@article {pmid42291329,
year = {2026},
author = {Zeng, Y and Jiang, Y and Huang, Y and Yin, S and Yang, Z and Zhang, F},
title = {The dialogue between breast cancer and microorganisms.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1738739},
pmid = {42291329},
issn = {2235-2988},
mesh = {Humans ; *Breast Neoplasms/microbiology/pathology/therapy ; Female ; Tumor Microenvironment ; *Microbiota ; Animals ; Dysbiosis ; Cell Transformation, Neoplastic ; Estrogens/metabolism ; },
abstract = {Breast cancer is a complex pathological process involving multiple factors and stages, characterized by pronounced molecular and phenotypic heterogeneity. Its global incidence and mortality rates have shown a continuous upward trend. With the advancement of microbiome research, microbial communities have been recognized as key determinants influencing host health and disease states. Increasing evidence suggests a close association between breast tissue-resident and systemic microbiota and the initiation and progression of breast cancer. Specifically, microorganisms may be associated with abnormal proliferation and malignant transformation of mammary epithelial cells through diverse mechanisms, including the modulation of estrogen metabolism, production of bioactive metabolites, induction of chronic inflammation, and remodeling of the tumor microenvironment. In addition, certain microbes may directly interact with host cells, potentially inducing DNA damage and contributing to the transition from normal to malignant phenotypes. This review systematically summarizes the origins and compositional characteristics of the breast microbiota, with a particular focus on current evidence regarding its roles in breast cancer initiation, progression, metastasis, therapeutic response, and prognosis. Currently, the majority of evidence originates from cross-sectional studies and in vitro/in vivo model, to better evaluate the current evidence, the limitations of different research designs and the levels of evidence are summarized in Table 1, aiming to provide new theoretical insights and research perspectives for microbiota-based strategies in breast cancer diagnosis and therapy.},
}

Humans
*Breast Neoplasms/microbiology/pathology/therapy
Female
Tumor Microenvironment
*Microbiota
Animals
Dysbiosis
Cell Transformation, Neoplastic
Estrogens/metabolism

@article {pmid42291330,
year = {2026},
author = {Arishi, RA and Cheema, AS and McEachran, JL and Gridneva, Z and Vlaskovsky, P and Norrish, I and Bilston-John, SH and Zhou, X and Lai, CT and Payne, MS and Geddes, DT and Stinson, LF},
title = {Concentrations of selected human milk components influence the infant oral microbiome to a greater degree than estimated intakes.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1765736},
pmid = {42291330},
issn = {2235-2988},
mesh = {Humans ; *Milk, Human/chemistry ; Infant ; *Microbiota ; Female ; *Mouth/microbiology ; Breast Feeding ; Lactose/analysis ; RNA, Ribosomal, 16S/genetics ; Australia ; Male ; Micronutrients/analysis ; Adult ; },
abstract = {BACKGROUND: Human milk is characterised by its complex composition, consisting of nutrient and bioactive components that play a crucial role in infant health. Although the infant oral cavity is directly exposed to these components during breastfeeding, their effects on the developing oral microbiome remains underexplored. This study aimed to assess associations between the concentrations and daily estimated intakes of human milk components (including minerals, lactose, and antimicrobial proteins) and the oral microbiome of exclusively breastfed infants.

METHODS: We profiled infant oral samples collected at 3 months of age using full-length 16S rRNA gene sequencing, alongside paired analyses of human milk components from 45 mother-infant dyads in the Western Australian BLOSOM cohort. Concentrations of milk lactose, antimicrobial proteins (AMPs), and micronutrients (16 components in total) were measured, and their daily estimated intakes were calculated based on 24-hour milk intake.

RESULTS: The composition of the infant oral microbiome was significantly associated with a number of AMPs and micronutrients, with concentration exerting a far stronger effect than estimated intakes. Lactose, the major sugar in human milk, was not associated with any feature of the infant oral microbiome. Both concentrations and estimated intakes of lactoferrin (P = 0.032 and P = 0.005, respectively), as well as estimated intakes of sodium and iodine (P = 0.041 and 0.022, respectively) were negatively associated with infant oral Shannon diversity. While some associations were consistent when both estimated intakes and concentrations were analysed, some appeared only in one analysis, suggesting differing mechanisms of action.

CONCLUSION: These findings underscore the influence of human milk composition on the developing oral microbiome during early life, highlighting that local, concentration-driven mechanisms are the primary drivers of these effects.},
}

Humans
*Milk, Human/chemistry
Infant
*Microbiota
Female
*Mouth/microbiology
Breast Feeding
Lactose/analysis
RNA, Ribosomal, 16S/genetics
Australia
Male
Micronutrients/analysis
Adult

@article {pmid42291363,
year = {2026},
author = {Trachu, N and Sensorn, I and Khiewngam, K and Monnamo, N and Chantratita, W and Sirachainan, E and Reungwetwattana, T and Oranratnachai, S},
title = {Gut microbiome in advanced non-small cell lung cancer: effect of chemotherapy and impact on efficacy.},
journal = {Translational lung cancer research},
volume = {15},
number = {5},
pages = {127},
pmid = {42291363},
issn = {2218-6751},
abstract = {BACKGROUND: While evidence linking the gut microbiome (GM) to cancer immunotherapy is growing, data regarding its role in chemotherapy remains limited. This study aims to investigate the effect of chemotherapy on GM composition and its potential as a predictive biomarker for treatment outcomes in advanced non-small cell lung cancer (NSCLC).

METHODS: Advanced NSCLC patients treated with chemotherapy at Ramathibodi Hospital were prospectively enrolled. Clinical data and stool samples were collected at three time points: baseline, post-evaluation, and at progression of disease (PD). Fecal bacterial DNA was extracted, followed by PacBio Sequel II sequencing and comprehensive bioinformatic analysis. Clinical data were summarized using descriptive statistics. Progression-free survival (PFS) and overall survival (OS) were estimated by the Kaplan-Meier method, and predictive factors were identified using Cox-regression analysis.

RESULTS: This study analyzed 54 stool samples from 27 NSCLC patients treated with platinum-doublet chemotherapy. The median PFS and OS were 5.3 months [95% confidence interval (CI): 2.4-8.4] and 13.8 months (95% CI: 5.2-not reached), respectively. Post-chemotherapy changes (n=20 paired samples) showed a significant decrease in microbial richness, as evidenced by reduced abundance-based coverage estimator (ACE) (P=0.02) and Chao1 (P=0.03) alpha diversity indices. Taxonomically, the relative abundance of Enterobacter was significantly decreased post-chemotherapy (P=0.03). Regarding treatment response (n=26 evaluable patients; 13 PD, 13 clinical benefit), baseline alpha diversity was not predictive of outcome. However, the relative abundance of Akkermansia was notably higher in the clinical benefit group, approaching statistical significance (P=0.07).

CONCLUSIONS: Chemotherapy significantly reduced GM by decreasing species richness (as measured by the ACE and Chao1 index), while species diversity (as measured by the Shannon and Simpson index) remained unchanged. Therefore, confirming the definitive role of the GM as a predictive biomarker in chemotherapy-treated NSCLC patients necessitates further investigation in a larger, more robustly powered cohort.},
}

@article {pmid42291470,
year = {2026},
author = {Agzamova, SA and Babadjanova, FR},
title = {Gut Microbiome and Short-Chain Fatty Acid Alterations After Cardiopulmonary Bypass are Associated with Nutritional and Functional Impairment in Young Children with Congenital Heart Defects.},
journal = {Clinical and experimental gastroenterology},
volume = {19},
number = {},
pages = {600414},
pmid = {42291470},
issn = {1178-7023},
abstract = {BACKGROUND: Cardiac surgery with cardiopulmonary bypass (CPB) in young children is associated with systemic stress, gastrointestinal dysfunction, and impaired nutritional recovery. The role of gut microbiome disruption and short-chain fatty acid (SCFA) metabolism in these processes remains insufficiently studied.

OBJECTIVE: To evaluate changes in gut microbiome composition, SCFA profiles, and nutritional status in children aged 0-3 years after CPB, and to assess their association with postoperative feeding intolerance and impaired growth.

METHODS: This prospective observational study included 20 children undergoing cardiac surgery with CPB. Stool samples were collected preoperatively and during the early postoperative period. Microbiota composition was assessed using culture-based microbiological methods, and fecal SCFA concentrations were measured by gas chromatography. Clinical, anthropometric, and laboratory parameters were assessed, and their associations with CPB characteristics and microbiome alterations were analyzed.

RESULTS: The postoperative period was characterized by significant intestinal dysbiosis, including reduced abundance of beneficial bacteria (Bifidobacterium, Lactobacillus, Bacteroides) and decreased SCFA-producing taxa. Fecal butyrate and propionate levels were significantly reduced. These changes were associated with increased intestinal inflammation, feeding intolerance, impaired nutrient absorption, and insufficient weight gain. The severity of dysbiosis correlated with CPB duration.

CONCLUSION: CPB in early childhood is associated with disruption of gut microbiota and reduced SCFA production, which are linked to postoperative feeding intolerance and impaired nutritional recovery. Targeted monitoring and modulation of the gut microbiome may improve clinical outcomes in pediatric cardiac surgery patients.},
}

@article {pmid42291758,
year = {2026},
author = {Zhang, S and Shoaie, S and Carpenter, GH},
title = {Suprathreshold non-volatile flavour perception is associated with multiple species rather than any single species via bacterial metabolism.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2686537},
pmid = {42291758},
issn = {2000-2297},
abstract = {BACKGROUND: The microbiome is the characteristic microbial community inhabiting a well-defined habitat with distinct physicochemical properties. During eating, food is masticated and mixed with saliva to form a bolus; non-volatile flavour molecules are released into the saliva and delivered to receptors on the tongue. Throughout this process, the oral microbiome is in direct contact with non-volatile flavour molecules. In this cross-sectional study, we hypothesised that the oral microbiome interacts with non-volatile flavour molecules to modulate suprathreshold taste perception.

MATERIALS AND METHODS: Fifty-three participants were included, with suprathreshold sensory data, salivary microbiome data (including both taxonomic and functional profiles), and salivary metabolome data. Associations were explored using fixed-effects linear-regression models and unsupervised clustering.

RESULTS: Suprathreshold non-volatile flavour perception was associated with the salivary microbiome via multispecies interactions rather than single-species effects. Taurine (an amino acid and confirmed bacterial metabolite) and ethanolamine (a phospholipid-related metabolite and confirmed bacterial metabolite) showed the greatest number of associations with suprathreshold taste perception in this study (6 of 8 sensory solution each).

CONCLUSION: This study suggested that suprathreshold taste perception was associated with inferred microbial metabolic pathways via multispecies interactions. Because inferred microbial metabolic pathways are encoded by multiple bacteria, they may better capture multispecies contributions than species-level taxonomic profiles.},
}

@article {pmid42291953,
year = {2026},
author = {Finlayson, CR and Hansen, NM and Stewart, S and Smith, M},
title = {Aetiology and Management of Acute Septic Arthritis and Prosthetic Joint Infection Presentations to Orthopaedics: An Evaluation of Tertiary Centre Performance.},
journal = {Cureus},
volume = {18},
number = {5},
pages = {e108830},
pmid = {42291953},
issn = {2168-8184},
abstract = {Background Septic arthritis (SA) and prosthetic joint infection (PJI) are common emergency referrals to orthopaedics in the United Kingdom. These infections carry a significant risk of harm due to chondrolysis and arthropathy and are a potential source of sepsis, requiring prompt assessment, investigation, and treatment. A joint aspirate is routinely sent for microscopy, culture , and sensitivities to aid treatment. In suspected PJI, this must be taken under sterile conditions to reduce the risk of iatrogenic PJI. Empirical antibiotics should then commence per the British National Formulary (BNF) or local policy. Due to the risks of delayed or ineffective treatment, evaluating local practice may identify areas to optimise treatment delivery and efficacy. Aims This study will evaluate the incidence of SA and PJI within a tertiary orthopaedic centre over 12 months. The culprit organisms and sensitivities, delivery of timely and appropriate antibiotics, serum infection markers, length of stay (LOS), and mortality will be reviewed. Methods Admissions to the orthopaedic unit between November 2023 and October 2024 were screened using the ICD-10 codes for pyogenic arthritis, prosthesis infection, or infection following a procedure. Further review confirmed cases of SA or PJI, excluding unsuitable admissions. Each patient's electronic record was examined for demographics, serum infection markers, LOS, 30-day mortality, relevant imaging, time to aspirate relative to admission, culture results, and timing and type of antibiotics initiated. Antibiotics used were compared to sensitivities and BNF recommendations to determine efficacy. Results A total of 27 admissions with SA and 24 of PJI were seen, accounting for 51 (1.9%) of 2,670 total admissions, relative to a mean annual arthroplasty incidence of 1,204 across the health board. The median age of PJI patients was 72 years, significantly higher than the median SA patient age of 52 years (p<0.01). Median LOS was also higher in PJI patients at 13.5 days compared to nine days in SA (p=0.036). Most infections were hip and knee joints at nine (33.3%) cases in SA, and 11 (45.8%) total knee replacements in PJI cohorts. Staphylococcus aureus was the most prevalent organism in each group; however, 11 (40.7%) of the SA aspirate cultures were negative. The median aspiration time, relative to admission, was 5.6 and 10.2 hours in SA and PJI, respectively. The median time to initiate antibiotics was 7.1 and 17.9 hours in SA and PJI, respectively. The majority of admissions received appropriate antibiotics at 20 (74.1%) of SA and 17 (70.8%) of PJI patients. Culture results confirmed sensitivity to recommended antibiotics in 14 (51.8%) of SA and 18 (75%) of PJI cases. The most initiated antibiotic overall was flucloxacillin. There was no significant difference in infection markers. Conclusion This study finds that PJI patients were typically older, with a greater LOS and comorbidity. Large joint infections, such as hips and knees, were the commonest presentation. The majority of each cohort was appropriately treated per the BNF, with S. aureus being the commonest cause. Factors such as prehospital antibiotics may reduce the bacterial yield of aspirations. Both groups show prolonged time taken to aspirate and treat, in which quality improvement interventions may reduce. Other centres may benefit from similar evaluations of the infective microbiome and the speed and efficacy of septic joint treatment.},
}

@article {pmid42292075,
year = {2026},
author = {Beattie McAliley, R and Hooper, L and Hoss, K and Vigerust, DJ},
title = {Test, Treat, Repopulate™ method reduces red complex bacteria and stabilizes the oral microbiome.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1839034},
pmid = {42292075},
issn = {2673-4915},
abstract = {Despite advances in dental hygiene and clinical interventions, preventable conditions such as tooth decay and gum disease remain widespread public health concerns. Recent research implicates complex, polymicrobial interactions as central drivers of disease pathogenesis, which often limits the effectiveness of traditional therapeutic approaches. Here, researchers evaluate the effectiveness of the Test, Treat, Repopulate method, a multi-phase oral health protocol combining scaling and root planing, targeted antibiotic therapy, use of a pH-balanced, prebiotic containing toothpaste and rinse, and daily oral probiotic use on the health of the oral microbiome. Retrospective analysis of RT-qPCR salivary diagnostic data from 38 de-identified U.S. patients, collected before and after treatment during routine care, demonstrated significant and sustained reductions in key oral pathogens following the combined treatment approach. Seven bacterial species were significantly reduced post-treatment, including Treponema denticola, Tannerella forsythia, Prevotella intermedia, Campylobacter rectus, Fusobacterium nucleatum, Fusobacterium nucleatum subsp. animalis, and Streptococcus mutans. Additional pathogens, including Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis, were also reduced. The protocol had minimal impact on the fungal species Candida albicans, highlighting an area for potential optimization. Additionally, four viral targets were assessed pre- and post-protocol, making this one of the first studies to evaluate a dental intervention's effects on oral viruses. Comparison of the cohort with 35,570 pre-treatment salivary diagnostic tests across the United States shows that baseline pathogen distributions reflect national patterns, supporting the generalizability of the protocol. A structured protocol for patients with elevated red complex bacteria is detailed, providing clinicians with a data-driven, reproducible framework for precision oral healthcare. These findings underscore the potential for microbiome-focused interventions to achieve measurable, lasting improvements in oral health across diverse populations.},
}

@article {pmid42292333,
year = {2026},
author = {Reynolds, A and Glenn, E and Lavoie, B and Ishaq, SL and Li, Y},
title = {Plant-derived bioactives, the gut-brain axis, and neurodegenerative diseases: mechanistic roles of diet-microbiota interactions.},
journal = {Frontiers in neuroscience},
volume = {20},
number = {},
pages = {1815972},
pmid = {42292333},
issn = {1662-4548},
abstract = {Diet is increasingly recognized as a potential upstream modulator of the gut-brain axis (GBA) through its effects on the microbiome, microbial metabolites, and host immune and endocrine responses. The GBA is a complex, bidirectional network connecting the gastrointestinal tract and central nervous system, with diet influencing microbial community structure and metabolic output. Plant-based diets, such as Mediterranean and MIND, have been associated with increased production of anti-inflammatory microbial metabolites and improved barrier function, while high calorie/low nutrient diets are often linked to increased immune activation and barrier dysfunction. However, while microbial metabolites, especially short-chain fatty acids, indoles, bile acids, and isothiocyanates, have been proposed as mediators of neuroprotective effects, their role in neurodegenerative diseases remains an area of active investigation, with evidence largely derived from preclinical and associative human studies. Cruciferous vegetables, especially broccoli sprouts, are an emerging focus of research for their bioactive compound sulforaphane, which activates Nrf2-centered cytoprotective pathways. Animal and early human studies suggest sulforaphane can improve cognitive and behavioral outcomes, though larger clinical trials are needed. Personalized, microbiota-targeted dietary interventions may offer scalable strategies for managing neuroinflammatory and neurodegenerative conditions, and we emphasize the need for integrated research across diet, microbiome, and brain health.},
}

@article {pmid42292359,
year = {2026},
author = {Zhang, Y and Qin, Y and Cheng, Z},
title = {Innate immune regulation of adaptive immunity: mechanisms, implications, and bias.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1847470},
pmid = {42292359},
issn = {1664-3224},
mesh = {Humans ; *Immunity, Innate ; *Adaptive Immunity ; Animals ; Signal Transduction ; Hypersensitivity/immunology ; Trained Immunity ; Epigenesis, Genetic ; Immune Tolerance ; },
abstract = {Innate immunity is not merely an early defensive system but a key regulator of adaptive immune fate. Through pattern-recognition receptor signaling, antigen presentation, cytokine production, and metabolic-epigenetic reprogramming, innate immune responses shape the strength, duration, and direction of T- and B-cell immunity. This review summarizes how innate immune regulation of adaptive immunity contributes to immune dysregulation in infection, autoimmunity, and allergic disease. We focus on three major mechanisms: remodeling of antigen presentation and costimulation, reshaping of cytokine microenvironments that guide T helper cell polarization, and metabolic-epigenetic programming associated with trained immunity or immune tolerance. We further propose that disease outcomes can be interpreted through three regulatory dimensions of innate immune signaling: insufficient signal strength promotes defective pathogen control and weak adaptive priming; persistent or excessive activation sustains autoimmune inflammation and loss of tolerance; and type 2-biased epithelial-innate signaling drives allergic inflammation through the alarmin-ILC2-Th2-IgE axis. By integrating molecular signaling, innate immune cell crosstalk, metabolic regulation, and epigenetic remodeling, this review provides a concise framework for understanding how innate immune imbalance shapes adaptive immune dysfunction and highlights therapeutic opportunities targeting interferon pathways, inflammasomes, epithelial alarmins, metabolic programs, and microbiome-related immune regulation.},
}

Humans
*Immunity, Innate
*Adaptive Immunity
Animals
Signal Transduction
Hypersensitivity/immunology
Trained Immunity
Epigenesis, Genetic
Immune Tolerance

@article {pmid42292378,
year = {2026},
author = {Gargaro, M and Fallarino, F and Zelante, T},
title = {Editorial: Host-microbe immunometabolic chat: a new era of organismal communication.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1882702},
doi = {10.3389/fimmu.2026.1882702},
pmid = {42292378},
issn = {1664-3224},
}

@article {pmid42292405,
year = {2026},
author = {Xiao, J and Duan, L and Yang, J and Deng, Y and Pang, S and Wang, H and Yin, X and Wang, H and Qiu, Y and Li, X and Gong, Y and Li, H},
title = {The landscape of cellular immune alteration in systemic lupus erythematosus.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1755310},
pmid = {42292405},
issn = {1664-3224},
mesh = {Humans ; *Lupus Erythematosus, Systemic/immunology/metabolism/therapy ; Animals ; *Immunity, Cellular ; Dysbiosis/immunology ; Gastrointestinal Microbiome/immunology ; Autoantibodies/immunology ; },
abstract = {Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by multi-organ inflammation and profound immune dysregulation. Aberrant interactions among adaptive and innate immune cells-including T cells, B cells, dendritic cells, macrophages, neutrophils, and natural killer cells-disrupt immune tolerance and perpetuate chronic inflammation. This review provides a comprehensive overview of the dysfunctional cellular immune landscape in SLE, focusing on the pathogenic crosstalk among immune cell subsets and its contribution to disease progression. We highlight the imbalance of T cell subsets (Th1, Th17, Tfh, Treg), B cell hyperactivation, and impaired regulatory cell function. Furthermore, we discuss how excessive NETosis, type I interferon signaling, and impaired apoptotic clearance amplify autoantibody production and immune complex-mediated injury. Emerging evidence positions gut microbiome dysbiosis as a critical environmental driver of immune dysregulation in SLE, characterized by depletion of beneficial butyrate-producing commensals and enrichment of pro-inflammatory taxa. This dysbiosis contributes to disease pathogenesis through gut barrier dysfunction, molecular mimicry, and short-chain fatty acid deficiency. Finally, we examine potential therapeutic strategies, including immune checkpoint modulation, metabolic interventions, and novel cellular therapies, aimed at restoring immune equilibrium in SLE.},
}

Humans
*Lupus Erythematosus, Systemic/immunology/metabolism/therapy
Animals
*Immunity, Cellular
Dysbiosis/immunology
Gastrointestinal Microbiome/immunology
Autoantibodies/immunology

@article {pmid42292406,
year = {2026},
author = {Sun, B and Wang, T},
title = {The microbiota-metabolite-immune axis in colorectal cancer: mechanistic insights and emerging clinical applications.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1768792},
pmid = {42292406},
issn = {1664-3224},
mesh = {Humans ; *Colorectal Neoplasms/immunology/metabolism/microbiology/etiology ; *Gastrointestinal Microbiome/immunology ; Animals ; Tumor Microenvironment/immunology ; Dysbiosis/immunology ; Signal Transduction ; },
abstract = {Colorectal cancer (CRC) results from a complex interplay of host genetics, environmental factors, and gut microbiota. Increasing evidence suggests that intestinal microorganisms significantly affect the initiation and progression of CRC through metabolic and immunological reprogramming. Dysbiosis, defined as an imbalance between beneficial and harmful microbial species, leads to chronic inflammation, genotoxic stress, and disruption of epithelial homeostasis. Microbial metabolites, such as short-chain fatty acids, secondary bile acids, and tryptophan derivatives, function as signaling molecules that influence epithelial proliferation, apoptosis, and immune cell activity. These metabolites regulate essential oncogenic and inflammatory pathways, including Wnt/β-catenin, NF-κB, and STAT3, and alter the tumor microenvironment by affecting regulatory T cells (Tregs), Th17 cells, macrophages, and myeloid-derived suppressor cells. Specific bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, illustrate how particular microbes can promote tumorigenesis through metabolite-mediated signaling and immune modulation. This review summarizes recent advances in understanding how gut microbiota and their metabolites contribute to colorectal carcinogenesis by influencing inflammatory signaling, epithelial homeostasis, and tumor immune responses. These mechanistic insights highlight the microbiota-metabolite-immune axis as a crucial driver of CRC initiation and progression. The increasing recognition that microbial alterations occur alongside early neoplastic changes and affect tumor behavior emphasizes their translational potential. Although further validation in large, well-controlled clinical settings is necessary, microbiome- and metabolite-based markers could enhance current strategies for the early detection, risk assessment, and therapeutic guidance of CRC. Ultimately, deepening our understanding of the intricate interactions between intestinal microbes, host metabolism, and immune regulation will facilitate the development of microbiome-informed approaches for CRC monitoring and intervention in the future.},
}

Humans
*Colorectal Neoplasms/immunology/metabolism/microbiology/etiology
*Gastrointestinal Microbiome/immunology
Animals
Tumor Microenvironment/immunology
Dysbiosis/immunology
Signal Transduction

@article {pmid42292417,
year = {2026},
author = {Wang, Y and Dong, C and Xiao, Y},
title = {Polystyrene nanoplastics promotes inflammation and aging in young mice through the oral-gut microbiome axis.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1806158},
pmid = {42292417},
issn = {1664-3224},
mesh = {Animals ; *Polystyrenes/toxicity/adverse effects ; *Aging/drug effects/immunology ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Inflammation/chemically induced/metabolism ; Cytokines/metabolism ; Mice, Inbred C57BL ; Male ; *Microplastics ; *Nanoparticles/toxicity ; *Mouth/microbiology ; Inflammation Mediators/metabolism ; Dysbiosis/chemically induced ; Cellular Senescence/drug effects ; },
abstract = {With the escalating global pollution of nanoplastics, their impacts on organismal health have become a focal concern. The oral-gut microbiota axis plays a pivotal role in host health regulation, yet how nanoplastics influence this axis and drive inflammation and aging in young organisms remain undefined. This study aimed to investigate whether polystyrene nanoplastics (PS-NPs) promote inflammation and aging in young mice by disrupting the oral-gut microbiota axis. Therefore, we established a free-feeding model with 1000 μg/L PS-NPs using 8-week-old C57BL/6 mice. We quantified tissue inflammatory cytokines and cellular senescence markers to assess PS-NPs-induced inflammatory and aging effects, while 16S rRNA sequencing was employed to characterize oral and gut microbiota structural changes. We found that PS-NPs exposure significantly increased the expression levels of cellular senescence markers p21[Cip1/Waf] and p16[Ink4a] in lung and liver. Meanwhile, PS-NPs promoted the release of inflammatory cytokines such as IL-1β, IL-6 and TNF-α, by modulating the p38 MAPK pathway. In addition, PS-NPs also decreased the expression levels of antioxidant genes. Furthermore, 16S rRNA sequencing analysis revealed that PS-NPs exposure caused dysbiosis in oral and intestinal microbiota, manifested as significant alterations in microbial diversity and community structure. Our work provided mechanistic insights into nanoplastic toxicity and theoretical basis for developing preventive strategies.},
}

Animals
*Polystyrenes/toxicity/adverse effects
*Aging/drug effects/immunology
*Gastrointestinal Microbiome/drug effects
Mice
*Inflammation/chemically induced/metabolism
Cytokines/metabolism
Mice, Inbred C57BL
Male
*Microplastics
*Nanoparticles/toxicity
*Mouth/microbiology
Inflammation Mediators/metabolism
Dysbiosis/chemically induced
Cellular Senescence/drug effects

@article {pmid42292476,
year = {2026},
author = {Zhou, Y and Li, Z and Chu, Y and Zhou, Z and Zhang, T and Yi, N and Sun, W and Yan, J and Yan, Z and Zhu, A},
title = {Reframing precision nutrition in irritable bowel syndrome: a mechanism-informed conceptual framework for responder prediction and clinical translation.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1809221},
pmid = {42292476},
issn = {1664-3224},
mesh = {Humans ; *Irritable Bowel Syndrome/diet therapy/microbiology/metabolism ; *Gastrointestinal Microbiome ; FODMAP Diet ; *Precision Medicine/methods ; Multiomics ; Translational Research, Biomedical ; },
abstract = {BACKGROUND: The low-Fermentable Oligosaccharides, Disaccharides, Monosaccharides and Polyols (FODMAP) diet is widely used for irritable bowel syndrome (IBS), but response varies markedly across patients. This heterogeneity has shifted the field from testing average efficacy toward forecasting individual benefit and translating microbiome science into practical precision-nutrition tools.

METHODS: We present a conceptual analysis grounded in evidence mapping from human IBS studies that paired dietary interventions (primarily low-FODMAP pathways) with baseline microbiome and/or multi-omics measurements. Findings are organized within a "microbiome-to-model" roadmap that specifies responder endpoints, candidate data layers (taxa, functions, metabolites and volatile signatures), modeling choices, and the validation and implementation requirements needed for clinical decision support.

RESULTS: Three recurring signals emerge across cohorts. Baseline microbial ecology can stratify response, but taxonomic features alone often fail to transport across studies. Functional readouts, including metabolites and volatile signatures, are closer to symptom mechanisms and can improve interpretability; however, clinical deployment is still limited by endpoint heterogeneity, imperfect exposure and adherence measurement, batch effects, and insufficient external validation and calibration.

CONCLUSION: IBS is well suited for microbiome-informed responder prediction, provided that models are developed with deployment in mind. Progress will depend on validation-first study designs, harmonized responder endpoints and adherence capture, robust multi-omics pipelines, and biologically interpretable decision rules that can be prospectively tested and monitored for temporal instability in real-world care.},
}

Humans
*Irritable Bowel Syndrome/diet therapy/microbiology/metabolism
*Gastrointestinal Microbiome
FODMAP Diet
*Precision Medicine/methods
Multiomics
Translational Research, Biomedical

@article {pmid42292489,
year = {2026},
author = {Zhang, L and Gu, Y and Deng, R and Ouyang, Y},
title = {Dual role of IL-17A in COPD: amplifier of inflammatory cascades and mediator of airway remodeling and alveolar destruction.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1828172},
pmid = {42292489},
issn = {1664-3224},
mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/immunology/pathology/metabolism/drug therapy ; *Interleukin-17/metabolism/immunology ; *Airway Remodeling/immunology ; Animals ; Signal Transduction ; Inflammation/immunology ; *Pulmonary Alveoli/pathology/immunology ; },
abstract = {Corticosteroid resistance remains a central challenge in managing chronic obstructive pulmonary disease (COPD). This refractory phenotype is primarily driven by persistent, neutrophil-dominated airway inflammation. Interleukin-17A (IL-17A) bridges innate and adaptive immunity and helps sustain this refractory inflammation, although it operates within a redundant cytokine network and its pathogenic contribution is clearest in a defined molecular subset of patients. Following an overview of upstream drivers including lung-gut microbiome dysbiosis and Th17/Treg immune imbalance, the downstream effector network of IL-17A is analyzed. In sustaining inflammation, IL-17A stabilizes pro-inflammatory transcripts via ACT1-mediated post-transcriptional regulation and produces a self-amplifying positive feedback loop with neutrophil extracellular traps (NETs). In tissue remodeling, IL-17A induces alveolar epithelial ferroptosis via the ACT1-TRAF6-p38 MAPK cascade to drive emphysema. It also mediates irreversible structural alterations in the airway and alveolar parenchyma by inhibiting fibroblast autophagy through the PI3K/AKT/mTOR pathway and inducing epithelial mucus hypersecretion. Given the lack of significant clinical benefit from early non-selective IL-17A blockade in unselected populations, precision intervention strategies guided by clinical endotypes are evaluated. Optimizing next-generation targeted therapies in COPD necessitates biomarker-driven patient stratification, coupled with upstream signal interception and the restoration of systemic immune homeostasis. Together, these strategies support a shift from symptomatic management toward endotype-specific disease modification.},
}

Humans
*Pulmonary Disease, Chronic Obstructive/immunology/pathology/metabolism/drug therapy
*Interleukin-17/metabolism/immunology
*Airway Remodeling/immunology
Animals
Signal Transduction
Inflammation/immunology
*Pulmonary Alveoli/pathology/immunology

@article {pmid42292620,
year = {2026},
author = {Zhou, Q and Lai, C and Zhang, M and Li, R and Li, K and He, W},
title = {Pediatric health: mechanistic insights into inflammatory diseases and emerging therapeutic pathway-targeted approaches.},
journal = {Translational pediatrics},
volume = {15},
number = {5},
pages = {195},
pmid = {42292620},
issn = {2224-4344},
abstract = {Pediatric inflammatory diseases, including juvenile idiopathic arthritis, pediatric inflammatory bowel disease, asthma, Kawasaki disease, and multisystem inflammatory syndrome in children, are an increasing global health concern. These conditions arise from dysregulated immune responses shaped by genetic susceptibility, environmental exposures, and the distinctive features of the developing pediatric immune system. This review presents a mechanism-centered overview of pediatric inflammation, emphasizing immune ontogeny, innate and adaptive immune dysregulation, cytokine signaling, inflammasome activation, oxidative stress, and the gut-immune axis. It also highlights emerging pathway-targeted therapies, including cytokine blockade, JAK inhibitors, microbiome-based interventions, and gene-editing strategies, with attention to their relevance for pediatric precision medicine. Early, mechanism-based intervention during critical developmental windows may improve long-term outcomes and reduce the lifetime burden of inflammatory disease. Overall, this review provides a concise, pediatric-focused perspective on how developmental immunology and targeted therapeutics can inform more precise and effective management of childhood inflammatory disorders.},
}

@article {pmid42292737,
year = {2026},
author = {Qiu, C and Guo, C and Xue, X and Feng, P and Zhang, Q and Li, Y and Liu, S and Li, Y and Bukhari, I and Ren, F and Zhang, Y and Zheng, P and Mi, Y},
title = {Exposure to calcium stearyl lactylate induces hepatointestinal toxicity and gut microbiota dysbiosis in mice.},
journal = {Current research in toxicology},
volume = {10},
number = {},
pages = {100301},
pmid = {42292737},
issn = {2666-027X},
abstract = {Calcium stearyl lactylate (CSL) is a widely used food emulsifier, particularly in pasta products. In this study, we investigated the potential toxicological effects of CSL exposure on organ health and gut microbiota in mice. Over a 12-week period, mice were administered CSL at 50, 500, and 5000 mg/kg·bw. Our study found that CSL exposure induced liver and colon inflammation, significantly elevating hepatic injury markers (ALT and AST). In parallel, key intestinal functional markers (CXCL-1, CXCL-2, IL-1β, TNF-α, ZO-1, and Occludin) were markedly altered, indicating compromised gut barrier integrity. 16S rRNA sequencing revealed that CSL administration disrupted gut microbial diversity, characterized by decreased beneficial bacteria (e.g., Bifidobacterium and Lactobacillus) and increased potentially harmful genera, including Anaerotruncus, Desulfovibrio, and Helicobacter. These findings indicate that long-term CSL intake can induce hepatointestinal damage and provoke significant dysbiosis of the gut microbiome.},
}

@article {pmid42292847,
year = {2026},
author = {You, Q and Jin, M and Zhou, B and Huang, C and Lin, Z and Hu, J and Xue, J and Chen, X and Xiao, Y and Li, R and Zong, Y and Wu, M and Zhang, T and Liu, H},
title = {Gut microbiome components predict response to neoadjuvant short-course radiotherapy followed by camrelizumab and chemotherapy in locally advanced rectal cancer (UNION): a prospective study.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1829108},
pmid = {42292847},
issn = {1663-9812},
abstract = {BACKGROUND: Although the gut microbiome shapes responses to anti-tumor immunotherapy and chemotherapy, its predictive value for neoadjuvant short-course radiotherapy (SCRT) followed by camrelizumab (CAM) and CAPOX in patients with locally advanced rectal cancer (LARC) has not been defined. This exploratory study aimed to evaluate whether the gut microbiome is associated with response to neoadjuvant SCRT followed by CAM and CAPOX.

METHODS: We obtained a total of 77 fecal samples from 36 patients with LARC, including 17 assigned to the long-course chemoradiotherapy (LCRT) group and 19 to the SCRT group. Samples were collected at three time points: baseline, after radiotherapy, and after chemoimmunotherapy. DNA was extracted, followed by metagenomic sequencing to profile microbiota dynamics during neoadjuvant treatment.

RESULTS: In this pilot analysis, we observed significant differences in the gut microbiota between the SCRT and LCRT treatment cohorts. Specifically, Bifidobacterium and Dorea were significantly enriched following completion of SCRT sequential CAM and CAPOX therapy. Further analysis revealed that the relative abundances of these two genera changed significantly only before and after the SCRT regimen, with no notable changes observed in the LCRT group. Preliminary ROC analysis suggested potential utility of these taxa for predicting treatment response, though validation in larger cohorts is needed.

CONCLUSION: The gut microbiome offers potential biomarkers that may stratify response to SCRT followed by CAM and CAPOX, representing a promising exploratory finding with potential clinical relevance.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/, identifier NCT04928807.},
}

@article {pmid42292951,
year = {2026},
author = {Li, M and Hao, L and Shi, X and Wang, J and Li, H and Wang, Y and Khambalkar, P and Sun, X and Rima, S and Guo, X and Fang, X and Ma, L},
title = {Solanaceous vegetables and Fusarium oxysporum interactions: pathogen genomics, pathogenesis, host resistance, and emerging microbiome-driven disease management.},
journal = {Horticulture research},
volume = {13},
number = {6},
pages = {uhag074},
pmid = {42292951},
issn = {2662-6810},
abstract = {Solanaceous vegetables are continuously threatened by Fusarium wilt disease, which is mainly caused by Fusarium oxysporum (Fo), a fungal species complex comprising many devastating soil-borne pathogens, resulting in severe yield losses worldwide. Over the past decade, significant and numerous advances have been made in dissecting the molecular and genomic basis underlying the interaction between solanaceous vegetables and Fo, particularly owing to the emergence of the tomato-Fo pathosystem as a powerful model system for studying the molecular basis of resistance and susceptibility in solanaceous vegetables against vascular wilt pathogens. In this review, we summarize recent advances driven by improvements in genome sequencing and assembly of Fo infecting solanaceous vegetables, the virulence strategies and diverse arsenals employed by Fo to modulate and suppress host immunity, as well as the identification and functional characterization of race-specific resistance genes in solanaceous vegetables and their corresponding Fo determinants. We address the potential downstream signaling pathways involved in activating solanaceous vegetable immunity against Fo. In addition, we explore emerging insights into microbiome-based strategies for disease control, emphasizing the potential use of beneficial and synthetic microbes in the sustainable management of Fusarium wilt in tomato. Collectively, this review provides an integrated perspective on pathogen genomics, pathogenesis, host resistance, and microbiome-driven control of Fusarium wilt in tomato, offering promising avenues for developing durable and broad-spectrum resistance against various Fo strains in solanaceous vegetables.},
}

@article {pmid42293013,
year = {2026},
author = {Suo, Y and Zhang, X and Li, L and Si, X and Xu, F and Wang, X and Cheng, P and Li, Q and Yan, M},
title = {Impact of wheat straw incorporation and fertilizer reduction on peanut yield and soil functions.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1828860},
pmid = {42293013},
issn = {1664-462X},
abstract = {INTRODUCTION: Balancing crop productivity with sustainable soil management is a critical challenge in modern agriculture.

METHODS: We conducted a three-year randomized complete block field experiment (2022-2024) to evaluate the integrated effects of wheat straw incorporation regimes and fertilizer reduction on the plant-soil-microbe nexus in peanut (Arachis hypogaea L.) production. Six treatments were compared: no straw return (CT), conventional straw incorporation (SI), deep straw incorporation with a decomposition accelerator (SD), deep incorporation with accelerator and a 25% fertilizer reduction (SDR), surface mulching (SM), and SM with a 25% fertilizer reduction (SMR).

RESULTS: Relative to CT, deep straw incorporation (SD and SDR) significantly increased the three-year mean peanut yield by 12-25%. Notably, the SDR regime maintained final yields, plant nutrient uptake, and soil aggregate stability statistically equivalent to the fully fertilized SD treatment (P > 0.05), successfully substituting for a 25% reduction in mineral inputs. Mechanistically, deep straw incorporation actively reshaped the rhizosphere microenvironment. Deep straw incorporation actively reshaped the rhizosphere microenvironment, enriching beneficial functional microbial taxa including Bacillus, Sphingomonas, and Trichoderma, which subsequently elevated the activities of carbon, nitrogen, and phosphorus-cycling extracellular hydrolases and oxidative enzymes by 1.4- to 2.6-fold. This microbially mediated acceleration of nutrient cycling enhanced soil organic carbon, microbial biomass carbon, and available nutrient pools, thereby improving soil nutrient availability and peanut production capacity.

DISCUSSION: Our findings demonstrate that deep straw incorporation with targeted microbial decomposition accelerators, combined with a 25% reduction in mineral fertilizer, provides a practical, low-input strategy to sustain high peanut yields, optimize root-zone functions, and advance climate-smart agricultural systems.},
}

@article {pmid42293143,
year = {2026},
author = {Kocaadam-Bozkurt, B and Aslan, S and Bozkurt, O and Bodur, M and Agagündüz, D and Budán, F},
title = {Gerobiotics and neuroprotection: effects on the gut-brain axis in age-related neurodegenerative diseases.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1814234},
pmid = {42293143},
issn = {1663-4365},
abstract = {As the global population ages, effective strategies to attenuate or prevent neurodegenerative processes are becoming increasingly important. Gerobiotics, an emerging class of probiotic strains and their derived postbiotics, are considered promising geroprotective agents because of their potential to target fundamental mechanisms of aging, modulate the gut-brain axis, and attenuate age-related cognitive and functional decline. This review aims to synthesize existing evidence from preclinical and clinical studies on the neuroprotective effects of gerobiotics, with particular emphasis on ageing-related changes in gut microbiota composition, systemic inflammation, and the pathophysiology of neurodegenerative diseases. Preclinical animal studies show that gerobiotics ameliorate memory impairment, preserve synaptic integrity, and attenuate neuroinflammation. Furthermore, clinical results suggest improvements in cognitive performance, mood regulation, and gastrointestinal function, particularly in the early stages of neurodegenerative disorders and among individuals with mild cognitive impairment. The microbiota-gut-brain axis has emerged as a relevant therapeutic target, with gerobiotic supplementation representing a multidimensional approach to support healthy cognitive ageing and counteract neurodegenerative processes. The underlying mechanisms, manifested mostly through modulation of microbial metabolites, include the restoration of intestinal and blood-brain barrier integrity, the reduction of neuroinflammation, the enhancement of neurotrophic factors, and the modulation of immunological pathways. Although current evidence is promising, heterogeneity in probiotic strains, dosages, and study designs indicates the need for further rigorous investigation. Further well-designed, large-scale clinical studies are required to establish efficacy, optimize intervention protocols, and support the translation of gerobiotics into evidence-based clinical practice for the prevention and management of age-related neurodegenerative diseases.},
}

@article {pmid42293159,
year = {2026},
author = {Ike, I and Teymouri, F and Crook, C and Guzman, S and Hazeltine, M and Castillo, D and Li, D and Brar, G},
title = {The interplay between bile acid metabolism and gut microbiome in biliary tract cancers.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1774429},
pmid = {42293159},
issn = {2813-4338},
abstract = {The gut microbiota and bile acids (BAs) exist in a tightly regulated, bidirectional relationship that influences host metabolism, immune function, and disease. Primary BAs synthesized in the liver are chemically transformed by intestinal microbes into a diverse pool of secondary BAs, which exert antimicrobial effects and activate host signaling pathways including Farnesoid X Receptor (FXR), Takeda G protein-coupled receptor 5 (TGR5), and sphingosine-1-phosphate receptor 2 (S1PR2). These pathways regulate BA homeostasis, epithelial barrier integrity, inflammation, and carcinogenesis. Disruption of this BA-microbiome axis has been implicated in biliary tract cancers (BTCs), a group of aggressive malignancies with rising global incidence and limited therapeutic options. Secondary BAs and BA receptor signaling contribute to tumor initiation and progression through NF-κB activation, oxidative stress, and altered cell survival, whereas reduced FXR signaling and obstructed enterohepatic circulation further promote inflammatory dysregulation. Emerging evidence demonstrates that microbial dysbiosis and altered BA metabolism are associated with distinct BTC microbial profiles, enriched in taxa such as Fusobacterium, Salmonella, Prevotella, and Actinomyces, alongside depletion of commensals including Lactobacillus. These taxa influence inflammatory signaling, BA transformation, and epithelial injury, contributing to carcinogenesis. Microbiome-BA interactions also shape anti-tumor immunity and responses to immune checkpoint inhibitors (ICIs). Specific microbial signatures-particularly enrichment of Lachnospiraceae, Erysipelotrichaceae, Bacteroidetes, and Alistipes-correlate with enhanced immune activation and improved clinical outcomes in hepatobiliary cancers. Modulation of gut microbiota through antibiotics, probiotics, or fecal microbiota transplantation can influence BA composition, immune surveillance, and therapeutic efficacy. Collectively, these data highlight the central role of the BA-microbiome axis in BTC pathogenesis and treatment response. Microbial and BA metabolite profiling represent promising avenues for biomarker development, while targeted manipulation of BA signaling and microbial ecology offers potential therapeutic strategies to improve BTC outcomes.},
}

@article {pmid42293160,
year = {2026},
author = {Han, Y and Zhang, H and Zhang, J},
title = {Altered early-life gut microbiota in offspring of pregnancies complicated by CHD-associated pulmonary hypertension.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1785707},
pmid = {42293160},
issn = {2813-4338},
abstract = {BACKGROUND: Pulmonary arterial hypertension is a progressive disease involving the pulmonary vasculature and is defined as a mean pulmonary arterial pressure (mPAP) >20 mmHg at rest. Pulmonary arterial hypertension during pregnancy is associated with increased maternal mortality and adverse fetal outcomes. The present study aimed to investigate differences in the initial meconium microbiota between neonates born to mothers with congenital heart disease-associated pulmonary arterial hypertension (CHD-PAH) and those born to mothers with congenital heart disease (CHD) alone, thereby elucidating the potential influence of pulmonary arterial hypertension on the establishment of the early-life gut microbiome.

METHODS: We collected first-pass meconium samples from neonates in the pulmonary hypertension group (PH group, n = 23) and the control group without pulmonary hypertension (NC group, n = 17) and characterized microbial profiles using 16S rRNA sequencing.

RESULTS: The PH group showed lower alpha diversity, with reduced Shannon and observed features indices (both P < 0.05), whereas Bray-Curtis beta diversity showed substantial overlap between groups. At the phylum level, the overall gut microbial structure was broadly comparable between the PH and NC groups, with no statistically significant differences in the relative abundance of dominant taxa. At the genus level, the mean relative abundance of Streptococcus was significantly lower in the PH group than in the NC group (0.20% vs. 2.09%, P = 0.0072). Predicted functional profiling suggested potential differences in dominant metabolic pathways between groups, including enrichment of ubiquinone biosynthesis and aromatic amino acid/chorismate biosynthesis pathways in the PH group.

CONCLUSION: Collectively, these findings extend current evidence on PAH-related alterations in early-life microbial ecosystems and provide a plausible microbiome-based basis for investigating the biological mechanisms underlying adverse maternal-fetal outcomes associated with pulmonary arterial hypertension.},
}

@article {pmid42293161,
year = {2026},
author = {Nunez, H and Straub, TJ and Imam, N and Goad, D and Mueller, NT and Mars, RAT and Sew Hoy, C and Paullin, T and Sukhum, KV},
title = {Age-specific early-life gut microbiome associations with eczema and food allergies during early immune development.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1804117},
pmid = {42293161},
issn = {2813-4338},
abstract = {INTRODUCTION: Eczema and food allergy commonly emerge during infancy and are linked to changes in the gut microbiome, yet it remains unclear when microbiome differences associated with allergic disease first appear during development.

METHODS: We analyzed age-stratified shotgun metagenomic data from 97 children aged 4-36 months, including physician-confirmed cases of eczema or food allergy and non-allergic controls, excluding recent antibiotic or probiotic exposure. Microbial taxa, functional pathways, and composite microbiome metrics were evaluated across three developmental stages: early infancy (4-6 months), mid-infancy (6-12 months), and toddlerhood (12-36 months).

RESULTS: Differences between allergic and non-allergic children were minimal before 6 months of age but became more apparent during mid-infancy and persisted into toddlerhood. Allergic conditions were associated with reduced abundance of fiber-fermenting and butyrate-producing taxa, enrichment of facultative and inflammation-associated microbes, lower microbiome maturation scores, and shifts in metabolic and inflammatory functional capacity.

DISCUSSION: These findings suggest that gut microbiome divergence associated with allergic disease becomes more apparent during mid-infancy, highlighting a developmentally relevant period for understanding early immune disruption. The results support further longitudinal and interventional studies aimed at clarifying whether earlier microbiome-targeted strategies may help modify progression along the atopic march.},
}

@article {pmid42293186,
year = {2026},
author = {Chen, K and Jin, S and Nie, Y and He, N and Chen, H and Yuan, J and Li, X and Liong, MT},
title = {Efficacy of Bifidobacterium lactis BLa80 in preventing early childhood eczema and respiratory infections via gut microbiome and immune modulation.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1727191},
pmid = {42293186},
issn = {2296-861X},
abstract = {BACKGROUND: Early childhood is a critical period for immune development, with eczema and respiratory infections representing common health challenges. This study investigated the efficacy of Bifidobacterium animalis subsp. lactis BLa80 in reducing these conditions potentially through gut microbiome modulation.

METHODS: In a randomized, double-blind, placebo-controlled trial, 360 formula-fed infants and children aged below 3 years old with elevated allergy risk received daily B. lactis BLa80 (5 × 10[9] CFU) or placebo for 180 days. Primary outcomes included eczema incidence and symptom burden, with secondary outcomes assessing respiratory infections, gastrointestinal symptoms, gut microbiota composition (16S rRNA sequencing), functional pathways (KEGG analysis), and fecal immune markers (ELISA).

RESULTS: The probiotic group demonstrated significantly reduced eczema incidence (27.6% vs. 69.5%, RR: 0.398, p < 0.001) and upper respiratory tract infections (19.4% vs. 42.5%, RR: 0.457, p < 0.001). Significant reductions were observed in symptom burden, including nasal congestion, vomiting, milk aspiration, and irritability. Microbiota profiling showed enrichment of beneficial taxa (Akkermansia, Fusicatenibacter) with enhanced metabolic pathways including tryptophan metabolism, vitamin biosynthesis, and xenobiotic degradation. Immunological profiling showed maintained human beta-defensin-2 (p = 0.005), increased secretory IgA (p < 0.001), and reduced calprotectin (p < 0.001).

CONCLUSIONS: B. lactis BLa80 supplementation effectively reduces eczema and respiratory infections associated with gut microbiome remodeling that may enhance barrier function, immune regulation, and metabolic capacity, supporting its use as a preventive nutritional strategy in early childhood.

CLINICAL TRIAL REGISTRATION: ChiCTR2300074956.},
}

@article {pmid42293192,
year = {2026},
author = {Shahbazi, S and Aminzadeh, S and Taati Moghadam, M and Rajabi, S and Vaziri, SS and Rostamian, M},
title = {Ramadan intermittent fasting and the gut microbiome: modulation of diversity and implications for metabolic health.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1767573},
pmid = {42293192},
issn = {2296-861X},
abstract = {Ramadan fasting (RF), a culturally embedded form of time-restricted eating, involves daily abstinence from food and drink from dawn to sunset and provides a real-world human model to examine the potential impact of intermittent fasting on the gut microbiome and metabolic health. This review synthesizes evidence from human studies, predominantly observational in design, to evaluate the associations between RF, microbial composition and diversity, and metabolic outcomes. Current evidence suggests that RF may be associated with changes in gut microbial richness and community structure, including reported increases in taxa such as Akkermansia muciniphila, Faecalibacterium prausnitzii, Roseburia, and Bacteroides, many of which are linked to short-chain fatty acid (SCFA) production and intestinal barrier function. However, findings across studies are not entirely consistent, particularly with respect to microbial taxa abundance and SCFA levels. Observational studies also report concurrent changes in anthropometric and metabolic parameters, including body weight, lipid profiles, glycemic markers, and inflammatory indices, although these associations may be influenced by confounding factors such as dietary composition, lifestyle changes, and weight loss during Ramadan. Proposed mechanisms include alterations in feeding-fasting rhythms and microbiota-related pathways such as bile acid metabolism and gut barrier function; however, these mechanisms are largely inferred from related experimental models and should be considered hypothesis-generating in the context of RF. Therefore, while RF represents a relevant ecological model for studying time-restricted eating in humans, the current evidence remains limited by small sample sizes, interindividual variability, and methodological heterogeneity. Further well-controlled, longitudinal, and multi-omics studies are required to clarify causal relationships and determine the extent to which RF-associated microbial changes contribute to metabolic health.},
}

@article {pmid42293200,
year = {2026},
author = {Shi, Y and Zhu, S and Chen, Z and Chao, K and Huang, Z and Gao, X},
title = {Gastrointestinal dysfunction score for mortality prediction in intensive care unit patients with pre-existing digestive system disease: a prospective observational study.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1831897},
pmid = {42293200},
issn = {2296-861X},
abstract = {BACKGROUND: Gastrointestinal (GI) dysfunction has been increasingly recognized as a common and clinically important problem in patients in the Intensive Care Unit (ICU). GI dysfunction may affect nutrition, immune function, and microbiome homeostasis, which has been associated with adverse outcomes in ICU patients. However, conventional organ failure scores such as the Sequential Organ Failure Assessment (SOFA) score do not adequately account for GI dysfunction, particularly in patients with pre-existing digestive system disease.

OBJECTIVE: This study aimed to evaluate the performance of the Gastrointestinal Dysfunction Score (GIDS) in adult ICU patients with pre-existing digestive system disease and to examine whether integrating GIDS with SOFA improves discrimination for 28-day mortality compared to SOFA alone.

METHODS: This single-center, prospective observational study included adult patients admitted to the ICU, excluding pregnancy, ICU readmission, cessation of active treatment, loss to follow-up and death within 24 h of ICU admission. Patients were stratified into GI and non-GI cohorts based on the presence of pre-existing digestive system disease at ICU admission. GIDS, SOFA and acute gastrointestinal irnjury (AGI) gades were recorded daily for the first ICU week. We compared baseline clinical characteristics and 28-day mortality between cohorts and evaluated whether adding GIDS to SOFA improved discrimination.

RESULTS: A total of 486 patients were included, with 359 in the GI cohort. Using the score of the first day in ICU, GIDS (AUC = 0.701) outperformed AGI (AUC = 0.614). When combined with SOFA, GIDS+SOFA had the highest AUC of 0.764, compared with SOFA alone (AUC = 0.739). In the GI cohort, GIDS+SOFA also demonstrated superior discrimination (AUC = 0.754) compared to SOFA alone (AUC = 0.723).

CONCLUSION: GIDS provides a meaningful stratification of 28-day mortality risk, especially in patients with pre-existing digestive system disease. Adding GIDS to SOFA modestly improved discrimination for 28-day mortality and warrants external validation. These findings support further validation and potential incorporation of GIDS into clinical practice.},
}

@article {pmid42293219,
year = {2026},
author = {Abu Dheir, N and Radwan, H and Hasan, H and Papandreou, D and Zeb, F and Abdelrahim, DN and Abdelaziz, MA and Abdoh, NN and Mohamad, MN and Al Dhaheri, AS and Stojanovska, L and Cheikh Ismail, L},
title = {Breastfeeding and prevention of childhood obesity: a narrative review of behavioral, hormonal, and microbiome programming.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1800487},
pmid = {42293219},
issn = {2296-861X},
abstract = {Childhood obesity has emerged as a major public health concern worldwide, with increasing prevalence in high-income countries. Growing evidence suggests that early-life nutrition, particularly breastfeeding, plays a critical role in reducing obesity that shaping long-term metabolic health. This narrative review highlight association between breastfeeding duration, exclusivity, and childhood obesity risk, synthesizing current evidence while exploring potential biological and behavioral mechanisms. Most studies report that breastfeeding, particularly when exclusive and sustained for longer durations, is associated with a reduced risk of childhood overweight and obesity. Evidence consistently shows that breastfed infants exhibit healthier growth trajectories, lower rates of rapid weight gain, and reduced adiposity compared to formula-fed infants. Several studies also identify plausible biological mechanisms, including appetite regulation, favorable insulin responses, and the influence of bioactive components in human milk, such as leptin, adiponectin, ghrelin, insulin-like growth factors (IGFs) and gut microbiome modulating factors. Nonetheless, some studies show weak or non-significant associations, often attributable to methodological differences, inconsistent breastfeeding practices, or inadequate adjustment for confounders such as maternal BMI and socioeconomic status. Current literature indicates that breastfeeding may serve as a protective factor against childhood obesity, highlighting its relevance in early-life nutrition and long-term health outcomes. This review underscores that promoting exclusive breastfeeding for at least 6 months should be a cornerstone of public health strategies to prevent childhood obesity.},
}

@article {pmid42293411,
year = {2025},
author = {Liu, M and Gong, J and Liu, Y and Yu, J and Hu, Z and Liu, Z},
title = {Multi-omics reveals circadian regulation of bone homeostasis by gut microbiota metabolites: mechanisms and chronotherapeutic implications.},
journal = {Frontiers in immunology},
volume = {16},
number = {},
pages = {1719445},
pmid = {42293411},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Animals ; *Homeostasis ; *Circadian Rhythm ; *Bone and Bones/metabolism/physiology ; Bone Remodeling ; Metabolomics ; Fatty Acids, Volatile/metabolism ; Osteogenesis ; },
abstract = {The gut-bone axis plays a pivotal role in skeletal health, yet the integration of multi-omics approaches to elucidate circadian metabolite-bone interactions remains limited. This review synthesizes evidence from metagenomics, metabolomics, and germ-free models to uncover how microbiota-derived metabolites-including short-chain fatty acids (SCFAs), bile acids, tryptophan derivatives, and gaseous molecules-orchestrate bone remodeling in osteoporosis, osteoarthritis, and bone malignancies. Many studies demonstrate that SCFAs inhibit osteoclastogenesis via GPR43/HDAC signaling and promote osteoblast metabolic reprogramming, while bile acids enhance osteogenesis through FXR/Wnt/β-catenin activation. Tryptophan metabolites repair intestinal barrier integrity and modulate osteoimmunity via the AhR pathway. Single-cell omics reveal circadian oscillations of metabolite receptors (e.g., GPR43, FXR) in bone stromal cells, linking microbial diurnal rhythms to epigenetic regulation of bone turnover. We propose a novel "metabolite-immune-bone triad" model, highlighting microbiome-driven immunometabolic reprogramming as a central regulator of skeletal homeostasis. These insights advance precision microbial therapeutics and chrono-nutritional strategies, bridging multi-omics discoveries with clinical applications for bone disorders.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Animals
*Homeostasis
*Circadian Rhythm
*Bone and Bones/metabolism/physiology
Bone Remodeling
Metabolomics
Fatty Acids, Volatile/metabolism
Osteogenesis

@article {pmid42293516,
year = {2026},
author = {Zou, Y and Liu, L and Chen, H and Luo, Z and Zhu, Z and Li, Z and Lin, B and Zhuang, Z and Li, W and Yang, Q and Yang, X and Zhou, H and Luo, M and Dai, D},
title = {Study protocol for a randomized controlled trial of fecal microbiota transplantation via different routes in children with moderate-to-severe autism spectrum disorder.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829532},
pmid = {42293516},
issn = {1664-302X},
abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) shows promise for autism spectrum disorder (ASD) by modulating the gut-brain axis, but the optimal delivery route remains unknown. Our previous single-arm study suggested efficacy of nasojejunal FMT in children with moderate-to-severe ASD, yet could not exclude placebo effects or compare routes. This randomized controlled trial aims to determine the most effective and tolerable FMT administration route.

METHODS: This single-center, randomized, triple-blind, double-dummy, placebo-controlled, three-arm parallel-group trial will enroll 75 children (aged 3-16 years) with moderate-to-severe ASD [Childhood Autism Rating Scale, Second Edition (CARS-2) ≥36]. Participants are randomized 1:1:1 to: (1) FMT via nasojejunal tube + sham colonoscopy (FMT-NJT); (2) active FMT via colonoscopy with transendoscopic enteral tube placement (first session) + two subsequent infusions via the indwelling tube + sham nasojejunal intubation (FMT-C); (3) placebo via both routes (sham procedures). Three FMT/placebo sessions (5 mL/kg, max 100 mL) are administered over 5 days. Primary outcome is change in CARS-2 score from baseline to Week 24. Secondary outcomes include changes in Social Responsiveness Scale, Autism Behavior Checklist, Gastrointestinal Symptom Rating Scale, Short Sensory Profile, Children's Sleep Habits Questionnaire, gut metagenomic profiles (baseline, Weeks 2,6,12,24,48), and adverse events.

RESULTS: This is a study protocol; no results are available.

CONCLUSIONS: This first head-to-head comparison of FMT routes in pediatric ASD will provide high-level evidence to guide treatment standardization, directly addressing the translational gap identified in our preliminary work.},
}

@article {pmid42293528,
year = {2026},
author = {Seth, N and Bansal, M and Mazumdar, S and Mazumdar-Leighton, S and Lakhanpaul, S and Vats, S and Arafat, Y and Babu, CR},
title = {Functional diversity in bacterial communities of an integrated constructed wetland used for in situ bioremediation of sewage.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1803785},
pmid = {42293528},
issn = {1664-302X},
abstract = {Constructed wetlands (CWs) offer effective, economical, environment-friendly and energy-efficient solution to growing challenges of increasing sewage and wastewater loads in urban areas. Although microbial communities form an integral component of constructed wetlands for sewage treatment, functional processes and their dynamics during sewage bioremediation in constructed wetlands remain largely uncharacterized. Moreover, the association of specific bacterial taxa with remediation of different sewage and water quality parameters remains largely unclear. This study explored the functional diversity likely associated with microbial communities of a constructed wetland system used for in situ remediation of 1 MLD (Million Liters per Day) sewage without external energy input since 2014. Different bacterial functional groups in the sludge from a stabilization pond and from rhizospheric sediments of the integrated constructed wetland were predicted using a 16S rRNA gene metagenomic sequencing dataset. Correlation analysis, multivariate statistics and a co-occurrence network were used to assess the bacterial groups associated with changes in water quality as it flows through different components of the integrated CW and highlight association patterns predicting major exchanges which might be operating in the microbial communities. While stabilization pond microbiome was dominated by bacterial groups such as Firmicutes, Desulfobacterota and Methylomirabilota known to be involved in carbon fermentation, sulphate reduction and methanogenesis, the rhizospheric sediments showed prevalence of bacteria associated with nitrogen reduction including Nitrospirota and Planctomycetota contributing to improved sewage quality parameters. Such results indicated complex microbial interactions involving bacteria from diverse functional groups sustaining bioremediation in the CW. The identification of primary bacterial taxa along with their putative functions can help in designing strategies to improve sustainable, nature-based wastewater treatment by CW systems.},
}

@article {pmid42293540,
year = {2026},
author = {Velaz Martín, M and Rießland, H and Rabe, KS and Niemeyer, CM},
title = {Primer choice shapes microbial community interpretation across habitats and informs short-term structured enrichment in environmental and applied systems.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1838890},
pmid = {42293540},
issn = {1664-302X},
abstract = {Microbial communities play central roles in ecosystem functioning across natural and engineered environments, yet their accurate characterization remains challenging due to methodological biases in amplicon sequencing. Primer choice can strongly influence taxonomic resolution, diversity estimates, and ecological interpretation. Here, we systematically compared primer performance across multiple ribosomal marker genes (16S, 18S, 28S rRNA, and ITS) and contrasting habitats, including soil, wastewater, and a photobioreactor-derived suspension. Amplicon-based profiles were benchmarked against shotgun metagenomic data. Primer choice significantly affected community composition, diversity metrics, and concordance with metagenomic profiles across all habitats and markers. Although 16S rRNA gene primers targeting the V3 region showed the highest agreement, no primer set fully reconstructed community structure. Applying the best-performing primer to a structured soil enrichment system using MESIF chips revealed rapid divergence from native soil and convergence toward less diverse communities, consistently favoring copiotrophic, surface-associated taxa while characteristic soil taxa declined. Across the 21-day incubation period, MESIF-associated communities diverged strongly from native soil, whereas medium-specific differences were comparatively smaller. This suggests that early enrichment was dominated by colonization of the structured matrix, while longer incubations and functional analyses will be needed to resolve substrate-specific selection. Overall, our findings highlight primer selection as a critical factor in microbial community analysis and show that combining optimized amplicon sequencing with structured cultivation enables reproducible enrichment, improved community monitoring, and targeted recovery of functionally relevant microorganisms. These insights are relevant for environmental monitoring, wastewater treatment, biotechnology, and controlled environment agriculture.},
}

@article {pmid42293542,
year = {2026},
author = {Liu, L and Liu, J and He, J and Xing, Y and Zhang, D and Zhang, X and Ma, C and Xu, M and Li, R and Peng, M and Mei, S},
title = {Multi-kingdom gut microbiota analysis identifies bacterial-viral association in multiple myeloma.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1798330},
pmid = {42293542},
issn = {1664-302X},
abstract = {INTRODUCTION: Alterations in the gut microbiome are closely associated with the progression of multiple myeloma (MM). Previous research has predominantly focused on the bacterial components of the microbiota; however, the virome, a significant component of the microbiota, also plays a critical role, with bacteriophages influencing bacterial community composition and evolution.

METHODS: This study utilized shotgun metagenomic sequencing of fecal samples to explore the interaction between the gut microbiota and MM development. Fecal samples from 28 MM patients and 20 healthy controls were analyzed to evaluate microbial diversity. Taxonomic profiling of both bacterial and viral communities was performed using the Kraken2 classifier.

RESULTS: Our analysis confirmed microbial dysbiosis in MM patients and revealed concomitant changes in both bacterial and viral communities. At the phylum level, this study identified a significant increase in the relative abundance of Pseudomonadota (from 1.63 to 8.88%, p < 0.001) and a decrease in Bacillota in MM patients compared to controls. Furthermore, several viral taxa were notably enriched in the MM cohort, including the phylum Heunggongvirae (linear discriminant analysis [LDA] = 4.74, p = 0.00003), phylum Uroviricota, and genus Punavirus (specifically Punavirus RCS47). Functional analysis demonstrated shifts in microbial metabolic pathways associated with MM, including a reduced capacity for amino acid and secondary bile acid biosynthesis and an enrichment of pathways associated with biofilm formation and cationic antimicrobial peptide (CAMP) resistance.

DISCUSSION: This multi-kingdom metagenomic analysis reveals distinct bacterial and viral signatures associated with MM, enhancing our understanding of gut microbial dysbiosis in the disease. These findings lay the groundwork for future mechanistic investigations and highlight the importance of validating these results in larger, independent cohorts.},
}

@article {pmid42293547,
year = {2026},
author = {Wei, X and Tian, N and Mei, W and Li, J and Liu, M and Zhou, H and Yang, Z and Yang, C and Hu, Y},
title = {Progress in understanding the infection mechanisms, soil microecological imbalance, and integrated control strategies of tobacco black shank.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1856708},
pmid = {42293547},
issn = {1664-302X},
abstract = {Tobacco black shank (TBS), caused by the oomycete pathogen Phytophthora nicotianae, is a destructive soilborne disease that seriously threatens tobacco production worldwide. This review summarizes recent progress in the infection biology of P. nicotianae, the disturbance of rhizosphere microbial communities under disease pressure, and integrated strategies for disease management. Current evidence indicates that TBS development is not only associated with direct pathogen infection, but also with rhizosphere microecological imbalance, including the decline of beneficial microbes, enrichment of opportunistic pathogens, reduced microbial diversity, and weakened soil suppressiveness. These changes may further promote pathogen persistence and disease recurrence. Based on this understanding, effective management should combine crop rotation, biological control, rational chemical intervention, resistant cultivars, and reductive soil disinfestation to suppress pathogen pressure while restoring soil microbial balance. Future research should further integrate multi-omics analysis, microbiome-based regulation, and intelligent monitoring to support early warning and precision control. This review provides an integrated perspective on pathogen-host-soil microbiome interactions and offers a theoretical basis for sustainable management of tobacco black shank.},
}

@article {pmid42293552,
year = {2026},
author = {Aldriwesh, MG and Bin Shuraym, H and Asiri, NY and Asiri, WY and Abukhalid, NF and Alasiri, A and Alghoribi, MF},
title = {Microbiome and One Health in GCC countries: current status, research gaps, and future directions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1821688},
pmid = {42293552},
issn = {1664-302X},
abstract = {BACKGROUND: Microbiome science has emerged as a central component of the One Health framework, linking human, animal, and environmental health. Although global microbiome research has expanded rapidly, a comprehensive evaluation of microbiome research development and integration across the Gulf Cooperation Council (GCC) countries remains lacking. This systematic review aimed to characterize microbiome research in the GCC countries, identify major research gaps, and evaluate alignment with One Health principles while proposing a strategic framework to support coordinated regional development.

METHODS: This systematic review followed PRISMA 2020 guidelines. A structured search of PubMed, ScienceDirect, Google Scholar, and EBSCO databases identified microbiome-related studies published up to January 31, 2025. Eligible studies included original research conducted in the GCC countries (Saudi Arabia, Qatar, Kuwait, United Arab Emirates, Oman, and Bahrain) investigating human, animal, or environmental microbiomes. Findings were synthesized descriptively to assess study distribution, research design, analytical methodologies, and thematic focus.

RESULTS: A total of 110 studies met the inclusion criteria. Human microbiome studies accounted for 49% of publications, followed by environmental microbiome studies (40%) and animal microbiome studies (11%). Research output increased substantially after 2020 but remained uneven among the GCC countries, with Saudi Arabia contributing 44% of publications, whereas Bahrain and Oman together accounted for fewer than 7%. Most studies were observational and primarily used 16S rRNA gene sequencing on Illumina platforms. Human studies focused mainly on gut and oral microbiomes and frequently investigated metabolic disorders such as obesity and diabetes. Animal microbiome research was limited and largely centered on camels, with minimal investigation of livestock relevant to food security. Environmental studies predominantly examined soil and desert environments. No included study simultaneously investigated human, animal, and environmental microbiomes within an integrated One Health study design.

CONCLUSION: Microbiome research in the GCC countries is growing but remains uneven and largely disconnected across human, animal, and environmental studies, with limited adoption of One Health approaches. A coordinated regional strategy integrating governance, infrastructure, funding, and workforce development is needed to advance translational microbiome research and strengthen the GCC's contribution to global health, food security, and environmental sustainability.},
}

@article {pmid42293560,
year = {2026},
author = {Tenea, GN and Jarrín-V, P and Reyes, P},
title = {Metagenomic insights into postbiotic-mediated modulation of strawberry surface microbiome and metabolic activity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1841388},
pmid = {42293560},
issn = {1664-302X},
abstract = {INTRODUCTION: The increasing demand for sustainable alternatives to chemical disinfectants in postharvest fruit handling has incentivized exploration into microbiome-based interventions. We evaluated the impact of lactic acid bacteria (LAB)-derived postbiotic formulations (FF1, FF2, FF3) and a commercial disinfectant (CD) on the microbial community structure of the strawberry fruit surface.

METHODS: Taxonomic and functional changes in the microbial communities were evaluated using shotgun metagenomic sequencing, enabling comprehensive profiling of microbial composition and functional potential through gene family abundance, EggNOG functional categories, KEGG pathways, and MetaCyc metabolic reconstruction. The tested formulations consisted of a precipitated peptide-protein extract (PP) from Weissella cibaria UTNGt21O (FF2), used as the antimicrobial agent, and an exopolysaccharide (EPS) from W. confusa UTNCys2-2 (FF3), serving as a biopolymer carrier, applied in combination (FF1: PPGt21O + EPSCys2-2) or individually.

RESULTS: Our integrated analysis revealed that the highly suppressive formulation, FF1, outperformed the CD by fundamentally restructuring the microbial landscape. Taxonomically, FF1 notably reduced the abundance of key opportunistic spoilage or hazardous organisms. Rather than acting as an indiscriminate biocide, FF1 functioned as a targeted ecological disruptor. Functional profiling (eggNOG, KEGG, and MetaCyc) suggested potential shifts in functional capacity, including a reduced relative abundance of genes associated with translation machinery, cellular membrane expansion (stearate biosynthesis), and host lipid degradation (fatty acid β-oxidation). In parallel, the FF1-treated microbiome showed a higher relative abundance of genes linked to stress-response functions, including heat shock proteins and cell wall-related processes such as peptidoglycan maturation. In contrast, less restrictive formulations (FF2 and FF3) permitted the proliferation of opportunists such as Pseudomonas spp. and Xanthomonas fragariae, accompanied by active energy-consuming and tissue-degrading metabolic signatures.

CONCLUSION: These findings suggest possible underlying mechanisms of LAB-derived postbiotics, demonstrating that FF1 forces the surface microbiome into a metabolically restricted, non-degradative survival state, potentially contributing to the preservation of postharvest strawberry quality.},
}

@article {pmid42293567,
year = {2026},
author = {Vougiouklaki, D and Prountzou, E and Siatelis, A and Ladias, K and Papaparaskevas, M and Tsakali, E and Polanska, M and Van Impe, JFM and Houhoula, D},
title = {Decoding the seminal microbial fingerprint and semen quality: insights from the first Greek pilot study.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1829292},
pmid = {42293567},
issn = {1664-302X},
abstract = {BACKGROUND: Recent evidence suggests that human semen harbors a complex microbiome that may influence semen quality and male fertility. However, comprehensive characterization of bacterial and fungal communities in semen remains limited, particularly using long-read sequencing technologies.

METHODS: In this pilot study, 80 semen samples from 80 men were analyzed and classified based on conventional semen-analysis findings into normozoospermic (n = 48) and abnormal (n = 32) groups. The abnormal group included men with asthenozoospermia and oligoasthenozoospermia. Microbial profiling was conducted using full-length 16S rRNA gene and internal transcribed spacer (ITS) sequencing on the Oxford Nanopore MinION platform.

RESULTS: Phylum-level analysis revealed distinct microbial profiles between groups. Normozoospermic samples were dominated by Bacillota (64.13%), followed by Actinomycetota (14.61%) and Pseudomonadota (12.95%). In contrast, abnormal samples showed reduced Bacillota abundance (2.32%) and enrichment of Campylobacteriota (10.82%). At the genus level, normozoospermic samples were characterized by predominance of Enterococcus, Cutibacterium, Streptococcus, Finegoldia, and Staphylococcus, whereas abnormal samples showed increased abundance of Campylobacter, Stenotrophomonas, and Agrobacterium. Species-level profiling identified Enterococcus faecalis as the dominant species in normozoospermic samples (41.3%), while Campylobacter ureolyticus predominated in abnormal samples (49.6%). ITS sequencing did not detect fungal DNA in any semen sample, whereas all fungal controls amplified successfully, confirming methodological reliability.

CONCLUSION: Our findings demonstrate significant differences in seminal microbiome composition between normozoospermic and abnormal semen samples parameters. Alterations at the phylum, genus, and species levels were associated with impaired semen parameters, suggesting a potential link between microbial dysbiosis and male reproductive health. Furthermore, the absence of detectable fungal communities indicates that fungi may be rare or absent in human semen under physiological conditions. This study provides novel insights into the bacterial and fungal landscape of the seminal microbiome using long-read sequencing technology.},
}

@article {pmid42293685,
year = {2026},
author = {Shen, Y and Lu, SM and Yang, L and Li, Y and Zhang, Y and Liang, LG},
title = {Engineered bacteria in disease diagnosis and therapy: A synthetic biology perspective.},
journal = {Synthetic and systems biotechnology},
volume = {14},
number = {},
pages = {459-470},
pmid = {42293685},
issn = {2405-805X},
abstract = {Synthetic biology is an interdisciplinary field that integrates knowledge and techniques from modern biology and many other disciplines to design and construct novel biological systems or to modify existing life forms. Its core technologies include gene editing (e.g., CRISPR/Cas9), DNA assembly, in vivo directed evolution, and integration with artificial intelligence. The development of these technologies has greatly advanced the application of synthetic biology in medicine. In disease diagnosis, engineered bacteria have shown considerable promise. They can be designed to sense disease-specific signals and produce detectable reporter outputs, thereby establishing new paradigms for early diagnosis and real-time disease monitoring. For example, bacteria engineered via synthetic biology have been developed as "living sensors" to detect disease biomarkers. In therapeutic applications, synthetic biology offers a fresh perspective on using microorganisms to treat diseases. Researchers can design and construct microorganisms with tailored functions for targeted drug delivery, immunotherapy, and microbiome modulation. These applications not only improve the precision and efficacy of treatments but also offer innovative solutions to overcome the limitations of conventional therapeutic approaches. However, despite their considerable potential, the clinical translation of engineered bacteria still faces numerous challenges, such as ensuring stable in vivo colonization, controlling immunogenicity, standardizing large-scale production, and establishing robust regulatory and ethical frameworks. This review summarizes engineering strategies aimed at enhancing the safety and efficacy of bacterial therapies, with the goal of optimizing bacterial functions and expanding their potential in diagnostics and precision medicine.},
}

@article {pmid42293984,
year = {2026},
author = {Li, Y and Huang, M and Mao, Z and Liu, C and Qu, W and Ni, J and Xu, W and Li, A and Bao, J and Han, D and Yu, F and Shen, Y and Wang, Y and Chen, W and Zheng, S},
title = {Ventilation-Associated Differences in Lower Airway Microbial Signatures and Peripheral Blood Transcriptome Among Critically Ill COVID-19 Patients.},
journal = {Infection and drug resistance},
volume = {19},
number = {},
pages = {586598},
pmid = {42293984},
issn = {1178-6973},
abstract = {BACKGROUND: Invasive mechanical ventilation (IMV) is a critical intervention for severe respiratory failure and has been widely used in the clinical management of COVID-19 patients. The relationship between such microbiota changes and the host transcriptome in IMV patients remains poorly documented.

METHODS: We prospectively enrolled 69 critically ill COVID-19 patients, among whom 41 received IMV. Correlation analyses were conducted to investigate the relationship between the lung microbiome and host immune status in IMV COVID-19 patients.

RESULTS: Compared to the Non-mechanical ventilation (NMV) group, patients in the IMV group exhibited significantly reduced alpha diversity, while no significant difference was observed in beta diversity. The abundance of Streptococcus genus was significantly higher in the NMV group, primarily dominated by Streptococcus oralis and Streptococcus mitis. Transcriptomic enrichment analysis revealed significant upregulation of inflammation-related pathways in the IMV group, including "positive regulation of inflammatory response" and "cellular response to interleukin-1". The decreased relative abundance of Streptococcus genus in the IMV group showed significant correlations with upregulation of genes including CXCL8, PLAU, SELENOK, SDC4, RPL17, RPS23, TOMM7, and PLK3. These upregulated genes promoted the recruitment of immune cells to inflammatory sites through activation of pathways including chemotaxis, leukocyte migration, and leukocyte cell-cell adhesion, ultimately triggering a robust innate immune response.

CONCLUSION: IMV COVID-19 ARDS patients demonstrated significantly reduced pulmonary microbial diversity, with a marked decrease in the abundance of Streptococcus-primarily Streptococcus oralis and Streptococcus mitis. Transcriptomic profiling further revealed substantial upregulation of inflammatory pathways in IMV patients, including "positive regulation of inflammatory response".},
}

@article {pmid42294020,
year = {2026},
author = {Lamberti, L and Rusiñol, C and Guisande, A and Peñalba, F and Irastorza, M and Konik, F and Parada, A and Iglesias, C and Mendive, P and Riera, N and Garrido, G},
title = {Clinical and sociodemographic characterization of a sibling-matched cohort of children with autism Spectrum disorder in Uruguay.},
journal = {Frontiers in child and adolescent psychiatry},
volume = {5},
number = {},
pages = {1835921},
pmid = {42294020},
issn = {2813-4540},
abstract = {This study characterized clinical, sociodemographic, psychiatric, and gastrointestinal variables in 55 families, comparing children with Autism Spectrum Disorder (ASD) to neurotypical siblings. Primary objectives were to delineate sociodemographic profiles and systemic barriers, establish a clinical-nutritional baseline for Uruguayan children, and generate metadata for future microbiome research. We conducted a cross-sectional, case-control study including children aged 4-10 years and sibling controls. Professionals collected data via clinical interviews. Findings indicate a higher male prevalence in the ASD group. Mothers predominantly participated in caregiving and interviews. In the ASD group, 60% of pregnancies had complications, including 12 twin pregnancies. No significant differences were found regarding parental age, delivery method, prematurity, or birth anthropometry. Head circumference at birth did not associate with regression or severity. All children with ASD showed sensory particularities; 94.3% reported gastrointestinal symptoms. We observed a 20-month diagnostic gap and 65% regression rates between 12 and 36 months. These data highlight the need for improved early detection and provide essential local evidence for the Uruguayan ASD population. This interdisciplinary approach bridges clinical practice and research, advancing contextualized care in Uruguay.},
}

@article {pmid42294507,
year = {2026},
author = {Kristiana, H and Kartawijaya, M and Tuentifiany, L and Hartanti, AW and Tjandrawinata, RR},
title = {Acute and sub-chronic oral toxicity evaluation and gut microbiota modulation of indigenous Lactobacillus helveticus strains from Indonesia in rats.},
journal = {Toxicology reports},
volume = {16},
number = {},
pages = {102286},
pmid = {42294507},
issn = {2214-7500},
abstract = {Probiotics are widely used to support gastrointestinal health, but their safety must be evaluated on a strain-specific basis. Lactobacillus helveticus DLBSA201 and DLBSA202 are indigenous strains with previously demonstrated probiotic potential in vitro. However, their in vivo safety profile has not been fully assessed. This study aimed to evaluate the acute and sub-chronic oral toxicity of these strains and their effects on selected gut microbial parameters in Wistar rats. In the acute toxicity study, rats received a single oral dose of L. helveticus DLBSA201 or DLBSA202 at 2.5 × 10[10], 2.5 × 10[11], or 5 × 10[11] CFU/rat. In the sub-chronic study, rats were orally administered a 1:1 mixture of both strains daily for 90 days at doses of 1 × 10[9], 1 × 10[10], or 1 × 10[11] CFU/rat/day. Clinical observations, hematological and biochemical parameters, histopathology, bacterial translocation, bacterial enzyme activity, and fecal microbiological analyses were evaluated. No mortality or treatment-related adverse effects were observed, and the LD50 of both strains was estimated to be greater than 5 × 10[11] CFU/rat. No significant treatment-related toxicological abnormalities were detected in the sub-chronic study, with a NOAEL of 1 × 10[11] CFU/rat/day. Probiotic administration was also associated with reduced harmful bacterial enzyme activity and altered selected fecal bacterial populations. In conclusion, L. helveticus DLBSA201 and DLBSA202 were well tolerated in Wistar rats at the tested dose range and study duration, and warrant further investigation using comprehensive microbiome and clinical approaches.},
}

@article {pmid42294611,
year = {2026},
author = {Cui, Y and Li, L and Wu, S and Zhang, X and Wang, L and Yang, H and Yan, Z},
title = {Salivary Proteome-Microbiome Profiling in Burning Mouth Syndrome Might Highlight Mucin-Related Host-Microbe Features.},
journal = {Journal of oral rehabilitation},
volume = {},
number = {},
pages = {},
doi = {10.1111/joor.70242},
pmid = {42294611},
issn = {1365-2842},
support = {82170967//National Natural Science Foundation of China/ ; },
abstract = {OBJECTIVE: This pilot study was designed to analyze salivary proteomic and microbiome profile in burning mouth syndrome (BMS) and to explore the potential role of salivary mucins in barrier-related host-microbe interactions.

METHODS: Unstimulated saliva samples from BMS patients and healthy controls were analyzed using data-independent acquisition (DIA)-based proteomics and 16S rRNA gene sequencing. A multi-step strategy was applied to identify BMS-associated core salivary proteins. Biofilm formation, epithelial adhesion and injury, as well as molecular permeability using a transwell model were conducted to assess the mucosal barrier-microbe interactions.

RESULTS: Proteomic profiling defined 29 BMS-associated core proteins with MUC5B showing prominent differential expression. Microbiome analysis showed altered community structure in BMS saliva, including increased relative abundance of Rothia. Further in vitro explorations revealed that mucin triggered dispersal of the formed biofilms, reduced bacterial adhesion to oral epithelial cells, attenuated epithelial cell injury and decreased FITC-dextran permeability in a concentration-dependent manner.

CONCLUSION: BMS might be associated with mucin-related alterations in the salivary microenvironment, including reduced MUC5B and increased relative abundance of Rothia. Together with the in vitro findings, this might suggest that mucin-related barrier changes may be linked to altered host-microbe interactions in BMS.},
}

@article {pmid40555926,
year = {2025},
author = {Wiele, N and de Melo Pereira, GV and da Silva Vale, A and de Mello Sampaio, V and Ribeiro-Barros, AI and Diniz de Souza, AF and Dos Santos, DVN and Góes-Neto, A and Soccol, CR},
title = {Comparative microbiomes reveal microbial signatures in coffee fermentation and flavor development across distinct Brazilian biomes.},
journal = {World journal of microbiology & biotechnology},
volume = {41},
number = {7},
pages = {207},
pmid = {40555926},
issn = {1573-0972},
support = {440343/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; UIDB/00239/2020//Fundação para a Ciência e a Tecnologia/ ; },
abstract = {Recent studies underscore the pivotal role of microbial terroir in shaping coffee fermentation and quality. However, the specific influence of regional microbiomes on flavor development remains underexplored. This study explored the link between the coffee farm microbiome and the resulting spontaneous fermentation process in Brazil’s Atlantic Forest and Semi-arid Cerrado biomes. Using Illumina-based amplicon sequencing, 972 prokaryotes and 435 eukaryotes were identified from coffee fruits, leaves, depulped coffee beans, over-ripe beans, soil, and temporal fermentation samples. During the fermentation process, microorganisms present in the pulped fruit (viz., Leuconostoc and Kazachstania) were the main microbial groups driving fermentation process across the two biomes, leading to the accumulation of primary (ethanol and lactic acid) and secondary (esters, aldehydes, higher alcohols, and ketones) metabolites. However, Leuconostoc and Kazachstania communities were significantly higher in the pulped fruit samples from the Atlantic Forest compared to the Cerrado biome. Therefore, the Atlantic Forest farm showed more stable microbial dynamics during the fermentation process and the formation of key flavor metabolites, such as methyl salicylate, linalool, ethyl linoleate, benzeneacetic acid ethyl ester, and phenylethyl alcohol. In contrast, the Cerrado samples exhibited higher microbial richness, leading to the emergence of co-dominant species such as Pantoea, Cutaneotrichosporon, Hyphopichia, Wickerhamomyces, and Cladosporium. Sensory evaluation revealed higher overall scores for the Atlantic Forest coffee, characterized by fruity, floral, and caramel notes, compared to earthy and herbal characteristics of Cerrado coffee. The findings demonstrate the influence of terroir-driven microbial communities on coffee fermentation and coffee quality, providing insights into optimizing fermentation for enhanced coffee flavor development and contributing to the growing field of microbial-assisted coffee production.},
}

@article {pmid41182402,
year = {2025},
author = {Tekgül, ZB and Adıgüzel, A},
title = {Microbial viability assessment with PMA-qPCR: challenges, opportunities, and future directions.},
journal = {Archives of microbiology},
volume = {207},
number = {12},
pages = {343},
pmid = {41182402},
issn = {1432-072X},
abstract = {Since molecular analyzes are insufficient to distinguish living and non-living cells, lead to misleading results, and dead cells also multiply their DNA/RNA, a method that can give more sensitive results was needed. PMA (propidium monoazide), which is used to prevent the DNA of dead cells from negatively affecting the experimental results, is a viability indicator that binds only to the DNA of damaged cells and prevents them from being multiplied by PCR, and was first introduced in 2006. Recently the interest in the use of PMA in many fields such as microbiome and metagenomic studies, environmental microbiology, food microbiology, antibiotic and disinfectant effectiveness tests, clinical microbiology and diagnosis, and cell culture and biotechnology has increased considerably. Therefore, the purposes of use, principles, applications in various fields and limitations of PMA have been investigated. The current review of this vitality marker, which has a history of less than 20 years, will lead to its use of many new scientific studies and will provide convenience to scientists by bringing together studies on the use of this dye.},
}

@article {pmid41329407,
year = {2025},
author = {Wang, W and Liang, Y and Cheng, T and Du, J and Zhang, Y and Jiang, L and Luo, X and Wang, Y},
title = {Gut Microbiota-Driven Modulation of Intestinal Barrier Function, Antioxidant Capacity, and Immune Response in Green-Footed Chicken by Dietary Fermented Chinese Herbal Compounds.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41329407},
issn = {1867-1314},
support = {16ZG6103//National Defense Basic Research Program/ ; },
abstract = {After the ban on antibiotics, fermented herbs have become an alternative. In the experiment, 960 one - day - old green - footed chickens were divided into four groups: T1 (basal ration), T2 (1% fermented herbs), T3 (3% fermented herbs), and T4 (5% fermented herbs). The experiment was conducted over a 69-day period. The health and growth of the chickens were assessed by evaluating growth performance, serum biochemistry, and gut microbiota. The results showed that during days 22–42 and 43–69, the average daily weight gain of T4 group chickens was significantly higher than that of T1 group (P < 0. 05). Serum biochemistry analysis showed that the IgA and IgG levels of T2, T3 and T4 group chickens were significantly higher than those of T1 group (P < 0. 05), while ALT activity was significantly lower than that of T1 group (P < 0. 05). In addition, the CD4+/CD8 + cell content in the blood of T2, T3 and T4 groups also increased (P < 0. 05). Notably, the Bursa of Fabricius Index in the T4 group was significantly enlarged (P < 0. 05). Gut immune and sequencing analyses showed that the villus height of the jejunum and duodenum increased significantly (P < 0. 05). 16s microbiome sequencing results showed that the gut markers of the test groups were Coriobacteriia, Subdoligranulum, and unidentified Actinobacteria. This study shows that fermentation of astragalus, cypress, dandelion, Scutellaria baicalensis, and honeysuckle herbs can modulate the intestinal microbial community structure through multiple pathways, promote gut health in broiler chickens, and thereby enhance growth performance.},
}

@article {pmid41372737,
year = {2025},
author = {Shah, A and Doshi, G},
title = {Stress and neurodegeneration: mechanistic insights and therapeutic opportunities for preserving brain resilience.},
journal = {Acta neurologica Belgica},
volume = {},
number = {},
pages = {},
pmid = {41372737},
issn = {2240-2993},
abstract = {Neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and Amyotrophic Lateral Sclerosis are strongly influenced by persistent stress, which accelerates both their onset and progression. This review explores the intricate interplay between chronic stressors, oxidative and metabolic imbalances, protein misfolding, inflammatory responses, and psychosocial adversity, and their cumulative impact on the aging brain’s capacity for homeostasis. The loss of cellular resilience due to prolonged stress leads to maladaptive outcomes, including mitochondrial dysfunction, sustained neuroinflammation, breakdown in proteostasis, and disruption of hypothalamic-pituitary-adrenal axis signaling, all of which amplify neuronal vulnerability. The detailed molecular pathways that underlie these phenomena, the article identifies key mediators such as Reactive Oxygen species, mitochondrial regulators, heat shock proteins, and proinflammatory cytokines that drive neurodegeneration. A comprehensive literature search was conducted using PubMed, Scopus, Web of Science, and Google Scholar up to 2025. Eligible publications included original research articles, clinical studies, and systematic reviews focusing on stress-related molecular pathways, oxidative metabolism, proteostasis, neuroinflammation, and therapeutic interventions in aging and neurodegenerative diseases. A qualitative synthesis of these studies was performed to identify key mechanisms, biomarkers, and emerging treatment strategies relevant to stress-induced neurodegeneration. Further, the review evaluates both established and emerging interventions aimed at mitigating these stress-driven processes. Lifestyle modifications such as aerobic exercise, calorie restriction, and cognitive behavioural therapies complement pharmacological agents like antioxidants, chaperone modulators, and anti-inflammatory drugs to enhance brain resilience and delay disease onset. Recent advances in the field, including integrated multi-omics profiling, biomarker discovery, and medicine approaches, promise to refine our ability to satisfy patients and deliver targeted therapies based on individual stress profiles. Additionally, the article discusses the neuroimmune-gut axis and the potential for interventions targeting microbiome-related inflammation. Early detection of stress-related biomarkers and personalized strategies holds considerable promise for improving clinical outcomes, enabling earlier diagnosis, and fostering tailored therapies that preserve cognitive function and independence in aging populations.},
}

@article {pmid41417288,
year = {2025},
author = {Deng, J and Ji, J and Khan, A and Wang, Z and Xiang, W and Qiao, H and Salama, ES and Gu, J and Mao, C and Liu, P and Li, X},
title = {Antimicrobial Proteins from Limosilactobacillus fermentum GR-9 Inhibit Pathogens and Alleviate Salmonella Paratyphi B Infection in Mice.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41417288},
issn = {1867-1314},
support = {24ZDWA005//Natural Science Foundation of Gansu Province/ ; },
abstract = {Probiotics employ defense molecules that include antimicrobial peptides (AMPs) and lytic enzymes to inhibit pathogens; however, translating these mechanisms into applications remains challenging. In this study, Limosilactobacillus fermentum GR-9, isolated from “Jiangshui”, secretes AMPs and NlpC/p60 hydrolase, exhibiting 64%-77% of inhibition against both Gram-positive and Gram-negative pathogens. In mice model, GR-9 treatment reduced 93% of Salmonella Paratyphi B intestinal pathogen colonization effectively, similar to the antimicrobial norfloxacin. Moreover, GR-9 promoted beneficial microbiota, including Ligilactobacillus spp. and Bifidobacterium, highlighting its dual role in pathogen clearance and microbiome restoration. GR-9 further alleviated inflammation by modulating the immune response, significantly reducing the levels of pro-inflammatory cytokine (both TNF-α and IL-6) by 16% in both serum and intestinal tissues. Ultimately, this treatment highlights that probiotic-producing therapeutic compounds in situ offer a viable alternative to synthetic AMP production, addressing its critical challenges while providing a sustainable tool against antimicrobial-resistant pathogens.},
}

@article {pmid41432892,
year = {2026},
author = {Seenivasan, SN and Vasudevan, SA and Raghupathy, AK and Rajan, F and Selvan, E and Sharma, SM and Muthusamy, RK and Paramasivam, L and Seethalakshmi, SP and Yogeswaran, S and Velmurugan, G},
title = {Intratumoural microbial metabolites in breast cancer: a longitudinal study on association with metastatic progression.},
journal = {Molecular and cellular biochemistry},
volume = {481},
number = {2},
pages = {1045-1057},
pmid = {41432892},
issn = {1573-4919},
support = {SRG/2020/001867//Science and Engineering Research Board/ ; },
abstract = {Delayed diagnosis and metastasis remain major challenges in breast cancer. While the gut microbiome’s influence on tumour progression is established, the presence and role of intratumoural microbial metabolites in breast cancer and their association with metastasis remain unexplored. Paired tumour and adjacent tissues were collected from 50 breast cancer patients at baseline. Patients were followed for five years; 10 who developed distant metastasis were classified as pre-metastatic, and 10 who remained disease-free formed the non-metastatic group. Untargeted LC–MS/MS-based metabolomics was performed to profile host and microbial metabolites. Multivariate analysis and pathway enrichment were used to identify discriminatory signatures. Elevated levels of carnitine, indole, tryptophan-derived metabolites, ceramides and polyamines were observed in tumour tissues on comparison with adjacent tissues. Interestingly, these metabolites were downregulated in tumour tissues of patients who progressed for metastasis (pre-metastatic) with increase in N-methylhistamine and taurolithocholic acid sulfate, suggesting metabolic reprogramming during metastatic priming. Baseline host–microbial metabolic disruptions in breast tumours are linked to future metastasis, with metabolites like indoles, bile acids, and polyamines showing promise as early biomarkers and therapeutic targets in precision oncology.},
}

@article {pmid41452511,
year = {2025},
author = {Al-Adham, ISI and Ali Agha, ASA and Al-Remawi, M and Al-Akayleh, F and Al-Sheikh, A and Aburub, F and Collier, PJ},
title = {Probiotics, Psychobiotics, Paraprobiotics, and Postbiotics in Gut-Brain Axis Modulation: Multi-Omics and AI-Driven Precision Nutrition for Cognitive Health.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41452511},
issn = {1867-1314},
abstract = {The gut-brain axis has emerged as a key regulatory interface in cognitive function and neurological health, influenced by diet-driven microbial metabolism and host-microbiome interactions. Integrating multi-omics approaches with AI-driven precision nutrition offers novel insights into how diet modulates neuroimmune, neuroendocrine, and metabolic pathways. This article explores recent advances in microbiome research, highlighting the role of microbiota-derived extracellular vesicles (MEVs) as bioactive carriers that facilitate gut-brain communication by transporting neuroactive metabolites and immune modulators. These findings reveal an underexplored mechanism by which dietary interventions can reshape brain function at the molecular level. Additionally, synthetic biology and CRISPR-mediated microbiome engineering are advancing targeted interventions, allowing precise modulation of microbial gene expression to enhance neuroprotective pathways and mitigate neuroinflammation. Emerging strategies such as psychobiotics, paraprobiotics, and postbiotics further expand this therapeutic landscape, offering novel microbiome-based tools to influence neurotransmission, neuroimmune regulation, and cognitive resilience. Artificial intelligence (AI)-driven multi-omics integration further enables predictive modeling of microbiome-neurotransmitter interactions, hence refining personalized nutritional strategies for cognitive resilience and neuroprotection. However, challenges such as inter-individual variability, algorithmic biases, and ethical considerations in AI-driven dietary recommendations must be addressed to ensure the suitability of potential therapies. Future research should focus on in vivo validation of AI-guided dietary interventions through multi-modal neuroimaging, metabolomics, and transcriptomics. These advances position precision nutrition as a transformative tool in neuroscience, bridging microbiome science, AI, and personalized medicine to optimize brain health and mitigate neurodegenerative risks.},
}

@article {pmid41455009,
year = {2025},
author = {Safari, F and Golafshan, F and Malekpour, E and Mirzaei, SA and Rouzbahani, H and Hajarzadeh, MO and Nasir Harandi, S and Nasirharandi, S and Noursina, A},
title = {Functional Proteins of Akkermansia Muciniphila: Impacts on Host Health and Metabolism.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41455009},
issn = {1867-1314},
abstract = {Akkermansia muciniphila, a mucin-degrading bacterium endemic to the human gut microbiome, plays a crucial role in modulating host physiology through the action of its functional proteins. This review compiles the latest insights into these proteins, elucidating their molecular mechanisms and their influence on host health. Notable proteins include Amuc_1100, Amuc_1631 (P9), Amuc_2109, and Amuc_1434, each of which is involved in key physiological processes. Amuc_1100 functions as an immune rheostat, engaging TLR2 and TLR4 pathways to modulate immune responses. Amuc_1631 enhances glucose homeostasis by promoting GLP-1 secretion, thereby linking gut microbiota to metabolic regulation. Amuc_2109 is implicated in the reinforcement of tight junctions, contributing to intestinal barrier integrity. In contrast, Amuc_1434 has demonstrated anti-tumor effects through the induction of apoptosis in colorectal cancer cells. Beyond these functions, these proteins also facilitate mucin degradation, support microbial cross-feeding, and promote resilience to gastrointestinal stressors. The review emphasizes their therapeutic potential for a range of conditions, including metabolic disorders, inflammatory bowel disease, cancer, and neuropsychiatric disorders. However, it also identifies translational hurdles such as the need for robust human clinical trials and the development of optimized delivery systems to harness their benefits fully. These findings position the proteins of A. muciniphila as promising targets for microbiota-centric therapeutic interventions.},
}

@article {pmid41483122,
year = {2026},
author = {Aghdam, MM and Rezagholizadeh, L and Fazaeli, A and Moradi, A and Ojarudi, M},
title = {Nutritional modulation of metabolic signaling within the tumor microenvironment for cancer therapy.},
journal = {Molecular and cellular biochemistry},
volume = {481},
number = {3},
pages = {1155-1182},
pmid = {41483122},
issn = {1573-4919},
abstract = {The tumor microenvironment (TME) constitutes a complex ecosystem of cellular and non-cellular components. Together, these constituents exert a critical influence on cancer progression. A principal mechanism underlying this influence is metabolic reprogramming, in which tumor cells alter glucose, amino acid, and lipid metabolism to promote growth, survival, and immune evasion. Metabolic adaptation is further regulated by nutrient-sensing pathways, including mammalian target of rapamycin (mTOR), AMP-activated protein kinase (AMPK), and hypoxia-inducible factor (HIF), which often exhibit context-dependent and sometimes opposing functions in tumor and immune cells within the TME. Given this complexity, targeting metabolic vulnerabilities has become a promising therapeutic approach. In this context, nutritional interventions, such as caloric restriction, ketogenic diets, fasting-mimicking diets, protein or amino acid modulation, and lipid metabolism adjustments, aim to deprive tumors of essential nutrients, remodel the immunosuppressive TME, and increase cancer cell sensitivity to chemotherapy, radiotherapy, and immunotherapy. However, the efficacy of these interventions varies according to cancer type, oncogenic drivers, and immune contexture, and there is a risk of impairing anti-tumor immune function. Addressing these challenges will require personalized nutrition strategies that integrate tumor genetics, metabolic profiling, and the gut microbiome, together with technological advances for real-time monitoring. Progress in this area depends on a deeper mechanistic understanding of nutrient-immune interactions and the optimization of combination approaches for improved metabolic targeting in precision oncology. Accordingly, this review addresses a critical gap by synthesizing mechanistic and translational literature and outlining actionable priorities to advance nutritional modulation from preclinical research to clinical application.},
}

@article {pmid41493541,
year = {2026},
author = {Dhiman, I and Nandni, and Poria, V and Kumar, S and Yadav, R and Shaik, T and Bedwal, S and Wati, L},
title = {Plant growth promoting rhizobacteria (PGPR) mediated amelioration of plant tolerance to abiotic stresses: Drought, salinity, and heavy metals.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {100},
pmid = {41493541},
issn = {1432-072X},
abstract = {Plants, being sessile organisms, are perpetually subjected to a spectrum of escalating abiotic stresses, which have detrimental repercussions on agriculture worldwide. In the forthcoming era of climate change and ecosystem degradation, fostering the use of beneficial microbiota in agroecosystems represents a major challenge towards sustainability. Some plant-associated bacteria, called Plant Growth Promoting Rhizobacteria (PGPR), may confer growth-promoting advantages to the host plant through enhancing nutrient uptake, altering hormone homeostasis, and/or improving tolerance to abiotic stress factors (drought, heavy metal, and salinity stress) in plants. These include promoting plant growth through the activation of antioxidant enzymes to detoxify reactive oxygen species, accumulation of compatible solutes to maintain osmotic homeostasis, suppression of lipid peroxidation to conserve membrane integrity, and emission of volatile organic compounds to induce systemic resistance. Additionally, PGPR synthesize phytohormones and exopolysaccharides that reinforce their persistence in soil, improve plant-water relations, and optimize nutrient uptake efficiency. In this regard, exploring the key ecological and evolutionary interactions between plants and their microbiomes is a prerequisite to developing innovative approaches and novel natural products that will complement conventional farming techniques. Collectively, these interactions fortify plant defense mechanisms, enhance physiological homeostasis, and promote adaptive plasticity in adverse environments. Herein, we describe the role of plant-microbe interactions in mitigating abiotic stress and fostering sustainable crop production. Leveraging multifactorial PGPR in agroecosystems strengthens the adaptive resilience of plants, reduces dependency on synthetic fertilizers, maintains soil microbiome integrity, cellular homeostasis, nutrient cycling, improves water retention, and ensures sustainable productivity in stress-prone and resource-limited regions.},
}

@article {pmid41524778,
year = {2026},
author = {Sundaray, JK and Roy, D and Mohapatra, M and Mohanty, D and Das, II and Parida, CK},
title = {Metagenomic profiling of fish-associated microbiota: ecological perspectives from freshwater to marine environment-a review.},
journal = {Archives of microbiology},
volume = {208},
number = {2},
pages = {105},
pmid = {41524778},
issn = {1432-072X},
support = {Project Code: 1006449//Centre for Agricultural Bioinformatics (CABin) Project/ ; },
abstract = {Microorganisms play pivotal roles in maintaining host physiology and ecosystem balance, with fish-associated microbiomes offering unique insights due to the diverse habitats and feeding behaviours of their hosts. This review comprehensively explores the diversity, composition, and functional roles of gut and skin-associated microbial communities in fish across freshwater, brackish, and marine environments, with emphasis on recent advancements in metagenomic methodologies. Culture-independent techniques, particularly high-throughput and third-generation sequencing technologies, have revolutionized our ability to uncover microbial diversity, gene functions, and interspecies interactions. The fish gut microbiome, heavily influenced by factors such as diet, habitat, and host species, contributes significantly to nutrient metabolism, immune modulation, and physiological adaptation. Similarly, the skin microbiota provides a critical first line of defence, offering protection through competitive exclusion and antimicrobial activity. Functional metagenomics reveals microbial contributions to host metabolism, energy homeostasis, xenobiotic degradation, and environmental adaptation via the gut-brain axis and metabolic pathways. Emerging evidence highlights the bidirectional relationships between microbiota and host phenotypic plasticity. This review underscores the importance of integrative metagenomic approaches to decode complex microbial functions and their ecological relevance in aquaculture, with implications for sustainable fish health management, disease prevention, and improved productivity.},
}

@article {pmid41642480,
year = {2026},
author = {Chriaa, O and Gdoura-Ben Amor, M and Mathlouthi, NEH and Slima, AB and Mhalhel, K and Turki, M and Kacem, FH and Germanà, A and Ben Ali, M and Gdoura, R},
title = {Probiotic intervention attenuates hypercholesterolemia and modulates gut microbiota in high-fat diet-fed rats.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {2},
pages = {74},
pmid = {41642480},
issn = {1573-0972},
abstract = {Hypercholesterolemia is a major risk factor for cardiovascular diseases and is often associated with lipid metabolism disturbances, liver dysfunction, and gut microbiota imbalances. Probiotics have emerged as promising agents to improve cholesterol management through gut microbiome modulation and anti-inflammatory effects. This study investigated the impact of probiotics on weight, lipid profiles, liver function, and gut microbiota composition in high-fat diet (HFD)-induced hypercholesterolemic rats. Rats were divided into five groups: normal diet (NG), HFD, HFD + Rosuvastatin (SG), HFD + probiotics (Lactobacillus spp.) (PG), and HFD + Rosuvastatin + probiotics (PSG). Probiotic supplementation significantly attenuated weight gain, reduced triglycerides (TG), total cholesterol (TCH), and LDL-C levels, and improved liver enzyme profiles (ALT, AST) compared to the HFD group. Histological analysis revealed that probiotics mitigated HFD-induced hepatocellular degeneration and decreased pro-inflammatory cytokine expression (IL-1β, TNF-α) in liver tissues. Gut microbiota analysis showed that probiotics modulated the relative abundance of key bacterial phyla and families, increasing beneficial taxa such as Lachnospiraceae and Lactobacillaceae. These findings suggest that probiotics can serve as a potential therapeutic strategy for managing hypercholesterolemia by improving lipid metabolism, protecting hepatic health, and reshaping the gut microbiome.Trial registration: CEREASFS4625/4022 (https//www.medecinesfax.org/fra/pages/518/projetscereas).},
}

@article {pmid41697296,
year = {2026},
author = {Chengcheng, L and Yanduo, Z and Zhebin, W and Jianzhang, L and Yangtao, Z and Jun, L and Yu, L and Felemban, HR and Alyahyawy, OY and Alhomodi, AF and Hadadi, F and Shaibah, A and Bingzhi, L and Xianwei, W},
title = {Metagenomic analysis of fecal microbial communities in dairy goats from different farms.},
journal = {Protoplasma},
volume = {263},
number = {3},
pages = {1031-1045},
pmid = {41697296},
issn = {1615-6102},
abstract = {This study aims to investigate the differences in the microbial community structure of goat manure under various breeding environments, providing scientific evidence and theoretical support for healthy breeding practices. Gut microbiota is a key determinant of feed conversion, disease resistance and overall productivity in ruminants. The gut microbiome is an integral part of the digestive system. Its composition and functional traits markedly influence digestive efficiency, immune development, gut homeostasis and reproductive performance. Using four goat dairy farms in the Yangling, Shaanxi Province as study subjects, fecal samples were collected and analyzed using 16S rRNA sequencing technology, combined with α-diversity indices and β-diversity analysis. The results revealed significant differences in the microbial community structure of goat feces across different farms, with each farm exhibiting unique microbial communities. Each farm harboured distinct microbial signatures and functional profiles, providing microbiota-based targets for precision management of Guanzhong dairy goats.},
}

@article {pmid41731166,
year = {2026},
author = {Zhang, X and Su, Q and Chen, X and Wang, S and Du, J and Chen, L and Xu, Q and Liu, C and Zhao, J},
title = {Inference of drowning sites of cases in the Pearl river based on microbial community profiling and random forest algorithm.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {41731166},
issn = {1437-1596},
support = {82371901//National Natural Science Foundation of China/ ; 2024B04J0022//Funding by Science and Technology Projects in Guangzhou/ ; 2022JC35//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; 2022JC26//Grant-in Aids for Scientific Research from Ministry of Public Security of the People's Republic of China/ ; },
abstract = {Accurate inference of drowning sites remains a critical challenge in forensic investigations, particularly for corpses recovered from dynamic aquatic environments. Conventional methods, such as diatom testing, are limited by the absence or scarcity of diatoms in certain water bodies, labor-intensive morphological identification, and challenges in distinguishing morphologically similar species. In this study, we explored the feasibility of inferring drowning sites in human cases by integrating pulmonary microbial community profiling with machine learning. A total of 56 lung tissue samples from confirmed drowning victims were collected from four regions of the Pearl River’s Guangzhou section, including the central urban waterfront (site1), mid-reach brackish transition zone (site2), southern estuarine outflow zone (site3), and eastern tributary confluence (site4). High-throughput sequencing of the 16 S rRNA gene (V3 – V4 region) was performed to characterize microbial community composition. Significant spatial heterogeneity in pulmonary microbiota was observed across drowning sites, as demonstrated by alpha diversity analysis, unweighted UniFrac-based principal coordinates analysis, and differential abundance testing. Linear discriminant analysis effect size (LEfSe) further identified 111 differentially abundant microbial taxa, providing biological interpretation of spatial microbial variation among groups. To enable drowning site inference, microbial features at the genus level were subjected to feature engineering using a hybrid strategy combining variance thresholding and the Boruta algorithm. Through this process, 32 genera—including Ralstonia, Sphingomonas, Akkermansia, and Faecalibacterium—were selected as key microbial markers for geolocation. Multiple classification models, including Random Forest (RF), Decision Tree (DT), Support Vector Machine (SVM), and Logistic Regression (LR), were constructed and compared. The RF model exhibited the superior predictive performance, achieving a test set accuracy of 92.3% and a macro-average area under the receiver operating characteristic curve (AUC) of 0.949. External validation using five independent cases further confirmed the model’s practical utility, correctly predicting the drowning sites for four of the victims. Overall, This study preliminarily demonstrates the feasibility of inferring drowning locations through pulmonary microbiome analysis combined with machine learning in human samples, demonstrating the novel application of this approach to human cases. Future efforts should expand geographic sampling and integrate environmental metadata to enhance methodological robustness.},
}

@article {pmid41733709,
year = {2026},
author = {Sahariah, P and Saikia, L and Bharali, A and Law, D and Sen, S and Dutta, PP},
title = {Modulation of mitochondrial biogenesis by flavonoids via SIRT1 signalling in metabolic syndrome: a systematic review.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {41733709},
issn = {1573-4978},
abstract = {Metabolic syndrome (MetS) is a complex cluster of metabolic abnormalities, including insulin resistance, central obesity, dyslipidemia, and hypertension. Dysregulated mitochondrial biogenesis has emerged as a key pathogenic feature of MetS, while flavonoids are increasingly recognised for their ability to modulate mitochondrial function through SIRT1-dependent pathways. This review aims to critically evaluate the role of flavonoids in modulating mitochondrial biogenesis via SIRT1 signalling in MetS, with emphasis on mechanistic evidence. A systematic review was conducted with a mechanistic focus, integrating preclinical and translational evidence to assess the role of flavonoids in MetS through SIRT1. A comprehensive literature search was performed in PubMed, Scopus, and Web of Science up to 2025 using the keywords “flavonoids,” “flavonols,” “SIRT1,” “AMPK,” “GLUT4,” and “metabolic syndrome.” Flavonols have emerged as the most extensively studied subclass of flavonoids in MetS models, with compounds such as quercetin, myricetin, and luteolin demonstrating consistent protective effects. These effects were mediated by AMPK activation, GLUT4 translocation, and mitochondrial biogenesis via SIRT1 signalling, thereby improving insulin resistance, dyslipidemia, and mitochondrial dysfunction. Despite robust mechanistic evidence, no clinical trials to date have evaluated flavonols in the context of MetS. Limitations, such as poor bioavailability, pharmacokinetic variability, and the absence of standardised formulations, continue to hinder their clinical translation. To overcome translational barriers, future research should prioritise randomised controlled trials, alongside innovative strategies such as nanoformulations, microbiome-targeted interventions, and flavonoid-inspired therapeutics. Addressing these gaps could establish the flavonoid–SIRT1 axis as a novel therapeutic avenue for MetS.},
}

@article {pmid41746458,
year = {2026},
author = {Almeida, LF and Li, L and de Vries, RP and Sun, P and Maitan-Alfenas, GP},
title = {Enzymatic production of prebiotic xylooligosaccharides.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {3},
pages = {},
pmid = {41746458},
issn = {1573-0972},
abstract = {Xylooligosaccharides (XOS) have been shown to have prebiotic activities and therefore have beneficial effects on human and animal health. Production of these oligosaccharides from xylan often results in diverse mixtures, largely due to the variation in the xylan structure and the substrate specificities of the enzymes used to generate them. In this review, we will shortly describe the xylan structure and its variations, and the enzymes that are involved in its degradation. The use of these enzymes for the production of XOS and how this affects the variation in XOS structures will be addressed, which will then be linked to their prebiotic effects, especially related to modulation of the gut microbiome. The resulting health benefits will be summarized and finally the remaining challenges will be highlighted and suggestions for further improvement of their production will be provided.},
}

@article {pmid41779114,
year = {2026},
author = {Medeiros, EB and Lidio, AV and Zabot, GC and Fenilli, GP and de Bem Silveira, G and Keller, GS and Carrion, FRA and De Felice, FG and Kluwe-Schiavon, B and Walls-Bass, C and Barichello, T and Budni, J},
title = {Exploring the Gut-Brain Connection: Are Probiotics the Next Frontier in Alzheimer's Disease Treatment?.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12602-026-10927-w},
pmid = {41779114},
issn = {1867-1314},
abstract = {Alzheimer’s disease (AD) is the most common form of dementia, historically considered exclusively as a neurological condition treated primarily with cholinergic and glutamatergic inhibitors. Recent evidence highlights the significant influence of peripheral systems, particularly the gut-brain axis, on AD pathology. The gut microbiota plays a critical role in both physiological and psychological functions, and its interactions may impact the integrity of the blood-brain barrier, potentially contributing to neurodegenerative processes. Emerging therapeutic strategies targeting the gut microbiome, including both pharmacological and non-pharmacological approaches such as probiotics and prebiotics, offer promising avenues for intervention. This review synthesizes current literature and illustrative data to elucidate the connections among the gut-brain axis, neuroinflammation, and neuroprotection, and their implications for the pathogenesis and potential treatment of AD.},
}

@article {pmid41793457,
year = {2026},
author = {Hussain, B and Haouala, F and Fariduddin, Q},
title = {From night hormone to green signal: The journey of melatonin.},
journal = {Protoplasma},
volume = {},
number = {},
pages = {},
pmid = {41793457},
issn = {1615-6102},
support = {grant number IMSIU-DDRSP-RP25).//Deanship of Scientific Research at Imam Mohammad Ibn Saud Islamic University (IMSIU)/ ; },
abstract = {Melatonin (MT), once considered exclusive to animals, is now recognized as a universal and multifunctional molecule in plants, playing pivotal roles in growth regulation, stress tolerance, and antioxidant defense. Since its discovery in plants in the mid-1990s, the presence of MT has been reported to be prevalent across diverse plant taxa. MT modulates plant responses to abiotic stresses such as heat, cold, salinity, drought, heavy metals, and UV radiation, as well as biotic stresses including pathogen attack and herbivory, primarily by regulating antioxidant enzymes, stress-responsive genes, hormone signaling pathways, and production of secondary metabolites. Advanced analytical techniques such as HPLC, LC-MS, and NMR have facilitated sensitive detection and structural characterization of MT in various plant species. Molecular studies have identified receptors of MT and its roles in regulating different processes, highlighting its integration with other phytohormones and signaling molecules. Genetic engineering tools have been proven effective in raising the level of endogenous MT levels, which has immense potential for enhancing crop resilience. Emerging evidence points to the role of MT in modulating the plant microbiome and systemic signaling, offering new avenues for research. Despite significant advances, key challenges remain in understanding the structure of receptors, signaling crosstalk, and the regulation of its biosynthesis under stress. This review discusses the methods for detecting MT in plants and evaluates its physiological, molecular, and functional aspects. Tracing the evolution of MT research in plants, from its initial discovery to the present day, key milestones, cross-talk, and signaling pathways of MT in plants have been discussed.},
}

@article {pmid41807782,
year = {2026},
author = {Stevanoska, M and Cremona, M and Beekmann, K and Sturla, SJ and Aichinger, G},
title = {Interindividual variability in gut microbial formation of the hop phytoestrogen 8-prenylnaringenin results in elevated but sub-toxic internal exposures.},
journal = {Archives of toxicology},
volume = {100},
number = {6},
pages = {2397-2409},
pmid = {41807782},
issn = {1432-0738},
support = {SCAHT-AP_22_02//Swiss Centre for Applied Human Toxicology/ ; },
abstract = {The gut microbiome converts the prenylated polyphenol isoxanthohumol (iXN), a natural constituent of hops found in beer, into 8-prenylnaringenin (8-PN), a potent phytoestrogen associated with endocrine-disrupting effects. Following oral exposure, interindividual differences in microbiome composition may lead to variable systemic 8-PN concentrations and consequently to differences in susceptibility to toxicity. To characterize the contribution of gut microbiota to health effects of hop polyphenols, a human physiologically based kinetic (PBK) model that includes microbial 8-PN formation was developed. Ex vivo fecal fermentation coupled to LC–MS/MS revealed substantial interindividual variation in biotransformation capacity. Derived kinetic parameters were incorporated into the PBK model, which was subsequently used to predict systemic 8-PN exposure while accounting for interindividual variability. Model simulations indicated that high iXN metabolizers experience approximately two-fold more internal 8-PN exposure than low metabolizers. Estrogenicity of the predicted uterine 8-PN concentrations was assessed via alkaline phosphatase induction in Ishikawa cells. Even in high metabolizers, systemic 8-PN concentrations appeared to remain below levels of concern regarding endocrine disruption. These findings highlight the importance of accounting for interindividual variability in gut microbial biotransformation when predicting xenobiotic toxicokinetics and illustrate the applicability of microbiome-competent PBK modeling for predicting the systemic fate of gut microbial metabolites.},
}

@article {pmid41831055,
year = {2026},
author = {Longoria, CR and DeSio, DD and Oydanich, M and Su, X and Chiles, EN and Kerkhof, LJ and Ibironke, O and Häggblom, MM and Wages, NP and Guers, JJ and Vatner, DE and Vatner, SF and Campbell, SC},
title = {Disruption of the gut microbiota in regulator of G protein signaling 14 knockout (RGS14 KO) mice alters the metabolome and reduces enhanced exercise capacity.},
journal = {European journal of applied physiology},
volume = {},
number = {},
pages = {},
pmid = {41831055},
issn = {1439-6327},
support = {826640//Office of Naval Research/ ; R01HL37368//NHLBI Division of Intramural Research/ ; R01HL106511//NHLBI Division of Intramural Research/ ; P30CA072720-6852//Division of Cancer Prevention, National Cancer Institute/ ; },
abstract = {Regulator of G-protein Signaling 14 Knockout (RGS14 KO) mice exhibit enhanced exercise capacity and health span, however the contribution of the gut microbiota to this phenotype remains unclear. This study integrated long-read rRNA operon amplicon sequencing and metabolomics to first determine how microbial composition and tissue metabolite profiles differ between RGS14 KO and their wild-type littermates. Next, we investigated how administration of antibiotics to perturb the gut microbiota may affect the RGS14 KO phenotype. Prior to antibiotic treatment (ABX), RGS14 KO mice outperformed WT littermates in maximal running distance and work performed, accompanied by elevated skeletal muscle citrate synthase, complex IV activity, and nitric oxide production. One week of ABX significantly reduced exercise capacity in both genotypes and markedly suppressed mitochondrial activity in RGS14 KO skeletal muscle. Gut microbiota profiling revealed similar phylum-level structure between genotypes but distinct species- and strain-level signatures. Metabolomics of brown adipose tissue (BAT) and quadriceps identified genotype-specific metabolic programs that were disrupted by ABX, including pathways related to amino acid metabolism, nucleotide turnover, and mitochondrial energetics. Collectively, these findings demonstrate that RGS14 KO mice harbor unique microbial and metabolic networks that support enhanced thermogenesis and exercise performance, and that microbiota depletion eliminates these advantages. This work establishes a mechanistic foundation connecting the gut microbiota to BAT and skeletal muscle metabolism, highlighting potential microbiome-targeted strategies to improve metabolic health and physical performance.},
}

@article {pmid41872932,
year = {2026},
author = {Imtiaz, H and Liu, R and Li, QH and Zhou, CZ and Ying, YT and Tan, X},
title = {Reduction in microbiota-derived short-chain fatty acids contributes to the pathogenesis of pulmonary arterial hypertension.},
journal = {Respiratory research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12931-026-03591-9},
pmid = {41872932},
issn = {1465-993X},
support = {31872444//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: Pulmonary arterial hypertension (PAH) is a progressive and fatal cardiopulmonary disorder, with growing evidence implicating proinflammatory gut dysbiosis in its pathogenesis. Fast growing broiler chickens (Gallus gallus) spontaneously develop PAH with histopathological features that closely resemble those of the human disease, providing a robust translational model. METHODS: Gut microbiota composition in PAH-afflicted broilers was compared to that of healthy controls to identify disease-associated microbial alterations. Microbiota depletion was achieved using a broad-spectrum antibiotic cocktail, and oral supplementation with calcium acetate, a short-chain fatty acid (SCFA) salt, was administered to assess therapeutic potential. Pulmonary cytokine expression was measured to evaluate inflammation. RESULTS: PAH-afflicted broilers exhibited gut microbial alterations similar to those observed in human patients, characterized by a reduction in bacterial genera involved in the production of anti-inflammatory metabolites, particularly SCFAs, and an increase in arginine- and tryptophan-producing taxa. Microbiota depletion selectively enriched SCFA-producing bacteria and prevented the onset of PAH. Calcium acetate supplementation significantly mitigated disease progression and reduced pulmonary expression of proinflammatory cytokines. CONCLUSIONS: These findings establish a causal relationship between microbiome-derived metabolites and pulmonary vascular remodeling, supporting SCFA-based interventions as a promising therapeutic strategy for PAH.},
}

@article {pmid41885972,
year = {2026},
author = {Peng, B and Feng, Q and Wang, S and Zhao, X and Sheng, T and Wang, S and Liu, W and Liu, W and Huang, W and Meng, S and Zeng, S and Lin, R},
title = {Salivary microbiota composition and caries status in children with hearing impairment: a cross-sectional comparative study.},
journal = {Clinical oral investigations},
volume = {30},
number = {4},
pages = {},
pmid = {41885972},
issn = {1436-3771},
support = {201904010085//the Science and Technology Planning Project of Guangzhou/ ; 2025-2027-12//the Key Project of Medicine Discipline of Guangzhou/ ; },
abstract = {OBJECTIVES: To characterize the salivary microbiota structure in children with hearing impairment using 16 S rRNA gene sequencing and explore its potential association with caries burden. METHODS: A total of 114 hearing-impaired children aged 6–16 years underwent oral clinical examination and completed a questionnaire. From this cohort, 20 children (HI group) and 20 age- and sex-matched healthy children (HS group) were randomly selected for salivary microbiome sequencing. Analyses included alpha and beta diversity, LEfSe, and caries-stratified subgroup comparisons. RESULTS: Hearing-impaired children carried a heavy caries burden (overall prevalence: 93.9%; mean DMFT/dmft: 6.4 ± 3.9). Oral hygiene practices were generally suboptimal, with only 54.5% brushing twice daily and 41.6% using fluoride toothpaste. Beta diversity analysis significantly differed between groups (ANOSIM, R[2] = 0.057, P < 0.05). The HI group exhibited trends of increased Proteobacteria, Neisseria, and Gemella and decreased Veillonella and Capnocytophaga (all P > 0.05). LEFSe analysis revealed richer signature taxa in controls (e.g., Selenomonas, Tannerella), whereas hearing-impaired children showed limited enriched taxa, especially in the low-caries subgroup, indicating microbiota simplification. CONCLUSIONS: The oral microbiome of hearing-impaired children displays alterations in overall community structure, characterized by reduced diversity of signature microbial taxa and a trend toward ecological simplification. CLINICAL RELEVANCE: These findings identify oral microbial trends associated with hearing impairment, providing potential insights for early caries risk assessment and tailored preventive interventions in this vulnerable population.},
}

@article {pmid41915144,
year = {2026},
author = {Liu, S and Zhang, H and Jin, C and Geng, X and Li, R and Wu, N and Wang, Y},
title = {Pediococcus pentosaceus JNL0053 Mitigates DSS-induced Colitis in Mice Via the IL-22-Gut Barrier Pathway.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {41915144},
issn = {1867-1314},
support = {2023YFC2506000//National Key R&D Program of China/ ; ZR2024QH412//Natural Science Foundation of Shandong Province/ ; JNL-2023010Q//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; },
abstract = {Ulcerative colitis (UC) is a chronic, relapsing inflammatory bowel disease that imposes a growing socioeconomic burden worldwide. Among emerging live biotherapeutics, the probiotic Pediococcus pentosaceus has shown therapeutic promise against UC, yet its molecular mode of action remains poorly understood. In this study, we isolated a novel strain P. pentosaceus JNL0053 from traditional Inner Mongolian cheese. By integrating transcriptomics, untargeted metabolomics, and 16 S rRNA gene profiling, we elucidated its protective efficacy in the dextran sulfate sodium (DSS)-induced murine colitis model. Mice receiving P. pentosaceus JNL0053 exhibited reduced body-weight loss, lower disease activity index scores and attenuated histopathological damage. This treatment reshaped the gut microbiota and was accompanied by a more balanced immune microenvironment, as evidenced by markedly decreased serum levels of pro-inflammatory cytokines interleukin (IL)-6 and IL-1β, alongside significantly elevated anti-inflammatory IL-10. N-acetylmuramate, identified as a key differential metabolite, potently promoted Th17 cell differentiation, leading to the secretion of IL-22 and IL-17 F. This, in turn, increased the expression of mucin 2 and occludin, thereby protecting the intestinal barrier against pathogens. Collectively, P. pentosaceus JNL0053 orchestrated multi-level crosstalk between host immunity and the gut microbiome to alleviate DSS-induced colitis. By activating the IL-22–MUC axis and restoring epithelial integrity, this food-derived P. pentosaceus JNL0053 represents a compelling therapeutic strategy for UC.},
}

@article {pmid41917507,
year = {2026},
author = {Suparmin, A and Cahyani, LE and Ngadiman, and Sudibyo, H and Handayani, DP and Kirana, RP},
title = {First genomic report of Enterobacter mori strain Pna8 from Pandanus conoideus with antagonistic activity against plant wilt pathogen Fusarium odoratissimum and Ralstonia solanacearum.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {4},
pages = {},
pmid = {41917507},
issn = {1573-0972},
support = {Academic Excellence Program C of Universitas Gadjah Mada 431/UN1.P1/KPT/HUKOR/2024//Universitas Gadjah Mada/ ; },
abstract = {Plant wilt diseases are among the most destructive threats to global agriculture, largely due to the rapid adaptive capacity and treatment resistance of their causal pathogens. Endophytic bacteria represent a promising, sustainable alternative for disease management. Here, we report the first isolation and characterization of an endophytic bacterium, Enterobacter mori strain Pna8, from Pandanus conoideus, a tropical plant whose microbiome has remained unexplored. Strain Pna8 displayed strong antagonistic activity, inhibiting the fungal pathogen Fusarium odoratissimum by 55.9% and suppressing the growth of the bacterial wilt pathogen Ralstonia solanacearum, demonstrating dual biocontrol potential against both fungal and bacterial wilt diseases. Whole-genome sequencing revealed a 4.81 Mb genome comprising 4,433 coding sequences enriched in functions related to carbohydrate metabolism, phytohormone biosynthesis, phosphate solubilization, and stress tolerance. Importantly, Pna8 lacks pectinolytic CAZymes commonly associated with pathogenic E. mori, supporting its non-destructive, endophytic lifestyle. The genome also encodes unique biosynthetic gene clusters, including a lassopeptide absent from pathogenic relatives and siderophore variants related to frederiksenibactin. Comparative genomic analysis identified 119 singleton genes involved in transcriptional regulation, ion transport, and biofilm formation, indicating niche-driven evolution and ecological specialization. Collectively, these results highlight E. mori Pna8 as a novel and promising biocontrol resource for sustainable agriculture and tropical crop protection.},
}

@article {pmid41998320,
year = {2026},
author = {Chaitra, HS and Pandiyan, K and Singh, J and Kalia, VK},
title = {Influence of sex and geographical location on culturable midgut bacterial diversity of pink bollworm, Pectinophora gossypiella larvae and their enzyme production potential.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {5},
pages = {},
pmid = {41998320},
issn = {1573-0972},
abstract = {Gut microbes play a dynamic role in many metabolic and physiological activities in insects. Recent studies have shown the difference in the gut microbiota associated with both sex and geographical locations. Deciphering the gut microbiota hosted with respect to their function in an economic pest like pink bollworm, Pectinophora gossypiella, is essential to understand the relationship between insect and its gut microbiome. In the present study, culturable midgut bacteria were isolated from Bt cotton resistant P. gossypiella larvae (male and female) collected from different cotton growing regions across India. A total of 37 bacterial isolates, 21 from male and 16 from female were obtained and identified based on 16S rRNA gene sequence. All the isolates belonged to two major phyla, Proteobacteria and Firmicutes. Only three isolates, Enterococcus casseliflavus, Enterobacter hormaechei subsp. xiangfangensis and Bacillus cereus were common to both the sexes, while the rest were specific to each sex. The study also indicated a higher bacterial diversity in populations collected from two locations, Adilabad and Khandwa. All the isolates were screened for extracellular hydrolytic enzyme production, protease, amylase, cellulase, xylanase and chitinase. The results revealed that, among 37 bacterial isolates, 33, 7, 6 and 4 isolates exhibited protease, cellulase, chitinase and amylase activity, respectively. Maximum production of protease was noticed in Pantoea dispersa GM2 (0.39 ± 0.02 U/ml), amylase from B. cereus RF2 (0.17 ± 0.04 U/ml), cellulase from Burkholderia contaminans KhF1 (endoglucanase – 8.29 ± 1.60 U/ml; exoglucanase – 12.77 ± 1.5 U/ml; β-glucosidase – 10.01 ± 0.7 U/ml) and chitinase from E. hormaechei subsp. xiangfangensis AuF (87 ± 0.02 U/ml). The findings suggest that the gut bacterial community is influenced by both sex and geographical locations and the enzyme production are confined to specific locations. Further molecular studies would reveal the factors responsible for microbial community diversity and enzyme production.},
}

@article {pmid42020671,
year = {2026},
author = {Cruz, D and Saati-Santamaria, Z and Achury-Arrubla, L and Garcia-Fraile, P},
title = {From Wild to Farm: Gut Bacteriome Differences and Probiotic Potential of Pantoea Agglomerans in Two-Spotted Cricket (Gryllus Bimaculatus) Rearing.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020671},
issn = {1867-1314},
abstract = {The gut microbiome plays a crucial role in insect nutrition and performance, yet its targeted exploitation in cricket farming remains underexplored. Here, we combined gut microbiota profiling of wild and farmed Gryllus bimaculatus with probiotic testing of host-derived bacterial isolates to explore microbiome-informed strategies for sustainable cricket farming. Wild crickets exhibited higher Shannon diversity but lower phylogenetic diversity than farmed counterparts. Wild populations were enriched in Oscillospiraceae and Christensenellaceae families, while farmed crickets showed higher abundance of Parabacteroides. From 199 bacterial isolates, wild populations showed higher frequencies of uricolytic capabilities (44% vs. 31%), related to nitrogen recycling, while farmed crickets had more pectinolytic isolates (70% vs. 50%), linked to plant fiber degradation. Pantoea agglomerans I53BLB, which demonstrated broad enzymatic capabilities, was selected for probiotic evaluation; we further provide its genome sequence and analysis to contextualize its metabolic and probiotic potential. A feeding experiment with a 2 × 3 factorial design (two diets × three probiotic treatments, n = 10 replicates per group) compared control chicken feed versus a high-fiber diet formulated with agricultural by-products, each supplemented with water, live or heat-inactivated P. agglomerans. A significant diet × probiotic interaction was observed for weight gain (χ[2] = 18.8, p = 0.0021) and adult emergence (χ[2] = 17.7, p = 0.0033). Live P. agglomerans enhanced performance only when combined with the high-fiber diet, with individuals reaching a mean wet weight of 0.602 g compared to 0.451 g (heat-inactivated, p = 0.035) and 0.427 g (water control, p = 0.003), and a significantly higher adult emergence rate (37%) compared to all other treatment combinations (13%, p < 0.05), suggesting a symbiotic effect likely related with carbohydrate digestion. No effects were observed on survival or reproductive output. Notably, the high-fiber diet alone performed comparably to commercial feed, suggesting potential for sustainable cricket production using agricultural by-products. These findings demonstrate the feasibility of microbiome informed probiotic strategies to enhance cricket farming efficiency while reducing feed costs.},
}

@article {pmid42020676,
year = {2026},
author = {Purohit, HV and Chakraborty, J and Kothari, RK and Bhatt, AR},
title = {Gene Exchange Mechanisms in Natural and Engineered Probiotics Within the Human Gut Implications for Antibiotic Resistance and Metabolic Modulation.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42020676},
issn = {1867-1314},
abstract = {The human gut microbiome is a dynamic and densely populated ecosystem where microbial gene exchange plays a central role in shaping both ecological interactions and host physiology. This review critically examines the mechanisms and implications of horizontal gene transfer (HGT) among natural and engineered probiotics within the human gut, with a specific focus on antibiotic resistance dissemination and metabolic modulation. We provide an in-depth analysis of the molecular pathways of conjugation, transformation, and transduction under anaerobic gut conditions, highlighting their roles in the spread of mobile genetic elements, including antibiotic resistance genes (ARGs) and functional metabolic traits. Special emphasis is placed on the dual nature of gene exchange: while beneficial traits such as vitamin biosynthesis and polysaccharide degradation can be horizontally acquired to enhance probiotic efficacy and host-microbe symbiosis, the uncontrolled dissemination of ARGs or synthetic constructs poses significant clinical and ecological risks. Through a synthesis of recent findings from metagenomics, microbial ecology, and synthetic biology, we explore how natural probiotics may act as reservoirs of ARGs, and how engineered strains—if not properly contained—may contribute to genetic instability in the gut. We also evaluate current containment strategies such as chromosomal integration, kill switches, auxotrophy, and orthogonal circuit design to limit horizontal spread, alongside emerging tools for in situ gene transfer monitoring. Finally, we discuss regulatory challenges and propose a context-dependent risk assessment framework in which the consequences of probiotic gene exchange are determined by cargo properties, host ecological niche, gut inflammatory status, and biocontainment design.},
}

@article {pmid42020691,
year = {2026},
author = {Vávrová, P and Janďourek, O and Coraça-Huber, DC and Spiegel, C and Nachtigal, P and Krátký, M and Konečná, K},
title = {Host soluble plasma factors increase dual-species Staphylococcus epidermidis and Candida albicans biofilm biomass without enhancing stress tolerance.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-49557-1},
pmid = {42020691},
issn = {2045-2322},
support = {SVV 260 664//Univerzita Karlova v Praze, Czechia/ ; NW24-05-00539//Ministerstvo Zdravotnictví Ceské Republiky/ ; },
abstract = {Staphylococcus epidermidis (S. epidermidis) and Candida albicans (C. albicans) are common members of the human microbiome and opportunistic pathogens, forming mixed biofilms, leading to catheter-associated bloodstream infections or wound infections. They are increasingly difficult to treat, highlighting the urgent need for new antibiofilm strategies. Understanding how host environmental factors affect microbial communities is crucial for their development. Based on our previous findings, we investigated whether higher levels of host soluble factors in human plasma (HP) and freeze-thaw lysed sheep red blood cells (FT-RBC) support the formation of S. epidermidis-C. albicans dual-species biofilm and increase resilience. Tryptic soy broth, RPMI 1640, and Lubbock media with HP or FT-RBC supplementation were used for in vitro biofilm formation. Total biomass, individual microorganisms, key matrix components (carbohydrates, proteins, eDNA), and antimicrobial tolerance were evaluated. Our results showed that although higher concentrations of HP in Lubbock medium support the formation of complex dual-species biofilm biomass, this does not correlate with enhanced antimicrobial tolerance. In contrast, higher adaptive resistance was detected in less heterogeneous biofilms formed under nitrogen-limited conditions in RPMI 1640-supplemented medium. These findings indicate that biofilm resilience is not solely dependent on biomass amount and complexity, underscoring the need to better understand host-biofilm interactions.},
}

@article {pmid42020874,
year = {2026},
author = {Xia, Y and Chen, S and Deng, Z and Ye, C and Wu, H and Wang, Y and Guo, S and Guo, N and Yang, J and Tao, Z and Xiong, X and Guo, Y and Shang, Y},
title = {Soil microbial succession for forensic estimation of postmortem interval and decomposition site identification.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42020874},
issn = {1437-1596},
support = {82402196//Natural Science Foundation of China/ ; 82572150//Natural Science Foundation of China/ ; 2024JJ6546//Natural Science Foundation of Hunan Province/ ; },
abstract = {Estimating the postmortem interval (PMI) and identifying decomposition sites are important challenges in forensic science. The soil microbiome has shown potential in both applications. This study used pig models to simulate human decomposition and analyzed soil microbial succession over both short (0–11 days) and mid-to-long-term (up to 10 months) intervals to develop a PMI estimation model, while simultaneously comparing control and decomposition soils to assist in identifying potential corpse deposition sites. We built KNN (K-nearest neighbors) models at the genus level, which achieved high performance in short-term PMI estimation. Furthermore, a Linear Discriminant Analysis (LDA) model demonstrated robust performance in long-term PMI estimation, relying primarily on animal-associated microbial genera. Additionally, the KNN machine learning model effectively distinguished soils impacted by cadavers. This study provides a promising tool for estimating PMI and identifying potential body deposition sites.},
}

@article {pmid42031861,
year = {2026},
author = {Kamyab, M and Motamedi, H},
title = {Introducing silica-solubilizing and plant growth-promoting bacteria from sugarcane as inducers of drought stress tolerance.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48745-3},
pmid = {42031861},
issn = {2045-2322},
abstract = {Today’s sugarcane cultivation is faced with abiotic stresses including drought, salinity, heat and water limitation leading to, its reduced growth, yield, and economic productivity. Given the significant role of silica in alleviating these negative effects as well as pathogens, silica solubilizing bacteria opens an eco-friendly and sustainable approach to overcome these challenges. The aim was to find native silicate solubilizing bacteria from sugarcane and assessment their plant growth-promoting potential. Extensive screening was done from five sugarcane fields and symbiont bacterial species were qualitatively and quantitatively selected with regard to silicate solubilization. The isolates were explored for plant growth-promoting traits. As a result, Pantoea ananatis ASEna, Pantoea dispersa E345Se, and Pseudomonas migulae DSb were identified as high silica solubilizers. These also exhibited antifungal activity; phosphorus and potassium solubilization; sulfur oxidation; protease and cellulose production; auxin, hydrogen cyanide, and ammonia synthesis; nitrogen fixation; tolerance to heat, salinity (10%), drought, and pH stresses. The identified genera are part of the core sugarcane microbiome, and this is for the first time that these species have been documented as possessing growth-promoting traits for sugarcane and silicate-solubilizing capabilities. Currently, sugarcane producers are seeking for solutions to mitigate biotic and abiotic stresses and enhance crop yield in sugarcane fields. The strategic selection of bacteria that not only solubilize silica but also possess growth-promoting traits and can supply other essential nutrients to stimulating plant growth through various mechanisms, can enhance the effectiveness of silicate-solubilizing bacteria and make them suitable candidates for development of biofertilizers.},
}

@article {pmid42032090,
year = {2026},
author = {Wang, R and Li, W and Yin, Y and Jiang, S and Yang, B and Yu, R},
title = {Human milk-derived Bifidobacterium longum subsp. infantis CCFM1269 alleviates food allergy by modulating gut microbiota and restoring intestinal barrier.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-50287-7},
pmid = {42032090},
issn = {2045-2322},
abstract = {Food allergy (FA) is an immune-mediated disorder increasingly linked to intestinal dysbiosis and epithelial barrier dysfunction. This study evaluated the protective effects of Bifidobacterium longum subsp. infantis CCFM1269, a human milk-derived probiotic, using a β-lactoglobulin-induced FA mouse model. Oral administration of CCFM1269 significantly reduced allergic symptoms, including poor weight gain, diarrhea, and elevated allergy scores. The probiotic restored immune balance by downregulating IL-4 and IL-17 A and upregulating IL-10 and IFN-γ in both serum and jejunal tissues. It also alleviated oxidative stress by increasing superoxide dismutase activity and decreasing malondialdehyde levels. CCFM1269 enhanced intestinal barrier integrity through the upregulation of tight junction proteins Occludin, Claudin-1, and ZO-1. Microbiome analysis showed that CCFM1269 reshaped the gut microbial structure by increasing Helicobacter and reducing Alloprevotella and Bacteroides, taxa strongly associated with FA severity. Correlation analysis confirmed that these microbial changes were linked to improvements in immune and barrier function. Collectively, these findings indicate that human milk-derived CCFM1269 alleviates FA through microbiota modulation and epithelial restoration, supporting its potential as a probiotic strategy for preventing and treating FA.},
}

@article {pmid42032553,
year = {2026},
author = {Somarathna, MT and Leuke Bandara, D and Gunasekare, SKV and Nawarathna, LS and Wijetunge, S and Paranagama, MP and Gunawardhana, ND},
title = {Molecular detection of Helicobacter pylori in saliva of Sri Lankan adults with periodontitis, gastritis or both conditions.},
journal = {BMC oral health},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12903-026-08421-4},
pmid = {42032553},
issn = {1472-6831},
support = {Multidisciplinary Research Grant -2024 (MRG) 500//University Research Council, University of Peradeniya, Peradeniya, Sri Lanka/ ; },
abstract = {BACKGROUND: Periodontitis is an immuno-inflammatory disease affecting the tooth-supporting structures, primarily caused by dysbiosis of the oral microbiome. The involvement of one of the gastric pathogens, Helicobacter pylori, has been reported among individuals with periodontitis. However, the evidence regarding the association between oral H. pylori, periodontitis, and gastritis remains inconsistent and has not been investigated in Sri Lanka. Therefore, this study aimed to detect the oral H. pylori in a cohort of Sri Lankan adults and to evaluate its association with periodontitis and gastritis. METHODS: This cross-sectional study recruited 214 adults from two tertiary care institutes in Sri Lanka. Participants were categorized into four groups: (A) periodontitis only (n = 60), (B) gastritis only (n = 51), (C) both periodontitis and gastritis (n = 48), and (D) healthy controls without periodontitis or gastritis (n = 55). Unstimulated saliva samples were collected, DNA was extracted, and H. pylori was detected using PCR targeting the 16S rRNA gene. Positive samples were confirmed by ureA gene amplification. Detection rates were compared using Fisher’s exact test with Holm correction for multiple comparisons (p < 0.05). RESULTS: H. pylori was detected in 44 of 214 participants (20.6%; 95% CI 15.4–26.5%): periodontitis only 20.0%, gastritis only 21.6%, both conditions 31.3%, and controls 10.9%. The highest detection rate was observed in individuals with both periodontitis and gastritis (31.3%; OR 3.71, 95% CI 1.31–10.55). Although this difference did not reach statistical significance after Holm correction (adjusted p = 0.084), it represents a biologically meaningful trend warranting further investigation with larger sample sizes. No significant associations were found with age or sex (p > 0.05). CONCLUSION: H. pylori DNA is detectable in the saliva of Sri Lankan adults, with the highest detection rate observed in individuals with both periodontitis and gastritis (31.3%). This clinically relevant trend suggests that the inflamed periodontium may provide a favorable niche for the pathogen, although larger studies are needed to confirm statistical significance. This study represents the first investigation in Sri Lanka to identify the oral cavity as a potential extragastric niche for H. pylori using salivary detection. However, PCR-based detection cannot distinguish viable colonization from transient contamination. Longitudinal studies with culture-based methods and viability testing are required to clarify whether the oral cavity serves as an active reservoir for H. pylori transmission and reinfection.},
}

@article {pmid42043454,
year = {2026},
author = {Oyedokun, PA and Alade, TA and Olawale, IJ and Laoke, TS and Adeyemi, MO and Oyedokun, MD and Olaolu, OA and A S, LS and Olayemi, SB and Ndako, JA},
title = {Translating microbial dysbiosis into brain health interventions: a focus on the oral-gut-reproductive inflammatory pathways.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043454},
issn = {1432-072X},
abstract = {Alterations in the microbial communities along the oral, gut, and reproductive (OGR) axis are increasingly recognized as major contributors to systemic inflammation, endocrine dysregulation, and neuroimmune pathophysiology. Scientific evidence has demonstrated that OGR dysbiosis is associated with neuroimmune signaling potentially by the leakage of lipopolysaccharides and cytokine cascades, with associated disruption of blood-brain barrier integrity, degeneration of the neurovascular unit, dysregulation of the hypothalamic-pituitary-adrenal axis, and disruption of neurotransmitter balance via abnormal tryptophan metabolism. The mechanisms have been implicated in the development of several neuropsychiatric and neurodegenerative disorders across preclinical and human observational models. Novel microbiome-targeted approaches, including antimicrobial therapy, prebiotics, probiotics, dietary modifications, and hormone-microbiota-targeting treatment, demonstrate potential to restore microbial balance and reduce neuroinflammation, with mechanistic effects on neurotransmitter production, barrier protection, and immune tolerance. However, these effects have been demonstrated predominantly in preclinical and animal models; robust evidence from well-powered human clinical trials is currently limited. Accordingly, these approaches should be considered exploratory and hypothesis-generating rather than established clinical strategies, and their translation to patient care requires rigorous evaluation in controlled human trials. This review addresses the gap in understanding how dysbiosis in these interdependent microbial ecosystems transmits inflammatory and metabolic signals that impair neurophysiology. This review presents a translational perspective on OGR-axis modulation as a frontier for the prevention and management of brain disorders, integrating microbial, immune, endocrine, and neural perspectives. Exploring these insights would birth a paradigm shift from symptom-management-based brain health interventions to microbiota-specific interventions.},
}

@article {pmid42043591,
year = {2026},
author = {Hu, Y and Lin, H and Jiang, M and Lin, C and Li, H and Sun, J and Chen, K and Yu, Y and Liu, C},
title = {Host-derived Bacillus velezensis enhances intestinal structure, antioxidant capacity, and pathogen resistance in the American bullfrog (Aquarana catesbeiana).},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {42043591},
issn = {1432-072X},
support = {KB23Y1101//Application Research and Extension of Fermented Chinese Herbal Medicine in Bullfrog Farming under the 2023 Rural Revitalization Strategy/ ; },
abstract = {The development of host-derived probiotics presents a forward-looking nutritional component strategy for sustainable aquaculture. However, research on host-associated probiotics for the globally farmed American bullfrog (Aquarana catesbeiana) is limited. The research put Bacillus velezensis (BLS) isolated from bullfrog guts determine its probiotic potential. Bullfrogs were divided into two groups: one fed a control diet and the other fed a diet enriched with 1 × 10[8] CFU/g BLS for 7 weeks. BLS supplementation significantly enhanced growth performance and markedly decreased mortality after challenge with Streptococcus agalactiae. Relative to controls, the BLS cohort demonstrated heightened activity of essential antioxidant enzymes (CAT, GSH-Px, and SOD) and lower malondialdehyde levels in liver and intestinal tissues. Moreover, BLS supplementation enhanced intestinal structure, demonstrated by markedly increased villus height and goblet cell count, alongside enhanced hepatocyte arrangement and tissue integrity. Gut microbiome analysis revealed that BLS elevated the proportion of Firmicutes while decreasing the proportion of harmful genera such as Elizabethkingia. These findings suggest that the probiotic effects are mediated through the modulation of gut barrier function and microbial community. In conclusion, dietary supplementation with B. velezensis BLS enhanced growth, pathogen resistance, antioxidant capacity, and bowel health in bullfrogs through enhanced intestinal morphology and microbiome regulation. Consequently, supplementation holds significant promise as a probiotic in bullfrog farming.},
}

@article {pmid42050727,
year = {2026},
author = {Ivanova, M and Svensmark, B and Bruun Jensen, EE and Aarestrup, FM and Vigre, H and Otani, S},
title = {Metagenomics provides broad detection of pathogens, antimicrobial resistance, and virulence genes in pig diarrhoea and complement conventional methods.},
journal = {Animal microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s42523-026-00577-2},
pmid = {42050727},
issn = {2524-4671},
abstract = {BACKGROUND: Post-weaning diarrhoea (PWD) remains a major cause of morbidity in pig production and is commonly associated with enterotoxigenic Escherichia coli (ETEC). Conventional diagnostics rely on culturing and targeted qPCR, which provide limited resolution of pathogen diversity, virulence and antimicrobial resistance. Here, we evaluated Oxford Nanopore Technologies (ONT) metagenomic sequencing as a diagnostic tool for direct detection of pathogens, virulence factors and antimicrobial resistance genes (ARGs) from diarrhoeal pig faeces. RESULTS: Twenty-six diarrhoeal and six healthy pig faecal samples were analysed using culture, qPCR and ONT metagenomics with both high-output and rapid workflows. Culturing recovered 26 haemolytic E. coli and nine Clostridium perfringens isolates. PromethION metagenomics detected a significantly higher diversity of bacterial species, virulence factors and ARGs compared with GridION. Direct read mapping achieved 71–96% genome coverage for six E. coli isolates. Fourteen high- and medium-quality E. coli metagenome-assembled genomes (MAGs) were reconstructed, of which seven clustered closely with corresponding cultured isolates. All virulence factors detected in isolates were captured by metagenomics, while metagenomics identified additional fimbrial and enterotoxin genes not recovered by culture. Metagenomic ARG profiling identified resistance to 16 antibiotic classes, compared to eight classes in cultured isolates. No ESBL, carbapenemase or mcr genes were detected. CONCLUSIONS: Long-read ONT metagenomics enables culture-independent, strain-resolved characterisation of the pig gut microbiome during PWD, capturing pathogen diversity together with virulence and antimicrobial resistance profiles. This approach reveals within-sample strain heterogeneity and functional potential that are not resolved by conventional culturing, supporting its value for studying microbial ecology and dysbiosis in diseased animal microbiomes.},
}

@article {pmid42280338,
year = {2026},
author = {Zhang, S and Liu, K and Shi, L and Yan, C and Wang, A and Liu, A and Guo, H and Xie, A and Kong, XJ},
title = {Development of a Metagenomics-Guided Personalized Synbiotic Protocol for Children with Autism Spectrum Disorder: An Exploratory Case Series.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280338},
issn = {2072-6643},
support = {92436//Boston Children's Hospital/ ; 233263//Massachusetts General Hospital/ ; },
mesh = {Humans ; *Synbiotics/administration & dosage ; *Metagenomics/methods ; Child, Preschool ; *Autism Spectrum Disorder/microbiology/therapy ; Male ; Child ; Female ; Pilot Projects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Treatment Outcome ; *Precision Medicine/methods ; },
abstract = {BACKGROUND/OBJECTIVES: Gut microbiota dysregulation has been increasingly implicated in the pathophysiology of autism spectrum disorder (ASD), yet clinical responses to standardized probiotic interventions remain inconsistent, likely reflecting substantial inter-individual variability in baseline microbiome composition, host-microbe interactions, immune tone, and metabolic function. Here, we present a pilot implementation of a metagenomics-guided, personalized synbiotic intervention in children with ASD using the Systematic Microbiome Assessment and Reconstruction Therapy (SMART) framework.

METHODS: Seven children (aged 5-12 years) underwent longitudinal fecal shotgun metagenomic profiling, and dietary habits, food sensitivities, and regional dietary background were recorded as contextual factors potentially influencing microbiome composition and response to intervention. Individualized synbiotic formulations were constructed based on microbial taxonomic composition and inferred functional capacity and iteratively refined over time. Gastrointestinal outcomes were assessed through caregiver-reported clinical observations, whereas behavioral changes were evaluated using standardized instruments.

RESULTS: Several participants demonstrated improvements in gastrointestinal symptoms and selected behavioral domains. Notably, in a subset of participants, improvements in gastrointestinal function preceded measurable behavioral changes.

CONCLUSIONS: Although limited by a small sample size and lack of a control group, these findings provide preliminary evidence supporting the feasibility of implementing a metagenomics-guided personalized synbiotic framework in ASD and generate hypotheses for future investigation. This work presents a preliminary conceptual framework for integrating microbial composition and inferred functional profiling into individualized intervention design and highlights the potential value of microbiome-informed stratification in future studies of treatment response. Larger controlled studies with objective outcome measures are warranted to further evaluate feasibility, reproducibility, and potential clinical utility.},
}

Humans
*Synbiotics/administration & dosage
*Metagenomics/methods
Child, Preschool
*Autism Spectrum Disorder/microbiology/therapy
Male
Child
Female
Pilot Projects
Feces/microbiology
*Gastrointestinal Microbiome
Treatment Outcome
*Precision Medicine/methods

@article {pmid42280343,
year = {2026},
author = {Biagioli, V},
title = {Probiotics, Maternal Microbiome, and Early-Life Programming: A One Health Perspective on Perinatal and Infant Health.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280343},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome/physiology ; *Infant Health ; Female ; Pregnancy ; Infant ; Infant, Newborn ; Developmental Origins of Health and Disease ; Maternal Nutritional Physiological Phenomena ; },
abstract = {In recent years, the role of the gut microbiota in regulating human health has gained increasing scientific attention, particularly during early life [...].},
}

Humans
*Probiotics/administration & dosage
*Gastrointestinal Microbiome/physiology
*Infant Health
Female
Pregnancy
Infant
Infant, Newborn
Developmental Origins of Health and Disease
Maternal Nutritional Physiological Phenomena

@article {pmid42280356,
year = {2026},
author = {Kim, EJ and Hong, DK and Choi, ID and Shim, JJ and Lee, JH and Jung, WK},
title = {Effect of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 on Serum Triglyceride Levels and the Gut-Metabolic Axis: A Randomized, Double-Blind, Placebo-Controlled Clinical Trial.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280356},
issn = {2072-6643},
mesh = {Humans ; Double-Blind Method ; *Triglycerides/blood ; *Probiotics/administration & dosage/therapeutic use ; Female ; Male ; *Gastrointestinal Microbiome ; Middle Aged ; *Hypertriglyceridemia/blood/therapy/microbiology ; Adult ; Cholesterol, LDL/blood ; Biomarkers/blood ; *Lactobacillaceae ; *Lactiplantibacillus plantarum ; Overweight/blood ; },
abstract = {Background/Objectives: Hypertriglyceridemia is a critical cardiovascular risk factor, and the probiotic combination of Latilactobacillus curvatus HY7601 and Lactiplantibacillus plantarum KY1032 (HY+KY) has emerged as a potential therapeutic strategy, though clinical validation in adults with mild hypertriglyceridemia (HTG) is needed. Methods: In this randomized, double-blind, placebo-controlled, 12-week trial, a total of 100 overweight participants with mild HTG were randomized (n = 50 per group). Ultimately, 80 participants completed the study without major protocol violations and were evaluated in the Per-Protocol Set (probiotics group: n = 41; placebo group: n = 39). Primary outcomes included changes in serum lipid profiles such as triglycerides (TG) and LDL cholesterol (LDL), metabolic biomarkers, and gut microbiota composition analyzed via 16S rRNA gene sequencing. Results: HY+KY supplementation led to significant reductions in serum TG (158.61 ± 23.17 to 139.54 ± 54.31 mg/dL, p = 0.009) and LDL (129.22 ± 28.45 to 111.34 ± 21.03 mg/dL, p = 0.005) compared to baseline, while the placebo group showed no significant changes. Furthermore, the HY+KY group exhibited a significant increase in Apolipoprotein CII (ApoC2, p = 0.034) and a reduction in fasting glucose levels (p = 0.021). Microbiome analysis revealed that HY+KY significantly increased alpha diversity (Shannon index, p = 0.012) and significantly altered the microbial community structure (beta diversity, p = 0.015). Co-occurrence network analysis identified Lactiplantibacillus as a highly connected central node that is strongly associated with the favorable shifts in clinical biomarkers. Conclusions: HY+KY supplementation was associated with improved fasting TG and LDL profiles in adults with mild HTG, alongside coordinated changes in ApoC2, fasting glucose, and gut microbiota structure. These findings support the potential of probiotic supplementation as a preventive nutritional approach in borderline HTG.},
}

Humans
Double-Blind Method
*Triglycerides/blood
*Probiotics/administration & dosage/therapeutic use
Female
Male
*Gastrointestinal Microbiome
Middle Aged
*Hypertriglyceridemia/blood/therapy/microbiology
Adult
Cholesterol, LDL/blood
Biomarkers/blood
*Lactobacillaceae
*Lactiplantibacillus plantarum
Overweight/blood

@article {pmid42280361,
year = {2026},
author = {Chiesa, A and Generali, L and Butera, A and Filippini, T and Lanteri, V and Veneri, F},
title = {Oral Microbiota Characteristics in Relation to Different Dietary Patterns: A Systematic Review.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280361},
issn = {2072-6643},
mesh = {Humans ; *Microbiota/physiology ; *Mouth/microbiology ; *Diet/methods ; Diet, Mediterranean ; Oral Health ; Female ; Diet, Vegetarian ; *Feeding Behavior/physiology ; Male ; Adult ; Diet, Vegan ; },
abstract = {Background: Diet is a key modifiable factor influencing oral health and may shape the oral microbiota. While individual nutrients, especially free sugars, have been widely studied, the role of overall dietary patterns remains unclear. This systematic review aimed to evaluate the association between dietary patterns and oral microbiota in humans. Methods: PubMed/MEDLINE, Embase, and Web of Science were searched up to 18 March 2026. Studies assessing defined dietary patterns (Mediterranean, vegan, vegetarian, omnivorous) and oral microbiota using sequencing-based methods in healthy individuals were included. Due to heterogeneity in study design, dietary assessment, and microbiome analysis, a narrative synthesis was conducted. Results: Six studies (n = 448 participants) were included. Dietary patterns showed limited impact on overall microbiota structure, with no consistent changes in alpha and beta diversity. However, differences were observed at the taxonomic level. The Mediterranean diet was generally associated with a lower abundance of periodontopathogenic taxa. Plant-based and omnivorous diets showed distinct microbial profiles, particularly involving Neisseria, Haemophilus, Prevotella, and Streptococcus. Functional activity and metabolomic profiles appeared more sensitive to dietary variation than taxonomic composition alone. Conclusions: The oral microbiota appears relatively stable across dietary patterns, although diet may influence specific taxa and functional pathways relevant to oral health. The Mediterranean diet shows the most consistent association with beneficial microbial shifts. However, evidence is limited by heterogeneity and cross-sectional designs, highlighting the need for longitudinal and interventional studies.},
}

Humans
*Microbiota/physiology
*Mouth/microbiology
*Diet/methods
Diet, Mediterranean
Oral Health
Female
Diet, Vegetarian
*Feeding Behavior/physiology
Male
Adult
Diet, Vegan

@article {pmid42280378,
year = {2026},
author = {Cabri, G and Bhatti, SFM and Hemeryck, LY and Boon, P and Volk, HA and Hesta, M and Verdoodt, F},
title = {Canine Idiopathic Epilepsy as a Natural Animal Model for Human Epilepsy: A Scoping Review Highlighting Metabolic Perspectives Beyond the Brain.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280378},
issn = {2072-6643},
support = {1297623N//Research Foundation - Flanders/ ; },
mesh = {Animals ; Dogs ; Humans ; *Disease Models, Animal ; *Epilepsy/metabolism/veterinary ; *Dog Diseases/metabolism ; Brain/metabolism ; },
abstract = {Background: Emerging evidence indicates that epilepsy extends beyond the brain, involving systemic metabolic, immune, and microbiome perturbations that shape neuronal excitability and treatment response. Canine idiopathic epilepsy (CE) offers a naturally occurring model with strong electrophysiological, pharmacological, and clinical homology to human epilepsies. Methods: This scoping review was conducted according to the PRISMA-ScR guidelines. A systematic literature search was performed in Web of Science and MEDLINE (PubMed) to identify original studies reporting metabolic, immunometabolic, or neurochemical alterations in CE compared with healthy controls. Eligible studies included peer-reviewed original research involving client-owned dogs diagnosed with CE according to international consensus criteria (IVETF guidelines). Studies focusing exclusively on genetics or neuroimaging without metabolic outcomes were excluded. Titles, abstracts, and full texts were screened for eligibility, and data were extracted from included studies using a standardized approach. Identified metabolic domains were synthesized narratively and grouped into functional systems, including amino acid and lipid metabolism, micronutrients, neurotransmission, oxidative stress, inflammation and immunology, endocannabinoid signalling, microRNAs, and gut-brain axis-related pathways. In a second step, the identified metabolic domains were evaluated for translational relevance through a targeted, non-systematic narrative synthesis of the human epilepsy literature. This approach aimed to assess cross-species parallels and to provide a conceptual framework to guide future research, rather than to perform a comprehensive systematic review of metabolic alterations in human epilepsy. Results: Across CE studies, consistent alterations were observed in multiple interconnected functional systems, including metabolic, immune, and gut-brain axis pathways, in agreement with findings reported for human epilepsy. These data support a model of epileptogenesis involving systemic dysfunction beyond the central nervous system. Translationally, these findings suggest opportunities for biomarker development, patient stratification, and mechanism-based interventions, including dietary and metabolic approaches (e.g., medium-chain triglyceride supplementation), microbiome modulation, and immunometabolic targeting. The current evidence is limited by small and heterogeneous cohorts, potential confounding effects of antiseizure medications, variability in dietary and fasting conditions, breed-related effects, and a predominance of associative over causal relationships. Conclusions: This review positions CE as a reference framework for future research into epilepsy metabolism, integrating current evidence and its translational relevance to human disease. The findings support a shift toward a systems-level view of epileptogenesis, involving interconnected metabolic, immune, and gut-brain axis pathways beyond the brain. CE represents a valuable translational model to identify shared mechanisms, inform biomarker discovery, and guide the development of mechanism-based therapeutic strategies across veterinary and human epilepsy.},
}

Animals
Dogs
Humans
*Disease Models, Animal
*Epilepsy/metabolism/veterinary
*Dog Diseases/metabolism
Brain/metabolism

@article {pmid42280379,
year = {2026},
author = {Xie, A and Yuan, L and Yang, B},
title = {Immune Responses Against Allergic Asthma Following Intervention with Lacticaseibacillus paracasei DMLA16017 and Vitamin D in Rats.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280379},
issn = {2072-6643},
mesh = {Animals ; *Asthma/immunology/therapy ; *Vitamin D/pharmacology/administration & dosage ; Rats ; Cytokines/blood ; Disease Models, Animal ; Male ; Gastrointestinal Microbiome/drug effects ; Lung/pathology/immunology ; Ovalbumin ; Immunoglobulin E/blood ; Rats, Sprague-Dawley ; },
abstract = {OBJECTIVES: Allergic asthma (AA) is an increasing public health concern. The aim of this study was to investigate the potential effects of immune responses against AA in rats following intervention with Lacticaseibacillus paracasei DMLA16017 and vitamin D (VD).

METHODS: L. paracasei DMLA16017 was identified using 16S rDNA sequencing, while a rat model of AA was established via ovalbumin (OVA) induction. Subsequently, samples were collected for biomarker analysis in peripheral blood and lung tissue (including serum OVA-immunoglobulin E (IgE) and cytokines) using enzyme-linked immunosorbent assays and assessment of the composition of the intestinal microbiota and species diversity using 16S rRNA sequencing.

RESULTS: In the rat model, OVA-induced sensitization induced significant physiological alterations, including pulmonary tissue damage, elevated white cell counts, increased serum levels of OVA-IgE and cytokines interleukin (IL)-4 and IL-17, and reduced levels of IFN-γ and TGF-β. These changes were accompanied by dysbiosis of the gut microbiota and decreased species diversity. Co-administration of VD and DMLA16017 effectively ameliorated the physiological disturbances and histopathological abnormalities in rats with AA, restored the balance between cellular and immune responses, and improved the composition of the gut microbiota and species diversity.

CONCLUSIONS: Combined intervention with VD and DMLA16017 can be used to treat AA disorders, with potential long-term modulation of the immune system.},
}

Animals
*Asthma/immunology/therapy
*Vitamin D/pharmacology/administration & dosage
Rats
Cytokines/blood
Disease Models, Animal
Male
Gastrointestinal Microbiome/drug effects
Lung/pathology/immunology
Ovalbumin
Immunoglobulin E/blood
Rats, Sprague-Dawley

@article {pmid42280407,
year = {2026},
author = {Acierno, C and Caturano, A and Barletta, F and Rinaldi, L and Sasso, FC and Adinolfi, LE and Nevola, R},
title = {Nutritional Interventions Targeting the Gut Microbiome in MASLD: From Prebiotics and Probiotics to Postbiotics and Fecal Microbiota Transplantation.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280407},
issn = {2072-6643},
mesh = {Humans ; *Prebiotics/administration & dosage ; *Fecal Microbiota Transplantation ; *Probiotics/administration & dosage ; *Gastrointestinal Microbiome ; *Fatty Liver/therapy/microbiology ; Synbiotics/administration & dosage ; Dysbiosis ; },
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) is a highly prevalent liver-centred manifestation of systemic metabolic dysfunction. The gut-liver axis provides a biologically credible therapeutic rationale because intestinal dysbiosis, impaired barrier integrity, microbial metabolites, bile acid signalling, short-chain fatty acids, and trimethylamine N-oxide may influence hepatic steatosis, inflammation, and fibrogenesis. This narrative review critically evaluates dietary patterns, prebiotics, probiotics, synbiotics, postbiotics, and fecal microbiota transplantation (FMT) as microbiome-directed strategies in MASLD. The comparative framework prioritises disease-specific human evidence, clinically meaningful endpoints, trial duration and sample size, reproducibility, safety, and feasibility. Dietary optimisation remains the most clinically grounded intervention, whereas probiotics and synbiotics show modest and heterogeneous signals on biochemical or metabolic surrogate endpoints. Prebiotics are mechanistically coherent but supported by limited liver-centred trials. Postbiotics and microbiome-mediated bioactives remain early-stage and require stricter definitional boundaries. FMT is investigational and should not be extrapolated from its established role in recurrent Clostridioides difficile infection. Most available evidence across all intervention categories relies principally on surrogate endpoints-including aminotransferases, insulin resistance indices, lipid parameters, and microbiome compositional shifts-rather than on validated liver-centred outcomes such as histological improvement or quantitative liver fat assessment; this constrains the strength of conclusions that can currently be drawn. Across all categories, microbiome modulation does not by itself establish liver disease modification, and no microbiome-targeted nutritional intervention has yet demonstrated histological benefit in MASLD. Future trials in this field should prioritise validated hepatic endpoints, phenotype-stratified patient enrolment, adequate follow-up duration, and direct comparisons between intervention categories to determine which microbiome-directed strategies, if any, deliver measurable and reproducible hepatic benefit beyond surrogate markers.},
}

Humans
*Prebiotics/administration & dosage
*Fecal Microbiota Transplantation
*Probiotics/administration & dosage
*Gastrointestinal Microbiome
*Fatty Liver/therapy/microbiology
Synbiotics/administration & dosage
Dysbiosis

@article {pmid42280409,
year = {2026},
author = {Ostrowska, M and Komoń-Janczara, E and Mikołuć, B and Iłowiecka, K and Jarczak, J and Zagórska, J and Zambrzycka, P and Turroni, S and Szczerba, H},
title = {Oral Mycobiome Alterations in Children with Phenylketonuria: Associations with Dietary Intake and Metabolic Context-A Pilot Study.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280409},
issn = {2072-6643},
support = {2022/06/X/NZ9/00519//National Science Centre/ ; },
mesh = {Humans ; *Phenylketonurias/microbiology/metabolism ; Pilot Projects ; Male ; Female ; Child ; *Diet ; *Saliva/microbiology ; *Mycobiome ; Child, Preschool ; Case-Control Studies ; *Mouth/microbiology ; *Fungi/classification ; },
abstract = {BACKGROUND: Phenylketonuria (PKU) is a metabolic disorder requiring a strict low-phenylalanine diet. Oral health impairment, including bacteriome dysbiosis, is common in PKU, yet the mycobiome remains poorly defined. This pilot study aimed to characterise the salivary oral mycobiome of children with PKU compared with controls and to explore associations with dietary intake.

METHODS: Saliva samples from 18 children, including 8 patients with PKU and 10 age-matched controls, were profiled using internal transcribed spacer (ITS) amplicon sequencing. Alpha/beta diversity, taxonomic composition, diet-fungi correlations, discriminative taxa and LEfSe were analysed.

RESULTS: Alpha diversity did not differ significantly between groups after correction for multiple comparisons, although exploratory subgroup analyses suggested lower evenness in PKU children aged <10 years compared with older controls. Beta diversity differed by diagnosis (PERMANOVA: F = 1.7251, p = 0.0062) and in the age-diagnosis model (F = 1.8502, p = 0.0004). Taxonomic analyses identified nominal differences in several fungal taxa, including Candida (p = 0.011), Saccharomycetales_fam_Incertae_sedis (p = 0.011), Naganishia (p = 0.020), and Aspergillaceae (p = 0.036) in PKU samples; however, these findings should be interpreted as exploratory because many did not remain significant after FDR correction. Diet-mycobiome analyses identified selected FDR-supported associations, including an inverse relationship between phenylalanine intake and Naganishia in PKU.

CONCLUSIONS: This pilot study suggests preliminary compositional differences in the oral mycobiome of children with PKU that may be related to dietary therapy and metabolic context. These exploratory findings require validation in larger cohorts with detailed oral health assessment and control of confounders.},
}

Humans
*Phenylketonurias/microbiology/metabolism
Pilot Projects
Male
Female
Child
*Diet
*Saliva/microbiology
*Mycobiome
Child, Preschool
Case-Control Studies
*Mouth/microbiology
*Fungi/classification

@article {pmid42280416,
year = {2026},
author = {Kim, J and Lee, J},
title = {Nutritional Regulation of Ovarian Bioenergetics: Implications for Reproductive Aging and Female Infertility.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280416},
issn = {2072-6643},
support = {RS-2025-00513071//National Research Foundation of Korea/ ; },
mesh = {Female ; Humans ; *Energy Metabolism/physiology ; *Infertility, Female/metabolism/physiopathology ; *Aging/metabolism/physiology ; *Ovary/metabolism ; Animals ; *Reproduction/physiology ; Mitochondria/metabolism ; },
abstract = {Ovarian function is critically dependent on tightly coordinated cellular energy metabolism, which governs follicular development, oocyte competence, and reproductive longevity. Increasing evidence indicates that metabolic dysregulation, including mitochondrial dysfunction, oxidative imbalance, and impaired NAD[+] metabolism, contributes to the pathophysiology of major ovarian disorders such as PCOS, ovarian aging, and DOR. In parallel, emerging studies suggest that nutritional factors influence ovarian function by modulating mitochondrial bioenergetics, redox homeostasis, and nutrient-sensing signaling pathways. This review summarizes current knowledge on the molecular basis of ovarian energy metabolism and its disruption in female reproductive disorders. We further discuss nutritional strategies targeting ovarian bioenergetics, including antioxidants, NAD[+] precursors, mitochondrial cofactors, and dietary metabolic interventions. In addition, we highlight recent advances in metabolomics, microbiome research, epigenomics, and multi-omics integration that are shaping emerging nutrition-based approaches in reproductive medicine. Collectively, positioning ovarian metabolism at the center of nutritional reproductive research may provide a conceptual framework for understanding metabolic regulation in ovarian function and for guiding future research on reproductive health.},
}

Female
Humans
*Energy Metabolism/physiology
*Infertility, Female/metabolism/physiopathology
*Aging/metabolism/physiology
*Ovary/metabolism
Animals
*Reproduction/physiology
Mitochondria/metabolism

@article {pmid42280426,
year = {2026},
author = {Arshad, F and Akbar, A and Chinnappan, R and Khan, MI and Yaqinuddin, A and Arora, I},
title = {Dietary Polyphenols and Selected Nutraceuticals in Hepatocellular Carcinoma: Mechanistic Insights, Translational Evidence, and Clinical Prospects.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280426},
issn = {2072-6643},
mesh = {Humans ; *Dietary Supplements ; *Liver Neoplasms/prevention & control ; *Carcinoma, Hepatocellular/prevention & control ; *Polyphenols/pharmacology/administration & dosage ; Animals ; Signal Transduction/drug effects ; Diet ; },
abstract = {BACKGROUND: Hepatocellular carcinoma (HCC) develops predominantly from chronic liver injury, with diet representing a clinically actionable yet mechanistically complex modulator of hepatic carcinogenesis. Despite advances in immunotherapy, long-term survival remains poor, underscoring the need for complementary preventive and adjunctive strategies.

METHODS: We conducted a narrative review of epidemiological, experimental, and clinical literature on dietary patterns, polyphenols, and non-polyphenol nutraceuticals for HCC prevention and management, with a focus on underlying molecular and cellular mechanisms.

RESULTS: Dietary polyphenols and selected nutraceuticals exert pleiotropic effects on signaling pathways implicated in HCC, including NF-κB, STAT3, TGF-β/SMAD, PI3K/AKT, and Wnt/β-catenin, while modulating hepatic stellate cell activation, immune cell polarization, and microbiome-derived metabolites. Preclinical studies suggest that some compounds may enhance antitumor immunity and sensitize tumors to systemic therapies; however, clinical translation is constrained by limited bioavailability, pharmacokinetic variability, formulation heterogeneity, and a lack of high-quality trials.

CONCLUSIONS: This review highlights the potential of dietary patterns and nutraceuticals in HCC prevention and as adjunctive therapies. It outlines key translational priorities, including etiologic stratification, biomarker-driven trial design, and rigorous safety evaluation.},
}

Humans
*Dietary Supplements
*Liver Neoplasms/prevention & control
*Carcinoma, Hepatocellular/prevention & control
*Polyphenols/pharmacology/administration & dosage
Animals
Signal Transduction/drug effects
Diet

@article {pmid42280436,
year = {2026},
author = {Hwang, JH and Choi, YK},
title = {Effects of Herbal and Natural Product Interventions on Gut Microbiota and Clinical Outcomes in Patients Receiving PPI-Containing Therapy: A Systematic Review and Meta-Analysis.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280436},
issn = {2072-6643},
support = {NRF-2022R1A2C1013518//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Biological Products/pharmacology/therapeutic use ; Helicobacter Infections/drug therapy/microbiology ; Treatment Outcome ; *Plant Preparations/pharmacology ; Helicobacter pylori/drug effects ; Female ; *Phytotherapy ; Male ; Middle Aged ; },
abstract = {Proton pump inhibitor (PPI)-containing regimens, including bismuth quadruple therapy, may perturb gut microbiota through combined exposure to acid suppression, antibiotics, bismuth, and underlying disease context. Herbal medicines and natural products have been proposed as adjunctive interventions to mitigate treatment-related microbiota perturbations; however, systematic synthesis of the clinical evidence remains limited. This systematic review and meta-analysis evaluated the effects of herbal and natural product interventions on gut microbiota and clinical outcomes in patients receiving PPI-containing therapy. Six databases (PubMed, EMBASE, Web of Science, Scopus, CENTRAL, and CNKI) were searched from their inception to March 2026. Risk of bias was assessed using RoB 2.0 and ROBINS-I. This review was prospectively registered in PROSPERO (CRD420261346672). Eighteen studies (17 randomized controlled trials, 1 observational study; n = 1984 participants) were included in the final analysis. Meta-analysis demonstrated significantly higher Helicobacter pylori eradication rates (pooled relative risk (RR) = 1.20, 95% confidence interval (CI) 1.14-1.27; I[2] = 33%). Chinese-style total effective rate was also higher in the herbal groups (RR = 1.19, 95% CI 1.14-1.25; I[2] = 0%), but this non-standardized outcome should be interpreted cautiously. Exploratory microbiome meta-analyses suggested higher post-treatment Bifidobacterium and Lactobacillus levels; however, substantial heterogeneity limited interpretability. Narrative synthesis revealed potential preservation of α-diversity and attenuation of pathobiont proliferation in herbal groups. Overall, herbal and natural product interventions may be associated with favorable clinical outcomes and potential microbiota-modulating effects in patients receiving PPI-containing therapy, but certainty remains limited due to methodological concerns, outcome indirectness, and heterogeneity. High-quality trials stratified by antibiotic exposure are warranted.},
}

Humans
*Proton Pump Inhibitors/adverse effects/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Biological Products/pharmacology/therapeutic use
Helicobacter Infections/drug therapy/microbiology
Treatment Outcome
*Plant Preparations/pharmacology
Helicobacter pylori/drug effects
Female
*Phytotherapy
Male
Middle Aged

@article {pmid42280437,
year = {2026},
author = {Samiksha, F and Singh, D and Harbool, SS and Di Martino, L and Kruithoff, C and S McCormick, T and Ghannoum, M},
title = {Fungal β-1,3-glucans: Cell Wall Constituents That Promote Gut Health Through Innate Immune Modulation.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280437},
issn = {2072-6643},
mesh = {Humans ; *beta-Glucans/pharmacology/immunology ; *Immunity, Innate/drug effects ; *Cell Wall/chemistry/immunology ; Animals ; *Gastrointestinal Microbiome/drug effects/immunology ; *Fungi/chemistry ; Innate Immunity Recognition ; Prebiotics ; Intestinal Barrier Function ; },
abstract = {Fungal β-1,3-glucans are structurally conserved polysaccharide components of the fungal cell wall that exhibit potent immunomodulatory activity. These molecules are recognized by pattern recognition receptors, Toll-like receptors, complement receptor 3, lactosylceramide, scavenger receptors, and EphA2. Binding of β-1,3-glucans through these receptors triggers coordinated innate and adaptive immune responses such as cytokine production, phagocytosis, and trained immunity. In addition to receptor-mediated immune activation, dietary β-1,3-glucans function as fermentable prebiotic fibers that modulate gut microbiota composition, increase short-chain fatty acid production, and strengthen epithelial barrier integrity. These combined immunological and microbiome-mediated effects position β-1,3-glucans as key regulators of gut homeostasis. Preclinical and emerging clinical evidence supports broad therapeutic potential across multiple disease domains, including inflammatory bowel disease, metabolic disorders, respiratory infections, and cancer. In oncology, β-1,3-glucans enhance anti-tumor immunity, improve responses to monoclonal antibodies and chemotherapy, and serve as promising adjuvants in vaccine-based strategies. Additionally, β-1,3-glucan is widely used as a biomarker for invasive fungal infections and represents a validated target of antifungal therapies such as echinocandins. Despite these advances, clinical translation remains limited by heterogeneity in glucan source, structure, and formulation, as well as a lack of appropriately powered, standardized human clinical trials. Future efforts should focus on clarifying mechanisms of action, as well as rigorous clinical evaluation, to fully define the therapeutic utility of fungal β-1,3-glucans.},
}

Humans
*beta-Glucans/pharmacology/immunology
*Immunity, Innate/drug effects
*Cell Wall/chemistry/immunology
Animals
*Gastrointestinal Microbiome/drug effects/immunology
*Fungi/chemistry
Innate Immunity Recognition
Prebiotics
Intestinal Barrier Function

@article {pmid42280469,
year = {2026},
author = {Ang, MY and Choo, SW},
title = {The Nutri-Exposome Intelligence Framework: Integrating Multi-Omics, Machine Learning, and Digital Nutrition for Precision Chronic Disease Prevention.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
pmid = {42280469},
issn = {2072-6643},
support = {Reference Number: 5000105//High-Level Talent Recruitment Program for Academic and Research Platform Construction/ ; Grant Number: KY20250604000448//IFIRI Talents Program/ ; },
mesh = {Humans ; Multiomics ; *Machine Learning ; Chronic Disease/prevention & control ; *Precision Medicine/methods ; Digital Health ; *Exposome ; Nutrigenomics/methods ; Data Analytics ; Diet ; },
abstract = {Background/Objectives: Precision nutrition is moving beyond population-based guidance and isolated gene-diet interactions toward integrative models of dietary response. However, current approaches remain fragmented across nutrigenomics, microbiome research, multi-omics profiling, digital health, and machine learning. This review proposes the Nutri-Exposome Intelligence Framework as a conceptual, data science-driven model for integrating cumulative dietary, environmental, microbial, molecular, clinical, and digital exposures for precision chronic disease prevention. Methods: This conceptual review synthesizes the literature on precision nutrition, nutrigenetics, nutrigenomics, exposomics, gut microbiome research, multi-omics integration, wearable and biomarker-based monitoring, and machine learning in nutrition studies. Evidence was organized into a framework linking exposure assessment, host susceptibility, microbiome-mediated biotransformation, molecular response profiling, computational modelling, personalized intervention, and longitudinal feedback. Results: The proposed framework consists of seven interconnected layers: diet, environment, and lifestyle exposures; host genome and microbiome; multi-omics molecular responses; machine learning-based integration; risk prediction and responder stratification; personalized dietary intervention; and wearable and biomarker-based feedback. It positions the nutri-exposome as a cumulative exposure-response system and highlights how machine learning can support data harmonization, feature engineering, predictive modelling, responder classification, explainable interpretation, and adaptive refinement of dietary recommendations. Key applications include obesity, type 2 diabetes, cardiovascular disease, metabolic dysfunction-associated steatotic liver disease, cardiovascular-kidney-metabolic syndrome, and broader cardiometabolic prevention. Conclusions: Nutri-exposome intelligence offers a structured pathway for transforming complex nutrition data into predictive, explainable, and adaptive precision nutrition strategies. Implementation will require longitudinal and multi-ethnic cohorts, standardized metadata, causal validation, interpretable machine learning, ethical governance, and equitable access to support responsible clinical and public health translation globally.},
}

Humans
Multiomics
*Machine Learning
Chronic Disease/prevention & control
*Precision Medicine/methods
Digital Health
*Exposome
Nutrigenomics/methods
Data Analytics
Diet

@article {pmid42280542,
year = {2026},
author = {Zhou, T and He, Y and Liew, A and Wang, M and Cheong, KL},
title = {Polysaccharides from the Peel of Hylocereus undatus Promote Wound Healing by Reshaping the Skin Microbiome and Regulating Immune Balance.},
journal = {Polymers},
volume = {18},
number = {11},
pages = {},
pmid = {42280542},
issn = {2073-4360},
support = {2025A1515010078//Natural Science Foundation of Guangdong Province/ ; 2024ZDZX2084//Key Research Project of High Education of Guangdong Province/ ; },
abstract = {Polysaccharides isolated from the peel of Hylocereus undatus exhibit promising anti-inflammatory activity; however, the underlying mechanisms-particularly their modulatory effects on cutaneous microbiota composition and host immune responses-remain incompletely characterized. This study investigates the therapeutic potential of polysaccharides isolated from the peel of Hylocereus undatus in the management of inflammatory cutaneous wounds. The polysaccharide extracted from the peel of Hylocereus undatus via ultrasound-assisted extraction is an acidic heteropolysaccharide, with galacturonic acid and rhamnose as its dominant monosaccharide components. It exhibits low crystallinity, a porous structure, and good thermal stability. In a mouse wound model, treatment with the polysaccharide extracted from the peel of Hylocereus undatus significantly accelerated wound closure as early as day 3 (** p < 0.01). By day 9, the wound closure rate approached that of the positive control group and remained significantly higher than that of the untreated group (** p < 0.01), exceeding 90%. Treatment with the polysaccharide advanced the inflammatory peak, as evidenced by elevated anti-inflammatory cytokines (IL-10 and TGF-β) and suppression of the pro-inflammatory cytokine IL-6. Immunofluorescence staining confirmed that polysaccharide promoted cell proliferation and neovascularization at the wound site. In conclusion, polysaccharides isolated from the peel of Hylocereus undatus accelerate skin wound healing by modulating the skin microbiota, enhancing the anti-inflammatory response, and promoting tissue regeneration, highlighting its potential as a natural wound dressing.},
}

@article {pmid42280664,
year = {2026},
author = {Hashemi, SM and Graeff, M and Nai, EA and Savidov, N},
title = {Cultivation System Dominates Cucumber Performance and Root-Zone Microbiomes Across Biochar Particle Sizes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280664},
issn = {2223-7747},
abstract = {Hydroponic (HP) and aquaponic (AQ) systems are widely known in greenhouse production; however, the combined effects of nutrient delivery system and substrate physical structure on crop performance and root-zone microbiomes remain insufficiently understood. Substrate physical properties influence water retention and aeration, which can affect root-associated microorganisms, plant growth, and yield. This study evaluated cucumber (Cucumis sativus L.) growth, yield, nutrient dynamics, physiological stress responses, and bacterial community composition under HP and AQ systems using bamboo-derived biochar substrates and coconut coir as a control. Vegetative growth was enhanced under AQ, with the greatest plant elongation (1102 ± 40.1 cm) and stem diameter (15.1 ± 1.0 mm) observed in biochar-grown plants. Total yield was consistently higher under AQ than HP, with the highest yield recorded in the coarse biochar treatment (28.6 kg m[-2]). Aquaponic systems were associated with greater nutrient availability under the conditions evaluated during mid to late season production, including nitrate concentrations of up to 226 mg L[-1]. Physiological stress monitoring indicated lower stress exposure under aquaponic conditions in plants grown in medium and coarse biochar substrates across both systems, with 78 to 81% of the growing season classified within low to balanced stress conditions. Bacterial community composition was primarily shaped by cultivation system, which explained 19.3% of the observed variation, whereas substrate treatment did not significantly alter overall bacterial community structure. Overall, cultivation system was the dominant factor associated with variation in cucumber performance and root-zone bacterial communities, while biochar substrates supported improved plant growth, yield, and reduced physiological stress.},
}

@article {pmid42280669,
year = {2026},
author = {Zhang, L and Dong, J and Zhao, J and Jiang, H and Zhang, W},
title = {Rhizosphere Functional Plasticity and the Keystone Taxon Sphingomonas Facilitate Sweet Cherry Adaptation to Semi-Arid Stress.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280669},
issn = {2223-7747},
support = {2023LHMS03007//Department of Science and Technology of Inner Mongolia Autonomous Region/ ; },
abstract = {Translocation of elite cultivars across distinct climatic regions often induces transplantation shock. Although the rhizosphere microbiome can facilitate host acclimation, the underlying functional mechanisms remain unclear. Here, we investigated microbiome-mediated adaptation in "Hongdeng" sweet cherry (Prunus avium L.) moved from a humid coastal region (Dalian, DL) to a semi-arid inland habitat (Hohhot, HS). We integrated plant physiological assays, metagenomic sequencing, and structural equation modeling (SEM) to compare the source population (DL), the introduced population (HS), and a locally acclimated reference cultivar ("Summit", HSY). The introduced trees adjusted physiologically to the semi-arid environment by elevating proline levels and antioxidant enzyme activities. Although environmental stress reduced microbial alpha diversity, the core taxonomic framework persisted. Community assembly analysis indicated that the semi-arid climate intensified environmental filtering. Network analysis identified Sphingomonas as a keystone taxon; notably, it maintained a highly connected topological role despite a stable relative abundance. Furthermore, structural equation modeling showed that the environmental stress index positively correlated with the upregulation of microbial DNA repair pathways (R = 0.81, p < 0.001). Ultimately, the SEM demonstrated that environmental stress primarily shapes microbial functional profiles rather than driving species turnover, thereby contributing to host adaptation. The successful establishment of introduced sweet cherry in semi-arid regions is tied more closely to rhizosphere functional plasticity than to taxonomic restructuring. These findings highlight the role of the keystone taxon Sphingomonas in maintaining rhizosphere homeostasis, offering a theoretical framework for targeted microbiome engineering to mitigate transplant shock and enhance crop resilience.},
}

@article {pmid42280740,
year = {2026},
author = {Ding, Y and Zhao, Y and Xie, Y and Sun, C and Yang, L and Sun, Z and Yang, L and Wang, Y and Zhang, J and Han, Z},
title = {Aspergillus neoalliaceus MR-86 Promotes the Growth of Saposhnikovia divaricata by Regulating the Rhizosphere Microbiome.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280740},
issn = {2223-7747},
support = {20260204099YY, 20260204045YY//Jilin Province Science and Technology Department/ ; JLAUHLRG20102006//Jilin Agricultural University high-level researcher grant/ ; D23007//The 111 Project, Northeast Advantageous Characteristic Resources and Health Food Discipline Innovation Introduction Base/ ; },
abstract = {Plant growth-promoting fungi (PGPF) have shown broad potential to improve soil conditions and enhance root growth and development. However, few studies have examined the effects of exogenous PGPF inoculation on the growth of the medicinal plant Saposhnikovia divaricata and the associated changes in the rhizosphere microbiome. In this study, Aspergillus neoalliaceus MR-86 exhibited phosphate solubilization, growth in nitrogen-free medium, potassium solubilization, IAA production, and siderophore production. PCR assays did not detect the aflatoxin biosynthesis-related genes aflR, aflS, and omtA in strain MR-86. Pot trials demonstrated that inoculation with MR-86 significantly increased the plant height and root dry weight of S. divaricata by 10.32% and 21.05%, respectively (p < 0.05). In the rhizosphere, soil pH decreased, whereas soil alkaline-hydrolyzable nitrogen and available phosphorus levels, as well as the activities of protease, urease, and cellulase, increased significantly. Illumina NovaSeq sequencing revealed that MR-86 inoculation altered the soil microbial community structure and specifically enriched several microbial taxa, including Talaromyces, Subulicystidium, and Aspergillus. Moreover, MR-86 inoculation did not alter the composition of dominant bacterial and fungal phyla, but significantly modified microbial interactions and the topology of microbial networks. Correlation analysis indicated that the specific microbial taxa Subulicystidium, Aspergillus, and Talaromyces were positively associated with soil nutrient indices, enzyme activities, and plant growth parameters. Functional prediction analysis indicated that MR-86 treatment was predicted to be enriched bacterial metabolic pathways, including flavone and flavonol biosynthesis and ether lipid metabolism, and was predicted to increase the relative abundance of functional fungal groups such as ectomycorrhizal and wood-decomposing fungi. In summary, A. neoalliaceus MR-86 may contribute to improved growth of S. divaricata by enhancing nutrient availability and transformation and by modulating the structure and function of the rhizosphere microbiome.},
}

@article {pmid42280750,
year = {2026},
author = {Liu, J and Haider, FU and Liu, Y and Zhang, P and Liu, T and Li, X and Li, S},
title = {Reframing Partial Root-Zone Irrigation: A Spatial Stress-Priming Mechanism for Crop Adaptation to Abiotic Stresses.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280750},
issn = {2223-7747},
support = {2024YFD1501500//The National Key R&D Program of China/ ; 20240101010JJ//Jilin Province Science and Technology Department/ ; },
abstract = {Abiotic stresses limit crop productivity by disrupting water relations, carbon assimilation, nutrient acquisition, membrane stability, and redox homeostasis. Partial root-zone irrigation (PRI), commonly implemented as partial root-zone drying (PRD), is often viewed as a deficit-irrigation strategy to improve water-use efficiency; however, this view underestimates the biological consequences of spatial root-zone heterogeneity. This review evaluates PRI as a spatially structured, priming-like framework for crop adaptation to abiotic stress. Available evidence indicates that localized drying and wet-side water uptake can coordinate root sensing, hydraulic-chemical signaling, abscisic acid delivery, hormone crosstalk, xylem-mediated regulation, and stomatal control. Beyond gas exchange, PRI is associated with photosynthetic maintenance, osmotic adjustment, antioxidant and redox regulation, root architectural plasticity, nutrient acquisition, and metabolic reprogramming. Evidence is strongest for drought, whereas responses to low temperature, salinity, heat-associated evaporative demand, and combined stresses remain more context-dependent. Emerging work also links PRI to rhizosphere restructuring and microbiome shifts, but the causal mechanisms and field reproducibility remain unresolved. We argue that future progress requires matched PRI-deficit-irrigation comparisons, standardized switching thresholds, shared physiological and molecular readouts across crops, high-resolution root biology, and commercially realistic field validation. This framing distinguishes conserved physiological outcomes from mechanisms that may differ among crops, genotypes, and irrigation designs.},
}

@article {pmid42280785,
year = {2026},
author = {Nunes, A and Minello, LVP and Oliveira, ER and Schneider, AR and Dutra, FS and Guizolfi, T and Santos, LRB and Gelli, VC and Granada, CE and Sperotto, RA and Moura, S and Maraschin, M and Lima, GPP},
title = {Impact of Kappaphycus alvarezii Biostimulant on Growth, Biochemistry, Essential Oil, and Rhizosphere of Basil (Ocimum basilicum) Plants.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280785},
issn = {2223-7747},
support = {2023/03886-1//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 25/2551-0002537-0//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 22/2551-0001641-3//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 88887.696139/2022-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 405949/2022-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 306495/2023-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 303956/2023-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 405779/2022-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 305135/2021-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 314977/2025-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 311719/2023-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 24/2551-0001302-4//Fundação de Amparo à Pesquisa do Estado do Rio Grande do Sul/ ; 2024TR002499//Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina/ ; 408526/2024-6//Institutos Nacionais de Ciência e Tecnologia/ ; },
abstract = {Seaweed-derived biostimulants are a promising strategy for improving crop performance in sustainable agriculture. In this context, this study evaluated the effects of foliar application of Kappaphycus alvarezii extracts, obtained from two Brazilian regions (São Paulo: Kal-SP and Santa Catarina: Kal-SC), at different concentrations (1%, 3%, 5%, and 7%) on the growth, biochemical profile, essential oil yield, and rhizosphere microbiome of Ocimum basilicum under field conditions. Morphological analysis indicated that the 5% and 7% concentrations increased plant height, biomass, root development, and inflorescence production, with biomass gains of up to 51% and essential oil production increases of up to 142% compared to the control. Biochemical responses varied by extract origin, with Kal-SC promoting greater increases in photosynthetic pigments, antioxidant activity, and carbon-related metabolites, whereas Kal-SP induced only minor metabolic changes. The algal biostimulant modulated essential oil yield and composition, promoting treatment-dependent shifts in major terpenoid compounds. Microbiome analysis showed no significant changes in alpha diversity, but significant shifts in beta diversity and functional groups, such as Bacillaceae, indicating rhizosphere reorganization. Overall, the effectiveness of K. alvarezii-based biostimulants depends on concentration and biomass source, highlighting their potential as sustainable agricultural bioproducts and the importance of standardized extraction for consistent outcomes.},
}

@article {pmid42280795,
year = {2026},
author = {Geng, H and Xin, Y and Jin, H and Zheng, Z and Pan, T and Zeng, Z},
title = {Physiological Responses, Molecular Basis, and Integrated Regulation of Heat Tolerance in Soybean.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
pmid = {42280795},
issn = {2223-7747},
support = {LQ24C130001//Zhejiang Provincial Natural Science Foundation/ ; CARS-04-CES33//China Agriculture Research System-Soybean/ ; 2022LFR109//Program for Research and Development of Zhejiang A&F University/ ; },
abstract = {Global warming has led to frequent occurrences of extreme heat, posing a huge threat to soybean (Glycine max L.) yield. As a major source of plant protein and oil, soybean is particularly sensitive to heat stress during its growth and development, especially in critical stages such as flowering and seed filling. Heat tolerance in crops is a complex trait governed by polygenic networks and environmental interactions; although existing studies have identified several heat-tolerance-related genes, the molecular regulatory networks regulating crop responses to heat stress remain elusive. This review synthesizes recent advances in soybean heat tolerance research, with a particular emphasis on physiological responses and molecular regulatory mechanisms under heat stress. We further evaluate the potential of modern technologies, including gene editing, marker-assisted selection, and pan-genomics, for the precise improvement of heat tolerance in soybean. Additionally, we outline sustainable agronomic practices and field management strategies to mitigate heat stress. The development of heat-tolerant soybean varieties depends not only on the identification of superior alleles but also requires a shift from gene-centric genetic improvement toward a system-wide solution that integrates "Genotype × Environment × Management".},
}

@article {pmid42281243,
year = {2026},
author = {Stanford, J and Hoedt, EC and Gómez-Martín, M and Clarke, ED and Duncanson, K and Burrows, T and Collins, CE},
title = {Contrasting dietary patterns remodel gut microbial function and generate multi-omic signatures associated with cardiometabolic markers.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2685381},
doi = {10.1080/19490976.2026.2685381},
pmid = {42281243},
issn = {1949-0984},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Multiomics ; Feces/microbiology ; Biomarkers/urine/blood ; Female ; Adult ; Male ; *Diet ; Australia ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Cross-Over Studies ; Middle Aged ; Metabolome ; Metabolomics ; Blood Pressure ; },
abstract = {Diet is a modifiable determinant of gut microbiome composition, yet the impact of contrasting whole-dietary patterns on microbial metabolic capacity and coordinated host metabolic signatures remains incompletely characterized. In a randomized crossover feeding trial, 34 Australian adults were provided with a Healthy Australian Diet (HAD), aligned with national dietary guidelines, and a Typical Australian Diet (TAD), reflecting average population intake for two weeks each, separated by a two-week washout. Fecal microbiome composition and function were assessed using shotgun metagenomics, plasma and urine metabolites by untargeted metabolomics, with cardiometabolic markers including blood pressure, plasma lipids, and glucose quantified. HAD was associated with reduced taxonomic and functional alpha diversity relative to baseline, with no change following TAD. Species-level responses were modest, 105 functional pathways differed between diets, with 99 increasing following HAD, predominantly related to amino acid and nucleotide biosynthesis and vitamin/cofactor metabolism. Multi-omic integration using DIABLO achieved strong discrimination of dietary responses (held-out accuracy 91.7%; permutation p = 0.005). In total, 77 individual omic feature-cardiometabolic outcome associations survived FDR correction (q < 0.05), spanning microbial gene functions, plasma metabolites, and urinary metabolites linked to cholesterol, blood pressure, and triglyceride responses. These exploratory findings suggest that integrated microbiome-metabolome profiling may capture inter-individual variation in dietary cardiometabolic responses, though replication in larger, independent, robustly designed studies is needed before translational personalized nutrition strategies can be assessed.},
}

Humans
*Gastrointestinal Microbiome/physiology
Multiomics
Feces/microbiology
Biomarkers/urine/blood
Female
Adult
Male
*Diet
Australia
*Bacteria/classification/genetics/isolation & purification/metabolism
Cross-Over Studies
Middle Aged
Metabolome
Metabolomics
Blood Pressure

@article {pmid42281266,
year = {2026},
author = {Hu, M and Li, Y and Zhao, L and Cha, S and Xue, Y and Han, Y and Xue, C and Dong, N},
title = {Engineered Lactococcus lactis for Oral Delivery of an Antimicrobial Peptide against Enterotoxigenic Escherichia coli in Weaned Piglets.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17784},
pmid = {42281266},
issn = {1520-5118},
abstract = {Food-grade strategies against foodborne pathogens while preserving intestinal health are gaining attention. Here, we developed a regulated delivery platform using Lactococcus lactis engineered to secrete a tandem dimeric antimicrobial peptide (SD). The engineered strain (SDLactis) exhibited stable growth, genetic stability, and tolerance to simulated gastrointestinal conditions. Chloride-responsive SD secretion enabled effective antibacterial activity against enterotoxigenic Escherichia coli (ETEC) K88 in vitro. In ETEC-challenged piglets, oral SDLactis alleviated diarrhea, improved growth, and reduced intestinal injury and inflammation. It strengthened intestinal barrier integrity by upregulating tight junction proteins (ZO-1, Claudin-1,Occludin) and downregulating CFTR. Microbiome analysis revealed that SDLactis partially restored gut microbial diversity, reducing Escherichia-Shigella while enriching Lactobacillus and short-chain fatty acid-producing genera. Overall, food-grade engineered lactic acid bacteria serve as controllable delivery vehicles for antimicrobial peptides, offering a nonantibiotic strategy for pathogen control and gut health management in food and feed applications.},
}

@article {pmid42281376,
year = {2026},
author = {Zhang, R and Li, X and Chen, X and Shen, A and Zhang, X and Peng, C and Qiu, J},
title = {Charge-Competition AIEgens Induce Mitochondrial Dysfunction for Selective Eradication of Candida albicans while Restoring Vaginal Microbiota.},
journal = {Journal of microbiology and biotechnology},
volume = {36},
number = {},
pages = {e2601074},
doi = {10.4014/jmb.2601.01074},
pmid = {42281376},
issn = {1738-8872},
mesh = {Female ; *Candida albicans/drug effects ; Animals ; *Antifungal Agents/pharmacology/chemistry ; *Candidiasis, Vulvovaginal/drug therapy/microbiology ; *Vagina/microbiology ; *Mitochondria/drug effects ; Biofilms/drug effects ; Lactobacillus/drug effects/growth & development ; Mice ; *Microbiota/drug effects ; Humans ; Disease Models, Animal ; },
abstract = {The principal therapeutic challenge in vulvovaginal candidiasis (VVC) is that the non-selective nature of conventional antifungal drugs, which frequently perturb vaginal microecological homeostasis and disrupt Lactobacillus barrier, lead to the emergence of recurrent infection and drug resistance. This study aims to develop novel antifungal agents capable of efficiently and selectively eradicating pathogenic fungi while protecting and promoting the growth of Lactobacilli, with real-time monitoring capabilities and significant potential for clinical application. Harnessing the principle of charge-competition, we engineered a cationic amphiphilic aggregation-induced emission luminogens (AIEgens, named as TPE-ET), where hydrophobic chain length served as a key determinant governing membrane affinity, aggregation propensity, and antimicrobial selectivity. This design empowered potent eradication of Candida albicans (C. albicans) while concomitantly favoring the proliferation of beneficial Lactobacilli. Moreover, TPE-ET disrupted C. albicans biofilms and suppressed virulence genes related to adhesion, invasion, and drug resistance. In a murine VVC model, TPE-ET reduced fungal burden by over 90%, facilitating the repair of damaged vaginal epithelium and the reconstitution of a Lactobacillus-dominat vaginal microbiome. Remarkably, TPE-ET outperformed clotrimazole in restoring healthy microecological balance, as manifested by diminished Proteobacteria abundance alongside increased Firmicutes (notably Lactobacillus) and Bacteroidetes. Mechanistic studies revealed that TPE-ET exerted its remarkable antifungal activity by targeting the mitochondrial inner membrane, disrupting the metabolism-inflammation axis and eliciting mitochondrial dysfunction. Collectively, this dual merits of membrane charge-selective targeting and AIEgens-mediated visualization established an innovative therapeutic strategy for VVC, featuring superior efficacy, exquisite selectivity, and real-time monitoring capability with significant clinical potential.},
}

Female
*Candida albicans/drug effects
Animals
*Antifungal Agents/pharmacology/chemistry
*Candidiasis, Vulvovaginal/drug therapy/microbiology
*Vagina/microbiology
*Mitochondria/drug effects
Biofilms/drug effects
Lactobacillus/drug effects/growth & development
Mice
*Microbiota/drug effects
Humans
Disease Models, Animal