education, Culture, Sports, Science and Technology/ ; #24K11527//Ministry of Education, Culture, Sports, Science and Technology/ ; },
mesh = {Humans ; Pilot Projects ; Male ; Adult ; *Gastrointestinal Microbiome/drug effects ; *Dietary Supplements ; Female ; *Immunity, Innate/drug effects ; Double-Blind Method ; *Polysaccharides/administration & dosage/pharmacology/adverse effects ; Phenotype ; Killer Cells, Natural/drug effects/immunology ; Young Adult ; Antioxidants ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; },
abstract = {BACKGROUND: Ascophyllan, a sulfated polysaccharide extracted from brown seaweed, has shown immunomodulatory and antioxidant effects in preclinical studies, yet human clinical evidence remains scarce. This randomized, double-blind, placebo-controlled pilot trial evaluated the safety and exploratory biological effects of daily ascophyllan supplementation in healthy adults.

METHODS: Twelve participants were randomized to receive either ascophyllan (n = 6) or placebo (n = 6) for 28 days. Safety was monitored through adverse event reporting and repeated laboratory assessments, including hematology, biochemistry, and inflammatory markers. Immune cell populations were analyzed via serial flow cytometry, serum total antioxidant capacity was measured at multiple time points, and gut microbiome composition was profiled using 16S rRNA gene sequencing. All analyses were exploratory in nature.

RESULTS: Ascophyllan supplementation proved well tolerated, with no adverse events observed and stable hematologic, renal, and biochemical parameters throughout the study. Exploratory longitudinal analyses suggested directional modulation of NK-cell-associated phenotypes during ascophyllan supplementation, including directional changes in CD57[+], NKp46[+], and NKG2D[+] NK-cell phenotypes; however, group × time interaction analyses did not remain statistically significant after correction for multiple comparisons. Serum antioxidant capacity showed inter-individual variability with a directional but non-significant increase in the ascophyllan group at intermediate time points. Exploratory microbiome analyses suggested modest directional compositional differences involving members of the Bacteroidaceae and Bifidobacteriaceae families; however, no taxon remained statistically significant after correction for multiple comparisons.

CONCLUSIONS: These preliminary findings indicate that ascophyllan is safe and well tolerated in healthy adults and may be associated with modulation of innate immune phenotypes, subtle microbiome compositional differences, and directional changes in antioxidant capacity. Larger, adequately powered clinical trials are warranted to confirm these observations and further investigate potential biological and clinical effects.},
}

Humans
Pilot Projects
Male
Adult
*Gastrointestinal Microbiome/drug effects
*Dietary Supplements
Female
*Immunity, Innate/drug effects
Double-Blind Method
*Polysaccharides/administration & dosage/pharmacology/adverse effects
Phenotype
Killer Cells, Natural/drug effects/immunology
Young Adult
Antioxidants
Middle Aged
RNA, Ribosomal, 16S/genetics

@article {pmid42347203,
year = {2026},
author = {Widyarman, AS and Udawatte, NS and Ma, SSSS and Theodorea, CF and Richi, M and Poedjiastoeti, W and Seneviratne, CJ},
title = {Nutritional Stunting Is Linked to Reduced Oral Microbiome Stability and Reconfigured Microbial Networks in Children: A Pilot Intervention Study.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060591},
pmid = {42347203},
issn = {2076-0817},
mesh = {Humans ; Child ; Pilot Projects ; Female ; Probiotics/administration & dosage ; Male ; *Microbiota ; *Growth Disorders/microbiology/complications ; Mouthwashes/administration & dosage ; *Mouth/microbiology ; Saliva/microbiology/chemistry ; Oral Health ; Bacteria/classification/genetics ; Oils, Volatile/administration & dosage ; },
abstract = {This non-randomized, open-labelled, controlled pilot trial investigated the impact of stunting on oral health and the oral microbiome, and evaluated the effect of 14-day probiotic or essential oil mouthwash interventions in children aged 8-12 years. Thirty-six participants (18 stunted, 18 non-stunted) were randomized into three parallel arms: probiotic lozenges (Limosilactobacillus reuteri DSM 17938 + ATCC PTA 5289), essential oil mouthwash, or water control. D-25OH level was assessed with ELISA, OHI-S, and PBI were examined, and oral microbiome was analyzed using 16S metagenomic sequencing. Stunted children demonstrated significantly higher gingival inflammation (PBI, F = 10.57, p = 0.002), reduced microbial alpha diversity, reductions in commensal Streptococcus spp., and increases in pathobionts, including Parvimonas micra, Fusobacterium nucleatum, and Tannerella forsythia. Beta-diversity analysis revealed distinct microbial communities (p = 0.001), with network analysis identifying these anaerobes as keystone hubs in stunted individuals. Salivary vitamin D and oral hygiene indices (OHI-S) also differed by stunting status. Fourteen-day interventions produced only modest, non-significant improvements in clinical indices and failed to induce significant shifts in microbial diversity or composition. These findings indicate that nutritional stunting is independently associated with oral dysbiosis and gingival inflammation. Short-term antiseptic interventions appear insufficient to reverse established microbial shifts, highlighting the need for sustained, integrated nutritional-oral health strategies.},
}

Humans
Child
Pilot Projects
Female
Probiotics/administration & dosage
Male
*Microbiota
*Growth Disorders/microbiology/complications
Mouthwashes/administration & dosage
*Mouth/microbiology
Saliva/microbiology/chemistry
Oral Health
Bacteria/classification/genetics
Oils, Volatile/administration & dosage

@article {pmid42347211,
year = {2026},
author = {Karthikeyan, A and Javaid, A and Charway, GNA and Tabassum, N and Kim, TH and Kim, YM and Jung, WK and Khan, F},
title = {Prophages in Skin Pathogens: From Virulence to Therapy.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060599},
pmid = {42347211},
issn = {2076-0817},
support = {RS-2023-00241461//Ministry of Education/ ; RS-2021-NR060118//Ministry of Education/ ; },
mesh = {*Prophages/genetics/physiology ; Humans ; Virulence ; Virulence Factors/genetics ; Animals ; *Skin Diseases, Bacterial/therapy/microbiology ; },
abstract = {Prophages are bacteriophage genomes that are part of bacterial chromosomes. They are not just dormant passengers; they actively shape pathogen biology. For example, in skin-infecting pathogens such as Staphylococcus aureus, Streptococcus pyogenes, and Pseudomonas aeruginosa, prophages carry important virulence factors, cytotoxins, superantigens, immune evasion clusters, and epigenetic regulators that directly affect the course of skin and soft tissue infections. This same prophage biology provides a therapeutic strategy: prophage-derived molecules, including endolysins, holins, spanins, and polysaccharide depolymerases, demonstrate potent antimicrobial and antibiofilm activity against drug-resistant skin pathogens, with several candidates now in clinical development. Engineered chimeric lysins, CRISPR-encoded prophage delivery systems, and the systematic mining of the skin microbiome phageome collectively enhance the translational potential of this biology. This review integrates mechanistic insights into prophage-mediated virulence. It assesses the translational landscape of prophage-derived therapeutics, delineating the conceptual and clinical frontiers that characterize the forthcoming chapter in this domain.},
}

*Prophages/genetics/physiology
Humans
Virulence
Virulence Factors/genetics
Animals
*Skin Diseases, Bacterial/therapy/microbiology

@article {pmid42347259,
year = {2026},
author = {Xu, ZY and Chen, GQ and Xue, J and Chi, YX and Jian, R and Guo, WP},
title = {Molecular Detection of Coxiella-like Endosymbionts in Ticks in Hebei, China.},
journal = {Pathogens (Basel, Switzerland)},
volume = {15},
number = {6},
pages = {},
doi = {10.3390/pathogens15060647},
pmid = {42347259},
issn = {2076-0817},
support = {C2022406003//Hebei Natural Science Foundation/ ; BJ2020024//Young Talent Program of Higher School in Hebei Province/ ; 202001//Scientific Research Foundation for High-level Talents of Chengde Medical University/ ; 213777109D//Key Research and Development Program of Hebei Province/ ; },
mesh = {Animals ; China ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Coxiella/genetics/isolation & purification/classification ; *Symbiosis ; *Haemaphysalis longicornis/microbiology ; DNA, Bacterial/genetics ; Chaperonin 60/genetics ; *Ticks/microbiology ; Polymerase Chain Reaction ; Sequence Analysis, DNA ; },
abstract = {Ticks are widely distributed in China and can carry and transmit a variety of pathogens that potential to cause serious impacts on public health and the economy. Little is known about the broader spectrum of Coxiella-like endosymbiont (CLE) in ticks under natural conditions in China. The aim of this study was to detect, analyze, and characterize phylogenetically CLE found in ticks in Hebei Province, China. A total of 947 ticks collected from Hebei Province were identified as Haemaphysalis longicornis based on morphological characteristics and cytochrome c oxidase gene PCR analysis of extracted DNA. Subsequently, DNA was analyzed via PCR for the IS1111 gene (frequently associated with Coxiella burnetii), and the amplified DNA was then sequenced and analyzed phylogenetically using a set of primers targeting the 16S rRNA, groEL, and rpoB genes. A total of 8.24% (78/947) of ticks from the Chengde, Baoding, and Cangzhou regions were positive in the IS1111 PCR. Phylogenetic analysis using the 16S rRNA, groEL, and rpoB genes revealed the presence of CLE in Ha. longicornis ticks from these regions and the formation of two distinct clades, suggesting horizontal gene transfer events. Our results strengthen the growing evidence that CLE, not Coxiella burnetii, is ubiquitously associated with ticks across diverse geographic locations-a distinction critical for accurately interpreting tick microbiome surveys and avoiding false assumptions of zoonotic risk.},
}

Animals
China
Phylogeny
RNA, Ribosomal, 16S/genetics
*Coxiella/genetics/isolation & purification/classification
*Symbiosis
*Haemaphysalis longicornis/microbiology
DNA, Bacterial/genetics
Chaperonin 60/genetics
*Ticks/microbiology
Polymerase Chain Reaction
Sequence Analysis, DNA

@article {pmid42347405,
year = {2026},
author = {Zheng, J and Chen, X and Jiang, J and Wu, F},
title = {Glyphosate Promotes the Spread of Antibiotic Resistance Genes in the Intestine: An Overlooked Environmental Risk.},
journal = {Toxics},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/toxics14060506},
pmid = {42347405},
issn = {2305-6304},
support = {42407569//National Natural Science Foundation of China/ ; 2024M750585//China Postdoctoral Science Foundation/ ; 2022GDASZH-2022010104-2//GDAS' Project of Science and Technology Development/ ; 2022GDASZH-2022020402-01//GDAS' Project of Science and Technology Development/ ; 2022GDASZH-2022020402-02//GDAS' Project of Science and Technology Development/ ; 2023B0303000006//Guangdong Major Project of Basic and Applied Basic Research/ ; 2023B1212060044//Guangdong Foundation for Program of Science and Technology Research/ ; },
abstract = {Glyphosate (Gly) is currently the most commonly used broad-spectrum herbicide in the world. The extensive residues of Gly and its major metabolite aminomethylphosphonic acid (AMPA) in food and the environment make it inevitable for humans to consume them. Although Gly has been shown to disturb the homeostasis of gut microbiome by inhibiting the shikimic acid pathway of microorganisms, the potential health effects [such as the occurrence of antibiotic resistance genes (ARGs)] remain unclear. Furthermore, as antibiotics that also act on the intestinal microbiota, their extensive residues inevitably lead to co-exposure with Gly. For these reasons, this study used zebrafish as experimental organisms to explore the effects of Gly/AMPA and oxytetracycline (OTC) exposure alone or in combination on ARGs in the intestine. Our results indicate that Gly exposure, rather than AMPA exposure, led to a 1.67-fold increase in the relative abundance of ARGs in the zebrafish intestine. Combined exposure to Gly and OTC led to a 2.30-fold increase in the relative abundance of ARGs in the zebrafish intestine, indicating a synergistic effect, whereas the additive effect of AMPA and OTC was negligible. In conclusion, the health risk of antibiotic resistance caused by Gly through the gut microbiota is a neglected hot topic. Further studies are needed to clarify Gly-induced functional drug resistance and to assess the human relevance of these findings using more appropriate model organisms.},
}

@article {pmid42347420,
year = {2026},
author = {Berber, AA and Akbulut, C and Demir, ŞN and Kurnaz, M},
title = {Microplastic Contamination in Amphibians and Reptiles: An Ecotoxicological Synthesis of Exposure, Mechanisms, and Risk Implications.},
journal = {Toxics},
volume = {14},
number = {6},
pages = {},
doi = {10.3390/toxics14060522},
pmid = {42347420},
issn = {2305-6304},
abstract = {Microplastic (MP) contamination has become a defining feature of twenty-first century environmental change, yet the toxicological and ecological consequences for amphibians and reptiles-two vertebrate classes already facing severe extinction pressures-remain fragmented across taxa, regions, and methodological traditions. Here, we synthesize field and experimental evidence from five continents to provide a taxonomically balanced, mechanistically grounded, and geographically explicit assessment of MP exposure, bioaccumulation, and toxicity in herpetofauna, drawing on a structured literature search in Web of Science, Scopus, and PubMed (January 2015-March 2026). Field detection rates of MPs in amphibian larvae range from 26% in conservatively screened Central European populations to 73-80% in anuran tadpoles from high-anthropogenic-pressure Anatolian catchments, with fibrous polyethylene terephthalate (PET), polyethylene (PE), and polypropylene (PP) particles dominating the detected burden. Mechanistic evidence converges on oxidative stress cascades, hypothalamic-pituitary-thyroid axis disruption, gut and cutaneous microbiome dysbiosis, and compromised antiviral and antifungal immunity, with the latter potentially amplifying vulnerability to Batrachochytrium dendrobatidis and to ranavirus. Among reptiles, sea turtles display near-universal MP ingestion with documented maternal transfer to eggs; freshwater turtles, terrestrial squamates, and crocodilians remain critically understudied. Three structural asymmetries constrain current ecotoxicological risk characterization: taxonomic bias toward anurans and sea turtles, geographic bias toward the Global North, and experimental bias toward acute, supra-environmental laboratory exposures using pristine, single-polymer particles that fail to capture the chemical complexity of weathered field mixtures. We argue that MP burden may warrant consideration as a candidate stressor criterion within IUCN Red List assessments and within environmental risk assessment frameworks for freshwater and terrestrial biodiversity once a robust quantitative relationship between MP burden and demographic decline or population-level fitness has been established, and propose six hypothesis-driven research priorities: methodological standardization, reptile toxicokinetics, transgenerational epigenetics, MP-pathogen microbiome interactions and their translation into population viability models, temperature × MP interaction under climate warming, and population-genetic consequences of contemporary MP-driven selection, as the most tractable avenues for ecotoxicological progress and for the development of herpetofauna-specific risk characterization frameworks.},
}

@article {pmid42347889,
year = {2026},
author = {Wang, M and Wu, OY and Wallen, OG and Mozaffarian, D},
title = {Artificial and Other Non-Nutritive Sweeteners, the Microbiome, and Cardiometabolic Health.},
journal = {Current atherosclerosis reports},
volume = {28},
number = {1},
pages = {},
pmid = {42347889},
issn = {1534-6242},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Non-Nutritive Sweeteners/adverse effects ; *Cardiovascular Diseases ; Animals ; *Diabetes Mellitus, Type 2 ; },
abstract = {PURPOSE OF REVIEW: In this narrative review complemented by a novel meta-analysis, we critically analyzed current scientific evidence from RCTs and cohort studies regarding the impact of non-nutritive sweeteners (NNS) on cardiometabolic health, and assessed the interplay with the gut microbiome as a potential mechanistic pathway. We focused on the question of direct physiological effects of NNS, rather than the additional effects of energy displacement by NNS, to inform future research and the development of dietary and clinical guidelines.

RECENT FINDINGS: Cohort studies assessing NNS from all dietary sources suggest that total NNS and each commonly used NNS are associated with higher risk of type 2 diabetes, and that total intake and specific agents are associated with certain cardiovascular disease outcomes. These findings are consistent with prior evidence from cohorts focusing on NNS in beverages. Such observational evidence may be confounded by reverse causation: people at higher cardiometabolic risk choosing to use NNS. However, our new meta-analysis of RCTs with non-caloric comparators and a recent RCT on glycemia outcomes with human-to-mice microbiota transplant suggest that NNS have harmful effects on glucose-insulin homeostasis including fasting insulin, HbA1c, and glucose area under the curve during oral glucose tolerance test (OGTT), potentially mediated by effects on the composition and functional potential of the gut microbiome. The summed evidence supports potential long-term risk of cardiometabolic diseases associated with NNS intake and short-term harmful effects of NNS on glycemia. Future clinical trials of physiologic effects and molecular mechanisms will strengthen interpretations and causal inference. Given potential for harm, caution is warranted for the use of NNS.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Non-Nutritive Sweeteners/adverse effects
*Cardiovascular Diseases
Animals
*Diabetes Mellitus, Type 2

@article {pmid42348069,
year = {2026},
author = {Ernst, S and Dirschka, T},
title = {The Bacterial Landscape of Facial Skin: From Homeostasis to Skin Conditions.},
journal = {Dermatology and therapy},
volume = {},
number = {},
pages = {},
pmid = {42348069},
issn = {2193-8210},
abstract = {The human facial skin microbiome is a complex and dynamic ecosystem that plays a central role in maintaining skin health, immune regulation, and preventing dermatological skin conditions. Cutibacterium acnes (C. acnes) and Staphylococcus epidermidis (S. epidermidis) are the most prominent bacterial species, with shifts in their relative abundance correlating with skin site, age, skin site, and health status. Exploring the facial microbiome offers exciting opportunities, though it requires careful methodological consideration. Sampling techniques vary in invasiveness and depth, which can influence the accuracy and reproducibility of microbiome profiles. While traditional cultivation methods provide valuable insights, they often miss nonculturable microbes, limiting the view of microbial diversity. Molecular approaches such as amplicon sequencing and metagenomics enable a more comprehensive understanding of microbial communities, even though they currently cannot distinguish between viable and nonviable microbes. Addressing these challenges will help unlock the full potential of facial microbiome research. A balanced facial skin microbiome is associated with healthy skin, whereas a dysbiosis of C. acnes and S. epidermidis is commonly observed in acne-prone skin and more pronounced clinically manifest acne. A comprehensive understanding of the diversity and distribution of C. acnes phylotypes, as well as distinct lineages of S. epidermidis associated with skin disorders, is crucial for developing targeted, microbiome-based cosmetic and medical treatments. Emerging strategies aim to restore microbial balance by leveraging the skin's native microbiota, including probiotic approaches. These strategies represent a promising yet still emerging approach, as current clinical evidence remains limited and further well-controlled studies are required, although they may offer benefits by enhancing microbial diversity and supporting skin barrier function.},
}

@article {pmid42348560,
year = {2026},
author = {Mani, K and Palanisamy, V and Shrestha, B and Vice, Z and Paudyal, S and Chitlapilly Dass, S},
title = {Insights into spatial dynamics of the microbiome and resistome across the conventional and organic dairy farms.},
journal = {PloS one},
volume = {21},
number = {6},
pages = {e0352336},
doi = {10.1371/journal.pone.0352336},
pmid = {42348560},
issn = {1932-6203},
mesh = {Animals ; *Dairying/methods ; *Microbiota/genetics ; Cattle ; Milk/microbiology ; Farms ; *Bacteria/genetics/drug effects/classification ; *Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics ; Organic Agriculture ; },
abstract = {Antimicrobial resistance (AMR) poses a serious global threat to human and animal health. While AMR has been reported in various environments, its distribution across different ecological compartments within dairy farms remains poorly characterized. In this study, we used large-scale shotgun metagenomic sequencing to characterize the microbiome and resistome across multiple sampling sites within one organic and one conventional dairy farm, including teats, liners, water troughs, feed area, milking parlour mats, bedding sand, and milk. Our results indicate that microbial community composition and resistance gene profiles were largely comparable between the two study farms, with sample type (ecological niche) exerting a stronger influence on community structure than farm management type. Pseudomonadota, Bacillota, and Actinomycetota were the dominant phyla, while Aerococcus, Glutamicibacter, and Pseudomonas were the most prevalent genera. Glycopeptide resistance genes were the most abundant ARG class, followed by lincosamide and tetracycline resistance genes. Milk samples exhibited a distinct microbiome and resistome composition compared to environmental samples. Strong correlations between microbiome structure, resistome profiles, virulence factors, and metal resistance genes were observed across farm niches, highlighting the interconnected nature of microbial communities and resistance elements across dairy farm environments. These findings provide foundational data for targeted surveillance and management strategies to mitigate antimicrobial resistance in dairy production systems.},
}

Animals
*Dairying/methods
*Microbiota/genetics
Cattle
Milk/microbiology
Farms
*Bacteria/genetics/drug effects/classification
*Drug Resistance, Bacterial/genetics
Metagenome
Metagenomics
Organic Agriculture

@article {pmid42348668,
year = {2026},
author = {Zhang, Y and Xie, Y and Zhang, Z and Gu, F and Xi, S},
title = {Elucidating the Pathophysiology and Diagnostic Biomarkers of Sepsis-Associated Encephalopathy: A Multiomics Approach.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002899},
pmid = {42348668},
issn = {1540-0514},
abstract = {Sepsis-associated encephalopathy (SAE) is a diffuse neurological injury that results from severe sepsis, and its underlying pathophysiological mechanisms remain largely unknown. This study aimed to elucidate the pathological basis of SAE and identify potential diagnostic biomarkers by integrating analyses of the intestinal microbiome, plasma metabolomics, and circulating microRNAs (miRNAs). We analyzed data from 50 patients who were divided into SAE or non-SAE groups. The results revealed significant differences in microbial composition between these groups, with a marked decrease in Bacteroides abundance and an increase in Enterococcus abundance in SAE patients. Compared with non-SAE patients, SAE patients presented notable alterations in LysoPC 18:3, linoleic acid, and miRNA PC-3p-535_63045 levels. Multiomics association analysis revealed positive correlations between Enterococcus and LysoPC 18:3, whereas Bacteroides and PC-3p-535_63045 were negatively correlated with linoleic acid. Gene prediction analysis indicated that PC-3p-535_63045 was enriched in PIK3R1, and a KEGG pathway analysis underscored the role of the PI3K‒Akt signaling pathway. PC-3p-535_63045 exhibited strong diagnostic performance, with an AUC of 0.850 (specificity of 0.867, sensitivity of 0.800). Comparative ROC analysis revealed no significant difference between PC-3p-535_63045 alone and the multiomics model. The integrated results from multiomics LASSO regression and random forest analyses suggest that PC-3p-535_63045 is a promising biomarker for the diagnosis of SAE. In conclusion, our multiomics analysis revealed a significant association among Bacteroides, PC-3p-535_63045, and linoleic acid, which suggests that the PI3K-Akt signaling pathway may play an important role in SAE progression. These findings deepen our understanding of the pathophysiological mechanisms underlying SAE and may ultimately enhance diagnostic and predictive capabilities for this condition.},
}

@article {pmid42348782,
year = {2026},
author = {Xia, H and Du, J and Kong, Y and Wang, Y and Xi, Y and Hu, C and Wang, W and Lei, L and Pan, X and Kang, L and Shi, J},
title = {Harnessing a Functional Rhizobial Partnership with Astragalus sinicus L. to Unlock Phytoremediation Potential for Soil Heavy Metals.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c01468},
pmid = {42348782},
issn = {1520-5118},
abstract = {Phytoremediation of heavy metal-contaminated soils is often limited by phytotoxicity and metal availability. This study evaluated the phytoremediation potential of Astragalus sinicus L. and its symbiotic rhizobia. A nationwide soil survey revealed significantly lower arsenic (As) in planted versus unplanted soils, and key factors governing metal retention were attenuated in planted soils, indicating plant-mediated interference. Pot experiments confirmed that A. sinicus L. cultivation significantly reduced soil cadmium (Cd) (33.33%), lead (Pb, 39.73%), copper (Cu, 12.92%), and As (23.70%). Among rhizobial isolates, Mesorhizobium sp. XS6-2 exhibited the highest heavy metal tolerance. Inoculation with XS6-2 increased plant biomass and specifically enhanced chromium (Cr) and Pb remediation. Microbiome analysis showed that XS6-2 reshaped the rhizosphere community and strengthened microbial interactions. Our findings demonstrate a potent plant-microbe synergy that alleviates phytotoxicity and increases metal availability, offering an effective strategy to advance phytoremediation.},
}

@article {pmid42348961,
year = {2026},
author = {Li, Y and Ye, Y and Lou, L and Yao, Z and Ma, Y and Feng, Y and Liu, W and Wu, H and Sun, Z and Cheng, Z and Zhao, Y and Lai, Q},
title = {Multi-omics analysis of the gill-gut axis in Scylla paramamosain under acute low-salinity stress: Implications for ion and osmotic regulation.},
journal = {Marine environmental research},
volume = {220},
number = {},
pages = {108219},
doi = {10.1016/j.marenvres.2026.108219},
pmid = {42348961},
issn = {1879-0291},
abstract = {The mud crab Scylla paramamosain is a euryhaline species with significant potential for aquaculture in low-salinity environments. However, abrupt exposure of this species to very low saline conditions may exceed its osmoregulatory capacity. Here, we evaluated the physiological, gill transcriptomic, and gut microbiome responses of S. paramamosain after 48 h of acute exposure to salinities of 1-5‰, with a control salinity of 15‰. The survival rate exhibited a sharp decline at salinities ≤5‰ (After 48 h of acute exposure, the survival rates were 33.3% at 1‰, 56.7% at 2‰, 70% at 3‰, 76.7% at 4‰, 86.7% at 5‰, and 100.0% at 15‰), accompanied by increased gill Na[+]/K[+]-ATPase activity, reduced hemolymph osmolality, and elevated hemolymph ammonia content. These results indicate that ion-regulatory responses were activated but were insufficient to sustain osmotic homeostasis under severe acute low-salinity stress. Gill transcriptome analysis between the 1‰ and 15‰ groups identified 1853 differentially expressed genes. Upregulated genes were enriched in ion transport, ABC transporters, calcium signaling, and mitochondrial energy-related pathways, whereas downregulated genes were mainly associated with chitin metabolism, steroid hormone biosynthesis, and molting-related transcriptional processes. Gut 16S rRNA sequencing showed that acute exposure to 1‰ salinity reduced microbial alpha diversity and altered community composition, including reduced abundance of several marine-associated genera such as Photobacterium and enrichment of Lactobacillus. BugBase and PICRUSt2 based analyses indicated differences in predicted microbial phenotypes and inferred functional potential between the 1‰ and 15‰ groups; these predictions should not be interpreted as direct evidence of microbial functional activity. Overall, S. paramamosain showed coordinated physiological, gill transcriptional, and gut microbial responses to acute low salinity. Nevertheless, severe hypoosmotic exposure impaired osmotic balance and reduced survival. These findings provide baseline information for evaluating low-salinity tolerance and suggest that gradual acclimation should be considered when introducing this species into low-salinity culture systems.},
}

@article {pmid42349034,
year = {2026},
author = {Abdel-Moneim, AS and Al-Balushi, MS and Al-Jabri, AA},
title = {Post-COVID-19 immune dysregulation and autoimmune sequelae.},
journal = {Virology},
volume = {623},
number = {},
pages = {111017},
doi = {10.1016/j.virol.2026.111017},
pmid = {42349034},
issn = {1096-0341},
abstract = {SARS-CoV-2 infection induces profound immune dysregulation, including hyperinflammation, lymphopenia, and innate/adaptive immune imbalance. In some individuals, these responses persist beyond viral clearance, creating conditions that may disrupt immunological self-tolerance and precipitate autoimmune phenomena. We critically review mechanistic and clinical evidence linking SARS-CoV-2 infection to autoimmunity. Viral entry via ACE2/TMPRSS2, endothelial injury, and renin-angiotensin system dysregulation generates a pro-inflammatory milieu. Immune pathways, including molecular mimicry, bystander activation, epitope spreading, and persistent antigenic stimulation, can trigger the activation of autoreactive lymphocytes. Emerging evidence further implicates SARS-CoV-2-associated oral-gut microbiome dysbiosis and alterations in tryptophan and arginine metabolic checkpoints as contributors to chronic inflammatory signaling and impaired tolerance maintenance. We propose a mechanistic cascade from viral infection to dysbiosis to metabolic perturbation to loss of tolerance to autoantibody generation. Clinical manifestations encompass neurological, hematological, endocrine, and systemic autoimmune syndromes, with evidence of autoantibody emergence and post-COVID-19 immune sequelae. SARS-CoV-2 acts as an amplifier of autoimmune reaction in genetically susceptible hosts. Understanding these mechanisms is critical for identifying at-risk individuals and informing preventive and therapeutic strategies for post-COVID-19 autoimmune sequelae.},
}

@article {pmid42349523,
year = {2026},
author = {Muqaddas, K and Mahnoor, and Hayat, O and Islam, A and Khan, R and Naz, S},
title = {Cutaneous Leishmaniasis Promotes Skin Microbial Dysbiosis and Exacerbation of Local Inflammatory Responses.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108655},
doi = {10.1016/j.micpath.2026.108655},
pmid = {42349523},
issn = {1096-1208},
abstract = {Cutaneous leishmaniasis (CL) is a neglected tropical disease caused by protozoan parasites belongs to the genus Leishmania transmitted to humans by the bite of the infected female sand fly. Increasing evidence suggested that alterations in the skin microbiome may influence local inflammatory responses and disease progression in CL. This study aimed to investigate the microbial community shifts associated with CL lesions using paired lesional and contralateral healthy skin samples from infected individuals (n = 8). Leishmania tropica was identified in all clinical samples by ITS-1 real-time PCR analysis. Microbiome profiling was performed using 16S rRNA gene amplicon sequencing followed by quality filtering, taxonomic classification using Kraken2/Bracken and statistical analysis. Phylum level analysis demonstrated altered microbial composition in lesional skin, with predominance of Proteobacteria. At the genus and species levels, lesional samples exhibited reduced microbial evenness and enrichment of opportunistic bacterial genera, including Stenotrophomonas, Pseudomonas, Acinetobacter, and Staphylococcus. In comparison, contralateral healthy skin indicated dominance of environmental and commensal bacteria such as Luteibacter, Methylobacterium, and Paracoccus, representing a relatively stable microbial community (FDR p ≥ 0.05). Alpha diversity analysis showed reduced microbial diversity in CL infected samples, whereas beta diversity analysis indicated clear difference between CL infected and contralateral skin microbiomes. The findings indicate that CL is associated with localized microbial dysbiosis characterized by altered community structure. These findings highlight the significance of skin microbiome as a contributing factor in CL pathogenesis and suggest that microbiome targeted approach may complement existing therapeutic strategies.},
}

@article {pmid42349666,
year = {2026},
author = {Tang, E and Xiang, Q and Wang, N and Zhou, H and Chen, Z and He, Q and Yang, X and Liao, W},
title = {Nobiletin Ameliorates Hepatic Insulin Resistance by Modulating the Gut-Liver Axis.},
journal = {The Journal of nutritional biochemistry},
volume = {},
number = {},
pages = {110452},
doi = {10.1016/j.jnutbio.2026.110452},
pmid = {42349666},
issn = {1873-4847},
abstract = {Insulin resistance (IR) is a core pathological feature of type 2 diabetes mellitus (T2DM), with hepatic IR serving as a hallmark of systemic IR. Nobiletin (NOB) shows great potential in exerting hypoglycemic effects and improving IR; however, its molecular mechanisms remain incompletely elucidated. This study aims to investigate the molecular mechanisms by which nobiletin (NOB) ameliorates hepatic IR. Our results demonstrated that NOB effectively ameliorated IR in both high-fat diet/streptozotocin (HFD/STZ)-induced mice and palmitic acid (PA)-treated HepG2 cells. NOB administration improved dyslipidemia and attenuated histopathological damage in mouse liver tissue. Additionally, NOB reduced lipid accumulation in both the mouse liver and HepG2 cells by inhibiting de novo lipogenesis (DNL) and free fatty acids (FFA) uptake while enhancing mitochondrial fatty acid β-oxidation (FAO). Moreover, NOB suppressed hepatic gluconeogenesis by activating the PI3K/AKT/FOXO1 signaling pathway. NOB also enhanced the intestinal barrier function, as evidenced by the upregulation of ZO-1, Claudin-1, and Occludin proteins. Furthermore, NOB increased gut microbiome diversity, reduced the F/B ratio, and enriched beneficial taxa, including Verrucomicrobia, Lachnospiraceae, and Akkermansia muciniphila, thereby ameliorating gut microbiota dysbiosis. This study pioneers the elucidation of the cooperative mechanisms by which NOB ameliorates IR through the gut-liver axis and multi-target regulation of hepatic lipid metabolism, establishing a foundation for the development of NOB-derived nutraceuticals and pharmaceuticals.},
}

@article {pmid42349674,
year = {2026},
author = {El-Sehrawy, AAMA and Aljumaili, OI and Baig, MR and Nematov, O and Sapaev, IB and Badr, IH and Smerat, A and Basunduwah, TS},
title = {Diagnostic and prognostic biomarkers in PCOS: Navigating insulin resistance, systemic inflammation, and endometrial receptivity.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {},
number = {},
pages = {121197},
doi = {10.1016/j.cca.2026.121197},
pmid = {42349674},
issn = {1873-3492},
abstract = {Polycystic ovary syndrome (PCOS) is a highly prevalent and phenotypically diverse endocrine disorder in which insulin resistance (IR) serves as a central molecular driver of major metabolic and reproductive complications, including infertility, obesity, and increased long-term cardiovascular risk. This review examines the complex pathophysiology of PCOS, emphasizing how chronic systemic low-grade inflammation, gut microbiome dysbiosis, and oxidative stress interact to worsen hyperinsulinemia and hyperandrogenemia. It also highlights the clinical value of emerging diagnostic and prognostic biomarkers to improve risk stratification and patient management. Systemic biomarkers, such as pro-inflammatory cytokines, circulating endotoxemia arising from increased intestinal permeability, and epigenetic regulators including miR-146a, may provide prognostic insight into the trajectory of metabolic deterioration. In parallel, endometrial biomarkers, including the glucose transporter GLUT4, implantation-associated genes such as HOXA10, and inflammatory mediators like TNF-α, can support evaluation of impaired uterine receptivity, prediction of assisted reproductive technology (ART) outcomes, and stratification of miscarriage risk. By mapping key interactions within the gut-immune-metabolic axis and detailing localized endometrial dysfunction, this review proposes a framework for integrating targeted biomarker profiling into clinical practice to enable personalized, biomarker-informed interventions aimed at restoring fertility and metabolic health in patients with PCOS.},
}

@article {pmid42349701,
year = {2026},
author = {Huang, J and Older, CE and Heckman, TI and Jordan, HR and Griffin, MJ and Allen, PJ and Grant Reifers, J and Goodman, PM and Yamamoto, FY},
title = {Autochthonous probiotic Lactococcus lactis MA5 improves recovery from acute hypoxia stress and resistance to Edwardsiella ictaluri in hybrid catfish (Ictalurus punctatus × I. furcatus).},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111544},
doi = {10.1016/j.fsi.2026.111544},
pmid = {42349701},
issn = {1095-9947},
abstract = {Dietary supplementation with probiotics is considered an effective strategy to enhance aquaculture production efficiency and disease resistance. Recent research has highlighted the value of using autochthonous probiotics in aquaculture. Herein, an autochthonous probiotic strain (Lactococcus lactis MA5) isolated from pond-raised hybrid catfish (Ictalurus punctatus × I. furcatus) in a previous study was investigated for its ability to improve host recovery from acute hypoxia and resistance to bacterial infection. Hybrid catfish were fed a control diet, or diets containing either 10[4] or 10[6] CFU/g MA5 for 56 days. After the feeding trial, subsets of fish were subjected to either acute hypoxia stress challenge or Edwardsiella ictaluri challenge. Fish fed MA5 exhibited enhanced growth performance without changes to body condition indices. Following acute hypoxia challenge, MA5-supplemented fish showed increased blood hemoglobin, red blood cell counts, and total protein concentration compared to the control. In addition, MA5 led to upregulated expression of gpx1, a gene encoding an antioxidant enzyme, in the intestine. Lastly, fish fed 10[6] CFU/g of MA5 displayed significantly higher survival when exposed to E. ictaluri. These data suggest dietary supplementation with the autogenous probiotic L. lactis MA5 can promote growth, support acute hypoxia recovery, and improve resistance to E. ictaluri in hybrid catfish.},
}

@article {pmid42349924,
year = {2026},
author = {Jeong, YS and Kim, KO and Park, YE and Lee, YJ and Seo, J and Kim, TW and Kim, BH and Yim, SV and Kim, HS and Lee, JY and Bae, JW and Choe, BH and Kang, B and Lee, CK},
title = {Age-Related Microbial Differences in Newly Diagnosed Crohn's Disease Reveal the Distinct Enrichment of Oral-Associated Taxa in Pediatric Patients.},
journal = {Gut and liver},
volume = {},
number = {},
pages = {},
doi = {10.5009/gnl260027},
pmid = {42349924},
issn = {2005-1212},
abstract = {BACKGROUND/AIMS: Crohn's disease (CD) presents differently by age of onset, but the microbial distinctions between pediatric and adult CD are currently unclear.

METHODS: In this study, the gut microbiota of fecal samples collected from newly diagnosed patients with CD (n=88; pediatric 44, adult 44) and their age- and sex-matched healthy controls (HCs, n=112) was analyzed using 16S rRNA gene amplicon sequencing. Differential abundance analysis was performed using MaAsLin2 to identify age-specific microbial signatures, and enterotypes were classified using Dirichlet multinomial mixture modeling.

RESULTS: Both pediatric and adult patients with CD exhibited shared dysbiosis characterized by reduced alpha diversity (p<0.001), enrichment of CD-associated pathobionts, such as Enterobacteriaceae and Enterococcaceae, and depletion of short-chain fatty acid-producing taxa within Ruminococcaceae and Lachnospiraceae. Notably, enterotyping revealed that individuals with CD converged toward a shared, pathobiont-dominated enterotype regardless of age, overriding the age-dependent stratification observed in HCs. Despite this shared convergence, differences in age-stratified comparisons were observed. Adult CD patients exhibited enrichment of resident pathobionts such as Ruminococcus gnavus and Clostridium innocuum, whereas pediatric CD patients exhibited unique and pronounced enrichment of Pasteurellaceae, Neisseriaceae, and Gemellaceae (false discovery rate <0.1).

CONCLUSIONS: In newly diagnosed patients, CD is characterized by shared dysbiosis and convergence toward a disease-specific enterotype across age groups. However, this was accompanied by distinct microbial features, specifically, the enrichment of taxa previously reported as prevalent in the oral microbiome in children versus resident pathobionts in adults. These findings suggest that age at disease onset is associated with age-stratified differences in microbial profiles in CD.},
}