@article {pmid42448878,
year = {2026},
author = {Kara, K and Pİrcİ, G},
title = {Dietary supplementation of lamiaceae aromatic oils: effects on performance, rumen fermentation, and ruminal microbiome in calves.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62392-8},
pmid = {42448878},
issn = {2045-2322},
support = {TSA-2024-13540//Erciyes Üniversitesi/ ; },
abstract = {This study investigated the effects of sage (Salvia officinalis), thyme (Thymus sp.), and lavender (Lavandula angustifolia) aromatic oils on growth performance, rumen fermentation, and microbial composition in Holstein calves. A total of 32 calves were randomly assigned to four groups: a control group (CONT) receiving unsupplemented milk and three experimental groups supplemented with 150 µL/day/calf of sage (SAG), thyme (THY), or lavender (LAV) aromatic oil, along with starter feed and forage. Sage (4.89 and 10.14%, respectively) and lavender (6.75 and 20.29%, respectively) oils significantly improved body weight and average daily weight gain at weaning, while all aromatic oils enhanced feedstuff dry matter (DM) intake (P < 0.05). Rumen ammonia nitrogen levels remained unaffected by sage and lavender oils but increased with thyme oil supplementation (P < 0.05). Sage oil increased the molar concentrations of acetic, iso-valeric, total (short chain fatty acids) SCFA (P < 0.01), straight SCFA (P < 0.01), and branched SCFA (P < 0.05). Both sage and lavender oils elevated propionic (P < 0.05) and butyric acid levels (P < 0.001). In terms of rumen microbiota, thyme oil increased the abundance of Bifidobacteriaceae by approximately 73% (P < 0.05), while sage oil significantly increased the relative proportion of Acidaminococcaceae by approximately 160% (P < 0.001). Sage and lavender oils reduced Prevotellaceae but increased Lachnospiraceae (P < 0.001). In conclusion, supplementation with 150 µL/day of sage, thyme, or lavender aromatic oils improved feedstuff DM intake, rumen fermentation, and microbial populations in Holstein calves. Sage and lavender oils showed the most pronounced benefits by increasing SCFA production and promoting potentially beneficial bacterial families such as Lachnospiraceae and Acidaminococcaceae, which are associated with enhanced carbohydrate fermentation and rumen development, while reducing Prevotellaceae abundance. Thyme oil increased Bifidobacteriaceae, suggesting a positive modulation of gut microbial balance. These findings indicate that aromatic oils, particularly sage and lavender, may support healthier rumen maturation and improved calf performance during early-life feeding.},
}

@article {pmid42448934,
year = {2026},
author = {Arora, K and Chowdhary, R and Shenoy, A and Kapadia, C and Paras, F and Vora, N and Arora, A and Chowdhary, R and Arora, A and Goyal, M and Matt-Amaral, L},
title = {Acute myeloid leukemia and gut microbiome: bidirectional effects and opportunities for intervention.},
journal = {Annals of hematology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00277-026-07176-w},
pmid = {42448934},
issn = {1432-0584},
abstract = {Acute myeloid leukaemia (AML) is characterized by substantial treatment-related morbidity that is not fully explained by cytogenetic or molecular risk stratification alone. Emerging evidence implicates the gut microbiome as a critical, modifiable determinant of AML pathogenesis, therapeutic response, and treatment-related complications. Patients with AML exhibit profound gut microbiome disruption at diagnosis, marked by reduced microbial diversity and depletion of short-chain fatty acid-producing commensals, which is further exacerbated by intensive chemotherapy, antibiotic exposure, and hematopoietic stem cell transplantation (HSCT). These perturbations impair intestinal barrier integrity, amplify systemic inflammation, and promote domination by opportunistic and multidrug-resistant organisms, thereby increasing the risks of mucositis, bloodstream infections, graft-versus-host disease, and mortality. Beyond complications, microbiome-derived metabolites modulate immune signalling, hematopoietic homeostasis, and inflammatory pathways relevant to clonal haematopoiesis and leukemogenesis, suggesting bidirectional interactions between the microbiome and AML biology. Observational and translational studies demonstrate that preserved microbial diversity and enrichment of specific taxa are associated with improved survival following HSCT, while dysbiosis correlates with inferior outcomes. Interventions aimed at microbiome preservation and restoration-including antibiotic stewardship, dietary modulation, autologous or donor fecal microbiota transplantation, and emerging postbiotic strategies-have shown feasibility and biologic efficacy, although definitive clinical benefit remains to be established. This review synthesizes current mechanistic, clinical, and translational evidence linking gut microbiome dysregulation with AML outcomes, highlights emerging therapeutic strategies, and outlines key challenges and future directions. Integrating microbiome-focused supportive care into AML management represents a promising avenue to reduce treatment toxicity and improve patient outcomes.},
}

@article {pmid42448967,
year = {2026},
author = {Sittipo, P and Park, JY and Tiffany, E and Oh, A and Moon, S and Lee, CH and Oh, JS and Kim, TY and Kweon, MN and Choi, J and Song, KH and Lee, DW and Nam, MH and Hong, SJ and Lee, EY and Jeon, SR and Song, HY and Kim, BS and Lee, YK},
title = {Gut microbiome modulation by Veillonella ratti induces resistance to EAE pathogenesis via microbe-derived metabolites.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42448967},
issn = {2092-6413},
support = {2021M3A9I4027993//National Research Foundation of Korea (NRF)/ ; RS-2023-00219563//National Research Foundation of Korea (NRF)/ ; 2021M3A9I4023974//National Research Foundation of Korea (NRF)/ ; },
abstract = {The progression of multiple sclerosis (MS) is potentially influenced by the microbiome. Elucidating host-microbiome interactions in MS may aid in developing microbiome-based applications; however, these interactions remain unclear. Here, we aimed to elucidate how Veillonella ratti MHL0042, isolated from human infant feces, modulates neuroinflammation and disease severity in experimental autoimmune encephalomyelitis, a murine MS model. Whole metagenomic sequencing revealed that V. ratti MHL0042 reshaped disrupted gut microbiota via microbial interactions throughout the intestinal tract. V. ratti MHL0042 administration significantly reduced central nervous system inflammation, notably decreasing CD4[+]IFN-γ[+] T cell populations and activated spinal cord microglia. Mechanistically, V. ratti MHL0042 depleted pldA-containing bacteria, involved in phosphatidylethanolamine metabolism, thus elevating dioleoyl phosphatidylethanolamine (DOPE) levels. Increased DOPE was not only detected in the intestinal tract but also extended systemically and reflected in the central nervous system. Exogenous DOPE administration recapitulated the attenuation of experimental autoimmune encephalomyelitis pathogenesis by suppressing microglial activation. These findings highlight the therapeutic applicability of the microbiome and underscore its potential in human disease treatment.},
}

@article {pmid42449053,
year = {2026},
author = {Maurice, K and Baldovini, N and Zaremski, A and Damay, J and Lehnebach, R and Estevez, Y and Ducousso, M},
title = {The Microbial and Chemical Terroir of Agarwood in French Guiana.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02824-0},
pmid = {42449053},
issn = {1432-184X},
support = {Acquilascent//Agence Nationale de la Recherche/ ; },
abstract = {Agarwood is a highly valued aromatic resinous wood formed in Aquilaria species following stress or infection, yet the putative microbial drivers of its quality remain poorly understood, particularly outside its native range. In this study, we investigated the bacterial and fungal communities associated with agarwood produced from Aquilaria crassna Pierre ex Lecomte planted in French Guiana and examined their relationships with volatile chemical compounds relevant to agarwood fragrance. Using high‑throughput sequencing and comprehensive chemical profiling, we characterized microbial community composition and agarwood volatile profiles across multiple cultivation plots. Despite spatial variability in microbial assemblages, agarwood samples exhibited a conserved chemical signature dominated by chromone derivatives and sesquiterpenoids, indicating the presence of a stable chemical terroir under Guianese environmental conditions. Network analysis revealed numerous bacterial and fungal taxa significantly associated with key chemical classes, suggesting potential microbial contributions to agarwood chemical complexity through plant-microbe interactions or microbial metabolic activity, although causality remains to be established. Comparative analyses with commercial agarwood samples from South-East Asia and the Middle East revealed a distinct chemical profile for Guianese agarwood, highlighting the influence of geographic origin on agarwood quality and supporting an extension of the terroir concept to woody aromatic products. Overall, this study demonstrates that Aquilaria trees cultivated in French Guiana can produce high‑quality agarwood and provides new insights into the interplay between microbial communities and agarwood chemistry. These findings lay the groundwork for the development of locally adapted, microbiome‑informed strategies for sustainable agarwood production.},
}

@article {pmid42449164,
year = {2026},
author = {Lin, D and Ganda, E and Silverman, J and Huang, J and Gottwald, KR and Hu, H and Niu, P and McArt, JAA},
title = {Toward disease-associated fecal microbiome signatures for domestic mammals.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10647-5},
pmid = {42449164},
issn = {2399-3642},
abstract = {Conserved fecal microbiome signatures of intestinal diseases across domestic mammals offer a non-invasive avenue to monitor animal health and advance One Health, yet systematic meta-analysis with cross-study, cross-disease, and cross-host validation remains lacking. We present a leave-one-dataset-out meta-analysis defining generalizable intestinal disease signatures in mammalian hosts. Analyzing 512 samples from four bovine diarrhea and three canine IBD studies, we identified 12 bovine and 8 canine stable signature genera marked by depleted short-chain fatty acid (SCFA) producers and enriched pathobionts through a compositional random-effects framework with per-study covariate-adjusted effect sizes. A minimal signature set matched full-feature models across five machine learning models, and study-aware transfer learning improved cross-study generalization. Across 367 samples, signatures outperformed for intestinal versus non-intestinal phenotypes in cross-disease prediction. Cross-host validation across equine, feline, caprine, swine, and human datasets (533 animal and 1,182 human samples) revealed canine IBD-associated signatures outperformed in feline intestinal disease prediction, while bovine diarrhea-associated signatures generalized better to herbivorous hosts and human intestinal diseases. These findings may support the existence of conserved microbial signatures across veterinary and human medicine, warranting further investigation toward diagnostic applications.},
}

@article {pmid42449405,
year = {2026},
author = {Ni, M and Wang, Q and Ye, T and Lei, H and Wang, Y and Yuan, Y},
title = {Targeting the gut microbiome: an integrated probiotic and prebiotic strategy for polycystic ovary syndrome management.},
journal = {Journal of ovarian research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13048-026-02164-0},
pmid = {42449405},
issn = {1757-2215},
support = {(No. 2024MS210)//the Science and Technology Project of the Sichuan Administration of Traditional Chinese Medicine/ ; (No. 2022SYF37)//the Luzhou Science and Technology Plan Project/ ; 2100601//the Central Finance Traditional Chinese Medicine Inheritance and Development Subsidy Project (Subproject: Evidence-Based Capacity Enhancement Project of Traditional Chinese Medicine)/ ; },
abstract = {Polycystic ovary syndrome (PCOS) is a prevalent endocrine-metabolic disorder in which gut dysbiosis acts as a key environmental driver. This review synthesizes how probiotics and prebiotics remodel the gut ecosystem and ameliorate PCOS through multi-pathway mechanisms:restoring intestinal barrier function, modulating microbial metabolites (e.g., short-chain fatty acids(SCFAs), bile acids(BAs)), attenuating chronic inflammation, and regulating androgen metabolism. We further propose a novel "integrated microbiome‑centric management" framework, demonstrating how microbiota-targeted interventions synergize with dietary, pharmacological, and behavioral strategies to enable personalized, multi-modal PCOS care. This work provides a transformative perspective for translating gut microbiome science into clinical practice across disciplinary boundaries.},
}

@article {pmid42449422,
year = {2026},
author = {Webster, SJ and Cock, IE and Matheson, C and Sweeney, EL},
title = {Vaginal microbiomes and their pertinent social context: a microbial ecological review proffering AMR-STI acquisition and emergence.},
journal = {Biology of sex differences},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13293-026-00953-2},
pmid = {42449422},
issn = {2042-6410},
support = {Research Training Program (RTP) Domestic Scholarship//Australian Government/ ; },
abstract = {BACKGROUND: In the landscape of sexual health, sex, gender, and sexuality are inextricably linked and highly relevant to sexually transmitted infections (STIs). Globally, key sexual and reproductive health concerns of women have been associated with the socioeconomic status of their country, indicating that social context bears influence over sexual health outcomes. Further, the increasing prevalence of antimicrobial resistant STIs (AMR-STIs) in the sexual networks of gay and bisexual men-who-have-sex-with-men (GBMSM) suggests an implicit connection between microbiological and social phenomena, although research to date is relatively limited and often fails to reflect the complexity and nuance of sexual networks. Vulval and vaginal microbiome composition may influence STI acquisition and transmission, yet the relationships between composition, microenvironment, and STIs remain largely overlooked, especially in the context of women and gender-diverse people. In this article, we explore the possibility that a combination of social, sexual, and behavioural factors, combined with biological features, shape the microbiological context of STIs within the vaginal microenvironment. MAIN: The human vaginal microbiome (VMB) forms an ecological niche home to a complex ecosystem of microorganisms. The microbial composition of the VMB is diverse between individuals, with variations observed across racial and ethnic groups, and intrapersonal fluctuations linked to a plethora of factors both within and outside of personal control. Importantly, VMB health is a crucial component of wellbeing for people assigned female at birth (AFAB), transgendered women with neovaginas, and their sexual partners. Clinical context also remains important; in Australia, doxycycline prophylaxis (Doxy-PEP) has recently become available to GBMSM networks aimed to protect against the acquisition of STIs. However, Doxy-PEP guidelines exclude AFAB people and fail to specify regarding use among gender diverse individuals. Given the high prevalence of AMR-STIs within GBMSM networks, the impact of this intervention on excluded partners should be thoroughly investigated. Factors in the VMB such as biofilm formation and necessary microbial balance with opportunistic pathogens renders this ecological microbial niche a hypothetically perfect platform for AMR development and emergence within the social context.

CONCLUSION: This review explores the social context of vaginal microbiomes, their potential influence on AMR-STI development, and highlight several important knowledge gaps to benefit from further research.},
}

@article {pmid42449539,
year = {2026},
author = {Chen, D and Ju, M and Li, H and Feng, J and Zi, X and Gong, X and Che, Y and Lei, X and Geng, Z and Deng, H and Zhao, K and Xie, J and Chen, XL and Peng, J},
title = {Combined application of Bacillus velezensis JDB15 and Trichoderma harzianum JDL4 suppresses banana Fusarium wilt under controlled conditions.},
journal = {Pest management science},
volume = {},
number = {},
pages = {},
doi = {10.1002/ps.71113},
pmid = {42449539},
issn = {1526-4998},
support = {SKLTCBQN202508//Project of State Key Laboratory of Tropical Crop Breeding/ ; 325MS119//Hainan Provincial Natural Science Foundation of China/ ; KJRC2025B10//Hainan Science and Technology Talent Innovation Project/ ; 1630042026002//Central Public-interest Scientific Institution Basal Research Fund/ ; NKLTCB202406//Open Funds of State Key Laboratory of Tropical Crop Breeding/ ; //Earmarked Fund for CARS-32/ ; },
abstract = {BACKGROUND: The development of biocontrol agents represents a promising strategy to manage banana Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4). Although many traditional approaches have isolated beneficial microorganisms from soil or the rhizosphere, studies seeking biocontrol resources from the perspective of banana root endophytes remain scarce.

RESULTS: Endophytic microbiome analysis revealed significant enrichment of Bacillota in the wilt-resistant cultivar. Among the isolated strains, Bacillus velezensis JDB15 exhibited the best inhibitory effect against Foc TR4. The fermentation broth of JDB15 significantly inhibited spore germination and caused hyphal membrane damage in pathogens. Mechanistic studies indicated that the lipopeptide surfactin C is a candidate active antimicrobial metabolite produced by JDB15, which disrupts pathogen cell membrane integrity, increases membrane permeability, and induces electrolyte leakage. Another isolated endophytic fungus, Trichoderma harzianum strain JDL4, also exhibited strong antagonistic activity against Foc TR4 probably through mycoparasitism. Combined application of cell-free filtrate from JDB15 and JDL4 demonstrated effective control against multiple plant diseases including banana Fusarium wilt, tomato Fusarium wilt, corn southern leaf blight, and rice blast under controlled conditions.

CONCLUSION: We suggest that the antimicrobial activity of JDB15 and JDL4 is most probably attributable to the metabolite surfactin C and likely mycoparasitism, respectively. Co-application of the fermentation filtrates of these two strains exhibited broad-spectrum disease control efficacy and significantly improved disease suppression compared with either strain alone. These findings provide novel biological agents for the control of banana Fusarium wilt and other plant diseases. © 2026 The Author(s). Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.},
}

@article {pmid42449649,
year = {2026},
author = {Machnicki, P and Czarnecka-Chrebelska, K and Kordiak, J and Lewandowski, K and Bielec, F and Płoszaj, T and Brzeziańska-Lasota, E and Pastuszak-Lewandoska, D},
title = {Lung Tissue Microbiome in NSCLC Patients: Metabarcoding Analysis Identifies Escherichia-Shigella as an Abundant Taxon.},
journal = {Cancers},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/cancers18132105},
pmid = {42449649},
issn = {2072-6694},
support = {Resolution No. 3/2025//Fundacja im. Jakuba hr. Potockiego, 02-202 Warszawa, ul. Drawska 14 lok. 11 (http://www.fpotockiego.org.pl; e-mail: fundacja@fpotockiego.org.pl)./ ; },
abstract = {Background: Non-small cell lung cancer (NSCLC) remains the leading cause of cancer-related mortality worldwide despite advances in diagnosis and treatment. Increasing evidence suggests that alterations in the lung microbiome may contribute to NSCLC development and progression; however, findings remain inconsistent due to heterogeneous biological materials and methodological differences among studies. Therefore, this study aimed to characterize the lung tissue microbiome in NSCLC using a paired tissue-based approach. Methods: Thirty-two patients with NSCLC were enrolled. For each patient, two samples were collected: primary tumor tissue and matched macroscopically unchanged adjacent lung tissue. The V3-V4 region of the 16S rRNA gene was amplified and sequenced, followed by bioinformatic analysis using the QIIME2 pipeline. Results: Tumor tissues demonstrated lower alpha (Shannon H = 9.60, q = 0.001) and beta (Jaccard pseudo-F = 1.26, q = 0.015) diversity compared with adjacent controls, indicating reduced microbial complexity within the tumor microenvironment. Escherichia-Shigella was the most abundant detected genus (~12%) in both groups, although without a statistically significant difference. Analysis of microbiome variation in relation to spatial distance between sampled tissues revealed a strong trend toward significance (p = 0.07) with a substantial effect size (R[2] = 0.207). Conclusions: The observed microbiome alterations in NSCLC were more evident at the ecological level than in overall taxonomic composition, supporting a model of microbial community simplification rather than complete compositional replacement. Our findings also suggest that tumor-adjacent lung tissue may not represent a fully neutral control due to the local field effect. The relatively high abundance of Escherichia-Shigella indicates that this taxon may warrant further investigation in NSCLC microbiome studies.},
}

@article {pmid42449656,
year = {2026},
author = {Clavo, B and Córdoba-Lanús, E and Martínez-Sánchez, G and Cánovas-Molina, Á and Federico, M and Galván, S and Ramchandani-Vaswani, A and Piñero, JE and Antonilli, C and Benítez, G and Cobiella-Hernández, L and Pérez-Rodríguez, D and Pérez-Santana, C and Martín-Alfaro, R and Fernández-Tagarro, M and Díaz-Garrido, JA and González-Martín, JM and Martínez-Pérez, R and Lorenzo-Morales, J and Rodríguez-Esparragón, F},
title = {Gut Microbiota Dysbiosis and CIPN: State-of-the-Art Evidence and a Microbiota-Ozone Therapeutic Framework.},
journal = {Cancers},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/cancers18132112},
pmid = {42449656},
issn = {2072-6694},
support = {PI23/01324//Institute of Health Carlos III/ ; CIGC/23-24//Cabildo de Gran Canaria/ ; CGC/2025/12551//Cabildo de Gran Canarias/ ; PIFIISC25/52//Fundación Canaria Instituto de Investigación Sanitaria de Canarias/ ; PIFIISC24/37//Fundación Canaria Instituto de Investigación Sanitaria de Canarias/ ; },
abstract = {BACKGROUND/OBJECTIVES: Chemotherapy-induced peripheral neuropathy (CIPN) affects up to 85% of patients receiving neurotoxic regimens, often leading to dose reduction and impaired quality of life, yet effective preventive or therapeutic options remain scarce. Emerging evidence implicates chemotherapy-induced gut microbiota dysbiosis in CIPN pathogenesis via a gut-nerve axis. Concurrently, rectal ozone insufflation (ROI) has been shown to modulate the gut microbiota and reduce inflammation in preclinical models. This article critically examines the evidence on the role of gut dysbiosis in CIPN, evaluates the microbiota-modulating capacity of rectal ozone therapy (OT), and assesses the biological plausibility of ozone as a microbiota-targeting intervention for CIPN, while explicitly distinguishing between established evidence and hypothetical mechanisms.

EVIDENCE SYNTHESIS: Neurotoxic agents induce dysbiosis marked by reduced microbial diversity, loss of short-chain fatty acid-producing bacteria, and expansion of pro-inflammatory taxa. Preclinical models demonstrate a causal role for specific microbial communities in CIPN, with microbiota depletion or fecal transplantation modulating neuropathic phenotypes. In human cohorts, dysbiosis severity correlates with CIPN symptoms. Preclinical studies show that ROI restores microbial balance, enhances short-chain fatty acid levels, and strengthens intestinal barrier function via Nrf2/HO-1 and SIRT1 pathways. Preliminary retrospective data from small case series (n = 7 and n = 15) report sustained symptom improvement in CIPN patients receiving OT. However, no human study has directly linked ozone-induced microbiota changes to clinical outcomes, and the clinical evidence for OT in CIPN remains limited to uncontrolled observations.

CONCLUSIONS: Convergent preclinical evidence supports a biological rationale for investigating ROI as a microbiota-targeting intervention in CIPN. However, this rationale remains largely hypothetical in the clinical setting. High-quality randomized controlled trials with longitudinal microbiome profiling are urgently needed to establish mechanistic causality and to determine whether the promising preclinical findings translate into clinically meaningful benefits. Until such evidence is available, the framework presented here should be regarded as hypothesis-generating rather than as a basis for clinical practice.},
}

@article {pmid42449723,
year = {2026},
author = {Grigoraș, A and Filip, B and Gavrilescu, MM and Scripcariu, DV and Huțanu, I and Aniței, MG and Scripcariu, V},
title = {Targeted Gut Microbiome Intervention to Reduce Anastomotic Leak in Colorectal Cancer Surgery: A Narrative Review and Potential Recommendations.},
journal = {Cancers},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/cancers18132181},
pmid = {42449723},
issn = {2072-6694},
support = {351058//The Health Program (PS) 2021-2027/ ; },
abstract = {Background/Objectives: Anastomotic leakage (AL) remains one of the most severe postoperative complications following colorectal surgery and is associated with increased morbidity, delayed adjuvant therapy, and impaired oncological outcomes in CRC patients. Increasing evidence suggests that alterations in the gut microbiome contribute to the pathogenesis of AL through effects on epithelial integrity, collagen metabolism, inflammatory pathways, and immune regulation. This review aimed to provide an updated overview of AL in CRC patients and to evaluate current evidence regarding the perioperative use of probiotics, prebiotics, and synbiotics as microbiome-modulating interventions in reducing AL after radical CRC surgery. Methods: A comprehensive literature review of randomized controlled trials (RCTs) investigating perioperative microbiome-targeted interventions in CRC patients undergoing colorectal surgery was conducted. Searches of PubMed, Embase, Cochrane Library, Scopus, and Clarivate databases identified 477 records, of which 21 RCTs met the inclusion criteria and were included in the final analysis. Results: Current evidence supports the role of probiotics in modulating postoperative immune and inflammatory responses. Four studies demonstrated a statistically significant reduction in AL incidence. Perioperative probiotic administration was additionally associated with lower rates of infectious complications, attenuation of systemic inflammatory responses, and earlier recovery of bowel function. Multi-strain formulations containing Lactobacillus and Bifidobacterium species appeared particularly promising. Overall, microbiome-targeted interventions were safe and well tolerated. However, treatment efficacy varied according to bacterial strain composition, dosage, and timing of administration. Conclusions: Perioperative microbiome modulation may contribute to restoration of gut microbial diversity and reduction in AL risk after radical CRC surgery. Multi-strain formulations containing Lactobacillus and Bifidobacterium species appear particularly promising. Nevertheless, further large-scale, standardized clinical trials are required before definitive recommendations can be established.},
}

@article {pmid42449926,
year = {2026},
author = {Mitova, N and Lazarova, Z},
title = {Microbial Composition of Carious Dentin and the Impact of Minimally Invasive Excavation Techniques: A Narrative Review.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135648},
pmid = {42449926},
issn = {1422-0067},
mesh = {Humans ; *Dental Caries/microbiology/therapy ; *Dentin/microbiology ; *Microbiota ; Biofilms/growth & development ; },
abstract = {Dental caries is a biofilm-mediated dysbiotic disease characterized by ecological shifts within the oral microbiome and progressive demineralization of dental hard tissues. The microbiological composition of carious dentin and the impact of minimally invasive excavation techniques on residual microbial communities remain subjects of ongoing investigation due to methodological heterogeneity and inconsistencies among published studies. This narrative review aimed to summarize current evidence regarding the microbial ecology of carious dentin, compare culture-based and molecular methods for microbiological assessment, and evaluate the microbiological outcomes associated with contemporary approaches to managing minimally invasive caries. The relevant literature on dentinal caries microbiology, microbial detection methods, and excavation techniques was analyzed. The available evidence indicates that carious dentin contains a highly diverse polymicrobial community composed of acidogenic, aciduric, anaerobic, and proteolytic microorganisms. Culture-based methods primarily detect viable and cultivable taxa, whereas molecular approaches reveal substantially greater microbial diversity, including uncultivable and low-abundance species. Comparative studies demonstrate that minimally invasive excavation techniques significantly reduce microbial load but rarely achieve complete microbial elimination. The available evidence suggests that successful caries management is associated with a reduction in and ecological modulation of the residual microbiota within a sealed environment. The integration of culture-based and molecular findings provides a more comprehensive understanding of the microbiology of carious dentin and supports biologically oriented, minimally invasive strategies for caries management.},
}

Humans
*Dental Caries/microbiology/therapy
*Dentin/microbiology
*Microbiota
Biofilms/growth & development

@article {pmid42449941,
year = {2026},
author = {Wojtyś, M and Górska, EB and Osińska, E and Stępień, W and Gozdowski, D and Gworek, B and Cunha, A and Garcia, INS and Kondras, M and Hewelke, E and Fidler-Jarkowska, J and Chmielewski, J and Orzechowski, S},
title = {Integrating Microbiological Indicators and Shotgun Metagenomics for the Assessment of the Rhizosphere Microbiome of Medicinal Plants.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135665},
pmid = {42449941},
issn = {1422-0067},
support = {UID/50006 + LA/P/0094/2020//Foundation for Science and Technology/ ; 8762E-385/SPUB /2018/31.07.2018//Ministry of Science and Higher Education/ ; },
mesh = {*Rhizosphere ; *Metagenomics/methods ; *Microbiota/genetics ; *Plants, Medicinal/microbiology ; *Soil Microbiology ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Medicinal plants are rich sources of bioactive secondary metabolites, yet their long-term effects on the rhizosphere (RS) microbial communities remain poorly understood, particularly with respect to microbial selection and functional potential. This study evaluated the number of selected groups of microorganisms culturable in vitro in the RS and bulk soil (BS) within 10-year monocultures of 11 medicinal plant species, and as a targeted case study, we performed shotgun metagenomic profiling for Allium ursinum. The abundance of microorganisms differed markedly among plant species, indicating species-specific RS selection. Azotobacter spp. showed the strongest variation: they were not detected in the RS of Allium ursinum, Thymus vulgaris, and Carum carvi, whereas higher counts were observed under Artemisia dracunculus (135.1 × 10[2] CFU g[-1] DM), Melissa officinalis (67.1 × 10[2] CFU g[-1] DM) and Calendula officinalis (38.8× 10[2] CFU g[-1] DM). Azotobacter spp. may serve as a sensitive candidate indicator of RS imbalance. Metagenomic analysis of the A. ursinum-associated soil revealed fine-scale taxonomic restructuring, while major functional categories remained broadly similar between the RS and BS. The novelty of this study lies in the development of the Integrated Microbiological Health Soil Index (IMHSI) and the proposal of a Nitrogen Enrichment Index (NEI) as exploratory composite metrics that integrate selected functional microbial groups.},
}

*Rhizosphere
*Metagenomics/methods
*Microbiota/genetics
*Plants, Medicinal/microbiology
*Soil Microbiology
Bacteria/genetics/classification
Metagenome

@article {pmid42450058,
year = {2026},
author = {Borowik, A and Wyszkowska, J and Zaborowska, M and Kucharski, J},
title = {Changes in Soil Bacteriobiome in Response to Organic Amendments and Cd[2+] Stress.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135783},
pmid = {42450058},
issn = {1422-0067},
support = {30.610.006-110//University of Warmia and Mazury in Olsztyn/ ; Regional Initiative of Excellence Program//Minister of Science/ ; },
mesh = {*Cadmium/toxicity ; *Soil Microbiology ; Humic Substances/analysis ; Soil/chemistry ; *Bacteria/drug effects/genetics/classification ; *Soil Pollutants/toxicity ; *Microbiota/drug effects ; Stress, Physiological ; Composting ; },
abstract = {Cadmium contamination of soils poses a global threat to food security and ecosystem stability. Soil bacteria play a key role in mitigating Cd-induced stress, and their adaptive capabilities can be modulated by the application of organic amendments such as compost, fermented bark, or preparations containing humic acid. This article presents the results of studies on soil bacterial communities using culture-dependent and next-generation sequencing approaches. Based on the obtained data, colony development indices and ecophysiological diversity indices were determined for organotrophic bacteria and actinobacteria. Alpha and beta diversity of bacteria were also assessed, common and unique genera occurring in the studied soils were identified, and the predicted metabolic functions of microorganisms were determined. It was found that cadmium reduced the abundance of organotrophic bacteria and actinobacteria by 54.5% and 12.9%, respectively, compared to the control, resulting in a shift in the bacterial community structure from r-strategists toward K-strategists. Humic acid increased the abundance of organotrophic bacteria and actinobacteria by 42.8% and 57.3%. Compost most effectively mitigated cadmium effects by stabilizing the colony development index and bacterial ecophysiological diversity. Cadmium strongly altered the soil bacterial microbiome, reducing the abundance of Actinomycetota while increasing that of Pseudomonadota and Bacteroidota. The application of organic amendments influenced the bacterial response to Cd[2+]-induced stress. Fermented bark was associated with an increased abundance of Sphingomonas, whereas compost was associated with an increased abundance of Cellulosimicrobium. Although none of the organic amendments affected the overall diversity index under these conditions, compost improved the evenness and ecological stability of the bacterial community. The dominance of aerobic chemoheterotrophs involved in the carbon cycle and the degradation of organic compounds was demonstrated. Compost most effectively supported biogeochemical processes.},
}

*Cadmium/toxicity
*Soil Microbiology
Humic Substances/analysis
Soil/chemistry
*Bacteria/drug effects/genetics/classification
*Soil Pollutants/toxicity
*Microbiota/drug effects
Stress, Physiological
Composting

@article {pmid42450074,
year = {2026},
author = {Sheng, L and Wang, Y and Lu, P and Han, G and Hao, Z and Hou, S},
title = {The Composition and Differentiation of the Seed-Associated Microbiome in Rapeseed Seeds as Studied Through 218 Rapeseed Transcriptomes.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135801},
pmid = {42450074},
issn = {1422-0067},
support = {CARS-12//China Agriculture Research System/ ; },
mesh = {*Seeds/microbiology/genetics ; *Transcriptome ; *Microbiota/genetics ; *Brassica rapa/microbiology/genetics ; Gene Expression Profiling ; Stress, Physiological ; *Brassica napus/microbiology/genetics ; },
abstract = {Rapeseed is one of the most important oil crops in the world. Its yield and quality are severely restricted by biotic stress and abiotic stress. Rapeseed seeds play a crucial role in the propagation process, and the microorganisms in the seeds can be vertically passed on to the next generation, which greatly affects the quality, yield and growth of rapeseed. However, from a group perspective, there is currently a lack of systematic research on the composition of seed-associated microbiome within rapeseed seeds. This study utilized the transcriptome data of 218 rapeseed seeds that have been published, focusing on analyzing and comparing the dynamic changes and functional differences in the composition of seed-associated microbiome in rapeseed seeds under normal growth and development, biologic stress and abiotic stress conditions. Since we used public transcriptome data without surface sterilisation control, we refered to the detected microorganisms as seed-associated microbiome. The advantage of this study lies in its application of this method to a large-scale sample of rapeseed populations, which systematically revealed the response characteristics of seed-associated microbiome under different stress conditions. Interestingly, some widely distributed genera were not detected, while rare taxa were found under specific conditions, warranting further verification. Since these microorganisms originated from the seeds, their compatibility with plants and colonization ability may far exceed those of soil-derived agents. In the future, high-throughput screening of strains with excellent antagonistic or repellent effects against major diseases and pests of rapeseed can be conducted from these unique seed-associated microbiome. These strains that were confirmed by culture-based, amplicon or metagenomic approaches can then be used to develop seed coating agents or soil inoculants.},
}

*Seeds/microbiology/genetics
*Transcriptome
*Microbiota/genetics
*Brassica rapa/microbiology/genetics
Gene Expression Profiling
Stress, Physiological
*Brassica napus/microbiology/genetics

@article {pmid42450138,
year = {2026},
author = {Getsina, M and Tsyba, N and Chernevskaya, E},
title = {Modern Approaches to Diagnosis and Evaluation of Survival Prognosis in Patients with Pancreatic Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135867},
pmid = {42450138},
issn = {1422-0067},
mesh = {*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism ; Humans ; Prognosis ; *Biomarkers, Tumor/metabolism ; Microbiota ; Metabolomics/methods ; Circulating Tumor DNA/blood ; Early Detection of Cancer ; },
abstract = {Pancreatic cancer is among the most aggressive malignancies, and late diagnosis remains a key challenge. For a systematic review of pancreatic cancer diagnosis and prognosis, Scopus and Web of Science databases were used for the period from 2016 to 2026. The search query included the following keywords and their combinations: pancreatic cancer, diagnosis, early detection, prognosis, biomarkers, metabolomic profiling, CA19-9, microbiome, metagenomic changes, circulating tumor DNA, genomic analysis. Inclusion criteria included only articles published in English. Exclusion criteria included case reports and studies that did not examine pancreatic cancer. Our analysis demonstrates that integrating multi-omics data, particularly combining traditional CA19-9 with circulating tumor DNA (ctDNA) and metabolomic profiles (lipids, amino acids, carbohydrates), significantly improves diagnostic accuracy. Microbiome composition and genomic alterations further refine risk stratification and prognostic assessment. The synergistic use of these biomarkers may facilitate the development of screening, early diagnosis, risk stratification, and treatment optimization. However, the introduction of new diagnostic approaches into clinical practice requires additional verification, standardization and prospective clinical studies.},
}

*Pancreatic Neoplasms/diagnosis/mortality/genetics/metabolism
Humans
Prognosis
*Biomarkers, Tumor/metabolism
Microbiota
Metabolomics/methods
Circulating Tumor DNA/blood
Early Detection of Cancer

@article {pmid42450165,
year = {2026},
author = {Xu, C and Qin, S and Sun, P and Meng, Y and Li, C and Wang, X and You, X and Li, G and Yang, X},
title = {Integrated Analysis of the Lung Microbiome and Metabolome Reveals Associations Between Amino Acid Metabolism and Pulmonary Fibrosis in a Bleomycin-Induced Mouse Model.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135895},
pmid = {42450165},
issn = {1422-0067},
support = {82204488//National Natural Science Foundation of China/ ; },
mesh = {Animals ; *Bleomycin/adverse effects ; *Amino Acids/metabolism ; *Metabolome ; Mice ; *Microbiota ; *Lung/microbiology/metabolism/pathology ; Disease Models, Animal ; *Pulmonary Fibrosis/metabolism/microbiology/chemically induced ; Male ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/metabolism ; Metabolomics/methods ; Mice, Inbred C57BL ; *Idiopathic Pulmonary Fibrosis/metabolism/microbiology/chemically induced/pathology ; },
abstract = {Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive lung disease with limited therapeutic options. To investigate the roles of the pulmonary microbiota and metabolism in fibrosis, we established a bleomycin (BLM)-induced mouse model at 14- and 28-day timepoints and performed integrated 16S rRNA gene amplicon sequencing and untargeted metabolomic analyses. Histological and Western blot analyses confirmed significant fibrotic changes and the upregulation of fibrotic markers. Microbiome profiling revealed marked dysbiosis after BLM exposure, characterized by reduced microbial diversity and enrichment of Klebsiella. LC-MS-based metabolomic analysis identified substantial perturbations in the lung tissue metabolome, particularly in lipid metabolism, amino acid metabolism, and energy pathways. Correlation analysis indicated a strong positive association between the abundance of Klebsiella and the levels of specific dipeptides, including Ala-Hyp-Gly, Asp-His, and Asp-Asn. The accumulation of these dipeptides may reflect increased collagen degradation and turnover in fibrotic lungs. Collectively, our findings demonstrate that BLM-induced pulmonary fibrosis is accompanied by coordinated alterations in the lung microbiome and metabolome. Notably, microbial dysbiosis, particularly the expansion of Klebsiella, may be associated with alterations in amino acid metabolism and fibrotic progression.},
}

Animals
*Bleomycin/adverse effects
*Amino Acids/metabolism
*Metabolome
Mice
*Microbiota
*Lung/microbiology/metabolism/pathology
Disease Models, Animal
*Pulmonary Fibrosis/metabolism/microbiology/chemically induced
Male
RNA, Ribosomal, 16S/genetics
Dysbiosis/metabolism
Metabolomics/methods
Mice, Inbred C57BL
*Idiopathic Pulmonary Fibrosis/metabolism/microbiology/chemically induced/pathology

@article {pmid42450223,
year = {2026},
author = {Mir, MM and Wani, JI and Mir, R and Alharthi, MH and Ayed, A and Nandi, P and Patel, AA and Mallick, AK and Alamri, MMS and O'haj, M and Khalid, TBA and Jehangir, A and Sonpol, HMA and Senbel, AM},
title = {Natural Products in Prostate Cancer: Crosstalk Among the Gut Microbiome, Androgen Receptor Signaling, and Epigenetic Regulation.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27135956},
pmid = {42450223},
issn = {1422-0067},
mesh = {Humans ; *Prostatic Neoplasms/drug therapy/metabolism/microbiology/genetics/pathology ; Male ; *Receptors, Androgen/metabolism/genetics ; *Epigenesis, Genetic/drug effects ; Signal Transduction/drug effects ; *Biological Products/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; Animals ; Tumor Microenvironment/drug effects ; },
abstract = {Prostate cancer remains one of the most biologically heterogeneous malignancies in men and continues to present major therapeutic challenges despite advances in androgen receptor-targeted therapy and molecular stratification. Increasing evidence suggests that prostate cancer progression is influenced not only by tumor-intrinsic genetic alterations but also by complex interactions involving androgen receptor signaling, inflammatory pathways, metabolic reprogramming, oxidative stress, epigenetic remodeling, immune dysregulation, and gut microbiome-associated signaling. Within this evolving systems-level framework, natural products have attracted increasing attention because of their ability to modulate multiple interconnected molecular pathways. This review examines the molecular basis of prostate cancer progression with particular emphasis on crosstalk among androgen receptor signaling, microbiome-associated regulation, epigenetic adaptation, inflammatory signaling, and tumor microenvironment remodeling. The emerging role of the gut microbiome in androgen metabolism, microbial metabolite production, immune regulation, and endocrine resistance is critically discussed, together with current evidence describing the biological effects of selected phytochemicals including curcumin, epigallocatechin-3-gallate, resveratrol, sulforaphane, quercetin, and genistein. These compounds may influence prostate cancer-associated pathways through modulation of inflammatory signaling, oxidative stress, metabolic adaptation, chromatin remodeling, and microbiome dynamics. Major translational limitations including poor bioavailability, pharmacokinetic variability, microbiome heterogeneity, inconsistent clinical evidence, and incomplete mechanistic understanding are additionally discussed. Rather than considering natural products as isolated anticancer agents, this review adopts a systems-level perspective in which dietary bioactive compounds may function as modulators of interconnected regulatory networks relevant to prostate cancer biology and therapeutic responsiveness.},
}

Humans
*Prostatic Neoplasms/drug therapy/metabolism/microbiology/genetics/pathology
Male
*Receptors, Androgen/metabolism/genetics
*Epigenesis, Genetic/drug effects
Signal Transduction/drug effects
*Biological Products/pharmacology/therapeutic use
*Gastrointestinal Microbiome/drug effects
Animals
Tumor Microenvironment/drug effects

@article {pmid42450287,
year = {2026},
author = {Zhao, Y and Lee, SM and Li, W and Floriolli, D and Chang, P and Narasaki, Y and You, AS and Kalantar-Zadeh, K and Rhee, CM and Liu, H and Tran, T and Paganini-Hill, A and Fisher, M and Lau, WL},
title = {Investigating the Kidney-Gut-Brain Axis in CKD: Uremic Toxins and Brain Microhemorrhages.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27136020},
pmid = {42450287},
issn = {1422-0067},
support = {R01NS113337//National Institutes of Health Clinical Center/ ; },
mesh = {Animals ; Female ; Male ; *Renal Insufficiency, Chronic/metabolism/microbiology/complications ; *Uremic Toxins/metabolism/blood ; Humans ; *Gastrointestinal Microbiome/drug effects ; Mice ; *Brain/metabolism/pathology ; *Kidney/metabolism ; *Cerebral Hemorrhage/etiology/pathology/metabolism ; Indican/blood ; Middle Aged ; Methylamines/blood ; Cresols/blood ; Aged ; Sulfuric Acid Esters ; },
abstract = {Alterations of gut microbiota are common in chronic kidney disease (CKD) and contribute to increased uremic toxins including indoxyl sulfate (IS), p-cresyl sulfate (pCS) and trimethylamine N-oxide (TMAO), which are linked to cerebrovascular disease risk. This study examined the kidney-gut-brain axis in CKD mice and in dialysis patients. Male and female mice with adenine-induced CKD were fed a high-amino-acid (HAA) diet to increase precursors of gut-derived uremic toxins. A subgroup of mice received antibiotics in drinking water to suppress gut microbiota and evaluate its role in toxin generation. Behavior tests, gut microbiome composition and brain histology for cerebral microhemorrhages were analyzed. CKD mice had higher serum levels of creatinine, cystatin C and gut-derived toxins, a 2.5-fold increase in brain microhemorrhages, and decreased locomotor activity. The HAA diet significantly increased serum TMAO but not IS and pCS, and all three toxins were reduced by antibiotic therapy. Sex differences were observed; in male animals, higher TMAO was associated with increased brain microhemorrhages, whereas in female mice, pCS was associated with brain microhemorrhage burden. The suppression of toxins with antibiotics improved working memory in male animals. Gut microbiota analysis revealed the expansion of Lactobacillus and Ileibacterium in CKD mice. The HAA diet and antibiotics altered gut microbiota composition without changing alpha diversity. The human study utilized biobanked serum samples and a retrospective review of brain imaging scans in a hemodialysis patient cohort; TMAO levels were associated with increased lobar microbleeds. Our study supports a role for bacterial-derived uremic toxins in the kidney-gut-brain axis and cerebral microhemorrhage formation in CKD.},
}

Animals
Female
Male
*Renal Insufficiency, Chronic/metabolism/microbiology/complications
*Uremic Toxins/metabolism/blood
Humans
*Gastrointestinal Microbiome/drug effects
Mice
*Brain/metabolism/pathology
*Kidney/metabolism
*Cerebral Hemorrhage/etiology/pathology/metabolism
Indican/blood
Middle Aged
Methylamines/blood
Cresols/blood
Aged
Sulfuric Acid Esters

@article {pmid42450290,
year = {2026},
author = {Kim, JH and Ahn, EK and Chang, HK and Kim, SJ and Kim, J and Park, SJ and Heo, J},
title = {Associations of Low-Carbohydrate High-Fat Dietary Patterns with Colorectal Tumor Burden and Gut Microbial Dynamics in an AOM/DSS Mouse Model.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27136023},
pmid = {42450290},
issn = {1422-0067},
support = {2020R1C1C1012694//Ministry of Science and ICT/ ; },
mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/drug effects ; *Diet, High-Fat/adverse effects ; Male ; *Colorectal Neoplasms/pathology/chemically induced/microbiology/etiology ; *Diet, Carbohydrate-Restricted ; Disease Models, Animal ; Dextran Sulfate/adverse effects/toxicity ; Mice, Inbred C57BL ; Azoxymethane ; Tumor Burden ; Colitis/chemically induced/pathology/complications ; Dietary Carbohydrates ; Dietary Fats ; Body Weight ; },
abstract = {Malignant tumors require substantial energy sources for proliferation, and dietary composition may influence colorectal carcinogenesis through metabolic and microbiome-related mechanisms. This study investigated the association of low-carbohydrate high-fat dietary patterns with macroscopic tumor burden, morphologic inflammatory cell infiltration, and gut microbiome alterations using an azoxymethane/dextran sulfate sodium (AOM/DSS)-induced mouse model of colitis-associated colorectal cancer. Male C57BL/6 mice received AOM followed by three cycles of DSS and were fed a standard diet (SD), high-carbohydrate diet (HCD), low-carbohydrate high-fat lard-based diet (HFL), or low-carbohydrate high-fat coconut oil-based diet (HFC). Body weight, colon length, splenic weight, macroscopic tumor formation, hematoxylin and eosin (H&E)-based inflammatory cell infiltration, and gut microbiome composition were analyzed. The HFL and HFC groups exhibited higher body weights and relatively preserved colon lengths compared with the SD and HCD groups. Tumor number and total tumor size were reduced in the HFL and HFC groups. Total lymphocyte-like inflammatory cell infiltration was not increased in the high-fat diet groups, whereas per-tumor values were interpreted cautiously because they are affected by tumor number. Gut microbiome analysis demonstrated altered microbial composition, increased alpha diversity, and distinct temporal microbial dynamics in the high-fat diet groups. Because the HFL and HFC diets simultaneously changed carbohydrate content, fat content, fat source, and caloric density, these findings should be interpreted as exploratory effects of low-carbohydrate high-fat dietary patterns rather than independent effects of carbohydrate restriction, total fat, or fat source.},
}

Animals
Mice
*Gastrointestinal Microbiome/drug effects
*Diet, High-Fat/adverse effects
Male
*Colorectal Neoplasms/pathology/chemically induced/microbiology/etiology
*Diet, Carbohydrate-Restricted
Disease Models, Animal
Dextran Sulfate/adverse effects/toxicity
Mice, Inbred C57BL
Azoxymethane
Tumor Burden
Colitis/chemically induced/pathology/complications
Dietary Carbohydrates
Dietary Fats
Body Weight

@article {pmid42450358,
year = {2026},
author = {Ohshima, J and Tanaka, N and Morita, M and Abe, S and Nakamura, E and Hayashi, M},
title = {Ectopic Olfactory Receptors in Oral Health and Disease: Molecular Links Between Chemosensing, Tissue Repair, Inflammation, and Cancer.},
journal = {International journal of molecular sciences},
volume = {27},
number = {13},
pages = {},
doi = {10.3390/ijms27136093},
pmid = {42450358},
issn = {1422-0067},
support = {24K19878, 26K20175, 24K22184, 26K20197//Japan Society for the Promotion of Science/ ; },
mesh = {Humans ; *Receptors, Odorant/metabolism/genetics ; Animals ; *Inflammation/metabolism ; *Oral Health ; Signal Transduction ; *Mouth Neoplasms/metabolism ; *Mouth Diseases/metabolism ; Mouth Mucosa/metabolism ; },
abstract = {Ectopic olfactory receptors (ORs) are G protein-coupled chemosensors expressed outside the olfactory epithelium, where they may couple local chemical inputs to cell-specific signaling. The oral cavity is continuously exposed to food-derived compounds, microbial metabolites, volatile organic compounds, and inflammation-associated metabolites, yet the molecular roles of oral ORs remain incompletely defined. This review critically synthesizes current evidence for OR expression and signaling in oral tissues and associated cell populations, with emphasis on ligand-receptor-signaling relationships and disease relevance. Functional OR signaling has been demonstrated in mammalian taste cells, while emerging transcriptomic studies in oral mucosa and transcriptomic/localization studies in the periodontal ligament indicate OR-related programs during tissue-specific or repair-associated states. Candidate metabolic axes, including short-chain fatty acids and lactate linked to OR51E1/OR51E2/Olfr78-related pathways in non-oral models, provide testable mechanistic hypotheses for microbiome-host communication in periodontitis and oral cancer; however, direct causal validation in oral disease models remains limited. We propose an evidence-tiered framework integrating spatial expression mapping, metabolomics-guided deorphanization, receptor perturbation, and longitudinal oral-fluid profiling. Oral ORs should currently be regarded as candidate molecular modulators and components of multimodal biomarker strategies rather than validated standalone diagnostic or therapeutic targets.},
}

Humans
*Receptors, Odorant/metabolism/genetics
Animals
*Inflammation/metabolism
*Oral Health
Signal Transduction
*Mouth Neoplasms/metabolism
*Mouth Diseases/metabolism
Mouth Mucosa/metabolism

@article {pmid42450554,
year = {2026},
author = {Lee, HJ and Suh, DH and Lee, S and Holzapfel, WH and Ji, Y and Runyon, MK and Jo, H and Hur, JY and Ryu, R and Jung, ES},
title = {Phytonutrient-Enriched Prebiotic Mixture Primes the Gut Environment to Enhance Probiotic Efficacy: Ex Vivo Screening and a Human Clinical Trial.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131006},
pmid = {42450554},
issn = {2079-7737},
support = {//Amway Research and Development/ ; },
abstract = {Phytonutrient-enriched prebiotic mixtures (PEPs), composed of phytonutrients and prebiotics serving as substrates for gut microbes, are recognized for their potential to modulate gut microbial metabolic activity. However, direct evidence of enhanced effects following co-administration with probiotics remains limited. Using a three-phase design integrating ex vivo evaluation and clinical validation, we assessed how PEP components influence microbial responses and whether co-administration with probiotics enhances these effects. PEP components increased acetate, butyrate, total short-chain fatty acids (SCFAs), and lactate, with fiber-rich components showing the strongest effects (all q < 0.0001 relative to negative control). Co-treatment with probiotics further enhanced butyrate and total SCFAs in a dose-dependent manner. In a randomized clinical study, all groups showed increases in fecal metabolites, with the combined group exhibiting the greatest increases in butyrate (+6.0 µmol/g, ~1.5-fold, p < 0.05) and total SCFAs (+22.9 µmol/g, ~1.3-fold, p < 0.05). Participants with constipation-type stool patterns shifted toward normal stool types across all groups. These findings support the utility of combined PEP and probiotic interventions for enhancing microbiome-derived metabolic activity.},
}

@article {pmid42450578,
year = {2026},
author = {Li, J and Cheng, S and Zhang, W and Qiao, S and Zhang, L and Yao, M and Zhang, Y and Wang, B and Wu, C},
title = {Mulberroside A Alleviates Scopolamine-Induced Cognitive Deficits by Suppressing Neuroinflammation and Oxidative Stress via the Dubosiella-Associated Microbiota-Gut-Brain Axis.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131030},
pmid = {42450578},
issn = {2079-7737},
support = {262102310255//Henan Provincial Science and Technology Key Project/ ; 26A180030//Key Scientific Research Foundation of Henan Colleges and Universities/ ; 252300423668//Natural Science Foundation of Henan/ ; ZKNUC2024030//Zhoukou Normal University High-level Talent Start-up Foundation/ ; },
abstract = {Mulberroside A (MsA) possesses neuroprotective effects, but whether it alleviates Alzheimer's disease (AD)-like cognitive impairment through the microbiota-gut-brain axis remains unclear. Using a scopolamine-induced mouse model of acute cognitive impairment (male ICR mice, n = 10/group), we demonstrated that daily administration of MsA (10, 20, and 30 mg/kg/day) for 5 weeks significantly ameliorated cognitive performance in novel object recognition and Morris water maze tests. At the optimal dose (30 mg/kg/day), MsA suppressed hippocampal microglial activation, reduced pro-inflammatory cytokines (IL-6, IL-1β, TNF-α), and attenuated oxidative stress by decreasing malondialdehyde (MDA) while restoring superoxide dismutase (SOD) and glutathione (GSH) levels. MsA also strengthened intestinal barrier integrity (ZO-1, occludin) and significantly altered the gut microbiota, notably increasing the beneficial genus Dubosiella. Brain metabolomics indicated that MsA reversed scopolamine-induced metabolic disturbances, mainly restoring phospholipid balance. Correlation analysis demonstrated a strong gut-brain connection, with Dubosiella abundance positively associated with neuroprotective phospholipids and negatively with stress markers. Furthermore, fecal microbiota transplantation from MsA-treated donors successfully replicated these behavioral improvements in recipient mice, underscoring the functional involvement of the reshaped microbiome rather than a simple autonomous recovery. These results suggest that MsA alleviates AD-like cognitive impairment by reducing neuroinflammation and oxidative stress through microbiota remodeling, enhancing the intestinal barrier, and modulating the Dubosiella-associated gut-metabolite-brain axis, making MsA a promising multi-target nutraceutical for ameliorating AD-like cognitive deficits.},
}

@article {pmid42450580,
year = {2026},
author = {Zamudio-López, A and García-De la Peña, C and Álvarez-Hernández, G and Barraza-Guerrero, SI and Meza-Herrera, CA and Sánchez-Loera, MG and Luna-Zapién, EA and Salazar-Nevárez, DE and Carrillo-Campos, J},
title = {Geographic Variation in the Bacterial Microbiota of Rhipicephalus sanguineus (Acari, Ixodidae) Across Environmentally Contrasting Regions of Mexico.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131032},
pmid = {42450580},
issn = {2079-7737},
support = {917536//Ministry of Sciences, Humanities, Technology and Innovation/ ; },
abstract = {Geographic and ecological variations are frequently associated with differences in the microbiota of arthropod vectors, with potential implications for pathogen transmission and public health. This study characterized and compared the bacterial microbiota associated with the brown dog tick (Rhipicephalus sanguineus) across three ecologically contrasting regions of Mexico: Cancun (Quintana Roo), Comarca Lagunera (Durango-Coahuila), and Hermosillo (Sonora). Non-engorged ticks collected from stray dogs were analyzed using 16S rRNA gene (V3-V4) sequencing. Amplicon sequence variants (ASVs) generated in QIIME2 were used for taxonomic, diversity, and predictive functional analyses. Proteobacteria dominated all samples, with Coxiella-like bacteria tentatively assigned as Coxiella mudrowiae identified as a dominant taxon across all localities. Significant geographic differences were observed in alpha and beta diversity, with Comarca Lagunera showing the highest diversity and Hermosillo the lowest. Sequences tentatively assigned to Rickettsia rickettsii were detected exclusively in two pools from Hermosillo. Functional predictions revealed a conserved metabolic repertoire alongside geographic variation in pathway abundance. Overall, the results support the existence of a stable symbiotic component accompanied by a geographically variable bacterial fraction associated with ecologically contrasting regions. These findings highlight the importance of geographic context in shaping tick-associated bacterial communities.},
}

@article {pmid42450613,
year = {2026},
author = {Jiang, Z and Chen, J and Ren, Y and Lin, T and Li, S and Shen, F and Qin, B and Li, L and Li, C and Ying, N and Zheng, H},
title = {Gut Microbiomes of Rainbow Trout and Atlantic Salmon: Nutritional Modulation, Mucosal Immunity, and Resistome Risk.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131066},
pmid = {42450613},
issn = {2079-7737},
support = {2024TD08//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025QT04//Central Public-interest Scientific Institution Basal Research Fund, ECSFR, CAFS/ ; 2025ZX03//Central Public-interest Scientific Institution Basal Research Fund, CAFS/ ; SF2407//Lianyungang Key Research and Development Program/ ; },
abstract = {The gut microbiome of rainbow trout (Oncorhynchus mykiss) and Atlantic salmon (Salmo salar) is increasingly recognized as a functional interface linking dietary inputs, epithelial barrier integrity, mucosal immunity, environmental stress, disease susceptibility, and antimicrobial-resistance risk in intensive aquaculture. Based on available salmonid studies and relevant evidence from broader fish and aquaculture systems, this review synthesizes current knowledge on salmonid gut microbial composition, nutritional modulation, microbiome-mucosal immune interactions, aquaculture stressors, antibiotic exposure, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metagenomics, multi-omics, and emerging microbiome-informed decision-support tools. Current evidence does not support a universally stable single-core microbiota in these species. Instead, community structure is shaped by developmental stage, freshwater-seawater transition, intestinal segment, digesta versus mucosa sampling, diet, temperature, stress, health status, and methodological workflow. Feed substitution and functional additives can remodel the gut microbiota, but these shifts should be interpreted alongside histology, barrier function, metabolic profiles, immune indicators, and disease-resistance phenotypes. Antibiotic exposure may reduce acute bacterial disease pressure while disturbing community structure and potentially enriching ARGs or ARG-MGE associations. Risk assessment should therefore move beyond ARG abundance toward host-ARG-MGE linkage using shotgun metagenomics, metagenome-assembled genomes, long-read sequencing, Hi-C, and externally validated multi-omics models. Machine learning and artificial intelligence approaches may support feature screening, risk stratification, and decision support, but their application in salmonid gut-health management remains at an early stage and requires external validation across sites, production stages, diets, and seasons.},
}

@article {pmid42450634,
year = {2026},
author = {Purec, D and Iorgoni, V and Iancu, I and Dégi, J and Pascu, C and Costinar, L and Badea, C and Gligor, A and Nistor, P and Udrea, A and Dreghiciu, IC and Herman, V},
title = {Gut Microbiome Disruption in Shelter Cats with Feline Panleukopenia: Virome Co-Detection and Enteric Dysbiosis.},
journal = {Biology},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/biology15131087},
pmid = {42450634},
issn = {2079-7737},
abstract = {Feline panleukopenia virus (FPV) causes severe enteric and systemic disease in cats, with particular importance in shelter environments where susceptible kittens, high population turnover, environmental contamination, and variable vaccination histories increase infection pressure. Recent virome and microbiome studies suggest that FPV-associated enteritis may occur within a broader context of viral co-detection and intestinal microbial disturbance, but direct FPV-specific bacteriome evidence remains limited. This review aims to synthesize current evidence on FPV-associated enteritis in shelter cats by integrating viral pathogenesis, diagnostic interpretation, enteric virome co-detection, gut dysbiosis, recovery dynamics, and intervention-related ecological effects. The literature was organized using an evidence-tier framework that distinguishes direct FPV/feline panleukopenia evidence from feline enteric microbiome proxy evidence and broader comparative or mechanistic microbiome studies. This approach was used to define the limits of inference and to separate evidence-supported conclusions from hypothesis-generating ecological models. Feline panleukopenia in shelter cats should be interpreted not only as an individual viral infection, but also as an ecological process shaped by host susceptibility, shelter exposure, diagnostic complexity, viral co-detection, and microbial community disturbance. Current evidence supports a cautious framework in which virome co-detection and dysbiosis-associated patterns are not treated as direct proof of causation. Future longitudinal, context-controlled, and multi-layer studies integrating validated FPV diagnostics, virome and bacteriome profiling, clinical metadata, treatment records, and functional endpoints are needed to clarify the biological and clinical significance of gut ecosystem disruption in feline panleukopenia.},
}

@article {pmid42450701,
year = {2026},
author = {Manguin, E and Dickson, RP and Jamon, J and Dubuc, V and Leclère, M},
title = {Inhaled Corticosteroids Influence Pulmonary Microbiota in Severe Equine Asthma.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16131994},
pmid = {42450701},
issn = {2076-2615},
support = {06090//Natural Sciences and Engineering Research Council of Canada/ ; },
abstract = {The use of inhaled corticosteroids (ICs) could influence the respiratory microbiota. In animals with asthma it is, however, difficult to separate the immunomodulatory effects of ICs from their indirect effects via improvement of ventilation. Our objective was to determine if ICs alter the pulmonary microbiota independently from their effects on lung function, using a blinded, controlled trial in an experimental model of asthma exacerbation in horses. We treated horses with severe asthma with either bronchodilators alone, or in combination with ICs. Twelve horses in exacerbation received long-acting β2-agonist (LABA, salmeterol) or ICs/LABA (fluticasone/salmeterol) by inhalation, for 2 weeks. Lung function and bronchoalveolar lavages (BAL) were performed before and after treatment. 16S rRNA gene quantification and sequencing were performed on BAL fluid, using digital droplet PCR and the Illumina MiSeq platform. Data were processed using the software package mothur v. 1.44.2. In the LABA group, pulmonary bacterial load and the relative abundance of Actinobacteria and Verrucomicrobia phyla decreased with treatment (p < 0.05 for both), and β-diversity differed from baseline (p = 0.007). The relative abundance of families and genera belonging to the Bacteroidetes phylum increased with ICs/LABA (p < 0.05). Lung function significantly improved with both treatments, suggesting that treatment-related differences in pulmonary microbiota could be attributed in part to medication, not solely to change in ventilation. However, it is not clear if these changes are positive or detrimental to the lung environment. Furthermore, lung function following treatment was not perfectly identical between groups.},
}

@article {pmid42450763,
year = {2026},
author = {Dettori, M},
title = {Informal Treatment Practices in Ornamental Aquaria: An Overlooked Interface Between Aquatic Animal Health, Antimicrobial Stewardship, and One Health.},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132056},
pmid = {42450763},
issn = {2076-2615},
abstract = {Ornamental aquarium keeping collectively involves millions of freshwater, marine, and reef systems in which fish, corals, invertebrates, biofilters, microbial communities, and human husbandry practices are closely interconnected. In these domestic aquatic animal systems, preventive and curative treatments may include antimicrobials, antiparasitics, antiseptics, oxidizing agents, copper-based products, dips, and commercial formulations targeting microbial proliferations or visible system deterioration. Many interventions occur without veterinary diagnosis, microbiological confirmation, standardized dosing, active-ingredient transparency, or post-treatment monitoring. This raises concerns for aquatic animal health and welfare, as whole-system treatments may affect not only the intended pathogen or pest but also non-target organisms, biofilter communities, animal-associated microbiota, and water quality stability. Digital communities and online platforms can rapidly circulate empirical treatment protocols, although they may also provide opportunities for stewardship education and improved husbandry guidance. Current evidence does not support interpreting ornamental aquaria as major independent drivers of antimicrobial resistance. The more defensible concern is stewardship: biologically active compounds may be used repeatedly and empirically in animal systems without diagnosis, professional guidance, or systematic monitoring. This Perspective argues that ornamental aquaria should be recognized as an overlooked interface between aquatic animal health, welfare, antimicrobial stewardship, and One Health. It proposes a research and communication agenda focused on treatment transparency, diagnosis, prevention, biofilter protection, and responsible care practices.},
}

@article {pmid42450776,
year = {2026},
author = {Zeng, D and Qin, Q and Yang, M and Wang, Z and Xiang, J and Wang, X and Hu, Y},
title = {Multi-Omics Reveals Gut Microbiota Shifts and Hepatic Metabolic-Immune Alterations in "Short-Leg" Malformed Frog (Pelophylax nigromaculatus).},
journal = {Animals : an open access journal from MDPI},
volume = {16},
number = {13},
pages = {},
doi = {10.3390/ani16132069},
pmid = {42450776},
issn = {2076-2615},
support = {25210010//Research and Demonstration on the Innovation of the Black-Spotted Frog Breeding Model/ ; 24B0625//Hunan Provincial Education Department Outstanding Youth Project/ ; 2026JJ60022//Natural Science Foundation of Hunan Province/ ; },
abstract = {Amphibian malformation syndromes significantly impact both conservation efforts and aquaculture, yet their underlying systemic pathophysiological mechanisms remain poorly characterized. This study comprehensively examines the multi-level pathological processes associated with the "short-leg" malformation syndrome in the black-spotted frog (Pelophylax nigromaculatus) using an integrated methodology, encompassing morphological, histopathological, gut microbiome, and hepatic transcriptomic analyses. Affected frogs demonstrated shortened limbs, impaired motor function, and a distinctive metabolic phenotype, including increased body weight despite a shorter body length, accumulation of visceral fat, and shortened intestines. Gut microbiota analysis identified significant compositional shifts, characterized by a decreased Firmicutes-to-Bacteroidota ratio, expansion of pro-inflammatory Proteobacteria, and reduction in beneficial Actinobacteriota, suggesting microbial niche restructuring that likely promotes metabolic and inflammatory disorders. Hepatic transcriptome profiling revealed 2617 differentially expressed genes, demonstrating a clear molecular dichotomy with concurrent up-regulation of immune-related pathways (e.g., neutrophil extracellular trap formation, complement cascades, and inflammatory signaling) and broad suppression of metabolic pathways (e.g., lipid oxidation, nutrient absorption, and PPAR and renin-angiotensin systems). This integrated analysis illustrates that the malformation syndrome represents a systemic pathophysiological state involving dysfunction of the gut-liver axis, characterized by the coexistence of gut microbiota alterations, hepatic metabolic suppression, and immune activation. These findings provide a framework for understanding amphibian malformations and suggest potential strategies to improve health outcomes in aquaculture.},
}

@article {pmid42451045,
year = {2026},
author = {Chen, Y and Gui, H and Zhao, T and Liu, C and Zhang, Y and Wang, M and Yang, R},
title = {Ultra-Processed Foods, MASLD, and Cognitive Aging: A Processing-Centered Gut-Liver-Brain Axis Perspective.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132041},
pmid = {42451045},
issn = {2072-6643},
mesh = {Humans ; *Liver/metabolism ; *Brain/metabolism ; *Cognitive Aging/physiology ; *Fast Foods/adverse effects ; *Fatty Liver/etiology ; Gastrointestinal Microbiome ; Animals ; *Brain-Gut Axis ; Cognitive Dysfunction/etiology ; },
abstract = {Background/Objectives: Ultra-processed foods (UPFs) are increasingly recognized as dietary exposures associated with cardiometabolic, hepatic, and neurocognitive outcomes. However, UPFs are often treated mainly as nutrient-poor foods, whereas their processing-related features may perturb gut-liver-brain communication. This review examines whether metabolic dysfunction-associated steatotic liver disease (MASLD) can be conceptualized as a hepatic metabolic amplifier linking UPF exposure to cognitive aging. Methods: We conducted a structured narrative search of PubMed/MEDLINE, Web of Science Core Collection, and Scopus from January 2010 to 11 May 2026 across four evidence modules: UPFs and MASLD/NAFLD; UPFs and cognitive aging or dementia; UPFs and gut-liver-brain mechanisms; and MASLD/NAFLD and cognitive aging. Representative studies were prioritized according to direct relevance to the proposed axis, study design, exposure and outcome validity, mechanistic specificity, and contribution to major evidence gaps. Results: Observational and mechanistic evidence links higher UPF consumption with liver steatosis, MASLD/NAFLD-related outcomes, cognitive decline, cognitive impairment, stroke, and dementia-related outcomes, although causality remains incompletely established and residual confounding is important. Candidate pathways include food-matrix disruption, rapid eating, displacement of microbial substrates, selected additives and processing-derived compounds, intestinal barrier dysfunction, metabolic endotoxemia, bile acid signaling, hepatic lipotoxicity, systemic inflammation, vascular dysfunction, and neuroimmune activation. Many pathways overlap with general cardiometabolic dysfunction; the processing-centered contribution lies in positioning industrial formulation as an upstream exposure and MASLD as a hepatic node that may amplify gut-derived and metabolic signals relevant to brain aging. Conclusions: A processing-centered gut-liver-brain framework integrates UPFs, MASLD, and cognitive aging as linked metabolic-aging phenomena. Future studies should test UPF substitution using liver imaging, microbiome profiling, metabolomics, bile acid and inflammatory biomarkers, neuroimaging, and cognitive assessment.},
}

Humans
*Liver/metabolism
*Brain/metabolism
*Cognitive Aging/physiology
*Fast Foods/adverse effects
*Fatty Liver/etiology
Gastrointestinal Microbiome
Animals
*Brain-Gut Axis
Cognitive Dysfunction/etiology

@article {pmid42451052,
year = {2026},
author = {Guzmán, TJ and Godínez-Méndez, LA and Soto-Luna, IC and Delgado-Rizo, V and García-López, PM and Romero-Velarde, E and Vargas-Guerrero, B and Hurtado-Díaz, I and Salazar-Montes, AM and Gurrola-Díaz, CM},
title = {Functional Soy and Lupin Protein-Based Beverages Modulate Gut Microbiome and Attenuate Metabolic Dysregulation in Adolescent Boys with Overweight and Obesity.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132049},
pmid = {42451052},
issn = {2072-6643},
support = {60283//Consejo Nacional de Ciencia y Tecnología-CONACYT/ ; Programa de Fortalecimiento de Institutos, Centros y Laboratorios de Investigación 2025:283628//University of Guadalajara/ ; },
mesh = {Humans ; Male ; Adolescent ; *Gastrointestinal Microbiome/drug effects ; *Soybean Proteins/administration & dosage/pharmacology ; Child ; *Beverages ; Double-Blind Method ; *Lupinus/chemistry ; *Overweight/microbiology ; Insulin Resistance ; Blood Glucose/metabolism ; *Pediatric Obesity/microbiology/metabolism/diet therapy ; Mexico ; Plasminogen Activator Inhibitor 1/blood ; },
abstract = {Background/Objectives: Given the rising prevalence of overweight and obesity in pediatric populations, identifying effective nutritional interventions for metabolic management is crucial. Beyond their nutritional value, soy and lupin proteins are recognized for their bioactive properties. We formulated two protein-enriched functional beverages and evaluated their impact on the metabolic profile and gut microbiota of adolescent boys with overweight or obesity. Methods: A randomized, double-blind clinical trial was conducted with 30 Mexican male adolescents (12-16 years old). Participants were randomly assigned to consume a functional beverage providing a daily 10 g portion of either soy or lupin protein for 5 weeks. Results: Following the intervention, both groups exhibited significantly attenuated fasting glucose (soy: 93.1 vs. 99.5 mg/dL; lupin: 92.3 vs. 97.9 mg/dL) and C-peptide levels. Consequently, insulin sensitivity, assessed via the HOMA2 index, improved significantly in both cohorts. The soy protein group showed a marked reduction in total cholesterol (-10.4%) and triglycerides (-17.1%). Furthermore, serum levels of plasminogen activator inhibitor-1 (PAI-1) and visfatin were decreased after both interventions. A post-treatment reduction in glucose-dependent insulinotropic polypeptide (GIP) was specifically observed in the lupin group. Regarding the gut microbiota, both protein-based beverage interventions correlated with enhanced 16S rDNA diversity and increased the abundance of the Bacillota phylum and butyryl-CoA transferase-positive bacteria. Conclusions: Our data suggests that the daily consumption of soy or lupin protein-based beverages could exert beneficial metabolic and endocrine effects in adolescent boys with overweight and obesity, potentially mediated by the modulation of the gut microbiome.},
}

Humans
Male
Adolescent
*Gastrointestinal Microbiome/drug effects
*Soybean Proteins/administration & dosage/pharmacology
Child
*Beverages
Double-Blind Method
*Lupinus/chemistry
*Overweight/microbiology
Insulin Resistance
Blood Glucose/metabolism
*Pediatric Obesity/microbiology/metabolism/diet therapy
Mexico
Plasminogen Activator Inhibitor 1/blood

@article {pmid42451055,
year = {2026},
author = {Kim, HH and Kim, SY and Kang, HM and Youn, YA},
title = {Meconium Microbiome Maturation Patterns Linked to Postnatal Growth Failure in Neonates.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132051},
pmid = {42451055},
issn = {2072-6643},
support = {RS-2023-00279932//National Research Foundation of Korea/ ; },
mesh = {Humans ; *Meconium/microbiology ; Infant, Newborn ; Gestational Age ; Female ; Male ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Infant, Premature/growth & development ; *Growth Disorders/microbiology ; *Bacteria/classification/genetics ; },
abstract = {Background/Objectives: This study investigated whether meconium microbial profiles differed according to postnatal growth failure (PGF) and whether gestational age (GA)-related microbial maturation patterns appeared to vary according to subsequent growth status. Methods: Meconium samples were collected from 310 neonates born at 22-40 weeks of gestation, and 16S rRNA sequencing was conducted. After excluding small-for-gestational-age infants, the analyses included 151 samples from PGF+ infants and 131 samples from PGF- infants. Microbial composition, alpha and beta diversity were compared according to PGF status. Distance-based redundancy analyses (dbRDA) were conducted to evaluate the independent association between PGF and microbiome composition. Results: The core meconium microbiome differed between groups. PGF+ infants showed a predominance of Proteobacteria (36.60% vs. 27.96%), whereas PGF- infants had relatively higher abundances of Firmicutes (35.47% vs. 30.64%) and Bacteroidetes (28.96% vs. 26.19%) than PGF+ infants. GA-related microbial maturation patterns also differed between groups. At the genus level, the PGF- group showed significant positive correlations with GA for Faecalibacterium, Sutterella, Dialister, Megamonas, Escherichia/Shigella, and Roseburia after false discovery rate correction, whereas no genus-level correlation remained significant in the PGF+ group. Alpha diversity did not differ significantly between groups, whereas beta diversity differed modestly (R[2] = 0.0087, p = 0.042). After adjustment for GA and birth weight, the PGF effect remained significant in the Bray-Curtis-based dbRDA model, whereas it was not significant in the Jaccard-based model. Conclusions: PGF was associated with abundance-based shifts within shared meconium taxa, suggesting subtle differences in early microbial developmental patterns among infants who later developed PGF.},
}

Humans
*Meconium/microbiology
Infant, Newborn
Gestational Age
Female
Male
RNA, Ribosomal, 16S/genetics
*Microbiota
Infant, Premature/growth & development
*Growth Disorders/microbiology
*Bacteria/classification/genetics

@article {pmid42451068,
year = {2026},
author = {Mohd Nawi, MN and Ibrahim, N and Bee Yong, T and Abd Rashed, A and Rmt Balasubramaniam, V},
title = {Pulses and Cancer Outcomes: A Scoping Review of Human Studies on Risk Reduction.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132064},
pmid = {42451068},
issn = {2072-6643},
mesh = {Humans ; *Neoplasms/prevention & control ; *Fabaceae ; *Risk Reduction Behavior ; *Diet ; },
abstract = {Background/Objectives: Pulses are nutrient-dense, low-glycaemic legumes rich in fibre and bioactive compounds that may modulate carcinogenesis through effects on diet quality, metabolism, and the gut microbiome. This scoping review mapped human evidence on pulses in relation to cancer risk reduction and related mechanistic and survivorship-relevant outcomes. Methods: Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) and Joanna Briggs Institute (JBI) Population, Concept and Context (PCC) guidance, we searched CENTRAL, Scopus and PubMed (2014-31 December 2025), supplemented by backward and forward citation tracking, for English-language human studies in which pulses were a defined exposure or intervention and cancer-specific clinical outcomes or biomarkers were reported. Exposures are described using the original 'legume' terminology, with pulse-specific interpretation restricted to FAO-defined pulses or clearly dry pulse forms and to pulse-dominant legume intake where the constituent items were predominantly pulses but preparation was not specified. Results: After screening 1244 records, 15 studies met the inclusion criteria, comprising five case-control studies, five 4-week randomised controlled trials (RCTs), one 8-week randomised crossover trial, one controlled feeding study, two prospective cohort studies, and one other prospective study. Observational data from a single pooled case-control study suggest that higher pulse-dominant legume intake is compatible with modestly lower colorectal cancer risk, although the findings are mixed and often attenuate after adjustment for lifestyle and dietary confounders. Evidence for breast and oesophageal cancer and all-cancer mortality is limited, frequently subgroup-specific or highly sensitive to confounder control, and survivorship endpoints are represented mainly by short-term mechanistic and feasibility trials in colorectal cancer survivors rather than by long-term clinical outcomes. Notably, five of these navy bean interventions were conducted by a single research group using similar protocols, which constrains the independence of replication. Conclusions: Pulses can be considered practical components of cancer-protective dietary patterns, especially for colorectal cancer, but the heterogeneity of study designs, short-term interventions, limited sample sizes, and lack of preparation-specific exposure data preclude firm causal inferences; longer-term, rigorously designed trials and detailed observational work are needed to refine pulse-based recommendations for cancer risk reduction and to clarify any role in survivorship care.},
}

Humans
*Neoplasms/prevention & control
*Fabaceae
*Risk Reduction Behavior
*Diet

@article {pmid42451089,
year = {2026},
author = {Hwang, AY and Lee, S and Yoon, J and Lee, KY and Suh, DH and Myung, S and Song, J and Jo, H and Sitnikov, D and Won, JH and Park, HY and Runyon, MK and Cho, D and Holzapfel, WH and Ji, Y and Jung, ES},
title = {Effects of Probiotic-Phytonutrient Blends on Defecation, Intestinal Barrier Function, and Gut Microbiota: A Randomized, Placebo-Controlled Trial.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132085},
pmid = {42451089},
issn = {2072-6643},
mesh = {Humans ; *Probiotics/administration & dosage/pharmacology ; *Intestinal Barrier Function ; Double-Blind Method ; Female ; Feces/chemistry/microbiology ; Male ; *Gastrointestinal Microbiome/drug effects ; *Defecation/drug effects ; Adult ; Tryptophan/metabolism ; Fatty Acids, Volatile/metabolism/analysis ; Middle Aged ; Haptoglobins ; Lactobacillus ; Bifidobacterium ; Protein Precursors ; },
abstract = {Background/Objectives: Probiotic interventions are widely used to improve intestinal health; however, comparative evidence on multi-strain formulations with different potencies, particularly when combined with plant-based complexes, remains limited. This study evaluated the effects of two probiotic blends containing phytonutrients: PBP1, comprising Lacticaseibacillus strains, and PBP2, comprising Lacticaseibacillus, Lactobacillus, and Bifidobacterium strains. The effects on bowel function, microbial metabolites, and gut barrier-related markers were investigated. Methods: In this randomized, double-blind, placebo-controlled trial, participants received PBP1, PBP2, or placebo for 8 weeks. Stool patterns (7-day Bristol Stool Form Scale (BSFS) diary), fecal short-chain fatty acids (SCFAs), tryptophan metabolites, zonulin, and gut microbiota were assessed at baseline and Week 8. Efficacy was evaluated by comparing each intervention group with the placebo group. Results: Both PBP1 and PBP2 significantly increased the proportion of normal stool types (BSFS types 3-5) compared with placebo (p < 0.05). Fecal SCFA levels, including acetate, propionate, and butyrate, were significantly increased in both intervention groups. Notably, butyrate levels were significantly elevated compared with placebo. Fecal tryptophan levels decreased, while indole metabolites showed increasing trends, with an inverse correlation observed between tryptophan and indole, particularly in the PBP2 group. Fecal zonulin showed a decreasing trend, with significant reductions in participants with 25.0 ≤ BMI < 30.0 kg/m[2]. Microbiome analysis revealed preserved alpha diversity with selective compositional shifts, including enrichment of Lactobacillus-related taxa. Conclusions: Supplementation with PBP1 and PBP2 improved bowel function and was associated with changes in microbiome-derived metabolites, including SCFAs and tryptophan-indole metabolism, with BMI-dependent changes in barrier markers. These findings suggest a potential role of microbiome-mediated metabolic modulation in intestinal health.},
}

Humans
*Probiotics/administration & dosage/pharmacology
*Intestinal Barrier Function
Double-Blind Method
Female
Feces/chemistry/microbiology
Male
*Gastrointestinal Microbiome/drug effects
*Defecation/drug effects
Adult
Tryptophan/metabolism
Fatty Acids, Volatile/metabolism/analysis
Middle Aged
Haptoglobins
Lactobacillus
Bifidobacterium
Protein Precursors

@article {pmid42451112,
year = {2026},
author = {Szukiewicz, D and Almeida-de-Souza, J and Gryka-Marton, M and Wątroba, M and Grabowska, AD},
title = {Relationships Between High Dietary Inflammatory Index Scores and Intestinal and Blood-Brain Barrier Integrity in the Context of Neurodegenerative Diseases.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132106},
pmid = {42451112},
issn = {2072-6643},
mesh = {Humans ; *Blood-Brain Barrier/metabolism ; *Neurodegenerative Diseases/etiology ; *Inflammation/etiology ; Intestinal Barrier Function ; *Diet/adverse effects ; Animals ; Gastrointestinal Microbiome ; Intestinal Mucosa/metabolism ; Permeability ; Diet, Western/adverse effects ; },
abstract = {The impact of diet on human health is constantly being researched. Nutrition is one of the most powerful tools for influencing gene expression, and dietary habits can promote the expression of genetic predisposition to obesity, diabetes, cardiovascular disease, cancer, and neurodegenerative diseases (NDs). The dietary inflammatory index (DII) is a numerical score that assesses the pro-or anti-inflammatory potential of a given diet. According to high DII scores, a Western diet or a standard American diet (SAD) has proinflammatory properties. By disrupting the gut microbiome, SAD creates an unfavorable environment in the intestine that is associated with a low-grade systemic inflammatory response and oxidative changes that may promote the development of NDs. An increased intestinal permeability and loss of blood-brain barrier (BBB) integrity play key roles in the pathomechanisms of diet-dependent NDs, leading to proinflammatory signaling via the gut-brain axis. The aim of this narrative review is to present in detail the current state of knowledge on the function of the gut-brain axis depending on the pro-/anti-inflammatory potential of the diet, measured by the DII, in the context of the contributions of intestinal and BBB permeability disorders to the development of NDs.},
}

Humans
*Blood-Brain Barrier/metabolism
*Neurodegenerative Diseases/etiology
*Inflammation/etiology
Intestinal Barrier Function
*Diet/adverse effects
Animals
Gastrointestinal Microbiome
Intestinal Mucosa/metabolism
Permeability
Diet, Western/adverse effects

@article {pmid42451116,
year = {2026},
author = {Jach, ME and Sajnaga, E and Ozimek, E and Serefko, A and Locatelli, M},
title = {Probiotic-Plant Bioactive Synergy in Gut Health: Mechanisms, Antimicrobial Activity, and Translational Challenges.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132112},
pmid = {42451116},
issn = {2072-6643},
support = {2024/1/7//John Paul II Catholic University of Lublin/ ; },
mesh = {*Probiotics/pharmacology ; Humans ; *Phytochemicals/pharmacology ; Animals ; *Gastrointestinal Microbiome/drug effects ; *Anti-Infective Agents/pharmacology ; Translational Research, Biomedical ; Intestinal Barrier Function ; },
abstract = {Background/Objectives: Antimicrobial resistance (AMR), microbiota disruption, and chronic inflammation have intensified the search for alternative and complementary antimicrobial strategies. Probiotics and plant-derived bioactive compounds (phytochemicals) are increasingly being investigated as microbiota-supporting, immunomodulatory, and antimicrobial agents. This review synthesizes the current evidence on probiotic-phytochemical interactions, with particular emphasis on mechanisms relevant to antimicrobial synergy, gut barrier reinforcement, microbiota modulation, and translational development. Methods: A narrative literature review with a structured search strategy was conducted using major scientific databases, including PubMed, Scopus, EBSCO, Google Scholar, SpringerLink, Wiley Online Library, and Taylor & Francis, and open repositories. Publications from January 2016 to April 2026 were considered, with an emphasis on experimental, preclinical, clinical, and mechanistic studies addressing the combined use of probiotics, postbiotics, plant extracts, or defined phytochemicals. Results: Available evidence indicates that selected probiotic-phytochemical combinations may enhance antimicrobial activity through complementary mechanisms, including pathogen membrane destabilization, inhibition of adhesion and biofilm formation, quorum-sensing interference, stimulation of probiotic viability and metabolite production, and biotransformation of phytochemicals into more active derivatives. These interactions may also support epithelial barrier integrity and immune regulation. However, the evidence remains heterogeneous and is strongly influenced by probiotic strain identity, phytochemical composition, dose, formulation, and the experimental model. Most studies are still limited to in vitro or animal models, and clinical validation remains scarce. Conclusions: Probiotic-phytochemical combinations represent a promising but insufficiently standardized strategy for antimicrobial and microbiota-targeted interventions. Future progress requires chemically characterized plant preparations, strain-level probiotic selection, harmonized synergy assays, advanced delivery systems, and well-designed clinical trials.},
}

*Probiotics/pharmacology
Humans
*Phytochemicals/pharmacology
Animals
*Gastrointestinal Microbiome/drug effects
*Anti-Infective Agents/pharmacology
Translational Research, Biomedical
Intestinal Barrier Function

@article {pmid42451117,
year = {2026},
author = {Ozeer, FZ and Kester, JC},
title = {Can Complex 3D Models Effectively Replace 2D and Animal Models to Investigate the Microbe-Tumor-Immune Axis in Pancreatic Cancer Studies?.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132113},
pmid = {42451117},
issn = {2072-6643},
mesh = {Humans ; *Pancreatic Neoplasms/microbiology/immunology/pathology/therapy ; Animals ; *Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology ; *Cell Culture Techniques, Three Dimensional ; Tumor Microenvironment/immunology ; Disease Models, Animal ; Spheroids, Cellular ; *Microbiota/immunology ; },
abstract = {The tumor microbiome has been implicated in pancreatic ductal adenocarcinoma (PDAC)'s poor response to treatment, demanding new methods for understanding host-microbe interactions in therapy. Traditional 2D systems, while widely used, fail to adequately recapitulate human PDAC due to insufficient representation of structural, immunological and stromal components. Differences in cancer-specific microbiomes, microbe-immune interactions, and the unique physiological and immunosuppressive features unique to PDAC have hindered the clinical translation of immune therapies. Reproducible 3D culture systems that integrate the human microbe-tumor-immune (MTI) axis represent a promising avenue for treatment research, yet they remain underexplored in PDAC. In this narrative review, we discuss the key microbial determinants of therapy resistance, explore the current 3D multicellular modeling approaches in other cancer types, and provide a path forward for similar integrative translational models in PDAC.},
}

Humans
*Pancreatic Neoplasms/microbiology/immunology/pathology/therapy
Animals
*Carcinoma, Pancreatic Ductal/microbiology/immunology/pathology
*Cell Culture Techniques, Three Dimensional
Tumor Microenvironment/immunology
Disease Models, Animal
Spheroids, Cellular
*Microbiota/immunology

@article {pmid42451168,
year = {2026},
author = {Li, A and He, Y and Walayat, B and Saleem, A and Zhao, J and Wang, Q and Zhang, X and Li, C and Liu, Y and Lu, S and Li, M},
title = {Gastric Microbiota Dysbiosis and Microbiome-Based Interventions in Chronic Atrophic Gastritis.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132165},
pmid = {42451168},
issn = {2072-6643},
support = {2024YF18PT036; 2024JJ212PT014//Dalian Science and Technology Innovation Project/ ; LJ212510161035//Liaoning Provincial Department of Education Basic Scientific Research Project/ ; },
mesh = {Humans ; *Gastritis, Atrophic/microbiology/therapy ; *Dysbiosis/microbiology/therapy ; Probiotics/therapeutic use ; *Gastrointestinal Microbiome ; Helicobacter pylori ; Helicobacter Infections/microbiology/therapy/complications ; Stomach Neoplasms/microbiology/prevention & control ; Gastric Mucosa/microbiology ; Chronic Disease ; Animals ; },
abstract = {Chronic atrophic gastritis (CAG) is a pivotal precancerous condition in gastric carcinogenesis, with progression typically following the classic Correa cascade. Although Helicobacter pylori (H. pylori) infection is widely recognized as the principal etiological factor, the persistence of gastric cancer (GC) risk in a subset of patients after successful eradication suggests that gastric microbiota dysbiosis may also contribute to CAG progression. In recent years, high-throughput sequencing technologies have revealed distinct microbial restructuring in patients with CAG, characterized by decreased microbial diversity, depletion of commensal taxa, and enrichment of opportunistic pathogens. These compositional changes are accompanied by metabolic dysfunction, activation of inflammatory signaling pathways, and disruption of immune homeostasis, which may contribute to a microenvironment permissive for precancerous transformation of the gastric mucosa. Probiotics and related microbiome-based therapeutics, including prebiotics, synbiotics, and postbiotics, have emerged as promising adjunctive strategies for H. pylori eradication and disease management. Their beneficial effects are mediated through multiple mechanisms, including remodeling of the microbial community, inhibition of pathogen colonization, modulation of host immune responses, and restoration of mucosal barrier integrity. However, whether these interventions can reverse established atrophic or metaplastic lesions remains unclear. In addition, how strain specificity, dose dependency, and interindividual heterogeneity influence clinical efficacy has yet to be fully elucidated. In this review, we summarize the compositional and functional features of gastric microbiota dysbiosis in patients with CAG, as well as the mechanisms and clinical applications of microbiome-based interventions. We further highlight current limitations in the field and discuss future directions for precision microecological therapies integrating multi-omics approaches, engineered probiotics, and artificial intelligence. These advances may provide a theoretical framework and practical guidance for the diagnosis and management of CAG and the prevention of GC.},
}

Humans
*Gastritis, Atrophic/microbiology/therapy
*Dysbiosis/microbiology/therapy
Probiotics/therapeutic use
*Gastrointestinal Microbiome
Helicobacter pylori
Helicobacter Infections/microbiology/therapy/complications
Stomach Neoplasms/microbiology/prevention & control
Gastric Mucosa/microbiology
Chronic Disease
Animals

@article {pmid42451191,
year = {2026},
author = {Taya, S and Ninchan, B and Umsumarng, S and Klinsoda, J and Wongpoomchai, R and Punvittayagul, C},
title = {Toxicological Assessment of Oligofructans Derived from Raw Sugar Fermentation by Bacillus subtilis TISTR 001 and Their Modulatory Effects on Rat Gut Microbiota.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132191},
pmid = {42451191},
issn = {2072-6643},
support = {FF016/2567//Fundamental Fund 2024, Chiang Mai University/ ; FRB670083/0162//Thailand Science Research and Innovation/ ; },
mesh = {Animals ; *Bacillus subtilis/metabolism ; Male ; Female ; Rats ; *Gastrointestinal Microbiome/drug effects ; Toxicity Tests, Acute ; Fermentation ; *Fructans/toxicity ; No-Observed-Adverse-Effect Level ; *Oligosaccharides/toxicity ; Rats, Sprague-Dawley ; Toxicity Tests, Subchronic ; },
abstract = {BACKGROUND/OBJECTIVES: Oligofructans are a category of non-digestible carbohydrates with beneficial effects on gut health and microbiota modulation. In this study, oligofructans were produced from raw sugar using Bacillus subtilis TISTR 001, and their safety and effects on the gut microbiota were assessed in rats.

METHODS: The acute toxicity assessment consisted of administering a single oral dose of 2000 mg/kg body weight (bw), whereas the subchronic toxicity assessment included oral dosages of 200, 600, and 2000 mg/kg/day for 90 days.

RESULTS: In the acute toxicity test, no mortality or toxicity was observed in the rats treated with a single dose of oligofructans during the 14-day observation period. The median lethal dose (LD50) of the oligofructans was >2000 mg/kg bw. In the subchronic toxicity study, daily oligofructans doses of 200, 600, and 2000 mg/kg bw for 90 days did not cause lethality or toxic clinical symptoms in rats of either sex. Furthermore, no treatment-related adverse effects of oligofructans on the hematological and biochemical parameters or organ histopathology were observed in the treatment and satellite groups. Hence, the no-observed-adverse-effect level (NOAEL) of oligofructans under the study's test conditions was confirmed as 2000 mg/kg/day.

CONCLUSION: No adverse effects were observed in either acute or subchronic toxicity studies at doses up to 2000 mg/kg/day. Moreover, oligofructans modulated the gut microbiota by promoting the growth of potentially beneficial commensal bacteria and reducing the taxa associated with inflammation or metabolic dysfunction. However, further studies are required to confirm these microbiome-related changes in humans.},
}

Animals
*Bacillus subtilis/metabolism
Male
Female
Rats
*Gastrointestinal Microbiome/drug effects
Toxicity Tests, Acute
Fermentation
*Fructans/toxicity
No-Observed-Adverse-Effect Level
*Oligosaccharides/toxicity
Rats, Sprague-Dawley
Toxicity Tests, Subchronic

@article {pmid42451209,
year = {2026},
author = {Wu, Y and Wang, J and Kang, L and Wan, X},
title = {The Interactions Between Circadian Rhythm, Gut Microbiota, and Anxiety: From Mechanisms to Intervention Strategies.},
journal = {Nutrients},
volume = {18},
number = {13},
pages = {},
doi = {10.3390/nu18132209},
pmid = {42451209},
issn = {2072-6643},
support = {31960676//National Natural Science Foundation of China/ ; 20242BAB20267//Natural Science Foundation of Jiangxi Province/ ; },
mesh = {Humans ; *Circadian Rhythm/physiology ; *Gastrointestinal Microbiome/physiology ; *Anxiety/microbiology/therapy/physiopathology ; Animals ; Melatonin ; Probiotics ; Fecal Microbiota Transplantation ; Prebiotics/administration & dosage ; },
abstract = {The circadian rhythm is an internal timing system formed by the body's adaptation to the Earth's rotation, which helps maintain homeostasis by regulating physiological, metabolic, and behavioral activities. The gut microbiota (GM), the largest microbial ecosystem in the human body, exhibits a bidirectional regulatory relationship with the host circadian clock. Emerging evidence indicates that circadian rhythm disruption (CRD) is linked to disturbances in the diurnal oscillations and compositional balance of the GM, accompanied by reduced short-chain fatty acid levels, increased lipopolysaccharide leakage, and altered tryptophan metabolism. These microbial abnormalities may be involved in anxiety-like behaviors through three major pathways: neuroendocrine (hyperactivation of the HPA axis), immune (microglia-mediated neuroinflammation), and neurotransmitter (imbalance of the serotonergic and dopaminergic systems). Conversely, microbial metabolites such as butyrate and secondary bile acids may reciprocally regulate peripheral clock gene expression, forming a complex "circadian rhythm-GM-anxiety" interaction network. This review summarizes the molecular basis of circadian-GM interactions, potential GM-mediated mechanisms linking CRD with anxiety, and emerging intervention strategies including chrononutrition (time-restricted feeding, sequential nutrient intake), microbiota-targeted therapies (probiotics/prebiotics, fecal microbiota transplantation), and light therapy and melatonin supplementation. Future directions should focus on cell-specific mechanisms using single-cell and spatial transcriptomics, developing personalized interventions that integrate chronotype and microbiome profiling, and conducting large-scale randomized controlled trials to facilitate clinical translation. This review provides a framework for understanding the integrative role of circadian biology and gut microbiota in anxiety and may help develop precision intervention paradigms.},
}

Humans
*Circadian Rhythm/physiology
*Gastrointestinal Microbiome/physiology
*Anxiety/microbiology/therapy/physiopathology
Animals
Melatonin
Probiotics
Fecal Microbiota Transplantation
Prebiotics/administration & dosage

@article {pmid42451600,
year = {2026},
author = {Garcia, J and Silva, J and Alves, MJ and Gouvinhas, I},
title = {Microbiome-Driven Bioactives for Chronic Wound Repair: Microbial Metabolites, Host-Microbe Mechanisms and Paths to Clinical Translation.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132229},
pmid = {42451600},
issn = {1420-3049},
mesh = {Humans ; *Wound Healing/drug effects ; *Microbiota ; Chronic Disease ; *Host Microbial Interactions ; Animals ; Probiotics/therapeutic use ; Skin Microbiome ; Biofilms ; Translational Research, Biomedical ; },
abstract = {Chronic wounds represent a substantial and growing clinical burden, yet durable healing remains difficult to achieve in a large proportion of patients. The skin microbiome plays a central role in this challenge: in healthy tissue, resident microorganisms support barrier integrity and calibrate immune responses, whereas in chronic wounds, community disruption-often combined with persistent biofilm formation-drives non-resolving inflammation, impairs re-epithelialisation, and increases antimicrobial tolerance. As antibiotic resistance escalates, these features strengthen the rationale for microbiome-directed strategies that target wound ecology while reducing reliance on conventional antimicrobials. Current evidence is still dominated by mechanistic and preclinical studies, with only early clinical signals for selected approaches; therefore, next-generation probiotics, including Lactiplantibacillus/Lactobacillus spp., as well as defined prebiotic and postbiotic formulations, should be interpreted as promising adjuncts rather than clinically established therapies. Causal mechanisms, optimal formulations, reproducibility, and patient-level determinants of response remain insufficiently defined, representing a critical knowledge gap that limits translation. Here, we synthesise current evidence linking microbial ecology to key wound-healing pathways and propose a precision framework that integrates metagenomics, transcriptomics, metabolomics, and spatial profiling to map host-microbe interactions, identify predictive biomarkers, and guide stratified therapy. We further highlight combinatorial approaches pairing ecological engineering with biofilm-disruptive materials and immune-modulatory molecules. Realising the potential of these interventions will require mechanism-resolved clinical trials, standardised outcome frameworks, and patient stratification tools-advances that could improve chronic wound management while reducing selective pressure for antimicrobial resistance.},
}

Humans
*Wound Healing/drug effects
*Microbiota
Chronic Disease
*Host Microbial Interactions
Animals
Probiotics/therapeutic use
Skin Microbiome
Biofilms
Translational Research, Biomedical

@article {pmid42451691,
year = {2026},
author = {Singh, AA and Arukha, AP and Song, M},
title = {Indole-Derived Compounds as Redox-Modulators: Antioxidant Mechanisms in Neuronal Protection.},
journal = {Molecules (Basel, Switzerland)},
volume = {31},
number = {13},
pages = {},
doi = {10.3390/molecules31132323},
pmid = {42451691},
issn = {1420-3049},
mesh = {Humans ; *Antioxidants/pharmacology/chemistry ; *Indoles/chemistry/pharmacology ; Animals ; *Neuroprotective Agents/pharmacology/chemistry ; Oxidation-Reduction/drug effects ; *Neurodegenerative Diseases/drug therapy/metabolism ; *Neurons/drug effects/metabolism ; Oxidative Stress/drug effects ; Signal Transduction/drug effects ; Reactive Oxygen Species/metabolism ; },
abstract = {Neurodegenerative diseases, such as Alzheimer's, Parkinson's, and Amyotrophic lateral sclerosis, are distinguished by progressive neuronal dysfunction caused primarily by oxidative stress, mitochondrial impairment, neuroinflammation, and redox imbalance. Growing evidence suggests that indole-derived compounds have significant neuroprotective potential due to their antioxidant, anti-inflammatory, and redox-modulating properties. This review summarizes the structural and biological significance of indole scaffolds, focusing on the mechanisms by which natural, endogenous, microbiota-derived, and synthetic indole compounds protect neuronal networks. Indole-3-carbinol, 3,3'-diindolylmethane, indole-3-propionic acid, and melatonin are major indole derivatives that control important neuroprotective pathways like Nrf2/ARE signaling, mitochondrial bioenergetics, neurotrophic factor expression, apoptotic regulation, and suppression of proinflammatory mediators. These compounds also maintain synaptic plasticity, reduce reactive oxygen species production, and improve neuronal survival in neurodegenerative disease models. Additionally, updated information from translational and clinical research indicates that indole-based compounds may have promising therapeutic applications; however, obstacles like low bioavailability, metabolic instability, and blood-brain barrier penetration continue to be major obstacles to clinical application. Development in nanoparticle delivery systems, microbiome-targeted interventions, and rational structural optimization may improve therapeutic efficacy and translational potential. Overall, indole-derived compounds are a versatile class of redox modulators with potential applications in the prevention and treatment of neurodegenerative diseases via integrated antioxidant and neuroprotective mechanisms.},
}

Humans
*Antioxidants/pharmacology/chemistry
*Indoles/chemistry/pharmacology
Animals
*Neuroprotective Agents/pharmacology/chemistry
Oxidation-Reduction/drug effects
*Neurodegenerative Diseases/drug therapy/metabolism
*Neurons/drug effects/metabolism
Oxidative Stress/drug effects
Signal Transduction/drug effects
Reactive Oxygen Species/metabolism

@article {pmid42452138,
year = {2026},
author = {Bodur, S and Asiloglu, R and Yazici, K},
title = {Soil Acidification Reshapes Microbial Trophic Interactions, with Implications for Plant Responses and Ecosystem Functioning in Tea Plantation Systems.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15131929},
pmid = {42452138},
issn = {2223-7747},
abstract = {Soil acidification is a widespread consequence of intensive agriculture and represents a major abiotic stress affecting plant performance, nutrient availability, and ecosystem functioning. Long-term tea (Camellia sinensis) plantations provide model systems of chronic acidification, where sustained low pH imposes strong environmental filtering on soil microbial communities. Although microbial responses to acidification have been extensively studied, research has focused predominantly on bacteria and fungi, leaving other key functional groups, particularly protists, largely overlooked. Here, we synthesize current knowledge on microbial communities in acidified soils and highlight trophic interactions, especially protist-mediated regulation, as a potentially critical but underexplored dimension linking abiotic stress to plant-soil processes. We propose that soil acidification may not only filter microbial community composition but also reshape trophic interactions. Based on evidence from other soil systems, protist-mediated trophic interactions could influence nutrient cycling, pathogen suppression, and ultimately plant responses under stress conditions. Integrating environmental filtering with trophic perspectives provides a conceptual framework for understanding microbiome dynamics in acidified soils. However, direct evidence linking protist-mediated trophic regulation to ecosystem functioning and plant performance in tea plantation soils remains limited and requires experimental validation. We further suggest that these systems provide unique opportunities to investigate how abiotic constraints and biotic interactions jointly shape plant performance. Addressing this gap is essential for advancing predictive understanding of plant-microbiome interactions under ongoing environmental change.},
}

@article {pmid42452193,
year = {2026},
author = {Sadvakasova, AK and Zaletova, DE and Bauenova, MO and Kossalbayev, BD and Xu, T and Kirbayeva, DK and Asylbekkyzy, L and Balouch, H and Botbayev, D and Abseyt, AA},
title = {Biocontrol Microbial Inoculants Suppress Fusarium oxysporum-Associated Disease Symptoms in Rice and Reshape Multicompartment Microbiomes.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15131986},
pmid = {42452193},
issn = {2223-7747},
support = {AP23488028//Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; },
abstract = {Fusarium oxysporum-associated disease symptoms in rice (Oryza sativa L.) seedlings represent an experimentally tractable model for evaluating microbiome-mediated disease suppression under controlled conditions. Biological control of Fusarium-associated disease development in rice provides a promising ecological alternative to chemical fungicides. However, the mechanisms underlying the spatial reconfiguration of the host plant multicompartment microbiome in response to complex inoculants remain insufficiently understood. In this study, we investigated the ability of the monoculture Bacillus amyloliquefaciens Bn1 (B. amyloliquefaciens Bn) and phototrophic-heterotrophic consortia composed of Nostoc sp. J-1 and B. amyloliquefaciens Bn1 to suppress Fusarium oxysporum infection, with parallel profiling of bacterial and fungal communities in rhizosphere soil, the root endosphere, and the phyllosphere using 16S rRNA and ITS amplicon sequencing. Phenotypic screening showed that microbial inoculant application significantly reduced the disease index by up to 55% while maintaining plant dry weight. The protective phenotype was not primarily associated with shifts in alpha diversity, but rather with compartment-specific reorganization of microbial communities. These findings suggest that biological control efficacy was associated less with the overall taxonomic scale of microbiome disturbance than with the formation of a functionally balanced, compartment-specific holobiont architecture but by the formation of a functionally balanced, compartment-specific holobiont architecture, providing a conceptual basis for the targeted design of next-generation phototrophic-heterotrophic biopreparations.},
}

@article {pmid42452235,
year = {2026},
author = {Zhu, C and Huang, Y and Tang, C and Sun, M and Hu, Y and Xu, X and Liu, J and Wu, P and Zhang, R and Zeng, J},
title = {Intercrops Maintain Orchard Soil Nutrients Accumulation with Variation in Soil Microbiome Composition and Function.},
journal = {Plants (Basel, Switzerland)},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/plants15132030},
pmid = {42452235},
issn = {2223-7747},
support = {2024YFD2300800//National Key Research and Development Program of China/ ; CARS-26//National Modern Agricultural (Citrus) Technology Systems of China/ ; KTP20240701 & KTP20240945)//Guangdong Rural Science and Technology Correspondent Project/ ; 2025D04J0077//Guangzhou Science and Technology Correspondent Project/ ; 2024760000390010100//Jiangmen Science and Technology Correspondent Project/ ; 2026CXTD24//Agricultural Product-Oriented Innovation Team Construction Project for Guangdong Modern Agricultural Industry Technology System/ ; },
abstract = {The intercropping system is used for weed control in orchards, but the intercrops need to be well-designed to fit into the row spaces of fruit trees. In this study, the citrus (Citrus reticulata cv. Chachiensis) row spaces were intercropped with either soybean (Glycine max (L.) Merr.) or sweet potato (Ipomoea batatas (L.) Lam.), and their effects on weed control, soil physiochemical properties, and soil microbiome were compared to the natural weeds. Both plant species were effective in reducing the orchard weeds, and their different varieties commonly improved soil organic matter, available P and K, and beneficial metal elements compared to the weeds. Even though the soil fungal and bacterial richness and diversity of the intercrops were not significantly altered, their composition, structure, and function were distinctive to those of the weeds. The soils of the intercrops generally enriched with the fungal genera of Talaromyces and Penicillium and the bacterial genera Sphingomonas, Knoellia, and Nocardioides. Accordingly, the altered microbial communities, in taxonomy, correlated to the enriched cellular functional pathways of glycolysis and gluconeogenesis, homologous recombination, nitrogen metabolism, lipoic acid metabolism, mismatch repair, DNA replication, nicotinate and nicotinamide metabolism. Taken together, these results imply that intercrops and weeds exert distinct effects on soil nutrient accumulation, and these effects are associated with their differential impacts on soil microbiomes-which are likely driven by the rhizosphere activities of the intercrops.},
}

@article {pmid42452334,
year = {2026},
author = {Salama, RAA and Msalat, OF and Fouad, MM and Alhammadi, M and Elsheikh, S and Nasser, RA},
title = {The Oral Microbiome-Nitrate-Nitrite-Nitric Oxide Axis and Cardiovascular Health: A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/jcm15134871},
pmid = {42452334},
issn = {2077-0383},
abstract = {Background: The oral microbiome has emerged as a potential contributor to cardiovascular physiology through its role in the enterosalivary nitrate-nitrite-nitric oxide pathway. Oral nitrate-reducing bacteria convert dietary nitrate into nitrite, which can subsequently be reduced to nitric oxide, a signaling molecule associated with vascular tone, endothelial function, platelet activity, and blood pressure regulation. Disruption of this pathway has been associated with reduced nitric oxide bioavailability and impaired vascular responses. Methods: This narrative review summarizes current evidence regarding the relationship between the oral microbiome, nitrate metabolism, and cardiovascular function. Relevant literature was identified through searches of PubMed/MEDLINE and Google Scholar up to May 2026. Evidence from mechanistic, observational, and interventional human studies was reviewed and synthesized thematically. Results: Available evidence suggests that oral nitrate-reducing bacteria may influence nitric oxide bioavailability and vascular function. Studies have reported associations between oral microbiome disruption and changes in blood pressure, endothelial responsiveness, plasma nitrite concentrations, and other surrogate cardiovascular markers. However, findings remain heterogeneous and are influenced by factors such as diet, oral hygiene practices, smoking status, medication use, oral health, and underlying cardiometabolic conditions. Most studies are limited by small sample sizes, short intervention durations, and reliance on surrogate outcomes rather than major cardiovascular events. Conclusions: The oral microbiome may influence cardiovascular health through its role in nitrate metabolism and nitric oxide bioavailability. However, current evidence is largely limited to surrogate vascular outcomes, while data on major cardiovascular events remain scarce. Further longitudinal and interventional studies are needed to clarify causality and evaluate microbiome-targeted interventions.},
}

@article {pmid42452393,
year = {2026},
author = {Goudman, L and Moens, M},
title = {Not All Microbiomes Reflect Chronic Pain: Evidence from the Urinary Tract in a Case-Control Study.},
journal = {Journal of clinical medicine},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/jcm15134931},
pmid = {42452393},
issn = {2077-0383},
abstract = {Background/Objectives: Chronic pain is increasingly conceptualized as a systemic condition characterized by central sensitization, autonomic dysregulation, and persistent neuroimmune and neuroendocrine alterations. These systemic changes have been linked to microbial dysbiosis, most prominently within the gut microbiome. In contrast, the relevance of the urinary microbiome outside primary urological disease remains poorly understood, particularly in non-urological chronic pain conditions. The objective of this study was to determine whether patients with chronic low back pain exhibit differences in urinary microbial diversity, community composition, or taxon-specific abundance compared with pain-free controls. Methods: In this age- and sex-matched case-control study, midstream urine samples were collected from ten patients with chronic low back pain and ten pain-free controls and analyzed using 16S rRNA gene sequencing (V4 region). Sequence data were processed using nf-core/ampliseq and DADA2. Alpha diversity, beta diversity, and differential abundance were assessed using depth-adjusted models, compositional and phylogenetically informed distance metrics, and ANCOM-BC2, with multiple sensitivity analyses to account for the low-biomass nature of urinary microbiome data. Results: After accounting for sequencing depth, no significant differences in alpha diversity were observed between patients and controls for any metric. Beta diversity analyses revealed no significant differences in overall community composition between groups across all distance measures, and dispersion was comparable between groups. Differential abundance analysis did not identify any bacterial taxa that differed significantly between patients and controls after correction for multiple testing. Conclusions: In this cohort, chronic low back pain was not associated with detectable alterations in the urinary microbiome. These findings suggest that, unlike the gut microbiome, urinary microbial communities may be relatively stable in the context of non-urological chronic pain, highlighting the importance of phenotype specificity and multidimensional approaches in microbiome-based pain research.},
}

@article {pmid42452620,
year = {2026},
author = {Berikkhanov, Z and Pilipenko, M and Ermakova, E and Sukhanova, M and Ivanova, M and Kotelnikov, A and Nikolaev, A and Razumovsky, V and Rakintsev, V and Shestakov, A and Tarabrin, E and Muraviev, S},
title = {From Microbiota Correction to Host Protection: A New Therapeutic Target for the Prevention and Treatment of Postoperative Complications.},
journal = {Journal of clinical medicine},
volume = {15},
number = {13},
pages = {},
doi = {10.3390/jcm15135161},
pmid = {42452620},
issn = {2077-0383},
abstract = {Background/Objectives. The intestinal microbiota is a key contributor to postoperative complications, yet direct interventions targeting dysbiosis-antibiotics, probiotics, and synbiotics-have produced inconsistent results. This paradox indicates a fundamental gap in understanding host-microbiota interactions under surgical stress. We aimed to re-examine the causal role of dysbiosis in postoperative pathogenesis and propose a revised therapeutic paradigm centered on host barrier protection. Methods. A narrative literature review was conducted, searching PubMed/MEDLINE, Scopus, and Web of Science for articles published between 2009 and 2025. Reference lists of included publications were additionally screened. Studies in English and Russian were eligible; 107 references were included. Results. We hypothesize that dysbiosis in surgical patients may, at least in part, represent a predictable ecological response to systemic hypoperfusion, pharmacological burden, and ischemia-reperfusion injury, rather than acting solely as an independent pathogenic agent. Microbial shifts, characterized by the depletion of short-chain fatty acid-producing commensals and the expansion of pathobionts, frequently accompany epithelial injury; however, available human data are predominantly observational and do not permit definitive determination of the temporal sequence. This hypothesis provides the conceptual foundation for the proposed therapeutic reorientation. Conclusions. The present findings support the rationale for transitioning from microbiome manipulation to a "host-first" strategy, which prioritizes the restoration of intestinal barrier integrity through the administration of cytoprotective agents and targeted metabolic substrates (glutamine and butyrate). We propose the Gut Resilience Index (GRI) as a theoretical construct to identify patients approaching a critical threshold necessitating rescue therapy. It must be emphasized that both the "host-first" strategy and the GRI remain hypothetical frameworks requiring prospective validation. The most critical next steps include the development and validation of the GRI in prospective cohort studies, as well as randomized controlled trials directly comparing barrier-oriented strategies with standard care.},
}

@article {pmid42453022,
year = {2026},
author = {Ishigami, Y and Takahashi, M and Nakatsukasa, H and Shibano, M and Kato, M and Takahashi, K and Uchida, J and Nakamura, Y and Kaneda, H},
title = {Clinical impact of opioid use in patients with urothelial carcinoma treated with pembrolizumab: a single center retrospective study.},
journal = {Immunotherapy},
volume = {},
number = {},
pages = {1-8},
doi = {10.1080/1750743X.2026.2702265},
pmid = {42453022},
issn = {1750-7448},
abstract = {BACKGROUND: Opioids may influence anti-programmed cell death-1/programmed death-ligand 1 antibody efficacy through effects on the gut microbiome and immune function. Although reduced efficacy has been suggested in non-small cell lung cancer, the impact of opioid use in urothelial carcinoma remains unclear. This study examined the impact of opioids on pembrolizumab efficacy in patients with urothelial carcinoma.

METHODS: We conducted a retrospective cohort study of patients with metastatic or unresectable urothelial carcinoma treated with pembrolizumab at our hospital between January 2018 and December 2021. Opioid use was defined as administration of opioid analgesics for pain control within 30 days before or after pembrolizumab initiation. Stabilized inverse probability of treatment weighting (IPTW) using propensity scores was applied to adjust for baseline imbalances and evaluate outcomes.

RESULTS: Of 76 recruited patients, 68 were eligible. In IPTW-weighted Cox regression analyses, opioid use was associated with shorter progression-free survival (median 6.7 vs. 4.1 months; hazard ratio [HR] 2.85, 95% confidence interval [CI] 1.67-4.88; p < 0.001) and overall survival (18.9 vs. 6.9 months; HR 4.06, 95% CI 1.73-9.55; p = 0.001).

CONCLUSION: Opioid use was associated with worse pembrolizumab outcomes in urothelial carcinoma, suggesting the need for careful, clinically appropriate opioid use during treatment.},
}

@article {pmid42453055,
year = {2026},
author = {He, S and Feng, P and Shao, X and Lu, H and Gao, Z and Yu, F and Chen, J and He, Z and Pei, S and Li, Z},
title = {Effects of Nonantibiotic Organic Pollutants on Soil Resistance and Element Cycling Functions in Greenhouse Soils: A Nationwide Survey in China.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.6c08091},
pmid = {42453055},
issn = {1520-5118},
abstract = {Greenhouse farming expansion worsens soil antimicrobial resistance. Environmental impacts of antibiotics are well-documented, yet nonantibiotic organic pollutants (NAOPs) remain vastly understudied. A nationwide soil comparison examined four common NAOP effects on elemental cycling genes (ECGs) and antibiotic resistance genes (ARGs) in paired greenhouse and open-field samples. Greenhouse soils held far richer nitrogen, phosphorus, and sulfur cycling genes and markedly higher ARG loads. Their microbiome featured more complex, tightly synergistic ecological interaction networks. Structural equation modeling revealed NAOPs regulate ARGs directly and indirectly via ECG-microbe cascades while suppressing native microbiota. Organophosphorus pesticides (OPPs) directly altered ARG profiles, dominating ARG abundance variation at 46.1%. The P═S functional group of OPPs was the key structural motif driving ARG accumulation. This study clarified NAOPs' resistance-fueling molecular mechanisms and offered valuable references for ecological risk evaluation in intensive agricultural production systems.},
}

@article {pmid42453107,
year = {2026},
author = {Rigerte, L and Sommer, A and Vlot, AC and Prada-Salcedo, LD and Reitz, T and Heintz-Buschart, A and Tarkka, MT},
title = {Synthetic rhizosphere bacterial communities induce systemic resistance to barley powdery mildew without major shifts in the native bacterial community.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818676},
pmid = {42453107},
issn = {1664-302X},
abstract = {INTRODUCTION: Synthetic microbial communities (SynComs) could help plants withstand biotic stress and reduce the need for pesticides. However, it remains unclear whether SynComs composed of host- or non-host-associated rhizosphere bacteria can trigger induced systemic resistance (ISR) in barley without causing major shifts in the native rhizosphere bacterial community.

METHODS: Here, we constructed two SynComs with known strain composition, composed of bacterial strains isolated from the host-associated barley rhizosphere and non-host-associated wheat rhizosphere. Their ability to trigger induced systemic resistance (ISR) against the barley powdery mildew pathogen Blumeria graminis f. sp. hordei (Bgh) was tested. To investigate plant-microbe interactions from both plant and microbial perspectives, we quantified Bgh propagation in leaves by DAF staining, analysed leaf transcriptomes, and profiled the rhizosphere microbiome using 16S rRNA gene amplicon sequencing and metatranscriptomics.

RESULTS: Both SynComs reduced fungal growth in barley leaves to a similar extent as the positive control strain, Pseudomonas simiae WCS417r, suggesting that ISR-like protection can also be achieved by defined multi-strain communities. Although both SynComs provided similar overall protection, the barley SynCom exhibited the strongest numerical reduction in fungal growth. These findings build on previous single-strain ISR studies and suggest that community-mediated protection is not restricted to host-derived bacterial consortia. Inoculations with both SynComs and WCS417r were not associated with statistically significant changes in the rhizosphere bacterial community structure. All treatments induced only subtle pre-infection transcriptional responses in barley leaves that were consistent with ISR-mediated priming. However, treatment with WCS417r yielded a higher number of differentially expressed genes than either SynCom. Rhizosphere metatranscriptomics revealed treatment-specific functional shifts. The two features K05516 and PF02868 were affected by all three treatments, implying the existence of shared changes related to stress adaptation and microbial activity. OTUs matching the inoculated SynCom members were still present in the rhizosphere at harvest, suggesting the persistence of at least some of the introduced communities.

CONCLUSION: Together, these findings suggest that SynCom-based ISR is potentially a more ecologically relevant approach to microbiome-mediated disease protection in barley.},
}

@article {pmid42453110,
year = {2026},
author = {Guo, J and Song, H and Xi, Z and Geng, W and Wang, F},
title = {The role of gut microbiome in antimicrobial resistance transmission between companion animals and livestock: mechanisms, drivers, and One Health implications.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1872946},
pmid = {42453110},
issn = {1664-302X},
abstract = {Antimicrobial resistance (AMR) poses a critical global public health challenge, with animal gut microbiomes serving as significant reservoirs and transmission hubs for antimicrobial resistance genes (ARGs). This review synthesizes current knowledge on the central role of gut microbiomes in companion animals and livestock in facilitating AMR dissemination. It examines key mechanisms that enable horizontal gene transfer within intestinal ecosystems: conjugation, transduction, and transformation. It also highlights how co-selection by heavy metals, disinfectants, and other non-antibiotic agents sustains resistance even without direct antibiotic use. The review analyzes major drivers of AMR, including antimicrobial usage, husbandry practices, and environmental pressures. It critically evaluates microbiome-based interventions such as probiotics, postbiotics, and fecal microbiota transplantation. A distinctive contribution is the integration of these elements into a network-centric One Health framework that explicitly maps cross-species transmission pathways from livestock and companion animals to humans via direct contact, food chains, and environmental dissemination. By moving beyond descriptive cataloging to provide a mechanistic and ecological synthesis, this review aims to guide the development of targeted, microbiome-informed intervention and surveillance strategies.},
}

@article {pmid42453337,
year = {2026},
author = {Gowda, H and Lu, W and Skaluba, P and Xiang, Y and McCann, JR and McCoubrey, LE and Rawls, JF and Venturelli, OS and Reker, D},
title = {Identifying Antibiotic Effects of Investigational Drugs on Commensal Bacteria with Machine Learning.},
journal = {ACS pharmacology & translational science},
volume = {9},
number = {7},
pages = {1756-1766},
pmid = {42453337},
issn = {2575-9108},
abstract = {Many human-targeted medications have been found to impact patients' gastrointestinal microbiomes, which has been proposed as an unrecognized source of drug side effects, comorbidities, and reduced treatment efficiencies. However, current methods for detecting such effects, such as patient sample analysis or in vitro high-throughput screening, are both labor- and resource-intensive. To accelerate the discovery of drug effects on the microbiome, we developed machine learning models that predict whether a small, drug-like molecule is likely to inhibit the growth of any of 40 representative human gut commensal microbes. We employed these models to virtually screen thousands of investigational drugs, revealing a strong propensity for human-targeted compounds to potentially modulate commensal microbes. Prospective in vitro validations uncovered two nonantibiotic drugs, the recently approved anti-cancer agent entrectinib and the clinical drug candidate PSI-697, to have previously unknown growth inhibition effects on multiple commensal gut microbes. Furthermore, we show that resistance to the effects of these drugs is mediated by known antibiotic resistance mechanisms BamB and TolC. Additionally, entrectinib significantly reduced microbial richness in a synthetic microbial model community. Taken together, our machine learning-assisted workflow and future extensions can triage microbiome-drug interactions to prioritize experimental testing and validation.},
}

@article {pmid42453369,
year = {2026},
author = {Cui, Y and Li, Q and Liu, Z and Yu, Y},
title = {Induced Sputum Microbial Diversity and Function Changes in Patients with Acute Exacerbations of Chronic Obstructive Pulmonary Disease by Metagenomic Sequencing: A Cross-Sectional Study.},
journal = {International journal of chronic obstructive pulmonary disease},
volume = {21},
number = {},
pages = {600218},
pmid = {42453369},
issn = {1178-2005},
mesh = {Humans ; *Sputum/microbiology ; *Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis ; Male ; Female ; Aged ; Cross-Sectional Studies ; *Metagenomics/methods ; *Bacteria/genetics/classification/isolation & purification ; Disease Progression ; *Microbiota ; Middle Aged ; *Lung/microbiology/physiopathology ; High-Throughput Nucleotide Sequencing ; China ; Phenotype ; Ribotyping ; },
abstract = {PURPOSE: The underlying pathogenesis of acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is closely related to airway microbiota dysregulation. Currently, there is a lack of systematic elaboration based on deep metagenomic sequencing regarding the species-level and functional characteristics of the microbiota during AECOPD, as well as its correlation with clinical phenotypes of the host. This study aims to systematically analyze the taxonomic composition and functional profile changes of the microbiota in induced sputum samples from COPD patients during the stable and acute exacerbation periods using metagenomic next-generation sequencing and to explore their correlations with clinical indicators through metagenomic methods.

PATIENTS AND METHODS: A total of 66 patients with COPD were recruited from the Department of Respiratory and Critical Care Medicine at Jiading District Central Hospital in Shanghai, China. Of these, 49 induced sputum samples were obtained from 47 patients (17 in the stable group; 30 in the acute exacerbation group) after the quality control with DNA extraction and deep metagenomic sequencing. The species annotation and functional analysis were conducted using bioinformatics procedures, and microbial α-diversity analysis, LEfSe analysis was performed to identify differentially expressed markers. Spearman correlation analysis was used to evaluate the correlation between microbial/functional characteristics and a series of clinical indicators.

RESULTS: The α-diversity of the sputum microbiota in AECOPD patients was significantly lower at the species level compared to the stable stage (p < 0.01), and the community structure also underwent significant changes. Functional annotation and comparative analysis further identified 9 KEGG pathways (ko00970, ko04112, ko03420, ko03440, ko03060/ko03070, ko03410, ko04930, and ko00680) and 1 eggNOG functional category (M: Cell wall/membrane/envelope biogenesis) that differed significantly between the two groups. Among them, pathways such as methane metabolism were downregulated in the exacerbation period.

CONCLUSION: This study revealed significant dysregulation of the airway microbiome in AECOPD patients at species-level diversity, community structure, and functional metabolism, providing a molecular basis for the discovery of functional biomarkers and therapeutic targets in the microbiome.},
}

Humans
*Sputum/microbiology
*Pulmonary Disease, Chronic Obstructive/microbiology/physiopathology/diagnosis
Male
Female
Aged
Cross-Sectional Studies
*Metagenomics/methods
*Bacteria/genetics/classification/isolation & purification
Disease Progression
*Microbiota
Middle Aged
*Lung/microbiology/physiopathology
High-Throughput Nucleotide Sequencing
China
Phenotype
Ribotyping

@article {pmid42453606,
year = {2026},
author = {Duda-Grychtoł, K and Oleś, K and Palacz-Wróbel, M},
title = {Microbiological diagnosis of the scalp and hair in 20-40 year olds - preliminary studies.},
journal = {Open life sciences},
volume = {21},
number = {1},
pages = {20251343},
pmid = {42453606},
issn = {2391-5412},
abstract = {Microbiome refers to the collection of microorganisms living in the human body. Skin, intestines and upper respiratory tract are particularly inhabited by microorganisms. The microbiota of the scalp and hair, though so far little understood, is particularly abundant in terms of microorganisms, which play an important role in maintaining the health of the scalp by inhibiting pathogens and promoting optimal skin condition. Dysbiosis of the scalp microbiota can be influenced by many factors, both exo and endogenous leading to the development of pathological conditions such as dandruff or seborrhoeic dermatitis. The aim of this preliminary study was the microbiological diagnosis of the scalp and hair in the group of individuals aged 20-40 years old. The samples for the research have been obtained from three different sites on the scalp of 6 individuals aged 20 to 40. The material for the study was collected using contact plates for total bacterial counts - Rodac Contact Test. The colonies grown on the microbiological media were characterised in terms of their size and shape. Subsequently, Gram staining was performed to assign the colonies of the bacteria to Gram-positive or Gram-negative bacteria, as well as fungi characterisation of the scalp and hair was conducted using a trichological camera. Finally, on the basis of the study following conclusions have been drawn. There were observed differences in the appearance of microbial colonies between younger and older people and in the group of 40-year-old, there was a significantly less colony diversity monitored. In terms of bacteria, Gram-positive cocci got isolated most frequently. In addition, yeast as well as filamentous fungi occurred abundant in the middle of the head of the research participants.},
}

@article {pmid42453631,
year = {2026},
author = {Lee, YR and Park, M and Cho, YS and Park, HY},
title = {Metabolomics and Precision Medicine in Resistant Hypertension: Pathophysiological Insights, Biomarker Discovery, and Translational Strategies.},
journal = {International journal of hypertension},
volume = {2026},
number = {},
pages = {9656975},
pmid = {42453631},
issn = {2090-0384},
abstract = {Resistant hypertension (RH), defined as uncontrolled blood pressure despite the use of at least three optimally dosed antihypertensive agents, including a diuretic, remains a major clinical challenge associated with elevated cardiovascular risk. Metabolomics offers a dynamic approach to characterize biochemical perturbations related to amino acid metabolism, lipid remodeling, mitochondrial dysfunction, oxidative stress, renal impairment, and gut microbiota-derived metabolites. However, current evidence remains limited by small sample sizes, cross-sectional designs, heterogeneous definitions of RH, inadequate exclusion of pseudoresistance, medication confounding, and limited external validation. This structured narrative review synthesizes RH-specific metabolomic evidence and distinguishes it from findings extrapolated from broader hypertension populations. We further discuss methodological challenges, replication gaps, pharmacometabolomic confounding, and validation standards required for clinical implementation. Integrating metabolomics with clinical phenotyping, genomics, proteomics, and microbiome profiling may eventually support RH phenotyping, treatment-response prediction, and biomarker-guided precision medicine, but large longitudinal cohorts with confirmed true RH are needed before clinical translation.},
}

@article {pmid42453715,
year = {2026},
author = {Correa, SS and Almansoori, AHMA and Nazzar, S and Sadaiappan, B and Ali, Q and Subramani, P and Mundra, S},
title = {Distinct functional responses of root endophyte and rhizosphere microbial communities in intercropping systems under arid conditions.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1809801},
pmid = {42453715},
issn = {1664-462X},
abstract = {INTRODUCTION: Sustainable strategies have been implemented to enhance plant development and productivity, including intercropping systems. This approach is particularly effective in arid regions, where diverse microbial populations associated with intercropping plants contribute significantly to stress tolerance and plant growthpromoting.

METHODS: We evaluated how intercropping and monocropping systems influence the diversity, functional traits, and stress tolerance of root-associated bacteria. Root endophytic and rhizosphere bacteria were isolated from intercropping and monocropping systems under arid conditions and evaluated for plant growth-promoting traits, enzymatic activities, exopolysaccharide and cellulose production, biofilm formation under drought stress, and tolerance to drought, salinity, and heat stress.

RESULTS AND DISCUSSION: Eighty bacterial isolates were characterized, most of which exhibited multiple plant growth-promoting traits and tolerance to environmental stress. Overall, Bacillus spp. were the dominant bacteria among endophyte and rhizosphere communities. In alfalfa-broad and Egyptian wheat-broad intercropping, Bacillus spp. were more common, whereas Pseudomonas spp. were more common in barley-mustard intercropping. Multivariate analysis of functional traits (NMDS) revealed that bacterial communities were primarily structured by niche (endophytic vs. rhizosphere) rather than by intercropping type. The results suggest that rhizosphere bacteria associated with intercropping enhanced nitrogen fixation compared to those from monocropping systems, and the exopolysaccharide produced by endophytic isolates from intercropping using glucose as a carbon source varied from monocropping. Based on our results, the intercropping system creates a favorable microenvironment for certain bacteria, such as Bacillus spp. and Pseudomonas spp., which possess specific plant growth-promoting traits suitable for harsh environments, such as arid regions. These findings support other studies showing that bacteria adapted to extreme conditions, and isolated from diverse and multiple cropping systems, can function as plant bioinoculants, supporting plant species under adverse conditions.},
}

@article {pmid42453735,
year = {2026},
author = {Shulga, S and Tigunova, O and Andriiash, H and Yemets, A and Blume, Y},
title = {Harnessing plant microbiomes to enhance crop resilience and restore war-affected soils in Ukraine.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1868751},
pmid = {42453735},
issn = {1664-462X},
abstract = {This review presents the current understanding of the rhizosphere microbiome and its potential application for the regeneration of damaged soils. The aim was to examine the issues of soil degradation associated with military actions and the latest developments in microbiome engineering for their application in the bioremediation of damaged lands. The review analyses recent developments and achievements in the study of the microbiome, its role in soil fertility, and plant protection against stress. Various directions and approaches to microbial profiling and addressing relevant pollution issues using developed bioengineered models and constructs have been examined. It has been shown that the most common explosive organic compounds - TNT, hexogen, and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine - and heavy metals - lead, cadmium, zinc, and antimony - account for the greatest soil contamination. The restoration of soils damaged as a result of military actions is feasible through the engineering of a specific soil microbiome (including genera Bacillus, Pseudomonas, and Arthrobackter, as well as arbuscular mycorrhiza). Military-related stress on soil is exerted by a mixture of organic pollutants and heavy metals, and the use of microbial consortia is a promising approach for mitigating their impact. The main economic advantage of such associations is that a consortium not only degrades toxic contaminants but also contains strains capable of nitrogen fixation and phosphorus mobilisation. The economic feasibility of applying synthetic microbial consortia and microbial engineering in war-affected regions is based on balancing the initial costs of research and development against substantial savings in capital investments compared with conventional land remediation methods.},
}

@article {pmid42453740,
year = {2026},
author = {Bosisio, M and Garcia, MA and Zani, A},
title = {Neurodevelopmental impairment in infants with necrotizing enterocolitis: a comprehensive review of mechanisms, outcomes, and emerging strategies.},
journal = {World journal of pediatric surgery},
volume = {9},
number = {4},
pages = {e001199},
pmid = {42453740},
issn = {2516-5410},
abstract = {Necrotizing enterocolitis (NEC) is a severe gastrointestinal condition predominantly affecting preterm infants and is characterized by intestinal inflammation, ischemia, and, in advanced cases, bowel necrosis. Although advances in neonatal care have improved survival, infants with NEC remain at substantially increased risk of long-term neurodevelopmental impairment (NDI), including cognitive, motor, sensory, and behavioral deficits. Clinical severity, surgical NEC, and comorbidities, including intraventricular hemorrhage and metabolic instability, further exacerbate neurodevelopmental risk. Neuroimaging and electrophysiological studies have consistently revealed structural and microstructural brain abnormalities that provide early prognostic markers. While prematurity contributes to baseline vulnerability, growing evidence indicates that NEC-specific factors, such as systemic inflammation, disruption of the gut-brain axis, and immune-mediated injury, play a central role in the pathogenesis of brain injury. Preclinical research targeting inflammation, oxidative stress, microbiome modulation, and high-mobility group box 1-Toll-like receptor 4 (HMGB1-TLR4) signaling has demonstrated promising neuroprotective effects, underscoring the need for translational strategies. This review comprehensively examines the literature on NDI in infants with NEC to compare the clinical outcomes of this population of babies with those of their preterm peers, evaluate the underlying mechanisms of brain injury associated with NEC, and discuss emerging preventative and therapeutic strategies to address this morbidity.},
}

@article {pmid42453861,
year = {2026},
author = {García-Del Río, M and Martin-Pozas, T and Sanchez-Moral, S and Cantarero, A and Castaño-Vázquez, F and Merino, Y and García-Velasco, J and Merino, S},
title = {Environmental Drivers on Blue Tit Nest Microbiome: An Experimental Study.},
journal = {Ecology and evolution},
volume = {16},
number = {7},
pages = {e74007},
pmid = {42453861},
issn = {2045-7758},
abstract = {Microclimate inside avian nesting cavities provides suitable growth conditions for microbial communities, which in turn may play a crucial role in influencing the well-being of the host. In this study, we investigated the microbiome of Blue Tit (Cyanistes caeruleus) nests subjected to experimental manipulations of temperature and humidity, aiming to evaluate the impact of these factors on fungal and bacterial communities. Additionally, we examined the associations between these microbial communities, parasitism and nesting birds' condition. Our results, based on metabarcoding analysis using 16S rRNA and the ITS2 region, indicated that while bacterial alpha diversity remained unaffected by the experimental manipulation, beta diversity differed significantly, particularly between nests with increased humidity and control nests. Similarly, elevated temperature and humidity increased fungal richness (alpha diversity) and altered fungal composition (beta diversity). We also observed that the abundances of bacterial and fungal phyla varied between treatments, with the differences being most pronounced in the case of fungi. We did not detect significant differences in potentially pathogenic bacteria between treatments. However, potentially pathogenic fungi, including dermatophytes, proliferated in humidified nests, potentially contributing to poorer nestling body condition compared to other nest treatment groups. The study also revealed significant correlations between microbial communities, ectoparasites and nestling body condition, indicating their potential interconnection. To our knowledge, this study represents the first experimental analysis of the microclimate effects on the nest microbiome. These findings highlight the complex interactions between nest microclimate, microbial diversity, ectoparasites and nestling development, offering new insights into the ecological effects of microclimatic conditions in avian nesting environments.},
}

@article {pmid42453984,
year = {2026},
author = {Bessa, LJ and An, Y and Li, Z},
title = {Editorial: The immune microenvironment-microbiome interactions in peri-implantitis and periodontitis.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1844086},
pmid = {42453984},
issn = {2235-2988},
}

@article {pmid42453986,
year = {2026},
author = {Zhang, B and Yun, Z and Yuan, Y and Li, L and Xiong, Z},
title = {A scientometric analysis of research related to the 'oral-placental axis' hypothesis: current status, hotspots, and future directions.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1864022},
pmid = {42453986},
issn = {2235-2988},
mesh = {Female ; Pregnancy ; Humans ; *Placenta/microbiology ; *Bibliometrics ; *Placenta Diseases/microbiology ; Computational Biology ; Pregnancy Outcome ; Microbiota ; *Mouth Diseases/microbiology ; Periodontal Diseases ; *Mouth/microbiology ; },
abstract = {Oral diseases and placental disorders are closely associated with adverse pregnancy outcomes, and accumulating evidence supports their crosstalk that constitutes the "oral-placental axis". This study integrated scientometric and bioinformatic approaches to systematically analyze global research trends, collaboration networks, research hotspots, and core molecular-microbial mechanisms of the oral-placental axis covering the period from 2016 to 2025. A total of 196 eligible publications were retrieved from the Web of Science Core Collection, Scopus, and PubMed. Bibliometric visualization was performed using VOSviewer, CiteSpace, and R-bibliometrix, and bioinformatic analysis was conducted to identify shared genes, signaling pathways, and microbial links between oral and placental diseases. The results revealed an annual publication growth rate of 5.03%, with the United States, China, and Australia as major contributing countries, the University of Queensland as the leading institution, and Gomez-Arango Luisa F. and Nitert Marloes Dekker as the most influential authors. Core keywords included preterm birth, periodontal diseases, gestational diabetes mellitus, and oral microbiome, reflecting a research shift from phenotypic association to mechanistic exploration such as microbial vertical transmission and inflammatory signaling. Mechanistic analyses identified shared hub genes (e.g., KRT19, ADAMDEC1, AQP9, SPAG4, PLAT) and key pathways, predominantly primary immunodeficiency and complement and coagulation cascades. Pathogenic bacteria including Fusobacterium nucleatum and Porphyromonas gingivalis mediated adverse pregnancy outcomes via hematogenous spread and placental barrier disruption. This study established a bidirectional regulatory model of the oral-placental axis involving shared risks, microbial transmission, and systemic inflammation, providing a theoretical basis for preconception oral intervention and precise prevention during pregnancy, and supporting the integration of oral care into routine perinatal management.},
}

Female
Pregnancy
Humans
*Placenta/microbiology
*Bibliometrics
*Placenta Diseases/microbiology
Computational Biology
Pregnancy Outcome
Microbiota
*Mouth Diseases/microbiology
Periodontal Diseases
*Mouth/microbiology

@article {pmid42454043,
year = {2026},
author = {Wendt, K and Schieck, M and Gille, C and Marschollek, M and Illig, T and Wolff, D and Nee, S},
title = {Biomarkers of post-acute infection syndrome: a systematic literature review.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1741761},
pmid = {42454043},
issn = {1664-3224},
mesh = {Humans ; *Biomarkers/metabolism ; Post-Acute COVID-19 Syndrome ; *COVID-19/complications ; *SARS-CoV-2 ; *Fatigue Syndrome, Chronic/diagnosis ; },
abstract = {BACKGROUND: Post-acute infection syndrome (PAIS) remained underrecognized before the COVID-19 pandemic, which further increased exposure by introducing a novel global cause. The global burden of post-acute COVID syndrome (PACS) and myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) alone is estimated at several tens of millions affected worldwide. Biomarker discovery is central to improving PAIS diagnosis and may provide therapeutic targets. This review summarizes current knowledge on biomarkers for PAIS, including PACS and ME/CFS.

METHODS: A systematic literature search was conducted in PubMed and Web of Science. Inclusion criteria were: (1) studies including PAIS patients; (2) reporting laboratory or omics biomarkers; and (3) investigating biomarkers or pathomechanisms of PAIS. Although Guillain-Barré syndrome (GBS) is not PAIS, we have included it as a separate mechanistic comparator due to its prevalence in search results and its clinical and immunological similarities to PAIS.

RESULTS: A total of 142 studies analyzing PAIS biomarkers were included. GBS was analyzed separately and later compared with the other results. Overall, the reviewed studies employed heterogeneous approaches. While similar types of data were frequently investigated, analytical methods varied and often focused only on a subset of molecules. The results indicate that amino acid, energy, and lipid metabolism, microbiome, mitochondrial stress, and miRNA networks are affected. All pathways are connected via NF-κB.

DISCUSSION: PAIS is a multisystem disorder rooted in persistent immune activation, metabolic reprogramming, and systemic inflammation, driven not by active viral infection, but by dysregulated host responses. The NF-κB pathway serves as a unifying hub, connecting molecular, cellular, and clinical phenotypes. Our framework enables a shift from symptom-based to mechanism-based classification, paving the way for biologically grounded interventions.

CONCLUSION: This review synthesizes a broad spectrum of biomarkers in PAIS, integrating findings across pathogens and molecular levels rather than restricting to individual conditions or symptom clusters. This study highlights the differences and commonalities among pathogens and diseases that lead to post-acute sequelae, fills a critical knowledge gap, and provides a foundation for future research and clinical practice. Future studies incorporating multi-omics approaches, longitudinal designs, and larger patient cohorts are needed to validate specific biomarkers and advance the understanding of PAIS.},
}

Humans
*Biomarkers/metabolism
Post-Acute COVID-19 Syndrome
*COVID-19/complications
*SARS-CoV-2
*Fatigue Syndrome, Chronic/diagnosis

@article {pmid42454214,
year = {2026},
author = {Dotan, I and Ben-Horin, S and Schwartz, D and Bar-Yoseph, H and Fischman, M and Shen-Orr, SS and Chowers, Y and Odes, S and Eliakim, R and Turner, D and , },
title = {The Israeli IBD Research Nucleus: collaborative advancements in Israeli IBD research.},
journal = {Therapeutic advances in gastroenterology},
volume = {19},
number = {},
pages = {17562848261463603},
pmid = {42454214},
issn = {1756-283X},
abstract = {Inflammatory bowel diseases (IBD) are increasing worldwide, requiring multidisciplinary care and coordinated research infrastructures. Leveraging Israel's integrated healthcare system with IBD centers of specific and complementary research expertise, a national collaborative consortium was established: the Israeli IBD Research Nucleus (IIRN). In this narrative article, we review a decade of IIRN structure, scientific outputs, and lessons learned. The IIRN included five tertiary academic IBD referral centers across Israel, with expertise in epidemiology, mucosal immunology, diet and microbiome, imaging, and psychosocial care. We summarized the IIRN key activities, findings, and contributions across these domains. Publications (2015-2025) were identified using a structured bibliometric approach and included studies aligned with core research programs of the IIRN. This collaborative consortium has been supported since its inauguration by the Leona M. and Harry B. Helmsley Charitable Trust, providing funding, advice, and partnership. The IIRN provided significant contributions in several domains. It established a population-based nationwide registry (epi-IIRN) that integrates data from the four national health maintenance organizations, enabling studies of disease prevalence, course, comorbidities, and treatment patterns. Prospective cohorts of patients with Crohn's disease provided longitudinal insights linking multidisciplinary programs, Mediterranean diet and lifestyle, and psychosocial interventions with patient-reported outcomes, inflammatory markers, and microbiome features. Integrating imaging, video-capsule endoscopy, and biomarker assessment informed monitoring strategies and treat-to-target concepts. Exploratory translational work in microbiome, transcriptomics, and therapeutic drug monitoring refined insights regarding treatment response and sequencing. Artificial intelligence applications explored image and report interpretation to predict Crohn's disease. The IIRN experience illustrates how coordinated national collaborations can leverage epidemiology, prospective cohorts, translational research, and multidisciplinary care programs. This experience highlights both the opportunities and challenges of shared research infrastructure and may inform similar collaborative efforts in other healthcare settings.},
}

@article {pmid42454291,
year = {2026},
author = {Toderescu, CD and Pogurschi, EN and Stefanache, A and Munteanu, MF and Trifunschi, S and Oancea, A and Bugi, MA and Cresneac, I},
title = {Dietary exposure to food additives in ultra-processed foods: implications for gut microbiome, metabolic health, and risk assessment.},
journal = {Frontiers in public health},
volume = {14},
number = {},
pages = {1843650},
pmid = {42454291},
issn = {2296-2565},
mesh = {Humans ; *Food Additives/adverse effects ; *Dietary Exposure/adverse effects ; Risk Assessment ; *Gastrointestinal Microbiome/drug effects ; *Fast Foods ; },
abstract = {BACKGROUND: The increasing consumption of ultra-processed foods has led to a substantial rise in dietary exposure to food additives, making them a consistent component of modern dietary patterns. While food additives are generally considered safe within established regulatory limits, their long-term health effects remain a subject of growing scientific interest, particularly from a nutritional epidemiology perspective.

METHODS: This narrative review, conducted following PRISMA-informed principles, synthesizes recent experimental, clinical, and epidemiological evidence on the health effects of major food additive categories, including emulsifiers, non-nutritive sweeteners, preservatives, and synthetic colorants. Literature searches were performed in Web of Science, Scopus, and PubMed, covering studies published between 2010 and 2024. A qualitative assessment of study quality was performed based on study design, sample size, and potential sources of bias. The results of this assessment are summarized in Table 2.

RESULTS: Dietary exposure to food additives through ultra-processed foods has been associated with changes in the gut microbiome, metabolic function, and low-grade inflammation. Experimental studies consistently report biological effects, particularly for emulsifiers and artificial sweeteners, whereas epidemiological findings remain heterogeneous and influenced by overall dietary patterns.

CONCLUSION: Current evidence supports the need to evaluate food additives within the context of dietary patterns rather than as isolated compounds. While most approved additives remain safe at regulated intake levels, emerging data suggest that cumulative exposure and diet-microbiome interactions may not be fully captured by existing risk assessment frameworks. Integrating nutritional context into future safety evaluations may improve their relevance for public health.},
}

Humans
*Food Additives/adverse effects
*Dietary Exposure/adverse effects
Risk Assessment
*Gastrointestinal Microbiome/drug effects
*Fast Foods

@article {pmid42454401,
year = {2026},
author = {Pettinga, D and Fonseca-García, C and Krause, G and Ploemacher, H and Wheeler, T and Clendinen, CS and Handakumbura, P and Egbert, R and Coleman-Derr, D},
title = {Rational reduction of a sorghum SynCom that preserves growth promotion reveals flavonoid-mediated plant-microbe interactions.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71425},
pmid = {42454401},
issn = {1469-8137},
support = {2019-67019-29306//National Institute of Food and Agriculture/ ; DE-AC05-76RL01830//Pacific Northwest National Laboratory/ ; CRIS 2030-12210-003-000D//Agricultural Research Service/ ; DE-AC05-76RL0183//Biological and Environmental Research/ ; },
abstract = {Plant growth is influenced by the composition of its associated microbiome. The inherent complexity and functional redundancy of natural plant microbiomes present a formidable barrier to understanding the myriad biological interactions therein. Efforts have been made to develop synthetic microbial communities (SynComs) that can provide a rigorous and generalizable framework for the rational design of next-generation microbial products for sustainable agriculture. We test multiple strategies for stable, plant growth promoting SynCom design and evaluate the phenotypic and molecular impacts of a successful plant-SynCom interaction. We designed four distinct, reduced-complexity variants of SynCom Sorghum Root Consortium 1 and assessed their capacities for colonization, stability, and plant growth promotion (PGP). To understand the impact on plant performance of our highest performing SynCom variant, we characterized the host's longitudinal transcriptional response to SynCom inoculation and corroborated the results with metabolomics analysis. The top-performing SynCom stably colonized Sorghum bicolor roots and rhizospheres, elicited PGP, and induced dynamic spatiotemporal gene transcription in S. bicolor roots and shoots defined by modulation of growth-defense trade-off machinery and enhanced flavonoid production. The resultant reduced-complexity SynCom is a highly stable, soil-independent, plant growth promoting, and demonstrates the utility of colonization-based selection criteria, integrated with longitudinal transcriptomic and metabolomic characterization.},
}

@article {pmid42454454,
year = {2026},
author = {Koedooder, R and Gao, XS and Schoenmakers, S and Budding, AE and Smeenk, JMJ and de Jonge, JD and Laven, JSE},
title = {Integrating Vaginal Microbiome Test Results into Shared Decision Making during In Vitro Fertilization Care.},
journal = {Medical decision making : an international journal of the Society for Medical Decision Making},
volume = {},
number = {},
pages = {272989X261463217},
doi = {10.1177/0272989X261463217},
pmid = {42454454},
issn = {1552-681X},
abstract = {BACKGROUND: The vaginal microbiota test predicts the success of in vitro fertilization (IVF), but with no therapy available to improve a low profile, couples must decide whether to proceed or postpone treatment. We aim to examine how couples interpret vaginal microbiome results and make postponement decisions within a shared decision making (SDM) framework.

METHODS: Women undergoing IVF or IVF-intracytoplasmic sperm injection (IVF-ICSI) treatment at 2 Dutch hospitals received the ReceptIVFity test™, which classified the vaginal microbiome as high (52.6% chance of conception), medium (23.6%), or low (5.9%) profile based on predicted implantation success after a fresh embryo transfer. Physicians discussed the results with couples using SDM, after which the couples decided whether to proceed or postpone treatment. The primary outcome was the patients' perceived involvement in shared decision making, assessed with the SDM-Q-9 questionnaire. The secondary outcome was the proportion of couples postponing treatment after a low microbiome profile.

RESULTS: Between October 2018 and November 2020, 728 women were enrolled. SDM-Q-9 responses showed high perceived involvement overall but lower scores for "exploring options," reflecting limited alternatives when the choice is to proceed or postpone treatment. A low profile was found in 35.4% (258/728). After the SDM consultation, 49.6% (128/258) chose to postpone treatment, with postponement rates increasing to over 80% among couples in later IVF cycles. Decisions were influenced by personal, emotional, and practical considerations, including the Dutch insurance reimbursement system (3 insured IVF or IVF-ICSI cycles regardless of postponement) and the absence of effective treatment to modify a low profile.

CONCLUSIONS: These findings demonstrate that couples can understand and use prognostic information when supported by SDM and that the ReceptIVFity test™ facilitated discussion about chances of success, timing of treatment, decisions to proceed or postpone, and personal values.},
}

@article {pmid42454489,
year = {2026},
author = {McCann, JR and Yang, C and Bihlmeyer, NA and Tang, R and Truong, T and Zhou, W and An, J and Jawahar, J and Ilkayeva, O and Muehlbauer, MJ and Hu, Z and Dressman, HK and Poppe, L and Granek, JA and Arnold, JW and David, LA and Oh, J and Shi, P and Gumus Balikcioglu, P and Shah, SH and Armstrong, SC and Newgard, CB and Seed, PC and Rawls, JF},
title = {Branched chain amino acid metabolism and microbiome in adolescents with obesity during weight loss therapy.},
journal = {The Journal of clinical investigation},
volume = {136},
number = {14},
pages = {},
doi = {10.1172/JCI196742},
pmid = {42454489},
issn = {1558-8238},
mesh = {Humans ; Adolescent ; *Amino Acids, Branched-Chain/blood/metabolism ; Female ; Animals ; Male ; Child ; Mice ; *Gastrointestinal Microbiome ; *Weight Loss ; *Pediatric Obesity/therapy/microbiology/metabolism ; Fecal Microbiota Transplantation ; },
abstract = {BACKGROUNDObesity and weight loss in adults have been associated with distinct metabolome and gut microbiome features, but the extent to which those associations apply to adolescent stages remain unclear.METHODSThe Pediatric Obesity Microbiome and Metabolism Study (POMMS) enrolled 220 adolescents aged 10-18 with severe obesity (OB) and 67 individuals who were healthy weight controls (HWCs). Blood, stool, and clinical measures were collected at baseline and after a 6-month obesity intervention for the OB group. Metabolomic profiling in serum using targeted quantitative mass spectrometry and microbiome profiling in stool were performed, and those features were assessed for associations with BMI, insulin resistance, and inflammation. Fecal microbiome transplants (FMT) were performed on germ-free mice using samples from both groups to assess effects on weight gain and metabolic pathways.RESULTSAdolescents with OB exhibited higher serum branched-chain amino acid (BCAA) but lower branched-chain ketoacid (BCKA) levels compared with HWC. This pattern was sex- and age-dependent and differed from adults with obesity who show elevated levels of both BCAA and BCKA. Longitudinal analysis identified metabolic and microbial features correlated with changes in health measures during the intervention. The fecal microbiomes of adolescents with OB and HWC had similar diversity but differed in membership and functional potential. FMT from both OB and HWC donors had similar effects on mouse body weight, but specific taxa were linked to weight gain in recipients of FMT.CONCLUSIONAdolescents with OB have unique metabolomic adaptations and microbiome signatures compared with their HWC counterparts and adults with OB.TRIAL REGISTRATIONClinicalTrials.gov Identifier: NCT03139877 (Observational Study) and NCT02959034 (Repository).FUNDING SUPPORTAmerican Heart Association Grants: 17SFRN33670990, 20PRE35180195; National Institute of Diabetes and Digestive and Kidney Diseases Grant: R24-DK110492.},
}

Humans
Adolescent
*Amino Acids, Branched-Chain/blood/metabolism
Female
Animals
Male
Child
Mice
*Gastrointestinal Microbiome
*Weight Loss
*Pediatric Obesity/therapy/microbiology/metabolism
Fecal Microbiota Transplantation

@article {pmid42454758,
year = {2026},
author = {Truong, VL and Rarison, RHG and Song, EJ and Nam, YD and Hong, YS and Jeong, WS},
title = {Diarylheptanoid Phytoestrogen from Curcuma comosa Attenuates Colitis and Colitis-Associated Colorectal Cancer by Inhibiting Inflammation and Oxidative Stress and Modulating Gut Microbiota.},
journal = {Journal of agricultural and food chemistry},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jafc.5c17732},
pmid = {42454758},
issn = {1520-5118},
abstract = {Diarylheptanoids are bioactive compounds primarily found in the rhizomes of Curcuma species and are traditionally used to treat inflammatory conditions. This study investigated the chemopreventive effects of 1,7-diphenyl-(4E, 6E)-4,6-heptadien-3-one (DPH), a diarylheptanoid isolated from Curcuma comosa ethanol extract (CCE), using in vitro and in vivo models. CCE/DPH administration significantly alleviated colitis and delayed colitis-associated colorectal tumorigenesis, accompanied by reduced expression of proinflammatory cytokines and mediators. Network pharmacology and experimental validation suggested potential involvement of the Toll-like receptor 4/mitogen-activated protein kinase/nuclear factor kappa B/signal transducer and activator of transcription 3 axis as a potential therapeutic target. Additionally, CCE/DPH upregulated the expression of the phase II antioxidant enzymes and tight junction proteins. Microbiome analysis revealed that CCE/DPH was associated with partial improvements in the gut microbial composition and metabolite profiles in experimental models. Overall, these findings support the preventive potential of CCE and DPH against experimental colitis and colitis-associated colorectal cancer.},
}

@article {pmid42454773,
year = {2026},
author = {Feng, Z and Yang, Y and Ayana, GU and Zhao, Y and Wang, Y and Zhou, W and Zhang, Q},
title = {Intestinal Microbiota and Metabolomics Analysis of Asian Swamp Eel (Monopterus albus) With Hemorrhagic Septicemia Caused by Aeromonas veronii.},
journal = {Journal of fish diseases},
volume = {},
number = {},
pages = {e70244},
doi = {10.1111/jfd.70244},
pmid = {42454773},
issn = {1365-2761},
support = {CARS-46//Earmarked Fund for China Agriculture Research System/ ; 2024YFD2401500//National Key Research and Development Program of China/ ; 22DZ2291200//The Science and Technology Commission of Shanghai Municipality/ ; },
abstract = {The Asian swamp eel (Monopterus albus) is an economically vital species in the Chinese aquaculture industry. However, outbreaks of the hemorrhagic septicemic disease caused by Aeromonas veronii have led to substantial economic losses in Asian swamp eel culture and its pathogenesis remains poorly understood. Therefore, this study isolated a pathogenic bacterial strain from diseased fish, which was identified as A. veronii and named the strain MaAv001 through phenotypic and 16S rRNA sequencing analyses. Artificial infection confirmed its high pathogenicity, with an LD50 of 4.12 × 10[4] CFU/g. Histopathological analysis revealed systemic damage, renal necrosis, splenic lymphocyte reduction, hepatic necrosis and intestinal sloughing. Virulence gene profiling identified six factors (aer, lip, gcaT, ser, alt, act) contributing to pathogenicity. The 16S rRNA of intestinal microbiota analysis revealed significant dysbiosis in the intestinal microbiota, marked by reduced beneficial Sphingomonas diversity and increased abundance of Vibrio. Non-targeted metabolomics identified 646 differential metabolites enriched in sulfur relay, glutathione, seleno-compound and cytochrome P450 pathways. This study elucidates the molecular pathogenesis of A. veronii as a primary pathogen of hemorrhagic septicemia in M. albus and its impact on the gut microbiome profiles and metabolomics. These findings provide a theoretical foundation for the diagnosis and prevention of Aeromonas infections in aquaculture.},
}

@article {pmid42454784,
year = {2026},
author = {Benlaïfaoui, M and Richard, C and Hunter, S and Méndez-Salazar, EO and Kourtian, S and Malo, J and Prifti, DK and Ponce, M and Khalfi, S and Belkaïd, W and Messaoudene, M and Boidot, R and Truntzer, C and Girhinghelli, F and Lehoux-Duboix, C and Ancuta, P and Elkrief, A and Marcil, V and Routy, B},
title = {Dietary intervention through bacterial-derived butyrate elicits anti-tumor activity and increases anti-PD-1 response.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2699457},
doi = {10.1080/19490976.2026.2699457},
pmid = {42454784},
issn = {1949-0984},
mesh = {Animals ; Humans ; Mice ; *Butyrates/metabolism/administration & dosage ; *Gastrointestinal Microbiome ; CD8-Positive T-Lymphocytes/immunology/drug effects ; *Programmed Cell Death 1 Receptor/immunology/antagonists & inhibitors ; Inulin/administration & dosage ; *Bacteria/metabolism/classification ; *Carcinoma, Non-Small-Cell Lung/immunology/therapy ; *Lung Neoplasms/immunology ; Mice, Inbred C57BL ; Dietary Supplements ; CD4-Positive T-Lymphocytes/immunology ; Female ; Dietary Fiber ; Fatty Acids, Volatile ; },
abstract = {The gut microbiome is increasingly recognized as a key modulator of cancer immunotherapy efficacy. Given that diet is one of the most important determinants of the gut microbiome composition and function, nutritional strategies have emerged as promising tools to modulate anti-tumor immune responses. Here, we demonstrate that dietary supplementation with inulin reduces tumor growth and enhances αPD-1 efficacy in mice. These effects were associated with increased frequencies of intra-tumoral CD8[+] and CD4[+] T cells, particularly CCR9[+]CXCR3[+] subsets, and enrichment of beneficial taxa such as Akkermansia and Lachnospiraceae, alongside elevated short-chain fatty acids (SCFA) levels. Among the SCFA, butyrate alone recapitulated the anti-tumor effect of inulin and had an additive effect when combined with αPD-1 therapy in a CD8[+] T cell-dependent manner. Butyrate exerted its anti-tumor effects by transcriptional changes in CD8[+] T cells involving activation of proliferation, trafficking, and metabolic pathways. In a cohort of 117 non-small cell lung cancer (NSCLC) patients amenable to immunotherapy, the median dietary fiber intake was lower than previously published studies but correlated with enrichment of Faecalibacterium praunitzii and metabolic pathways related to sucrose degradation and tryptophan biosynthesis. Collectively, our findings highlight the therapeutic potential of targeting diet-microbiome-immune system interactions to improve cancer immunotherapy outcomes.},
}

Animals
Humans
Mice
*Butyrates/metabolism/administration & dosage
*Gastrointestinal Microbiome
CD8-Positive T-Lymphocytes/immunology/drug effects
*Programmed Cell Death 1 Receptor/immunology/antagonists & inhibitors
Inulin/administration & dosage
*Bacteria/metabolism/classification
*Carcinoma, Non-Small-Cell Lung/immunology/therapy
*Lung Neoplasms/immunology
Mice, Inbred C57BL
Dietary Supplements
CD4-Positive T-Lymphocytes/immunology
Female
Dietary Fiber
Fatty Acids, Volatile

@article {pmid42454911,
year = {2026},
author = {Bellar, A and Sangwan, N and Miller, A and Kumar, A and Jaramillo, T and Mishra, S and Kannan, P and Attaway, A and Mishra, L and Welch, N and Dasarathy, S},
title = {Voluntary wheel running modulates murine gut microbiome during hyperammonemic stress.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0319425},
doi = {10.1128/spectrum.03194-25},
pmid = {42454911},
issn = {2165-0497},
abstract = {Exercise modulates multiple physiological systems, including skeletal muscle and the gut microbiome (GMB). Ammonia, a microbiome-derived cytotoxic metabolite, causes cellular hyperammonemic stress (HAS) in chronic diseases. We investigated the impact of voluntary wheel running (VWR) on GMB during HAS in a mouse model. Male C57BL/6J mice were randomized to treatment with either ammonium acetate (AmAc) (2.5 mmol/kg/day) or vehicle for 6 weeks. Stool 16S rRNA sequencing was performed at baseline, pre-intervention, and post-intervention. GMB diversity, taxa-level abundance, and correlation analyses were performed. Overall GMB composition remained stable between baseline and pre-intervention across groups (r > 0.57; P < 0.001). Following interventions, VWR or usual activity (UA), alpha-diversity was highest in AmAc-treated, specifically AmAc-VWR, mice. Eubacterium xylanophilum was reduced in AmAc-UA vs other groups (P < 0.05). Akkermansia abundance declined over time in UA mice, but in AmAc-VWR mice, this depletion was reversed (P = 0.002). Clostridium sensu stricto 1 and Eubacterium ventriosum were increased in AmAc-VWR mice (P < 0.05). Correlation analysis revealed high stability in PBS-UA (r = 0.667; P < 0.001), moderate restructuring in AmAc-VWR (r = 0.566; P < 0.001), and PBS-VWR (r = 0.385; P = 0.0099). HAS-induced GMB instability, with loss of beneficial taxa, including short-chain fatty acid-producing bacteria, was partially ameliorated by VWR. Exercise-mediated GMB modulation may be a strategy to mitigate HAS-induced complications in chronic diseases.IMPORTANCEVoluntary exercise is recommended in chronic diseases to improve outcomes, but biological responses in disease are not well characterized. Perturbations in the metabolism of ammonia, a microbiome-generated toxin, occur in chronic diseases that can be compounded by muscle-generated ammonia during exercise. Exercise-induced molecular responses are adversely affected by hyperammonemic stress of chronic diseases, including liver cirrhosis. We investigated gut microbiome changes during voluntary wheel running, which replicates human endurance exercise in a preclinical mouse model of hyperammonemia. Adverse impacts of Hyperammonemic stress included a reduction in short-chain fatty acid producers that were reversed by voluntary wheel running. Our data lay the foundation for future studies on how endurance-type exercise promotes a favorable gut microbial composition and strategies to use exercise as a regulator of hyperammonemic stress via targeting the gut microbiome.},
}

@article {pmid42454930,
year = {2026},
author = {Vogt, B and Kazarina, A and Sytsma, J and Adams, B and Rodela, L and Keller, R and Thompson, D and Winters, H and Jumpponen, A and Johnson, L and Lee, STM},
title = {Plant influence shapes Andropogon gerardii rhizobiome assembly strategies in response to decreasing precipitation.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0283225},
doi = {10.1128/spectrum.02832-25},
pmid = {42454930},
issn = {2165-0497},
abstract = {Predicted changes in precipitation threaten tallgrass prairies by altering microbial communities essential for plant resilience. Andropogon gerardii, a dominant tallgrass, spans the North American precipitation gradient. However, it remains unclear to what extent the rhizosphere microbiomes (rhizobiomes) are influenced by the plant-host-environmental interaction. To assess how environmental and host influences shape the rhizobiome, we surveyed A. gerardii populations across 25 remnant prairie sites within its native range in the United States, characterizing the microbiomes in the rhizosphere and soils using 16S amplicon sequencing. We demonstrated that while geographic location was the primary driver of community structure of both rhizosphere and soil communities, regional precipitation emerged as an influential determinant of the microbial community assembly. We observed distinct microbial divides across the dry and wet regions of the North American "arid-humid divide." Importantly, we found compelling large-scale evidence that regional precipitation has a profound influence on rhizobiome assembly. In the most arid regions, rhizosphere microbial communities exhibited significantly greater compositional convergence than local soil communities and harbored distinct, enriched sub-populations of taxa previously associated with host-benefiting functions. Our study aims to lay the groundwork for future investigations into the functional pathways through which limited precipitation shapes rhizobiome assembly, and how these effects are further impacted by host influence and local adaptation.IMPORTANCEIn this study, we conducted a biogeographical survey of the native tallgrass species Andropogon gerardii across 25 remnant prairie sites spanning the contiguous United States. Using 16S rRNA amplicon sequencing, we analyzed microbial communities from both local soils and plant-associated rhizobiomes. Our results demonstrate that regional precipitation is an influential driver of microbial community assembly, with clear compositional shifts observed across the 100[th] meridian, the North American "arid-humid divide." Critically, in the most arid locations, rhizobiomes converged toward a more homogeneous community structure, with both βNTI and RCBray indicating more deterministic assembly, consistent with intensified selective filtering under limited precipitation. These patterns establish a framework for future work to dissect the specific host and microbial mechanisms that enforce deterministic community assembly under precipitation stress.},
}

@article {pmid42454934,
year = {2026},
author = {Gonzalo, M and Liu, X and Dufour, YS and Shade, A},
title = {MATRIX: rapid quantification of total and active microbial cells with single-cell phenotypes for environmental microbiomes.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0030826},
doi = {10.1128/msystems.00308-26},
pmid = {42454934},
issn = {2379-5077},
abstract = {UNLABELLED: Quantifying the abundance and activity of bacteria within populations and communities is fundamental to systems microbiology and microbiome research. Yet direct microscopic cell counting remains low throughput, labor-intensive, and prone to user variability, leading many researchers to rely on indirect proxies such as optical density or multicopy marker-gene quantification. These indirect approaches do not distinguish between active and inactive cells and can obscure ecological interpretation. Here, we introduce microbial activity and total cell quantification via rapid imaging and extraction (MATRIX), an efficient workflow that integrates sample extraction, fluorescence staining, microscopy and automated image analysis, and Bayesian statistical inference to quantify total and redox-active cells and derive single-cell measurements for environmental bacterial populations and communities. We demonstrate its reproducibility and versatility using both cultured isolates and high-diversity soil communities. The resulting quantitative, phenotypic data sets provide rapid, direct measurements of bacterial population and community size and activity, enabling well-powered analyses that strengthen mechanistic insight into microbial responses and improve the ecological grounding of microbiome studies.

IMPORTANCE: Microbiome studies commonly rely on relative abundance data, which cannot distinguish whether compositional shifts reflect true population growth, declines in total community size, or both. Without explicit measurements of population and community sizes, the mechanistic interpretation of microbiome dynamics remains incomplete. Here, we present a rapid, throughput workflow, microbial activity and total cell quantification via rapid imaging and extraction (MATRIX), that quantifies both total and redox‑active bacterial cells from environmental samples. By integrating single‑cell phenotypes with community‑level metrics, this approach anchors microbiome data sets in direct ecological accounting rather than proxies. These measurements can clarify whether the observed changes in community structure represent shifts in abundance, activity, or both, improving inference about microbial responses to stress or environmental change. MATRIX offers an efficient way to incorporate quantitative ecology into systems microbiology and microbiome studies and to strengthen the link between microbial cellular physiology, community dynamics, and ecosystem function.},
}

@article {pmid42454945,
year = {2026},
author = {Oworae, KO and Rabacal, W and Hu, A and Wychrij, DA and Rayens, E and Chapman, TI and Bahl, J and Norris, KA},
title = {Evaluating the impact of immunization with the "pan-fungal" vaccine, NXT-2, on the gut mycobiome and microbiome in non-human primates (NHPs).},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0104726},
doi = {10.1128/spectrum.01047-26},
pmid = {42454945},
issn = {2165-0497},
abstract = {Fungal infections remain a significant public health concern with high mortality, morbidity, and increasing associated health costs. This burden is projected to rise due to expansion of at-risk populations, limited therapeutics, increasing drug resistance, and the emergence of new fungal pathogens. Even with these challenges, there are currently no approved vaccines. We previously developed a "pan-fungal" vaccine candidate, NXT-2, that confers protection against multiple invasive fungal infections such as pulmonary aspergillosis, pneumocystosis, and invasive candidiasis, as well as non-invasive vulvovaginal candidiasis. NXT-2 is a 90 amino acid consensus peptide designed from a conserved region of the fungal antigen (KEX1). We assessed the effect of NXT-2 immunization on gut microbial diversity, composition, and functional capacity in non-human primates. To do this, we monitored changes in the gut mycobiome and microbiome pre- and post-vaccination using ITS2 and metagenomic sequencing, respectively, in Japanese and rhesus macaque cohorts. NXT-2 elicited a robust antibody response without disrupting the gut microbial communities in both macaque species. The mycobiome exhibited stability with no significant changes in alpha and beta diversity, taxonomic composition, or functional guild distributions. The relative abundance of gut resident Candida and Aspergillus species remained stable and was not significantly altered following vaccination. The microbiome showed stability with preserved alpha and beta diversities, taxonomic composition, and functional capacity. Results from this study show the first cross-kingdom analysis demonstrating that antifungal vaccination can achieve protective immunity without perturbing gut microbial communities. This establishes a framework for microbiome-informed vaccine assessment beyond conventional immunogenicity and adverse effect monitoring.IMPORTANCEFungal infections cause millions of deaths annually, yet no vaccines are approved despite growing drug resistance and limited treatment options. NXT-2 is a pan-fungal vaccine that protects against multiple fungal infections such as pneumocystosis, candidiasis, and aspergillosis. Here, we demonstrate in NHPs that NXT-2 elicits robust protective antibody responses without altering gut bacterial or fungal communities. This is the first study to assess antifungal vaccination across both microbial kingdoms and establish that protective antifungal immunity can be achieved while preserving resident microbiota. This work provides a framework for incorporating microbiome assessment into vaccine development beyond conventional immunogenicity and adverse event monitoring.},
}

@article {pmid42454959,
year = {2026},
author = {Stern, L and Ter Horst, AM and Simpson-Johnson, KE and Gaudin, ACM and Emerson, JB},
title = {Host community activity, but not always composition, explains viral biogeography in bulk and rhizosphere soils over a tomato growing season.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag189},
pmid = {42454959},
issn = {1751-7370},
abstract = {The soil microbiome is key to plant health and nutrient acquisition, and viruses likely play important but largely unknown roles in these processes. To interrogate bulk and rhizosphere soil viral biogeography, we collected samples over a tomato growing season in California from an experiment testing arbuscular mycorrhizal fungi (AMF) treatment. We generated 78 viromes, 16S rRNA gene, and ITS1 amplicon datasets, and 33 rhizosphere metatranscriptomes. Of 67,038 DNA viral 'species' genomes (vOTUs), 25% were previously identified, predominantely in agricultural systems, suggesting habitat filtering and greater viral homogeneity across agricultural compared to natural soils globally. Rhizospheres had significantly higher DNA viral richness than bulk soils, whereas no significant richness differences were observed for other biota. 60% of vOTUs were shared between compartments, compared to only 21-23% of bacterial and fungal taxa. Although bulk soil viral biogeography resembled that of prokaryotes, with significant structuring by moisture content, greater virome similarity between high-moisture bulk soils and rhizospheres suggests that conditions with high host activity selected for similar viral communities. In rhizospheres, while bacterial and fungal communities differed most over time, DNA and RNA viral communities differed most by sampling location, matching prokaryotic transcriptional patterns and further implicating host activity in viral biogeography. Similarly, AMF treatment induced changes in the prokaryotic transcriptome but, across biota, only significantly affected DNA viral communities. Overall, results indicate strong viral responses to spatiotemporally localized conditions, with viral biogeography reflecting both dispersal opportunities (high between neighboring bulk and rhizosphere soils, low across fields) and selection via local host activity.},
}

@article {pmid42455161,
year = {2026},
author = {Zuberbier, T and Bonnekoh, H and Kocatürk, E and Kolkhir, P and Lionnet, L and Muñoz, M and Stevanovic, K and Metz, M},
title = {Insights into Pathogenesis of Chronic Spontaneous Urticaria.},
journal = {The British journal of dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1093/bjd/ljag277},
pmid = {42455161},
issn = {1365-2133},
abstract = {Chronic spontaneous urticaria (CSU) is a mast cell-mediated inflammatory disease marked by recurrent wheals and/or angioedema in the absence of identifiable external triggers. Once considered idiopathic, CSU is now recognized as a heterogeneous immunological disorder that results in mast cell activation. Two major endotypes have been described: autoallergic (type I) CSU, mediated by IgE autoantibodies directed against self-antigens, and autoimmune (type IIb) CSU, mediated by IgG autoantibodies targeting IgE or FcεRI on mast cells and basophils. Type IIb CSU is associated with higher disease severity, autoimmune comorbidities, low total IgE levels, and reduced responsiveness to antihistamines and omalizumab. Beyond classical autoantibody-mediated mechanisms, increasing evidence supports the contribution of non-IgE-dependent pathways in CSU pathogenesis. These include Mas-related G protein-coupled receptor X2 (MRGPRX2) - mediated mast cell activation, neuroimmune interactions, activation of coagulation and complement cascades, and persistent low-grade inflammation. Alterations of the gut microbiome and impaired barrier function have also been implicated in sustaining systemic immune activation and lowering mast cell activation thresholds in subsets of patients. Recent therapeutic advances, including biologics targeting type 2 inflammation and small-molecule inhibitors of intracellular signaling pathways such as Bruton's tyrosine kinase, highlight the clinical relevance of these mechanistic insights. However, a substantial proportion of patients remain inadequately controlled, underscoring the need for improved biomarkers, refined endotype stratification, and disease-modifying treatment strategies. This review summarizes current insights into the multifactorial pathophysiology of CSU, highlights remaining knowledge gaps, and discusses how emerging concepts may inform more precise, personalized, and potentially disease-modifying therapeutic approaches.},
}

@article {pmid42455235,
year = {2026},
author = {Radaelli, E and Palladino, G and Leuzzi, D and Scicchitano, D and Rampelli, S and Turroni, S and Randhawa, HS and Candela, M},
title = {Unraveling the Influence of Behavioural Ecotypes on Fish Gut Microbiome: Focus on the Atlantic cod (Gadus morhua) in Icelandic Waters.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02832-0},
pmid = {42455235},
issn = {1432-184X},
abstract = {This study investigated the gut microbiome of Atlantic cod in northern Icelandic waters to assess how resident (coastal) and migratory (frontal) behavioural ecotypes influence gut microbial community composition, with a focus on the effects of ecological adaptation and the potential drivers of microbial shifts within this species. A total of 81 intestinal samples from coastal and frontal Atlantic cod collected in northern Iceland in December 2021 and January 2024 were analysed using 16S rRNA gene metabarcoding. Environmental datasets from the Copernicus Marine Service were used to assess the relationship between annual shifts in microbiome composition and changes in environmental conditions. Our results highlight that the Icelandic cod gut microbiome is a highly dynamic system primarily shaped by environmental shifts, such as warming trends and anthropogenic stressors. Because different behavioural ecotypes are inherently exposed to distinct environmental configurations, these distinct macro-scale exposures may indirectly translate into ecotype-specific microbial signatures that shape the differentiation between coastal and offshore habitats; the effects were particularly evident in the coastal populations, underscoring the greater vulnerability of nearshore habitats to environmental shifts and anthropogenic stressors. These findings suggest the role of the microbiome in ecological plasticity of Atlantic cod; concurrently, they reveal distinct ecotype-specific sensitivities to environmental shifts, particularly those of anthropogenic origin, providing a valuable framework that may support future marine conservation strategies.},
}

@article {pmid42455447,
year = {2026},
author = {Zakrzewska, Z and Boruta, O and Skupień, D and Skoczeń, S},
title = {Microbiome and peptide alterations in children with acute lymphoblastic leukemia: current insights and future directions.},
journal = {Discover oncology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s12672-026-05551-7},
pmid = {42455447},
issn = {2730-6011},
abstract = {Acute lymphoblastic leukemia (ALL) is the most common type of pediatric leukemia, yet the mechanisms of leukemogenesis remain incompletely comprehended. Since the concept of brain-gut-microbiome has been established, microbiota dysbiosis has been considered to potentially impact on development of this cancer. This review focuses on microbiome and peptide alterations. In ALL pediatric patients during the time of diagnosis significant differences in comparison to healthy children were noted. While treatment and prophylaxis used in this group of patients is known to have an impact on gut microbiome, some changes in bacteria abundances could serve as predictors for infectious complications (e.g. Bifidobacterium longum), however it is not a standard practice. Probiotic supplementation with Bifidobacterium breve or Lactobacillus rhamnosus could reduce adverse symptoms of chemotherapy, but the legitimacy of their use in immunocompromised patients is controversial. Introducing new strategies, such as fecal microbiota transplantation (FMT) could lead to improvement in patients' outcomes in ALL treatment. The interaction between metabolic hormones, peptides and interleukins seems to be crucial for cancer cell metabolism and proliferation as well as immune regulation, inflammation and treatment response. Moreover, gut microbiota does not fully recover in the first year after treatment and even asymptomatic adult survivors of childhood ALL were found to have significantly altered abundances of bacteria species.},
}

@article {pmid42455612,
year = {2026},
author = {Peng, YY and Elsheikha, HM and Xun, Y and Liu, YL and Zhang, Y and Deng, YP and Hu, SF and Fu, YT and Liu, GH},
title = {Peribacillus suis sp. nov. Isolated From the Pig Louse Haematopinus suis Reveals Unexpected Pathogenic Potential in a Traditionally Benign Genus.},
journal = {Transboundary and emerging diseases},
volume = {2026},
number = {1},
pages = {e8640992},
doi = {10.1155/tbed/8640992},
pmid = {42455612},
issn = {1865-1682},
support = {32473057//National Natural Science Foundation of China/ ; 2024YFD1800103//National Key Research and Development Program of China/ ; 2025RC1053//Science and Technology Innovation Program of Hunan Province/ ; 2024JJ6548//Hunan Natural Science Foundation Youth Fund Project/ ; },
mesh = {Animals ; *Swine Diseases/parasitology/microbiology ; Phylogeny ; Swine ; Virulence ; *Lice Infestations/veterinary/parasitology ; Mice ; *Anoplura/microbiology ; },
abstract = {The pig sucking louse Haematopinus suis is a major swine ectoparasite and vector of pathogens, yet its microbiome remains understudied. Here, we described the isolation of a previously unrecognized bacterial strain, P8-9[T], from the intestinal tract of H. suis. A comprehensive polyphasic analysis, including phenotypic characterization, phylogenomics, and whole-genome comparisons, placed this isolate within Peribacillus. Genome-based metrics confirmed its novelty, with average nucleotide identity and digital DNA-DNA hybridization values (<80% and <27%, respectively) falling far below accepted species delineation thresholds. We, therefore, proposed the designation Peribacillus suis sp. nov. Unexpectedly, the genome of P8-9[T] encodes an extensive repertoire of 219 putative virulence-associated and antibiotic resistance genes; features atypical for a largely composed of environmental species considered saprophytic or beneficial. In vivo experiments revealed this pathogenic potential: intraperitoneal inoculation in mice resulted in all animals reaching predefined humane endpoints within 24 h, characterized by septicemia and widespread organ pathology, while oral exposure elicited splenomegaly, intestinal pathology, and a robust pro-inflammatory response. This work represents the first report of a Peribacillus species isolated from an ectoparasite and provides direct experimental evidence of virulence within a genus traditionally viewed as benign.},
}

Animals
*Swine Diseases/parasitology/microbiology
Phylogeny
Swine
Virulence
*Lice Infestations/veterinary/parasitology
Mice
*Anoplura/microbiology

@article {pmid42455624,
year = {2026},
author = {Signorelli, T and Walker, M and Robertson, J and Quizon, K and Zhang, Y and Reimer, AR and Eagle, SHC},
title = {Benchmarking DNA extraction protocols across use cases for culture-independent Nanopore metagenomics.},
journal = {Microbial genomics},
volume = {12},
number = {7},
pages = {},
doi = {10.1099/mgen.0.001738},
pmid = {42455624},
issn = {2057-5858},
mesh = {*Metagenomics/methods ; *Nanopore Sequencing/methods ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; *DNA, Bacterial/isolation & purification/genetics ; Humans ; Microbiota/genetics ; Feces/microbiology ; Nanopores ; *DNA/isolation & purification ; },
abstract = {Oxford Nanopore Technologies (ONT) sequencing offers several advantages for metagenomics, including long reads, rapid turnaround, low upfront cost, scalability and portability. However, for ONT metagenomics, DNA yield, quality and integrity are important considerations when selecting an extraction method. Many metagenomic extraction methods use harsh lysis conditions to extract a wide range of species and provide an accurate community composition, but these conditions can compromise DNA fragment length. Therefore, extraction methods for ONT metagenomics must balance DNA shearing and recovery with representative community lysis. We systematically evaluated DNA extraction methods for ONT metagenomic sequencing using a use case-oriented framework. Among nearly 50 extraction methods screened, 7 were selected for detailed comparison based on suitability for metagenomics, variation in methodology, availability, cost and processing time: Norgen BioTek Corp's Stool DNA Isolation (NG), Zymo Research's ZymoBIOMICS Quick-DNA HMW MagBead (ZMG), Qiagen's DNeasy Blood and Tissue (QBT), Macherey-Nagel's NucleoMag DNA Microbiome (MN), Zymo Research's ZymoBIOMICS DNA Mini Prep (ZMI), Qiagen's DNeasy PowerSoil/QIAamp PowerFecal Pro (PS) and Qiagen's QIAamp Fast DNA Stool Mini (QIA). Methods were tested using Zymo Research's ZymoBIOMICS Microbial Community Standard (MCS), a matrix-free mock community with known composition. DNA extracts were sequenced on an ONT PromethION using the Rapid Barcoding Kit, except QIA due to insufficient DNA yield. Metrics for the method, DNA extracts, sequencing and genomes were evaluated, revealing trade-offs between methods. The two magnetic bead methods, MN and ZMG, produced the highest mean read length N50 values (13.9 and 16.5 kb, respectively) but showed apparent community compositions skewed towards Gram-negative bacteria. In contrast, ZMI and PS maintained a community composition close to expected, with reduced mean read length N50 values (4.5 vs. 7.5 kb). Performance across various metrics is presented in the context of the following use cases: maximizing genome coverage and assembly completeness, preserving composition accuracy, targeting specific species and limiting required resources (equipment, time or budget). The metrics and use case considerations presented offer practical guidance for informed selection of DNA extraction methods for ONT metagenomics. For accurate community composition, ZMI or PS are recommended, while PS and ZMG perform best at maximizing genome coverage and assembly completeness. NG and QBT may be the most economical options, though performance trade-offs were observed. Finally, PS may be the preferred method for time-sensitive diagnostic or field applications.},
}

*Metagenomics/methods
*Nanopore Sequencing/methods
Sequence Analysis, DNA/methods
High-Throughput Nucleotide Sequencing/methods
Benchmarking
*DNA, Bacterial/isolation & purification/genetics
Humans
Microbiota/genetics
Feces/microbiology
Nanopores
*DNA/isolation & purification

@article {pmid42455639,
year = {2026},
author = {Silva Cerqueira, AE and Holley, JC and Hatcher, SC and Vidigal, PMP and Phillips, LE and Moran, NA},
title = {Neffella xylocopae gen. nov., sp. nov., a novel host-specific gut symbiont of Xylocopa carpenter bees in the family Orbaceae.},
journal = {International journal of systematic and evolutionary microbiology},
volume = {76},
number = {7},
pages = {},
doi = {10.1099/ijsem.0.007119},
pmid = {42455639},
issn = {1466-5034},
mesh = {Animals ; Bees/microbiology ; *Phylogeny ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry/analysis ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Base Composition ; Bacterial Typing Techniques ; *Symbiosis ; *Gastrointestinal Microbiome ; },
abstract = {Bee-associated Orbaceae species aid in the metabolism of plant polysaccharides, toxic sugars and urea and stimulate the immune system. In honeybees and other eusocial bees, microbial transmission occurs through hive contact and social interactions, favouring the emergence of host-specific strains. While most solitary bees acquire their microbiota from the environment, large carpenter bees (genus Xylocopa) exhibit facultative or incipient social behaviour that might enable direct transmission. This behaviour might have contributed to host specialization of Xylocopa-associated bacteria, such as the genus Xylocopilactobacillus and novel species belonging to the genus Lactobacillus and the family Bifidobacteriaceae. Evidence of an apparent Xylocopa-specific Orbaceae clade has also been observed. Here, we isolated and characterized AC157Xtp[T], a novel strain in the family Orbaceae, from the gut of Xylocopa tabaniformis parkinsoniae. The optimal growth occurs anaerobically at 30-35°C, 0-0.5% salinity and pH 6-7. The predominant fatty acids were C18:1 ω6c and/or C18:1 ω7c (45.9%), followed by C16:0 (35.0%) and C14:0 (7.8%), consistent with those reported for members of the family Orbaceae. The cell size of AC157XtpT was ~0.5-1.6 µm in length and 0.4-0.7 µm in width, with coccoid to small rod-shaped morphology under scanning electron microscopy. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) scores between AC157Xtp[T] and other Orbaceae ranged from 69.99 to 72.88% for ANIb, from 0.59 to 0.83 for TETRA values and from 20.1 to 26.7% for dDDH, measures far below species thresholds. Combined with the average amino acid identity (AAI) and percentage of conserved proteins (POCP) at the lower end of the Orbaceae-specific genus boundary range, and the phylogenomic tree placing AC157Xtp[T] in a separate monophyletic clade sister to Orbus and Frischella, these data support the classification of AC157Xtp[T] as a representative of a novel genus within the family Orbaceae. In conclusion, AC157XtpT (=NCIMB 15593T=ATCC TSD-486[T]) represents the type strain of Neffella xylocopae gen. nov., sp. nov. The GenBank accession numbers are CP133583 (genome) and PQ456091 (16S rRNA gene).},
}

Animals
Bees/microbiology
*Phylogeny
RNA, Ribosomal, 16S/genetics
Fatty Acids/chemistry/analysis
DNA, Bacterial/genetics
Sequence Analysis, DNA
Base Composition
Bacterial Typing Techniques
*Symbiosis
*Gastrointestinal Microbiome

@article {pmid42455659,
year = {2026},
author = {Hirakawa, R and Hisamatsu, M and Maekawa, S and Asai, E and Ohta, M and Matsuo, A and Okano, K and Miyazaki, T and Akiyama, M and Toyomizu, M and Islam, J and Furukawa, M and Nochi, T},
title = {Bursa of Fabricius-independent B cells establish an IgA-mediated intestinal barrier that safeguards gut-liver homeostasis.},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {123},
number = {29},
pages = {e2605569123},
doi = {10.1073/pnas.2605569123},
pmid = {42455659},
issn = {1091-6490},
support = {22H00393//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21K19176//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K18073//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 23K19328//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 25K18344//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; },
mesh = {Animals ; *Immunoglobulin A/immunology/metabolism ; Homeostasis/immunology ; *Bursa of Fabricius/immunology/cytology ; *B-Lymphocytes/immunology/metabolism ; Chickens/immunology ; *Liver/immunology/metabolism ; Intestinal Barrier Function ; Receptors, CXCR4/metabolism ; },
abstract = {The bursa of Fabricius (BF), a specialized lymphoid structure in birds, regulates avian B-cell development. However, the BF starts to regress posthatching, suggesting that as-yet-unidentified structures assume this function during maturation. This study reveals that BF-independent B-cell genesis involving the gut cecal tonsils (CTs) predominates over the BF-dependent pathway posthatching. Although B-cell progenitors originating from the bone marrow (BM) typically migrate to the BF, we identified a population that instead migrates to the CTs through CXCL12/CXCR4-mediated chemotaxis. These BF-independent CXCR4[+] pre-B cells acquired surface IgM expression within the CT follicular region (FR) and differentiated into immunoglobulin A (IgA)-producing plasma cells. Inhibition of CXCR4[+] cell influx from the BM impaired formation of the FR, altered the responsiveness of intestinal IgA to commensal bacteria, promoted gut dysbiosis, allowed translocation of pathogenic bacteria (e.g., Streptococcus alactolyticus) to the liver, and ultimately caused hepatic inflammation and metabolic dysfunction. These abnormalities were reversed by administering an IgA-enriched fecal preparation derived from healthy chickens. Collectively, these results reveal the existence of a population of BF-independent B cells that function in CTs. These cells represent a promising target for maintaining and improving the immunological and microbiological environment of the avian intestinal tract, which is closely linked to hepatic homeostasis.},
}

Animals
*Immunoglobulin A/immunology/metabolism
Homeostasis/immunology
*Bursa of Fabricius/immunology/cytology
*B-Lymphocytes/immunology/metabolism
Chickens/immunology
*Liver/immunology/metabolism
Intestinal Barrier Function
Receptors, CXCR4/metabolism

@article {pmid42455761,
year = {2026},
author = {Li, XS and Wang, M and Wang, Z and Fan, B and Tian, MY and Filippazzo, J and Lee, Y and Mallela, DP and Mao, K and Liu, Y and Lemaitre, RN and Xie, V and Diaz, E and DiDonato, JA and Tang, WHW and de Oliveira Otto, MC and Budoff, MJ and Owens, AP and Newman, AB and Cameron, SJ and Siscovick, DS and Lusis, AJ and Mozaffarian, D and Hazen, SL},
title = {Gut microbe-generated metabolite trimethylamine N-oxide and risk of abdominal aortic aneurysm: a cohort study.},
journal = {European heart journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/eurheartj/ehag489},
pmid = {42455761},
issn = {1522-9645},
support = {/NH/NIH HHS/United States ; //Office of Dietary Supplements/ ; R01 HL167831/HB/NHLBI NIH HHS/United States ; R01 HL103866/HB/NHLBI NIH HHS/United States ; P01 HL147823/HB/NHLBI NIH HHS/United States ; R01HL158801/HB/NHLBI NIH HHS/United States ; R01-HL147171/HB/NHLBI NIH HHS/United States ; HHSN268201200036C/HB/NHLBI NIH HHS/United States ; HHSN268200800007C/HB/NHLBI NIH HHS/United States ; HHSN268201800001C/HB/NHLBI NIH HHS/United States ; N01HC55222/HB/NHLBI NIH HHS/United States ; N01HC85079/HB/NHLBI NIH HHS/United States ; N01HC85080/HB/NHLBI NIH HHS/United States ; N01HC85081/HB/NHLBI NIH HHS/United States ; N01HC85082/HB/NHLBI NIH HHS/United States ; N01HC85083/HB/NHLBI NIH HHS/United States ; N01HC85086/HB/NHLBI NIH HHS/United States ; 75N92021D00006/HB/NHLBI NIH HHS/United States ; U01HL080295/HB/NHLBI NIH HHS/United States ; U01HL130114/HB/NHLBI NIH HHS/United States ; R01HL172803/HB/NHLBI NIH HHS/United States ; R01AG023629/NS/NINDS NIH HHS/United States ; /AG/NIA NIH HHS/United States ; //CHS/ ; },
abstract = {BACKGROUND AND AIMS: Abdominal aortic aneurysms (AAAs) are associated with increased mortality in older adults. The gut microbe-generated metabolite trimethylamine N-oxide (TMAO) has been linked to AAA risk and promotes AAA progression in animal models. Whether circulating TMAO levels in apparently healthy older adults predict AAA development and adverse AAA outcomes remains unknown.

METHODS: Plasma TMAO levels were quantified using stable isotope dilution liquid chromatography-tandem mass spectrometry in 4442 community-dwelling adults (aged ≥65 years) in the Cardiovascular Health Study. Participants underwent ultrasound screening and prospective follow-up. Multivariable models assessed associations of serial TMAO levels with AAA development and incident risk for adverse AAA events, adjusting for traditional risk factors, renal function, socioeconomic status, and cardiometabolic lifestyle factors.

RESULTS: Higher baseline TMAO levels were associated with larger infrarenal aortic diameter and increased AAA risk. Over a median 12.2-year follow-up (54 402 person-years), 79 participants experienced incident adverse AAA events (repair, rupture, or AAA-related death). Elevated TMAO levels were independently associated with higher risk of adverse AAA events, whether modelled continuously [adjusted hazard ratio (HR) 1.28, 95% confidence interval (CI) 1.07-1.54 per doubling], by quantiles (HR for tertile 3 vs tertile 1: 2.46, 95% CI 1.32-4.59), or using a clinical threshold (≥6.2 µM; HR 1.93, 95% CI 1.25-2.99).

CONCLUSIONS: In community-based older adults, higher TMAO levels were independently associated with increased risk of AAA development and adverse AAA events. Findings support TMAO as a novel risk factor for AAA and a potential therapeutic target for AAA prevention.},
}

@article {pmid42455902,
year = {2026},
author = {Lu, YQ and Dai, JH and Duan, YF and Qin, GJ and Huang, SW and Lin, L and Tan, XR and Zhu, XH and He, QM and Wang, JY and Zhang, MY and Feng, SY and He, SW and Si, N and Wu, JQ and Lv, GL and Liang, YL and Li, JY and Gong, S and Li, YQ and Li, L and Ma, J and Yue, JX and Liu, N},
title = {Culturomics reveals Fusobacterium-Prevotella mutualism as a hallmark of nasopharyngeal tumor microbiota.},
journal = {Science translational medicine},
volume = {18},
number = {858},
pages = {eaec4847},
doi = {10.1126/scitranslmed.aec4847},
pmid = {42455902},
issn = {1946-6242},
mesh = {Humans ; *Microbiota/genetics ; *Symbiosis ; *Nasopharyngeal Neoplasms/microbiology ; *Fusobacterium/physiology/genetics/isolation & purification ; *Prevotella/physiology/genetics/isolation & purification ; Nasopharyngeal Carcinoma/microbiology ; Transcriptome/genetics ; },
abstract = {The nasopharynx constitutes a critical niche in the upper respiratory tract, harboring a diverse microbiota linked to nasopharyngeal carcinoma (NPC), the mechanistic roles of which remain poorly understood. Here, we established the Nasopharyngeal Mucosal and Tumor-resident Bacterial Catalog (NMTBC) that comprises 5311 bacterial isolates representing 127 species, with 1006 of them being fully sequenced and annotated, providing a comprehensive culturable resource facilitating mechanistic dissection of the microbiome-tumor interactions. With NMTBC, we uncovered a Fusobacterium-Prevotella mutualism and revealed heterotypic bacterium-bacterium interactions involving transcriptional reprogramming and metabolic cross-talk. Using single-bacterial transcriptomics, we mapped a high-resolution transcriptomic trajectory, showing the ability of a single strain to differentiate into functionally distinct subpopulations that cooperate to sustain mutualism. By analyzing a multicenter NPC cohort, we showed that Fusobacterium and Prevotella co-colonization in NPC tumors correlated with unfavorable clinical outcomes after conventional radiochemotherapy. Analysis of RNA-seq data from two previous phase 3 clinical trials showed that coenrichment of Fusobacterium-Prevotella predicted better response to anti-PD-1 immunotherapy, highlighting their important role in microbiota-mediated immunomodulation. Overall, this study establishes a comprehensive nasopharyngeal bacterial catalog through culturomics, which offers valuable insights into microbiome-derived biomarker discovery and immunotherapy patient stratification in clinical practice.},
}

Humans
*Microbiota/genetics
*Symbiosis
*Nasopharyngeal Neoplasms/microbiology
*Fusobacterium/physiology/genetics/isolation & purification
*Prevotella/physiology/genetics/isolation & purification
Nasopharyngeal Carcinoma/microbiology
Transcriptome/genetics

@article {pmid42456442,
year = {2026},
author = {Wills, OC and Chua, XY and McEvoy, C and Fitzmaurice, M and El-Assaad, F and El-Omar, E and Probst, Y},
title = {A case-control study of the oral microbiome among Australian female adults with relapsing-remitting multiple sclerosis: A pilot study.},
journal = {Multiple sclerosis and related disorders},
volume = {113},
number = {},
pages = {107383},
doi = {10.1016/j.msard.2026.107383},
pmid = {42456442},
issn = {2211-0356},
abstract = {BACKGROUND: There is growing evidence investigating the role of the gut microbiome in the onset and progression of multiple sclerosis (MS). However, the role of the oral microbiome in MS is poorly understood, despite its importance in immune regulation and systemic health.

METHODS: A cross-sectional, case-control, pilot study comparing the oral microbiome among adults with relapsing-remitting MS to matched controls based on age, sex and body mass index (BMI), was conducted. Participants provided fasting oral swabs where DNA was extracted and shotgun metagenomic sequencing performed. Comparative analyses between cases and controls explored alpha-and beta-diversities including differential abundance testing.

RESULTS: Across 24 oral microbiome samples, 355 species from 12 phylum were detected. Alpha diversity was lower in MS at the species level, however, did not reach statistical significance for either richness or Shannon diversity. Beta diversity demonstrated a significant difference using Bray-Curtis dissimilarity with group status accounting for ∼6.7% of the total variation in microbial community structure. Differential abundance testing highlighted Veillonella parvula as the most enriched species among cases (coef=2.56, stderr=0.74, FDR=0.17), while Porphyromonas pasteri (coef=-3.57, stderr=1.02, FDR=0.17) and s__GGB4936_SGB6889 (coef=-4.29, stderr=1.30, FDR=0.17) were predominant among controls.

CONCLUSION: The oral microbiome of Australian females with RRMS differs in a subtle but detectable manner from those without MS, characterised by a non-significant trend towards reduced microbial diversity and distinct compositional clustering based on Bray-Curtis dissimilarity. Findings support the emerging concept of an oral-immune axis in MS, underscoring the need for longitudinal and functional studies to explore causality.},
}

@article {pmid42456685,
year = {2026},
author = {Steriade, C and Segata, N and Saxena, D},
title = {The role of the gut microbiome in mediating neuroinflammation in immune-based neurological disorders.},
journal = {The Lancet. Neurology},
volume = {25},
number = {8},
pages = {764-780},
doi = {10.1016/S1474-4422(26)00193-6},
pmid = {42456685},
issn = {1474-4465},
abstract = {The gut microbiome can influence brain health by modulating neuroinflammation through various mechanisms, including immune regulation, the production of metabolites that affect neural function, gut and blood-brain barrier integrity, upstream effects via the vagus nerve, upstream migration of gut-resident lymphocytes to the brain, bile acid signalling, and endocrine activity. Changes in gut microbiota have been observed in demyelinating conditions, autoimmune encephalitis, and epilepsy. Gut microbiota composition changes can affect neuroinflammation, disease progression, and treatment outcomes. Advances in microbiome research have improved the potential for clinical translation of findings; but limitations persist, driven by the largely correlational nature of clinical studies and the complexity of microbiome sequencing and interpretation. At present, only the ketogenic diet is routinely recommended by clinicians, whereas other microbiome-based interventions remain investigational. Multiple strategies for manipulating the gut microbiome, including dietary changes, prebiotics, probiotics, postbiotics, and faecal microbiota transplantation, might be used as disease-modifying therapies in the future.},
}

@article {pmid42456720,
year = {2026},
author = {Liang, X and Deng, Y and Zhao, L and Zhou, X and Li, Z and Xiao, G and Chen, SS},
title = {From Dysbiotic Gut to Malodorous Mouth: Targeting Microbial Metabolism for Gastrointestinal type halitosis.},
journal = {Journal of breath research},
volume = {},
number = {},
pages = {},
doi = {10.1088/1752-7163/ae8b14},
pmid = {42456720},
issn = {1752-7163},
abstract = {This article reviews the microbiological mechanisms of halitosis, the oral-gut axis, the role of the gut microbiome, related metabolic pathways, and their associations with gastrointestinal diseases, and explores intervention strategies based on microbial regulation. Halitosis is primarily caused by volatile sulfur compounds produced by oral microorganisms, especially gram-negative anaerobic bacteria, and volatile organic compounds in most extraoral etiologies. Studies have found that intestinal microbial dysregulation can affect the composition of oral flora through the oral-gut axis and aggravate bad breath. Gastrointestinal diseases, such as gastroesophageal reflux disease,Helicobacter pyloriinfection, ulcerative colitis and irritable bowel syndrome can directly or indirectly promote the occurrence of bad breath by changing the intestinal microenvironment and microbial metabolic pathways, such as protein spoilage or short-chain fatty acids imbalance, etc. For microbial interventions, traditional Chinese medicine can not only systemically regulate the oral-gut axis balance, but also effectively alleviate bad breath by targeting sterilization and inhibiting the metabolic activity of pathogenic bacteria. This review focuses on elucidating the complex links between halitosis and the gut microbiome, its metabolic pathways, and gastrointestinal diseases, emphasizing the key role of microbial metabolites in pathological mechanisms. It reveals the importance of the oral-gut axis in systemic health and provides a rationale for developing personalized halitosis management strategies based on microbiome regulation.},
}

@article {pmid42456801,
year = {2026},
author = {Thiruvengadam, V and Karuppannasamy, A and Kesavan, S},
title = {Insecticide Resistance Beyond Genetics: Integrating Microbiomes, Machine Learning, and Emerging Molecular Technologies.},
journal = {Current opinion in insect science},
volume = {},
number = {},
pages = {101576},
doi = {10.1016/j.cois.2026.101576},
pmid = {42456801},
issn = {2214-5753},
abstract = {Insecticide resistance has become a serious and escalating threat to global agriculture, undermining food security, farmer livelihood, and environmental health. Resistance is now widespread across major pest groups, including Lepidoptera, Hemiptera, Diptera, and Coleoptera, and affects nearly all major classes of insecticides. This review presents the recent progress in understanding the evolution of insecticide resistance at molecular, ecological, and evolutionary levels, while highlighting how modern technologies are reshaping resistance management. Advances in genomics and multi-omics approaches have revealed novel resistance genes, epigenetic regulation, and microbiome-driven detoxification pathways, showing that resistance is often a complex, polygenic trait. At the same time, innovations in surveillance such as molecular diagnostics, machine learning-based prediction tools, and globally integrated resistance databases are shifting resistance monitoring from reactive detection to early warning and prediction. Emerging tools, including RNAi-based bioinsecticides, CRISPR-mediated gene editing, nanotechnology, and microbial interventions, offer promising alternatives to overcome entrenched resistance. The review also emphasises the growing role of precision pest management, enabled by digital agriculture and decision-support systems, in improving insecticide stewardship. Beyond science and technology, it critically examines policy and governance gaps and stresses the need for coordinated, One Health-oriented strategies to achieve sustainable, long-term insecticide resistance management.},
}

@article {pmid42456880,
year = {2026},
author = {Zheng, Y and Li, J and Yu, Y and Wang, W and Fan, X and Sun, L and Tang, L},
title = {The gut-microbiota-brain axis mediates the neuroprotective effects of exercise against microgravity-induced cognitive impairment.},
journal = {Experimental neurology},
volume = {},
number = {},
pages = {115930},
doi = {10.1016/j.expneurol.2026.115930},
pmid = {42456880},
issn = {1090-2430},
abstract = {OBJECTIVE: Prolonged exposure to microgravity is associated with gastrointestinal dysfunction and cognitive decline, both of which are critically regulated by the gut-microbiota-brain axis. This study aimed to investigate whether exercise mitigates microgravity-induced cognitive deficits by restoring gut homeostasis.

METHODS: The hindlimb unloading (HU) mouse model, a well-established ground-based analog of microgravity, was used in this study. HU mice underwent 4-week weight-loaded treadmill running. After the intervention, gut homeostasis, hippocampal neuroplasticity, and cognitive function were assessed. To establish causality, fecal microbiota transplantation (FMT) from exercised donor mice to HU recipient mice was performed.

RESULTS: HU mice exhibited gut microbial dysbiosis, increased circulating lipopolysaccharide (LPS) levels, reduced short-chain fatty acids (SCFAs), and impaired learning and memory. Exercise intervention restored intestinal barrier integrity by upregulating zonula occludens-1 (ZO-1) and Occludin, normalized gut microbiota composition and diversity, enhanced hippocampal neuroplasticity by increasing postsynaptic density protein 95 (PSD95), growth associated protein 43 (GAP43), phosphorylated cAMP response element-binding protein (P-CREB), and the brain-derived neurotrophic factor (BDNF)/ tropomyosin receptor kinase B (TrkB) pathway, and improved cognitive function. FMT from exercised donors to HU recipients recapitulated these benefits.

CONCLUTION: These results support that physical activity counteracts microgravity-induced neural dysfunction via the gut-microbiota-brain axis, suggesting that microbiome-targeted interventions may help preserve cognitive health in extreme environments such as spaceflight.},
}

@article {pmid42457178,
year = {2026},
author = {Vimonpatranon, S and Ssemaganda, A and Phuang-Ngern, Y and Sajjaweerawan, C and Saetun, P and Shakery, T and Sukhumvittaya, S and Rathore, S and Rerknimitr, R and Ehrenberg, PK and Eiser, D and Ratnaratorn, N and Trautmann, L and Choi, S and Severini, G and Thomas, R and Sacdalan, C and Pinyakorn, S and Ananworanich, J and Cowden, J and Hsu, D and Vasan, S and Phanuphak, N and McKinnon, LR and Schuetz, A and , },
title = {Impact of early antiretroviral treatment on tissue resident memory CD4+ T cells in the gastrointestinal tract.},
journal = {The Journal of infectious diseases},
volume = {},
number = {},
pages = {},
doi = {10.1093/infdis/jiag358},
pmid = {42457178},
issn = {1537-6613},
abstract = {BACKGROUND: Tissue resident memory CD4+ T cells (CD4+ TRM) are long-lived, seldom-circulating cells that reside for long periods in most tissues. TRM can mount rapid, antigen-specific responses to pathogens and contribute to mucosal barrier homeostasis by regulating commensal interactions. At the intestinal mucosa, the main site of early HIV replication, CD4+ TRM may serve as virus targets; however, limited data are available regarding their dynamics during acute HIV-1 infection and antiretroviral treatment.

METHODS: Nested cross-sectional study within a longitudinal cohort.

RESULTS: Sigmoid CD4+ TRM (CD69+CD103+) had a higher expression of CCR5 compared to CD4+ non-TRM (CD69-CD103-), suggestive of increased susceptibility to HIV-1 infection. Consistent with this, sigmoid CD4+ TRM but not CD4+ non-TRM were depleted/non-replenished despite long-term ART, regardless of the Fiebig (F) stage treatment was initiated during acute HIV infection. In contrast, overall sigmoid CD4+ T-cells were comparable in abundance with people living without HIV if treatment was initiated in FI/II, but were significantly decreased if treatment was initiated >FIII, suggesting preferential early depletion/non-replenishment of CD4+ TRM. The loss/non-replenishment of sigmoid CD4+ TRM was associated with a lower abundance of short-chain fatty acid producing commensal bacteria that are crucial for the maintenance of mucosal homeostasis, a higher abundance of opportunistic pathobionts Desulfovibrio, and increased soluble biomarkers of systemic inflammation that drive non-AIDS mortality.

CONCLUSION: Sigmoid CD4+ TRM may be early mucosal targets of HIV-1 infection and that their persistent depletion contributes to decreased mucosal barrier function, warranting development of therapeutic strategies that can restore CD4+ TRM during HIV treatment.},
}

@article {pmid42457309,
year = {2026},
author = {Völkerer, A and Wernly, S and Semmler, G and Flamm, M and Ausserwinkler, M and Horejs-Hoeck, J and Berger, A and Hofer, H and Aigner, E and Datz, C and Wernly, B},
title = {Association between Helicobacter pylori infection and colonic diverticulosis: a retrospective observational study in an asymptomatic Austrian endoscopy-based screening cohort.},
journal = {BMJ open gastroenterology},
volume = {13},
number = {1},
pages = {},
doi = {10.1136/bmjgast-2026-002450},
pmid = {42457309},
issn = {2054-4774},
abstract = {OBJECTIVE: Colonic diverticulosis is highly prevalent in ageing populations, yet the role of microbial factors remains unclear. Helicobacter pylori (HP) exerts systemic and microbiome-modulating effects and has been linked to extragastric inflammatory states, rendering an association with diverticulosis biologically plausible. However, this hypothesis has not been examined in asymptomatic screening populations with simultaneous endoscopic diverticulosis classification and histological HP confirmation. This study aimed to investigate whether HP infection is associated with colonic diverticulosis in an asymptomatic Austrian screening cohort.

METHODS: We performed a retrospective observational study of 5646 asymptomatic adults undergoing screening colonoscopy with concurrent oesophagogastroduodenoscopy (2007-2020). Diverticulosis was classified endoscopically by distribution; HP status was determined histologically from gastric biopsies. Multivariable logistic regression adjusted for metabolic, sociodemographic and lifestyle factors. A subset with follow-up colonoscopy (n=510) was analysed descriptively.

RESULTS: Diverticulosis was present in 37% of participants and HP infection in 19%. No association was found between HP infection and diverticulosis in univariable (OR 1.01, 95% CI 0.88 to 1.15; p=0.935) or fully adjusted analysis (OR 0.86, 95% CI 0.72 to 1.02; p=0.078), with an effect size too small to be clinically meaningful. Subgroup analyses by diverticular distribution and interaction analyses across age, sex, metabolic syndrome and lifestyle factors showed consistent null results. In the longitudinal subset, diverticulosis prevalence at follow-up did not differ by baseline HP status (63.9% vs 62.1%; p=0.749).

CONCLUSIONS: In this large screening cohort with simultaneous endoscopic and histological confirmation, HP infection was not associated with colonic diverticulosis across subtypes or risk strata. These findings do not support HP status as a clinically useful marker of asymptomatic diverticulosis. In future microbiome-focused studies of diverticulosis, HP infection may be best regarded as a potential confounder or marker of broader host, socioeconomic or healthcare-related factors.},
}

@article {pmid42457389,
year = {2026},
author = {Tang, X and Gu, Y and Wang, L and Wu, X and Ren, Y and Zhou, S and Cai, Y and Du, X and Xia, X and Zhang, T},
title = {Sarcopenia Predicts Postoperative Cognitive Impairment and Poor Surgical Outcomes in Older Adults: A Prospective Cohort Study.},
journal = {Journal of cachexia, sarcopenia and muscle},
volume = {17},
number = {4},
pages = {e70346},
doi = {10.1002/jcsm.70346},
pmid = {42457389},
issn = {2190-6009},
support = {24LHLNYX1-13//Foundation of Chengdu Medical College/ ; 24LHLNYX1-24//Foundation of Chengdu Medical College/ ; 2024-YF05-00911-SN//Chengdu Key R&D Support Program for Technological Innovation/ ; KY2022QN0289//Sichuan Medical health Promotion Association general project/ ; 2023540//Chengdu Medical Research Projects/ ; },
abstract = {BACKGROUND: Sarcopenia is a progressive skeletal muscle disorder prevalent in older adults, yet its role as a risk factor for acute postoperative cognitive decline-an early manifestation within the spectrum of perioperative neurocognitive disorders (PND)-remains underexplored. We hypothesize that preoperative sarcopenia increases the incidence of early postoperative cognitive impairment and adverse surgical outcomes in geriatric patients.

METHODS: This prospective cohort study enrolled 443 older adult patients (mean age 72.8 ± 5.8 years, 58.3% male) undergoing elective noncardiac surgery at a single centre in China. Preoperative sarcopenia was diagnosed according to the 2019 Asian Working Group for Sarcopenia (AWGS) criteria, which included assessments of muscle mass, strength, and physical performance. Neurocognitive function was assessed via the Mini-Mental State Examination (MMSE) 1 day before and 3 days after surgery, with acute cognitive decline defined as a postoperative decrease of ≥ 2 points. Of the 443 patients, 391 (88.2%) completed 6-month telephone follow-up for assessment of longer-term functional outcomes. In an exploratory subset of 60 patients, preoperative faecal samples underwent 16S rRNA sequencing and untargeted metabolomics to characterize gut microbial and metabolic signatures.

RESULTS: The prevalence of preoperative sarcopenia was 28.0% (124/443). Acute postoperative cognitive decline occurred in 27.3% (121/443) of patients. Multivariate logistic regression identified preoperative sarcopenia (adjusted OR = 3.291; 95% CI: 1.295-7.531; p < 0.001) and frailty (adjusted OR = 4.012; 95% CI: 1.854-8.456; p < 0.001) as independent risk factors for acute cognitive decline. Sarcopenic patients exhibited significantly higher rates of postoperative complications (adjusted RR = 1.21; 95% CI: 1.12-1.44; p = 0.025) and ICU admission (adjusted RR = 2.41; 95% CI: 1.03-4.41; p = 0.008). Among the 391 patients with complete 6-month follow-up, the sarcopenia group exhibited elevated risks of falls (adjusted RR = 2.89; 95% CI: 1.55-5.08; p = 0.028) and all-cause mortality (adjusted RR = 3.07; 95% CI: 1.17-7.87; p = 0.016). Exploratory microbiome analysis revealed an elevated Firmicutes/Bacteroidetes ratio, reduced Bacteroides abundance, and upregulated faecal stercobilin and estradiol derivatives in sarcopenic patients who developed cognitive decline.

CONCLUSION: Preoperative sarcopenia is an independent risk factor for acute postoperative cognitive impairment and poor surgical outcomes in older adults. These findings support the integration of sarcopenia screening into preoperative risk stratification and suggest a potential role of the gut-muscle-brain axis in perioperative neurocognitive vulnerability.},
}

@article {pmid42457551,
year = {2026},
author = {Wang, X and Umemoto, R and Kato, M and Hayakawa, T},
title = {Gut microbiome changes in a captive giant panda with cardiovascular disease.},
journal = {The Journal of veterinary medical science},
volume = {},
number = {},
pages = {},
doi = {10.1292/jvms.26-0042},
pmid = {42457551},
issn = {1347-7439},
abstract = {The interaction between gut bacteria and their host is vital for the early diagnosis and treatment of disease in captive animals. Here, we report a 16S rRNA sequencing-based bacterial profile during the progression of cardiovascular disease and drug treatment in a captive giant panda (Ailuropoda melanoleuca). We observed changes in the composition of bacteria associated with inflammation and regulating nutrient metabolism. Predicted metabolic functions also exhibited alterations. The remarkably reduced gut microbiome diversity, along with the imbalance in community interaction networks, indicated possible gut dysfunction. Our findings represent the first description of gut bacterial changes in a giant panda with cardiovascular disease. Maintaining symbiotic bacteria diversity is crucial for preventing health issues in captive animals and advancing wildlife conservation efforts.},
}

@article {pmid42457685,
year = {2026},
author = {Wei, L and Cui, Z and Mu, Z and Li, Y and Deng, F},
title = {Comparative fecal microbiome and metabolome reveal enhanced lignocellulose-degrading potential in Cervus elaphus yarkandensis.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-01002-3},
pmid = {42457685},
issn = {2396-8370},
support = {ygzbhly2025102//School-level project fund of Chongqing Medical and Pharmaceutical College/ ; QN[2025]100//Guizhou Provincial Basic Research Program (Natural Science) Youth Guidance Project/ ; },
abstract = {Reed is rich in lignocellulose and is therefore challenging for many ruminants to use efficiently. The endangered Tarim red deer subspecies Cervus elaphus yarkandensis (TH) inhabits the Tarim Basin, where reed represents an important forage resource, whereas captive observations suggest that the closely related Cervus elaphus songaricus (TS) may exhibit poorer tolerance to reed-rich diets. Here, we compared fecal microbial composition, metagenomic functional potential, metagenome-assembled genome (MAG)-level carbohydrate-active enzyme (CAZyme) profiles, fecal enzymatic activities, in vitro reed-straw degradation capacity, and fecal and serum metabolomic profiles between TH and TS under the same reed-containing feeding conditions. Compared with TS, TH showed higher fecal microbial diversity and increased abundances of fiber-associated taxa, including Ruminococcaceae, Lachnospiraceae, and Alistipes. Shotgun metagenomics and MAG-level CAZyme analysis indicated that TH-associated microbial communities carried a broader repertoire of functions related to lignocellulose degradation and plant-polysaccharide deconstruction. Consistent with these functional profiles, TH fecal samples exhibited higher cellulase and hemicellulase activities, and TH fecal inocula showed greater reed-straw degradation capacity than TS fecal inocula in vitro. Untargeted metabolomics revealed group-specific fecal and serum metabolites related to carbohydrate fermentation, short-chain fatty-acid-related metabolism, and lipid metabolism, which were associated with TH-enriched fiber-degrading taxa and microbial functional pathways. In an exploratory mouse colonization experiment, TH-derived fecal microbiota was associated with changes in fiber-associated microbial taxa, metabolic pathways, fecal metabolites, body weight, and intestinal morphology in antibiotic-treated mice fed a reed-containing diet. Together, these results indicate that TH harbors fecal microbial and metabolic features associated with enhanced lignocellulose and reed-straw degradation capacity. These findings suggest candidate microbiome-associated pathways relevant to reed-rich forage utilization and may help identify microbial and enzymatic resources for lignocellulose bioconversion.},
}

@article {pmid42443402,
year = {2026},
author = {Goya-Jorge, E and Antoine, C and Gonza, I and Al-Chihab, M and Thonart, P and Druart, G and Mascolo, CT and Leroy, B and Boutaleb, S and Douny, C and Scippo, ML and Delcenserie, V},
title = {Screening psychobiotic bacteria in the human colonic microbiota under high perceived stress.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-62011-6},
pmid = {42443402},
issn = {2045-2322},
support = {Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; Microbiostress Project - Grant Agreement No 8509//Gouvernement Wallon/ ; },
abstract = {Psychobiotic bacteria hold promise for modulating the gut-brain axis, particularly under stress-induced dysbiosis. In this study, nine psychobiotic formulations were evaluated using a novel simplified batch version (M-batches) of the Simulator of the Human Intestinal Microbial Ecosystem, including the mucosal compartment (M-SHIME[®]), inoculated with fecal samples from highly stressed donors. Several treatments, particularly those containing Heyndrickxia coagulans [ATB-BCS-042] with either Levilactobacillus (Lv.) brevis [THT-030-201] or Lactiplantibacillus plantarum [THT-030-702], led to significant increases in Bifidobacterium and Akkermansia muciniphila. Modulations in butyrate-producing taxa were observed with H. coagulans + Lactobacillus (L.) gasseri [THT-031-301] and Enterococcus faecium [ATB-EFM-030] + Lactobacillus helveticus [THT-031-102]. Combinations of H. coagulans with either Lv. brevis, L. gasseri, or Lactobacillus johnsonii [THT-032-401] facilitated lactobacilli colonization. Dopamine levels increased with E. faecium + Lacticaseibacillus (Lc.) paracasei [THT-031-901] and H. coagulans + L. johnsonii, whereas other metabolites, such as Short Chain Fatty Acids (SCFA) and ammonia, remained largely unchanged across treatments. Metabolic outputs also included aryl hydrocarbon receptor (AhR)-activating metabolites, with the strongest effect seen for H. coagulans + L. gasseri, suggesting involvement with stress-related host signaling pathways. Among all probiotics, cocktails containing H. coagulans with either Lv. brevis or L. gasseri produced the most consistent and multifaceted effects. These findings underscore psychobiotic formulations that enhance gut microbiota resilience and boost metabolites potentially influencing host pathways under stress. Using fecal microbiota from highly stressed donors offers a promising in vitro approach that better reflects stress-related gut ecosystems for translational microbiome-brain axis research.},
}

@article {pmid42443604,
year = {2026},
author = {Sezgin, G and Yuksel, A},
title = {Mechanisms and clinical evidence of dietary patterns in axial spondyloarthritis.},
journal = {Rheumatology international},
volume = {46},
number = {8},
pages = {},
pmid = {42443604},
issn = {1437-160X},
mesh = {Humans ; *Axial Spondyloarthritis/diet therapy ; Diet, Mediterranean ; Diet, Gluten-Free ; Quality of Life ; Gastrointestinal Microbiome ; },
abstract = {Axial spondyloarthritis (axSpA) is a chronic inflammatory disease that significantly impairs quality of life. Despite pharmacological advances, there is increasing interest in adjunctive nutritional interventions. This review evaluates the efficacy, mechanisms, and safety of dietary models-including low-starch, gluten-free, dairy-free, vegan/vegetarian, and Mediterranean diets-for axSpA management. A comprehensive literature search was conducted across Medline/PubMed, EMBASE, Scopus, Web of Science, and the Directory of Open Access Journals (DOAJ) databases for peer-reviewed articles published up to June 1, 2026. The search strategy utilized Boolean operators (AND, OR) to combine Medical Subject Heading (MeSH) terms and free-text keywords encompassing concepts of 'axial spondyloarthritis' and various dietary interventions (e.g., Mediterranean, gluten-free, and low-starch diets). Studies focusing on isolated nutrient supplementations without a broader dietary framework were excluded. Restrictive diets (e.g., low-starch or gluten-free) offer theoretical anti-inflammatory benefits via gut microbiota modulation but pose risks for unsupervised micronutrient deficiencies. While the Mediterranean diet is a feasible and safe option for general health, evidence for specific dietary interventions in axSpA remains limited and predominantly observational, with few randomized controlled trials available. Integrating personalized nutritional counseling into the multidisciplinary management of axSpA may help safely prevent deficiencies, optimize body weight, and improve patient well-being. However, current evidence remains insufficient to universally recommend a specific dietary model for axSpA.},
}

Humans
*Axial Spondyloarthritis/diet therapy
Diet, Mediterranean
Diet, Gluten-Free
Quality of Life
Gastrointestinal Microbiome

@article {pmid42443654,
year = {2026},
author = {Zhang, X and Zou, Y and He, XQ and Xu, YH and Li, HX and Yang, F and Zhang, BC and Liao, LX and Cao, MX and Wang, RX and Hao, SF and Wang, MM and Zhang, J and Pei, XF},
title = {Short-term hot spring balneotherapy ameliorates sleep disorders: wrist-worn wearable-assessed sleep improvement associated with neuroimmune, tryptophan metabolic and gut microbiome alterations.},
journal = {International journal of biometeorology},
volume = {70},
number = {7},
pages = {},
pmid = {42443654},
issn = {1432-1254},
support = {2021ZYSF006//Yibin Science and Technology Planning Program/ ; },
mesh = {Humans ; Male ; *Balneology ; Female ; *Gastrointestinal Microbiome ; *Sleep Wake Disorders/therapy/metabolism/microbiology/blood ; Adult ; *Tryptophan/metabolism/blood ; *Wearable Electronic Devices ; Middle Aged ; Cytokines/blood ; Pilot Projects ; Prospective Studies ; Neuroimmunomodulation ; Biomarkers/blood ; },
abstract = {Balneotherapy is a potential complementary approach for sleep problems, but its short-term sleep effects and accompanying biological changes remain unclear. We conducted a prospective single-arm, self-controlled pilot study of 30 adults with sleep disorders, who completed a 10-day residential hot spring balneotherapy program (twice daily at 09:00 and 20:00, 30 min per session, 40-42 °C) at Tianhe Hot Spring, Sichuan Province, residing on-site and receiving identical meals throughout the intervention. Sleep quality was assessed using the Pittsburgh Sleep Quality Index (PSQI) and wrist-worn wearable tracking. Serum neurotransmitters, inflammatory cytokines and tryptophan-kynurenine metabolites were assayed, while 16 S rRNA-based gut microbiota profiles were profiled pre- and post-intervention. Post-intervention, PSQI scores decreased, while wearable metrics indicated longer total and nocturnal sleep duration, elevated deep-sleep duration and proportion, better sleep continuity, and a lower rapid eye movement (REM) percentage (P < 0.05). Blood pressure, anxiety/depression scores, and wearable-derived sleep-stress indices also improved. Biomarker profiling revealed elevated GABA, 5-HT, 5-HIAA, BDNF, and IL-10, alongside reduced IL-1β, IL-6, and TNF-α (P < 0.05). Trp metabolism shifted, characterized by decreased Trp and increased 3-HAA and PA (P < 0.05). Structurally, the gut microbiota exhibited an increased abundance of Blautia_A (P < 0.05), with LEfSe analysis identifying post-intervention enrichment of Turicibacter and pre-intervention predominance of Agathobacter. Cross-system network analysis further established 5-HT, IL-6, and IL-10 as the core candidate biomarker profile directly correlating with these multi-domain sleep improvements. Overall, short-term residential hot spring balneotherapy may improve subjective and wearable-derived sleep outcomes, accompanied by coordinated cardiovascular, stress-related, neuroimmune, tryptophan-metabolic, and gut microbiome changes, supporting a multi-system physiological basis for balneotherapy-related sleep improvement.},
}

Humans
Male
*Balneology
Female
*Gastrointestinal Microbiome
*Sleep Wake Disorders/therapy/metabolism/microbiology/blood
Adult
*Tryptophan/metabolism/blood
*Wearable Electronic Devices
Middle Aged
Cytokines/blood
Pilot Projects
Prospective Studies
Neuroimmunomodulation
Biomarkers/blood

@article {pmid42443738,
year = {2026},
author = {Carasso, S and Gefen, T and Bakria, R and Bar-Yoseph, H and Geva-Zatorsky, N},
title = {Microbiome changes associated with FMT-mediated clearance of antibiotic-resistant Klebsiella pneumoniae in a murine carriage model.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05354-4},
pmid = {42443738},
issn = {1471-2180},
support = {grant 1571/17 and 3165/20//Israeli Science Foundation/ ; grant FL-000969/FL-001245/FL-001381//CIFAR Azrieli Global Scholars/ ; grant CDA00025/2019-C//Human Frontier Science Program Career Development Award/ ; ERC, ExtractABact, 101078712//the European Union/ ; },
abstract = {Carbapenem-resistant Enterobacterales (CRE), including Klebsiella pneumoniae (KP), pose a significant public health threat due to their resistance to last-line antibiotics. Eliminating CRE colonization in asymptomatic carriers is crucial to prevent the spread of resistance, as carriage often serves as a reservoir that enables the transmission of resistant strains to vulnerable populations. Fecal microbiota transplantation (FMT) has emerged as a potential strategy to restore gut microbiome balance and eliminate CRE colonization. However, the mechanisms driving successful decolonization warrant further research. This study investigates the impact of FMT on gut microbiome composition, CRE-KP clearance and host response, in a mouse model of CRE-KP carriage. Mice colonized with CRE-KP, were treated with FMT or left untreated. Shotgun metagenomics of fecal samples were used to monitor changes in microbiome composition and function. FMT resulted in substantial changes in the gut microbiome, with successful clearance correlating with an expansion of commensal bacteria including Bifidobacterium and Lactobacillus species. Notably, a reduction in K. pneumoniae was also observed in some untreated control mice as the microbiome recovered naturally, also associated with Bifidobacterium expansion. Phage profiling revealed distinct viral populations that were associated with successful decolonization. Flow cytometry was employed to quantify bacterial populations bound by immunoglobulins, providing insight into host immune modulation. These findings suggest potential mechanisms for CRE carriage eradication using microbiome targeted therapies. The results emphasize the importance of microbiome resilience in combating antibiotic-resistant infections and suggest that phage-microbiome interactions could play a role in restoring microbial balance.},
}

@article {pmid42443770,
year = {2026},
author = {Liao, L and Zhou, X and Li, X and Gu, W and Lu, K and Huang, H and Yang, S},
title = {Endophytic microbiota and metabolites profile in gynoecious versus monoecious cucumbers.},
journal = {BMC plant biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12870-026-09459-w},
pmid = {42443770},
issn = {1471-2229},
support = {Guike AB23026076//Guangxi Key Research and Development Program/ ; Barenke 20220005//the Special Project of Bama Industry-Education Integration Research Institute of Guangxi University/ ; },
abstract = {Sex expression in cucumber (Cucumis sativus L.) is a critical agronomic trait governing fruit yield and cultivation efficiency. Although its genetic and hormonal regulation is well-characterized, the role of endophytes and their metabolic interplay remains largely unexplored. In this study, an integrated approach, combining high-throughput sequencing of endophytic bacteria and fungi with untargeted metabolomics was conducted to investigate differences in endophytic community structure between gynoecious versus monoecious cucumbers. We found that gynoecious plants harbored bacterial communities with significantly higher richness, evenness, and a greater number of unique operational taxonomic units (OTUs) than monoecious plants, whereas fungal diversity was not significantly different. Although Proteobacteria, Actinobacteriota, and Firmicutes were dominant in both genotypes, gynoecious were uniquely enriched in Verrucomicrobiota and Myxococcota, while Patescibacteria characterized monoecious. LEfSe analysis identified Myxococcota and Bdellovibrionota as key biomarkers in gynoecious cucumbers, implying a potential for enhancing pathogen suppression. Functional prediction indicated that gynoecious-associated microbiota possessed stronger capacities for hydrocarbon degradation and iron respiration, whereas the microbiota-associated communities were enriched in pathways for nitrogen and nitrate respiration. Metabolomic analyses revealed pronounced genotype-dependent differences, including tryptophan metabolism, plant hormone signal transduction, linoleic and linolenic acid metabolism, and indole alkaloid biosynthesis were significantly upregulated in gynoecious root. Meanwhile, key metabolites, such as L-tryptophan, tryptamine, serotonin, indole-3-acetic acid, jasmonic acid, and salicylic acid were also accumulated at higher levels in gynoecious roots. Furthermore, correlation network analysis revealed stronger associations between specific microbial taxa and hormone- or defense-related metabolites in gynoecious plants compared to monoecious plants.},
}