@article {pmid42035121,
year = {2026},
author = {Zhang, X and Chi, Y and Zhang, Z and Wang, Y and Yi, F and Wang, P and Liu, Y and Hao, W},
title = {Gestational diabetes: from pathogenesis to therapeutic intervention.},
journal = {Diabetology & metabolic syndrome},
volume = {18},
number = {1},
pages = {},
pmid = {42035121},
issn = {1758-5996},
abstract = {Gestational diabetes mellitus (GDM), affecting up to 15% of pregnancies worldwide, is a complex metabolic disorder arising from the interaction of pregnancy-induced insulin resistance and inadequate pancreatic β-cell compensation. This review synthesizes current advances in understanding the pathogenesis and therapeutic strategies of GDM. Mechanistically, GDM develops through a multifactorial network involving placental hormone–driven insulin resistance, impaired β-cell adaptive remodeling, genetic susceptibility, and epigenetic modifications that alter key metabolic regulators such as INSR and PDX1. Increasing evidence further implicates immunometabolic dysregulation—including neutrophil extracellular trap formation and placental inflammation—along with gut microbiota dysbiosis characterized by depletion of butyrate-producing bacteria and enrichment of lipopolysaccharide-producing taxa. Additional emerging contributors include circadian rhythm disruption and exposure to environmental endocrine-disrupting chemicals, both of which can interfere with glucose homeostasis and insulin signaling. These interacting mechanisms contribute not only to maternal hyperglycemia but also to adverse maternal and fetal outcomes, including macrosomia, preterm birth, and long-term cardiometabolic risk in both mothers and offspring. Current management strategies rely primarily on lifestyle interventions and pharmacotherapies such as insulin and metformin; however, novel therapeutic approaches—including GLP-1 receptor agonists, SGLT2 inhibitors, and microbiome-targeted interventions—are being explored, although their safety in pregnancy requires further validation. Looking forward, integrating multi-omics technologies, early biomarkers, and digital health monitoring may enable precision medicine approaches for earlier diagnosis, mechanistic subtyping, and individualized treatment of GDM, ultimately reducing its intergenerational metabolic burden.},
}

@article {pmid42278572,
year = {2026},
author = {Khanduja, R and Frye, RE},
title = {A Systematic Review of Folate and the Human Enteric Microbiome: Biological Mechanisms and Clinical Implications.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115048},
pmid = {42278572},
issn = {1422-0067},
mesh = {Humans ; *Folic Acid/metabolism ; *Gastrointestinal Microbiome/physiology ; Animals ; Probiotics ; Prebiotics ; },
abstract = {Folate (vitamin B9) is central to one-carbon metabolism, supporting nucleotide biosynthesis, methylation homeostasis, and epigenetic regulation. The gut microbiome both produces and consumes folate, creating a bidirectional axis influencing host health and disease. We systematically reviewed 159 original studies from MEDLINE, Google Scholar, Embase, and Scopus (inception through January 2026) examining enteric microbiota-folate interactions, with intervention evidence graded using the Oxford Centre for Evidence-Based Medicine 2011 framework. Only a minority of gut bacteria possess complete folate biosynthetic pathways; most depend on cross-feeding from prototrophic taxa including Bifidobacterium, Lactobacillus, and Streptococcus. Altered microbial folate metabolism was associated with metabolic, gastrointestinal, oncologic, neuropsychiatric, cardiovascular, immunologic, and reproductive disorders through convergent mechanisms of disrupted methylation, genomic instability, and immune dysregulation. Probiotic interventions achieved the strongest evidence, supported by multiple human controlled and observational trials and animal models. The evidence for prebiotic, dietary, and folate supplementation interventions was moderate due to the predominant animal models and in vitro data. Overall, the predominant associational and observational evidence base is insufficient to establish causal relationships, underscoring the need for adequately powered human randomized controlled trials with folate-specific endpoints, multi-omics integration, and precision approaches matching folate form and dose to individual microbiome and host genetic profiles.},
}

Humans
*Folic Acid/metabolism
*Gastrointestinal Microbiome/physiology
Animals
Probiotics
Prebiotics

@article {pmid42278576,
year = {2026},
author = {Kozhakhmetov, S and Kushugulova, A and Vinogradova, E and Rakhmankulova, A and Terzic, M and Bapayeva, G and Aimagambetova, G and Kamzayeva, N and Kim, Y and Primbetov, B and Imankulova, B and Kongrtay, K and Kadroldinova, N and Galym, M and Makhambetova, S and Nurgaliyeva, K and Abdiyeva, Z and Zhumakanova, Z and Baktybayeva, D and Smagulova, B and Ukybassova, T},
title = {Cervicovaginal Mycobiome Restructuring by HPV and Bacterial Community State Types in a Kazakhstani Shotgun Metagenomic Cohort: Lactobacillus iners as a Candida-Permissive Niche Associated with α-9 HPV in Cytologically Normal Women.},
journal = {International journal of molecular sciences},
volume = {27},
number = {11},
pages = {},
doi = {10.3390/ijms27115052},
pmid = {42278576},
issn = {1422-0067},
mesh = {Humans ; Female ; *Lactobacillus/genetics/physiology ; *Vagina/microbiology/virology ; *Candida/genetics/physiology ; *Cervix Uteri/microbiology/virology ; *Papillomavirus Infections/virology/microbiology ; *Mycobiome/genetics ; Metagenomics/methods ; Adult ; Microbiota ; Shotgun Sequencing ; Middle Aged ; *Human Papillomavirus Viruses/genetics ; },
abstract = {Cervicovaginal dysbiosis is an established co-factor of high-risk human papillomavirus (HPV) persistence and cervical neoplastic development, yet most studies address the bacterial compartment in isolation, leaving fungal communities and bacterial-fungal cross-kingdom interactions underexplored, particularly in Central Asian populations. We performed shotgun metagenomic sequencing (mNGS) of cervicovaginal samples from 311 Kazakhstani women undergoing routine cervical screening. HPV status was determined using combined PCR and mNGS methods, and cervical screening was completed using liquid-based cytology (NILM, ASC-US, LSIL, ASC-H). Bacterial, viral, and fungal taxa were profiled from a single shotgun dataset with Kraken2 pipeline. Bacterial community state types (CSTs) were determined based on dominant bacterial species, functional gene content was annotated against KEGG using eggNOG, and covariate-adjusted associations were estimated using MaAsLin3. Mycobiome β-diversity differed significantly by HPV status (p = 0.003). In particular, Candida positivity was significantly associated with HPV presence and with high-risk α-9 HPV in cytologically normal (NILM) samples (OR = 3.6, [1.6-9.6], p ≤ 0.001). Covariate-adjusted analysis was consistent with this positive association (q < 0.05). Concurrently, among CSTs, Lactobacillus iners-dominated CST III and dysbiotic Gardnerella vaginalis-dominated CST IV showed a 3-fold higher Candida albicans prevalence (p < 0.01). Further analysis demonstrated that, functionally, both of these CSTs had depleted capacity for lactate metabolism (ko00620, p < 0.0001) and, in particular, for the genetic capacity for pyruvate-dependent H2O2 generation (half that of the L. crispatus-dominated CST I). These findings support L. iners as a metabolically permissive rather than protective Lactobacillus and suggest cross-kingdom functional signatures as candidate biomarkers for HPV acquisition and persistence in Central Asia, a region previously absent from the cervicovaginal microbiome literature.},
}

Humans
Female
*Lactobacillus/genetics/physiology
*Vagina/microbiology/virology
*Candida/genetics/physiology
*Cervix Uteri/microbiology/virology
*Papillomavirus Infections/virology/microbiology
*Mycobiome/genetics
Metagenomics/methods
Adult
Microbiota
Shotgun Sequencing
Middle Aged
*Human Papillomavirus Viruses/genetics

@article {pmid42278930,
year = {2026},
author = {McPherson, EJ and Chowdhry, M and Lin, A and Stavrakis, AI and Su, L},
title = {"Antimicrobial Brachytherapy" Protocol for Chronic Periprosthetic Joint Infection in Total Knee Arthroplasty: A Preliminary Case Series with 2-Year Results.},
journal = {Journal of clinical medicine},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/jcm15114070},
pmid = {42278930},
issn = {2077-0383},
abstract = {Background: The success rates of treating chronic periprosthetic joint infection (PJI) have plateaued in the last two decades utilizing exchange protocols combined with extended parenteral antimicrobials. At the same time, extended systemic antimicrobials carry well-recognized adverse effects, including organ toxicity, metabolic derangements, and disruption of host-microbiome balance, which may themselves impair host inflammatory responses and tissue healing. The defined challenge is to intensify local site eradication while minimizing systemic antimicrobial exposure and its associated host harms. This study introduces a tactical treatment shift focusing on local microbial biocidal treatment, that we aptly name "antimicrobial brachytherapy" protocol (ABP). Methods: A consecutive case series of 25 patients with chronic PJI in total knee arthroplasty (TKA) were treated with the ABP from 2019 to 2023. In brief, the protocol includes: (1) local multimodal antimicrobial therapy applied during debridement to reach and extinguish microbial reserves, (2) eliminating parenteral antimicrobials and limiting oral antimicrobials to 3 weeks, and (3) employing variable explantation times (longer when needed) via a 1.5 exchange technique allowing individualized host and limb rejuvenation. Patients were graded according to McPherson host scoring. Musculoskeletal Infection Society (MSIS) tier levels were used to rate success. All patients had a minimum two-year follow-up. Results: Eighty percent of the patients were significantly compromised, consisting of B and C hosts having 2 and 3 limb scores. Outcomes using the MSIS tier rating show 16/25 (64%) tier 1 success (infection-free without antimicrobial suppression). In these 16 patients, three were still using their 1.5 implant at a mean 4.2 years (2-5.5 years). There were two (8%) tier 3C outcomes (aseptic revision at <1 year), and six (25%) tier 3E failures (amputation, resection arthroplasty or arthrodesis) with four amputations for continued infection, and two who underwent a repeat 1.5 exchange for recurrent infection. Of the four patients amputated, three had fungal microbes identified in post-resection aspirations. Lastly, there was one (4.15%) tier 4a outcome (mortality at <1 year). Conclusions: The ABP concept is a tactical shift focusing antimicrobial therapy within the zone of infection, avoiding long course systemic antimicrobials, and allowing variable explantation time for host and limb rejuvenation. Success was comparable to published MSIS tier 1 outcomes using traditional two-stage exchange protocols with extended parenteral antimicrobials. Given the small sample size and absence of a comparator, the results should be regarded as hypothesis-generating, and require validation in larger, randomized, controlled studies.},
}

@article {pmid42279022,
year = {2026},
author = {Babik, K and Bomze, Z and Szuba, M and Borek-Dzięcioł, B and Kociszewska-Najman, B},
title = {Impact of Early-Life Antibiotic Exposure on Gut Microbiome and Vaccine Immunogenicity in Infants: A Narrative Review.},
journal = {Journal of clinical medicine},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/jcm15114161},
pmid = {42279022},
issn = {2077-0383},
abstract = {Background: Neonatologists face a significant clinical challenge in balancing the life-saving effects of broad-spectrum antibiotics with an infant's ability to develop long-term vaccine-induced immunity. During the critical neonatal window, the gut microbiota acts as an essential endogenous adjuvant that promotes immune maturation through Toll-like receptor signaling and the production of microbial metabolites such as short-chain fatty acids. Methods: This narrative review was based on a comprehensive search of the PubMed and Google Scholar databases for studies published between 2014 and 2025. The search focused on the relationships between neonatal antibiotic exposure, gut microbiome development, and vaccine-induced immune responses in infants. Results: Early-life antibiotic exposure disrupts immune maturation by causing a marked reduction in commensal bacteria, particularly Bifidobacterium and Bacteroides. Clinical and epidemiological evidence indicates that this antibiotic-driven dysbiosis leads to significantly lower antibody titers following routine vaccinations, including PCV13, Hib, and DTaP, with measurable effects persisting up to 15 months of age. While antibiotics may paradoxically enhance oral rotavirus vaccine responses in resource-constrained settings by reducing environmental enteric dysfunction, an undisturbed native microbiota remains the optimal foundation for robust immunological memory. Conclusions: These findings highlight the necessity of improving antibiotic stewardship and exploring microbiota-restoring interventions, such as targeted probiotics, to optimize infant vaccination schedules and protect long-term immune health. Empirical antibiotic treatment should be promptly terminated once sepsis has been clinically excluded to preserve the gut-immune axis.},
}

@article {pmid42279061,
year = {2026},
author = {Szwajkowski, M and Szwach, J and Shefa, S and Karwowska, A and Głębocka, A and Pazdro-Zastawny, K and Dorobisz, K},
title = {Molecular Characterization of the Middle Ear Microbiome in Pediatric Otitis Media with Effusion: Diagnostic and Clinical Implications.},
journal = {Journal of clinical medicine},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/jcm15114200},
pmid = {42279061},
issn = {2077-0383},
abstract = {Background: Otitis media with effusion (OME) is a highly prevalent pediatric condition and a leading cause of conductive hearing loss in children. Its pathogenesis remains uncertain, and diagnostic and therapeutic challenges make management difficult. Objectives: This review evaluates current evidence on the middle ear microbiome in pediatric OME, focusing on the diagnostic value of 16S ribosomal ribonucleic acid (16S rRNA) gene sequencing and its potential clinical implications. Methods: A literature review was conducted using the PubMed database, including studies published between 2006 and 2026. Eligible studies involved pediatric patients with OME and examined the sources and characteristics of microbiota potentially involved in disease pathogenesis. Microbiome analysis was performed using next-generation sequencing (NGS) techniques. Results: Growing evidence indicates that OME is associated with microbial dysbiosis and biofilm formation rather than a sterile inflammatory process. The most frequently detected genera include Haemophilus, Moraxella, Streptococcus, and Alloiococcus, although substantial variability exists between studies. Pathogens are believed to reach the middle ear through the Eustachian tube from two main reservoirs: the nasopharynx and the adenoids. The potential role of Helicobacter pylori infection and gastroesophageal reflux disease (GERD) in OME pathogenesis remains uncertain and requires further investigation. NGS methods, including 16S rRNA sequencing, demonstrate higher sensitivity than conventional culture techniques, enabling the detection of fastidious and previously unrecognized microorganisms. Evidence also highlights the limited effectiveness of antibiotic therapy in OME, the persistent issue of antibiotic overuse, and the relative advantages of conservative management and microbiome-modulating approaches compared with antibiotics and surgical interventions. Conclusions: Current evidence suggests that OME is closely associated with microbiota dysbiosis and bacterial biofilm formation. Given the limited efficacy of antibiotics, microbiome-focused strategies-particularly probiotics-should be further explored. Molecular diagnostic methods, especially NGS, show clear advantages over traditional culture-based techniques. Future research should further evaluate microbiome modulation as a potential adjunctive or preventive strategy.},
}

@article {pmid42279243,
year = {2026},
author = {Radu, EA and Mocanu, E and Fulina, M and Rotar, V and Enache, F and Popescu, S and Șerbănescu, L},
title = {Maternal Oral Microbiome Dysbiosis and Adverse Pregnancy Outcomes: Microbial Signatures, Inflammatory Pathways, and Clinical Evidence.},
journal = {Journal of clinical medicine},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/jcm15114379},
pmid = {42279243},
issn = {2077-0383},
abstract = {Background/Objectives: Pregnancy is characterized by complex physiological, hormonal, and immunological changes that influence the oral environment and the microbial composition of the oral cavity. Emerging evidence suggests that maternal oral dysbiosis may be associated with systemic inflammatory responses and may potentially influence pregnancy outcomes. This systematic review aimed to evaluate the current clinical evidence regarding the association between maternal oral dysbiosis and adverse pregnancy outcomes, including preterm birth, low birth weight, and gestational complications. Methods: A systematic search of PubMed, Scopus, Web of Science, and Cochrane Library was conducted for studies published between January 2013 and September 2025. Observational studies and clinical trials examining the relationship between maternal oral dysbiosis or periodontal pathogens and pregnancy outcomes in pregnant women were included. Study selection was performed according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA 2020) guidelines, and the review was prospectively registered in PROSPERO (CRD420261383855). Data were extracted on the study design, population characteristics, microbiological assessment methods, and reported pregnancy outcomes. Ten studies met the inclusion criteria of this review. Results: Seven of the ten included studies reported significant associations between the increased prevalence of periodontal pathogens, including Porphyromonas gingivalis, Fusobacterium nucleatum, and Prevotella intermedia, and adverse pregnancy outcomes, particularly preterm birth and low birth weight (LBW). Several studies have identified oral bacterial DNA in placental tissues, supporting the potential hematogenous microbial translocation pathways. However, heterogeneity in microbiological assessment techniques and study designs limits the comparability of the findings. Conclusions: Current evidence suggests that maternal oral dysbiosis may be associated with the inflammatory pathways linked to adverse pregnancy outcomes. Further prospective studies and standardized microbiome analyses are required to clarify the role of the oral microbiome in maternal and fetal health. Integrating oral health assessments into prenatal care may be an important strategy for improving maternal and neonatal outcomes.},
}

@article {pmid42279278,
year = {2026},
author = {Liu, Z and Ang, MY and Kue, CS},
title = {Gut Microbiota in Colorectal Cancer: Mechanistic Insights, Clinical Strategies, and a Regional Perspective with a Focus on Sichuan, China.},
journal = {Cancers},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/cancers18111693},
pmid = {42279278},
issn = {2072-6694},
abstract = {CRC remains a major cause of cancer-related morbidity and mortality worldwide. In recent years, the gut microbiota has gained increasing attention in CRC research. Intestinal microbes are not passive bystanders in tumor development. They may promote persistent inflammation, disrupt epithelial barrier integrity, alter microbial metabolites, and affect host immune and signaling pathways. Emerging evidence also suggests that microbiota-related metabolites and microbial functional alterations may influence host epigenetic regulation, including DNA methylation and chromatin-associated signaling, thereby further shaping colorectal carcinogenesis. Together, these changes can create a microenvironment that favors tumor initiation and progression. Several bacterial species, including Fusobacterium nucleatum, Parvimonas micra, and Peptostreptococcus anaerobius, have been repeatedly associated with CRC. In contrast, beneficial commensal microbes and their metabolites, especially short-chain fatty acids, may help maintain intestinal homeostasis and limit tumor-promoting processes. Because the gut microbiota is strongly shaped by diet, lifestyle, and environmental exposure, regional differences are also relevant. This is particularly important in Sichuan, China, where distinctive dietary habits and environmental features may influence microbial patterns associated with CRC risk and disease behavior. This review summarizes the main mechanisms linking the gut microbiota to CRC, examines the regional context of Sichuan, China, and discusses current and emerging clinical strategies. These include dietary intervention, probiotics, fecal microbiota transplantation, and microbiome-informed approaches to prevention, diagnosis, and treatment.},
}

@article {pmid42279294,
year = {2026},
author = {Newell, LF and Twohey, E and Sweetnam, J and Skendzel, S and Stingle, J and Vartanian, KA and Davis, BA and Layman, CE and Carbone, L and Ray, K and Fei, SS and Karstens, L and He, FC and El Jurdi, N and Blaes, AH and Meyers, G and Cook, RJ and Baraki, A and Dengel, DR and Holtan, SG},
title = {Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.},
journal = {Cancers},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/cancers18111710},
pmid = {42279294},
issn = {2072-6694},
abstract = {Background: Chemotherapy and radiation accelerate aging of multiple systems, including the immune and musculoskeletal systems. Resistance training may mitigate some of the late physiologic effects of cancer therapy. Methods: We developed a community-based pilot study of resistance training for long-term cancer survivors meeting criteria for pre-frailty or frailty (N = 8; 6 allogeneic hematopoietic cell transplant, 1 autologous hematopoietic transplant, 1 breast cancer survivor) and their caregivers (N = 8 healthy controls) consisting of a baseline assessment, 10 weeks of personalized resistance training at least once weekly as a group and as many additional times on an individual basis as their schedule allowed, and an end-of-study assessment to measure change in strength and body composition. Blood samples were collected at the start of the study and after the 10-week training program to assess changes in peripheral blood mononuclear cell DNA methylation patterns, gene expression measured by RNA sequencing, and stool microbiome analysis using metagenomics. The median number of resistance training sessions was 25 sessions. Results: Cancer survivors and controls both more than doubled their squat and press volume after 10 weeks. At baseline, cancer survivors exhibited a pro-inflammatory transcriptomic and epigenetic profile with elevated interferon signaling and reduced naïve T cell signatures compared to healthy controls, consistent with immune senescence. After 10 weeks of resistance training, these differences normalized, suggesting that exercise exerted anti-inflammatory and immune-restorative effects in cancer survivors at both gene expression and methylation levels. Ten fecal microbial pathways that were lower in relative abundance in patients compared with controls at baseline were no longer significantly different post-exercise. Conclusions: Our data suggest that in addition to beneficial changes in body composition, resistance training may exert an immune restorative effect in cancer survivors.},
}

@article {pmid42279452,
year = {2026},
author = {Yang, L and Meng, W and Yang, T and Zhu, Y and Wang, Z},
title = {Microbiomics: Novel Biomarkers of Colorectal Cancer Diagnosis and Prognosis.},
journal = {Diagnostics (Basel, Switzerland)},
volume = {16},
number = {11},
pages = {},
doi = {10.3390/diagnostics16111582},
pmid = {42279452},
issn = {2075-4418},
abstract = {With colorectal cancer (CRC) accounting for over 1.9 million new cases and 930,000 deaths globally in 2020, there is a critical need for innovative indicators to forecast disease advancement and therapeutic outcomes. The gut microbiome has emerged as a fertile area for discovering such diagnostic and prognostic signals. This narrative review collected current evidence on intestinal microorganisms and their metabolic products as candidate markers for CRC control. Intestinal communities influence malignancy through diverse mechanisms, including metabolic shifts, immune modulation, inflammation, proliferation/apoptosis regulation, genotoxicity, and mucosal barrier disruption. Pathogenic species, such as Fusobacterium nucleatum and enterotoxigenic Bacteroides fragilis, facilitate tumorigenesis via FadA-mediated signaling and Th17/IL-17 responses. In contrast, beneficial taxa like Faecalibacterium prausnitzii and Akkermansia muciniphila provide protective effects through short chain fatty acid production. Macrophage phenotype physiological equilibrium is altered and inflammatory status fluctuates under the former. Metabolically, hydrogen sulfide damages mitochondrial DNA and secondary bile acids stimulate cellular proliferation. While 16S rRNA sequencing and shotgun metagenomics are established detection strategies, innovative platforms like organoids and gene arrays remain in the exploratory stage. Clinical data indicates that F. nucleatum aligns with advanced tumor stage, and its combined detection with colibactin-producing E. coli achieves high sensitivity for early-stage screening. Additionally, A. muciniphila levels can anticipate the efficacy of PD-1 blockade immunotherapy. Microbiota-derived tools represent a transformative direction in oncology. Future research must focus on standardizing protocols and validating multi-marker panels to enhance clinical translation.},
}

@article {pmid42279678,
year = {2026},
author = {Ali, A and Cui, L},
title = {Metabolomic Characterization of Baby Spinach Phenolics Transformation During Gastrointestinal Digestion and Microbiome-Mediated Metabolism.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15111893},
pmid = {42279678},
issn = {2304-8158},
abstract = {Gastrointestinal digestion and colonic fermentation determine phenolic transformation and reciprocal microbiome modulation, influencing the generation of gut-derived metabolites associated with epithelial integrity, inflammatory regulation, and metabolic homeostasis. Baby spinach phenolics possess antioxidant and microbiome-modulating potential; however, their functional efficacy is constrained by storage-induced degradation and limited gastrointestinal bioaccessibility. This study investigated phenolic transformation in fresh and stored baby spinach (4 °C and 25 °C) during simulated gastrointestinal digestion and subsequent colonic fermentation. Standardized in vitro digestion revealed limited phenolic bioaccessibility (10-15%), with storage at 25 °C accelerating oxidative degradation and reducing antioxidant capacity. Storage at 25 °C reduced TPC from approximately 465 to 265 µg GAE/g and decreased antioxidant activity by nearly 30%, whereas refrigerated storage (4 °C) better preserved phenolic stability and antioxidant capacity throughout the storage period. LC-MS/MS-based untargeted metabolomics characterized digestion-driven structural remodeling and identified diverse colonic metabolites generated during human fecal fermentation. Despite storage-induced alterations in precursor phenolics, 16S rRNA sequencing demonstrated microbiome relative microbial stability, with fermentation time exerting a stronger influence on community assembly than storage conditions. Microbial metabolism produced shared downstream metabolites, particularly phenylpropionic and flavonoid-derived intermediates. These results suggest that storage modifies phenolic availability during digestion, while gut microbial metabolism sustains the production of functionally relevant metabolites.},
}

@article {pmid42279781,
year = {2026},
author = {Yi, X and Deng, W and Gao, K and Ou, X and Tang, K and Zeng, Q and Ni, Y and Liang, X and Wu, Z and Wu, Y and Xie, Y and Chen, H and Yang, A},
title = {Genistein Pretreatment Attenuates Ovalbumin-Induced Food Allergy in Mice with Intestinal Barrier Preservation and Modulation of Gut Microbiota and Metabolites.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15111995},
pmid = {42279781},
issn = {2304-8158},
support = {No. 20225BCJ22022//Funding for Academic and Technical Leaders in Major Disciplines, Jiangxi Province, China/ ; No. 32260595//National Natural Science Foundation of China/ ; },
abstract = {Food allergy (FA) is an increasing public health concern, highlighting the urgent need for safe, bioactive-based preventive strategies. This study evaluated genistein, a plant-derived isoflavone, in an ovalbumin (OVA)-induced murine FA model. Genistein was administered before sensitization and throughout allergy induction. Clinical symptoms, rectal temperature, diarrhea, OVA-specific antibodies, mast cell responses, intestinal barrier markers, gut microbiota, short-chain fatty acids (SCFAs), and fecal metabolites were assessed using immunological, histological, microbiome, and metabolomic analyses. Genistein pretreatment prevented OVA-induced clinical symptom scores, rectal temperature decline, diarrhea occurrence, OVA-specific antibody responses, and mast cell responses. These changes were accompanied by preservation of jejunal tight junction-related markers and modulation of T-cell-associated immune responses. In vitro, genistein modulated antigen uptake, maturation-associated features of bone marrow-derived dendritic cells (BMDCs), and BMDC-driven CD4[+] T-cell polarization. In parallel, genistein-pretreated mice showed altered gut microbial structure, higher relative abundances of selected SCFA-associated taxa, increased fecal butyrate, and fecal metabolomic alterations involving purine metabolism, bile-acid-related metabolism, and tryptophan-related microbial metabolites. Consistently, correlation analyses indicated associations among microbial taxa, metabolites, immune indicators, and intestinal barrier markers. Together, these findings provide preliminary mechanistic insight into genistein in experimental FA and support further investigation of genistein as a dietary bioactive candidate for FA prevention.},
}

@article {pmid42279791,
year = {2026},
author = {Jiang, S and Sun, H and Zhang, C and Zhang, Y},
title = {Deep Learning and Microbiome Analysis Reveal the Preservation Mechanism of Cinnamomum cassia for Strawberry.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15112005},
pmid = {42279791},
issn = {2304-8158},
support = {52300027//National Natural Science Foundation of China/ ; KM202310011004//Beijing Municipal Education Commission/ ; },
abstract = {Strawberry preservation remains a critical challenge due to rapid postharvest microbial spoilage. This study investigated the preservative efficacy of Cinnamomum cassia and Punica granatum peel aqueous extracts, prepared via spray drying, on strawberries over 5 days of storage, with a specific focus on their regulatory impact on the fruit surface microbiome. Preservation tests demonstrated that the C. cassia extract was more effective in reducing visible mold development. High-throughput sequencing revealed that the C. cassia treatment reshaped microbial community structures, decreasing the relative abundance of spoilage-associated bacteria and the primary pathogenic fungus Botrytis (94.37%), while enriching potentially beneficial or antagonistic genera such as Sphingobium (28.72%), Sphingomonas (9.52%), and Cladosporium (0.62%). Using a probability threshold of 0.7, 121 compounds were identified as potential active candidates from a library of 675 C. cassia constituents. These compounds predominantly have a molecular weight between 100 and 250 and are characterized by prevalent functional groups including alkene (49.60%), hydroxyl (38.80%), and benzene rings (36.40%). In vitro antibacterial assays confirmed the inhibitory activity of vanillin and its isomers, validating the reliability of the computational predictions. These findings suggest that the preservative mechanism of C. cassia is likely mediated by the collective action of a multi-component matrix that modulates the microecological balance on the fruit surface, rather than the isolated effect of a single compound. This integrated approach provides an effective framework for developing plant-derived preservation strategies by combining microbiome dynamics with machine learning.},
}

@article {pmid42279801,
year = {2026},
author = {Guo, W and Li, Y and Han, J and Liu, X and Ni, L},
title = {Integrated Microbiome and Metabolomics Analysis Reveals That Ganoderma lucidum Triterpenoids Ameliorate Colitis Associated with the Modulation of the Gut Microbiota and Metabolic Profiles.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15112016},
pmid = {42279801},
issn = {2304-8158},
support = {XRC-25053//Research Project of Fuzhou University/ ; 2025M772970//China Postdoctoral Science Foundation under Grant/ ; },
abstract = {Colitis is a global health challenge that severely impairs quality of life, necessitating effective dietary interventions. This study investigated the protective effects of Ganoderma lucidum triterpenoids (GLTs) on pathological symptoms, inflammatory responses, and gut microbiota dysbiosis in a dextran sulfate sodium (DSS)-induced murine model. Our results demonstrated that GLT intervention significantly attenuated the disease activity index (DAI), prevented colon shortening, and fortified gut barrier integrity through upregulating the transcription of tight junction proteins. GLT inhibited the secretion of pro-inflammatory cytokines (TNF-α, IL-1β, and IL-6) and bolstered antioxidant defenses (CAT) by controlling the TLR4/NF-κB pathway and upregulating the Nrf2 pathway. Furthermore, 16S rRNA sequencing and non-targeted metabolomics revealed that GLT reshaped the gut microbial landscape (enriching Enterorhabdus and Lachnospiraceae NK4A136 group) and reconfigured amino acid metabolism to restore colonic homeostasis. Collectively, these findings highlight the potential of GLT as a functional food ingredient to prevent colitis, potentially linked to the modulation of the microbiota-metabolite-immune interplay, offering a novel nutritional strategy for inflammatory bowel disease management.},
}

@article {pmid42279810,
year = {2026},
author = {Alhaj, OA and Elsahoryi, NA and Jahrami, HA},
title = {Dairy Bioactive Compounds as Precision Modulators of Gut Microbiota: From Molecular Mechanisms to Personalized Immunometabolic Health.},
journal = {Foods (Basel, Switzerland)},
volume = {15},
number = {11},
pages = {},
doi = {10.3390/foods15112024},
pmid = {42279810},
issn = {2304-8158},
abstract = {The gut microbiota (GM) has become a key mediator of host health, with dietary manipulations promising ways of modulating the microbiome. This review focuses on the role of dairy bioactive (DB) compounds as precision modulators of intestinal microecology, including the whey proteins (WPs), including lactoferrin (LF), α-lactalbumin (LA), β-lactoglobulin, lysozyme (LZ), lactoperoxidase, glycomacropeptide (GMP), milk oligosaccharides (MOs), and bioactive peptides (BPs). This review compiles the existing evidence illustrating their dual-action mechanism through direct prebiotic activity and the promotion of beneficial taxa (Bifidobacterium, Lactobacillus, Faecalibacterium), along with selective antimicrobial activity and pathogen suppression. These compounds improve intestinal barrier integrity through tight junction (TJ) protein regulation, regulating short-chain fatty acid production, and modulating immune signaling pathways. Clinical evidence shows significant benefits in metabolism and inflammation among various populations. However, individual responses vary according to host factors such as enterotypes, FUT2 genotype, and baseline microbiota composition, suggesting the need for personalized intervention strategies. This review addresses critical knowledge gaps in dose-response relationships, long-term efficacy, and mechanistic pathways and suggests future directions for precision nutrition. By modifying molecular mechanisms in clinical applications, we have identified DB compounds as promising candidates for targeted modulation of the microbiota to optimize health and disease management. The review also brings together molecular mechanistic and clinically implementable, personalized dietary strategies, which have not been fully captured by previous reviews. It pinpoints gaps in knowledge related to dose-response characterization, long-term trial design, and multi-omics stratification that collectively define a new precision nutrition framework. In this approach, dairy-based intervention is planned for each person based on their microbial, genetic, and metabolic characteristics.},
}

@article {pmid42280315,
year = {2026},
author = {Jia, L and Lu, H and Jiang, C and Hu, W and Yu, G and Xiang, X and Shen, G and Tao, J and Chen, L and Miao, W},
title = {Torreya grandis Diester Oil Attenuates High-Fat Diet-Induced Pulmonary Inflammation with Superior Efficacy to Natural Torreya grandis Oil.},
journal = {Nutrients},
volume = {18},
number = {11},
pages = {},
doi = {10.3390/nu18111671},
pmid = {42280315},
issn = {2072-6643},
support = {2026C02A1023//Department of Science and Technology of Zhejiang Province/ ; },
mesh = {Animals ; *Diet, High-Fat/adverse effects ; *Plant Oils/pharmacology ; Oxidative Stress/drug effects ; Male ; Mice ; Lung/drug effects/metabolism/microbiology ; *Pneumonia/etiology/drug therapy/prevention & control/metabolism ; NF-kappa B/metabolism ; Mice, Inbred C57BL ; Cytokines/metabolism ; Seeds/chemistry ; PPAR gamma/metabolism ; Signal Transduction/drug effects ; Nitric Oxide/metabolism ; },
abstract = {BACKGROUND/OBJECTIVES: A high-fat diet (HFD) not only induces metabolic disorders but also causes oxidative damage to the lung tissue, triggering inflammatory responses. However, the detailed mechanisms by which HFD induces pulmonary oxidative stress and inflammation, particularly involving NF-κB/PPAR-γ signaling and lung microbiota, remain poorly understood, and effective dietary intervention strategies are still lacking. This study investigated the effects of HFD on lung tissue injury in mice and systematically evaluated the protective effects and potential mechanisms of Torreya grandis seed oil (TGO) and Torreya grandis seed diester oil (TGO-DG).

METHODS: After 12 weeks of HFD feeding, HFD group mice exhibited a marked increase in body weight (90.36%) compared with the control group, whereas body weight gain was significantly attenuated in the TGO (57.95%) and TGO-DG (55.78%) groups.

RESULTS: Biochemical analyses revealed that the levels of malondialdehyde (MDA), nitric oxide (NO), and pro-inflammatory cytokines (TNF-α, IL-6, IL-1β) were significantly elevated in the HFD group, indicating pronounced oxidative stress and inflammatory responses in lung tissue. These symptoms were significantly attenuated by TGO and TGO-DG, with TGO-DG showing a more marked effect. Western blot (WB) results showed that both TGO and TGO-DG suppressed IL-6 expression and altered the expression of proteins in the NF-κB and PPAR-γ signaling pathways, which may contribute to the alleviation of pulmonary inflammation. Lung microbiota analysis revealed that TGO was associated with an increased proportion of Lactobacillus species, which correlated with the restoration of pulmonary microbial homeostasis.

CONCLUSIONS: Overall, these results suggest that TGO and TGO-DG effectively alleviate HFD-induced oxidative stress and inflammation in lung tissue through regulation of inflammatory signaling pathways and lung microbiota composition. Notably, TGO-DG exhibited superior protective effects, highlighting its potential as a lipid ingredient.},
}

Animals
*Diet, High-Fat/adverse effects
*Plant Oils/pharmacology
Oxidative Stress/drug effects
Male
Mice
Lung/drug effects/metabolism/microbiology
*Pneumonia/etiology/drug therapy/prevention & control/metabolism
NF-kappa B/metabolism
Mice, Inbred C57BL
Cytokines/metabolism
Seeds/chemistry
PPAR gamma/metabolism
Signal Transduction/drug effects
Nitric Oxide/metabolism

@article {pmid42269619,
year = {2026},
author = {Guo, Y and Wang, Z and Li, D and Wang, L and Lan, H and Guo, F and Zhao, Z and Liu, Z and Meng, L and Shen, X and Wang, M and Zhao, W and Zhang, W and Kong, C and Shi, L and Sun, Y and Seim, I and Jiang, A and Ma, K and Su, Z and Zhang, N and Ji, Q and Chen, J and Chen, K and Qi, C and Li, B and He, B and Liu, Y and Zhou, J and Zheng, Y and Zhang, H and Wang, Y and Han, M and Yang, T and Tong, J and Zhang, Y and Wang, Z and Xu, X and Chen, J and Liu, Y and Chen, H and Zeng, T and Wei, X and Li, C and Yang, H and Wang, B and Liu, X and Shao, C and Zhang, W and Gu, Y and Xiao, X and Xu, X and Wang, J and Mock, T and Fan, G and Li, Y and Liu, S and Dong, Y},
title = {The genetic repertoire of deep-sea microbiome: From sequence to structure and function.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.05.009},
pmid = {42269619},
issn = {1934-6069},
abstract = {The deep sea, as the largest and maybe most hostile environment on Earth, is still underexplored, especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea microbial genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures and use it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity and substantial structural conservation of proteins. Especially, proteins involved in replication, recombination, and repair were identified as being under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as an evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.},
}

@article {pmid42269666,
year = {2026},
author = {Dewey, CW and Rojas, CA and Pomeroy, C and Gerardi, J and Ganz, HH},
title = {Fecal microbiota transplantation shows promise in slowing or reducing cognitive impairment in aging dogs.},
journal = {Journal of the American Veterinary Medical Association},
volume = {},
number = {},
pages = {1-6},
doi = {10.2460/javma.26.03.0231},
pmid = {42269666},
issn = {1943-569X},
abstract = {OBJECTIVE: To investigate potential effects of fecal microbiota transplantation (FMT) on cognitive scores and bacterial microbiota composition in dogs with suspected canine cognitive dysfunction (CCD).

METHODS: The study was conducted from September 19, 2024, to September 11, 2025. Dogs with presumptive CCD were given oral FMT capsules daily for 90 days. Each dog received 1 FMT capsule every 12 hours. Fecal samples and cognitive (disorientation, impaired social interactions, sleep disturbance, house soiling, learning and memory loss, activity changes, and anxiety and fear [DISHAA]) assessments were completed at baseline and on days 30, 60, and 90. Fecal samples were submitted for 16S rRNA gene sequencing.

RESULTS: 11 dogs were enrolled; 10 dogs had no adverse events from FMT treatment, and 1 dog developed gastrointestinal signs and was removed from the study. All 10 remaining dogs had complete microbiome data; however, owners of 4 dogs did not report final (90-day) DISHAA scores. Of the 6 dogs with complete data, cognition improved in 4 (mean, -8.25 points) but worsened in 2 (mean, +7 points) according to owner-reported DISHAA scores. Microbiome richness and diversity increased in 4 of the 6 dogs. Several dogs also showed positive modulation of microbiome composition including reductions in Streptococcus spp and increases in Peptacetobacter hiranonis, Prevotella copri, and Bacteroides spp.

CONCLUSIONS: These findings provided preliminary evidence that FMT may help improve cognitive function in dogs with CCD. However, the study sample size was small and ideal FMT dosing level and treatment duration remain undefined. A larger study with longer follow-up is warranted, based on our results.

CLINICAL RELEVANCE: FMT showed promise in slowing or reducing cognitive impairment in aging dogs and may be considered as adjunct therapy in these cases.},
}

@article {pmid42269934,
year = {2026},
author = {Zhao, Y and Wang, X and Ma, Q and Liu, E and Zhang, D and Liu, H and Cai, L and Wang, J and Feng, T and Schroyen, M and Chen, M},
title = {Persistent Benefits of Early Gestational Chenodeoxycholic Acid Supplementation on Late Pregnancy in Sows via Sustained Modulation of the Gut-Metabolism Axis.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101664},
doi = {10.1016/j.tjnut.2026.101664},
pmid = {42269934},
issn = {1541-6100},
abstract = {BACKGROUND: Our previous studies in pigs have identified chenodeoxycholic acid (CDCA) as a potent metabolic regulator during early gestation, capable of enhancing embryo implantation by optimizing maternal metabolic status and gut microbiota-host interactions, while the long-term impacts of early gestational CDCA on late pregnancy remain largely unexplored.

OBJECTIVE: This study investigated whether supplementation with CDCA during early gestation (gestational day 0-28) exerts a sustained metabolic modulation effect on maternal health and reproductive outcomes in late gestation in a sow model.

METHODS: Multiparous sows (n = 24) were randomly assigned to receive either a control diet or a diet supplemented with 0.15% CDCA during early gestation. The reproductive performance, oxidative stress, inflammatory status, gut microbiome, and serum metabolome in late gestation were subsequently evaluated.

RESULTS: Results showed that early CDCA intervention significantly increased the total and live litter sizes (P < 0.05). Furthermore, CDCA treatment alleviated maternal oxidative stress and systemic inflammation, and improved insulin sensitivity in late gestation (P < 0.05). Untargeted metabolomics revealed a distinct metabolic remodeling, characterized by the enrichment of beneficial metabolites, such as L-ornithine, and the depletion of proinflammatory and oxidative markers, including 1-palmitoylphosphatidylcholine, 2-lysophosphatidylcholine, 3-hydroxyanthranilic acid, and N-carboxymethyllysine. 16S rRNA sequencing indicated that CDCA exerted a targeted modulation rather than a global reconstruction of the gut microbiota. Specifically, CDCA suppressed potential harmful bacteria, including NK4A214_group, Clostridium_sensu_stricto_1, and Turicibacter, while enriching beneficial genera like Subdoligranulum. Multi-omics integration identified NK4A214_group as a key driver associated with exacerbated inflammatory status and unfavorable metabolic profiles.

CONCLUSIONS: Collectively, these findings demonstrate that early-gestational CDCA supplementation elicits a long-term protective effect on maternal metabolism via optimizing specific gut microbe-metabolite interactions, thereby ensuring optimal gestational outcomes.},
}

@article {pmid42270015,
year = {2026},
author = {Wang, S and Liu, Z and Jiang, C and Wei, Y and Liu, G and Pan, Y},
title = {The intratumoral microbiota: Orchestrating metabolic-immune crosstalk and shaping the therapeutic landscape in cancer.},
journal = {Biochimica et biophysica acta. Molecular basis of disease},
volume = {},
number = {},
pages = {168316},
doi = {10.1016/j.bbadis.2026.168316},
pmid = {42270015},
issn = {1879-260X},
abstract = {The intratumoral microbiota is now recognized as a key component of the tumor microenvironment, where it influences tumor metabolism, shapes immune activity, and modulates treatment responses. Microbial metabolites such as short-chain fatty acids regulate pathways that control energy use in cancer cells and modify immune signaling within tumors. Microbial imbalance disrupts metabolic homeostasis and promotes immune escape, contributing to cancer progression and resistance to therapy. Specific taxa including Fusobacterium nucleatum drive distinct protumorigenic effects through metabolic and immunologic routes. Spatial heterogeneity of microbial colonization further defines metabolic gradients and immune niches that influence treatment efficacy. Advances in sequencing, multi-omics, and spatial profiling have clarified these interactions and identified microbial signatures with diagnostic and prognostic potential. Therapeutic strategies such as precision probiotics, engineered bacteria, and nanotechnology-based delivery systems offer avenues to target microbial metabolic pathways and enhance treatment response. Continued integration of microbiology, oncology, and bioinformatics will support translation of these findings into personalized cancer therapies.},
}

@article {pmid42270094,
year = {2026},
author = {Deng, L and Gao, X and Guo, C and Hu, X and Qi, J and Wang, J and Huang, X and Zhang, Y and Hu, Z and Wang, H and Hong, B},
title = {Structural and Functional Alterations of Microbiome in Upper and Lower Respiratory Tract in Patients With NSCLC.},
journal = {Cancer control : journal of the Moffitt Cancer Center},
volume = {33},
number = {},
pages = {10732748261460118},
pmid = {42270094},
issn = {1526-2359},
mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/microbiology/pathology ; *Microbiota ; *Lung Neoplasms/microbiology/pathology ; Bronchoalveolar Lavage Fluid/microbiology ; Female ; Case-Control Studies ; Male ; Sputum/microbiology ; Prospective Studies ; Middle Aged ; *Respiratory System/microbiology ; Bacteria/isolation & purification/genetics ; Aged ; Fungi/isolation & purification ; },
abstract = {IntroductionThe airway microbiome plays a pivotal role in lung cancer development, but the microbiome characteristics in upper and lower respiratory tract of non-small cell lung cancer (NSCLC) patients remains unclear.MethodsThis was a prospective case-control study. The study included 60 samples from NSCLC patients and non-cancer controls: 23 sputum (SP) samples (14 NSCLC, 9 controls) and 37 bronchoalveolar lavage fluid (BALF) samples (21 NSCLC, 16 controls). Metagenomic sequencing was performed to characterize microbial composition and diversity, differential taxa, inter-kingdom networks, and functional profiles for bacteria and fungi.ResultsFor bacterial community, BALF samples from NSCLC tend to show higher alpha diversity than that of non-cancer controls (Shannon p = 0.046, Simpson p = 0.089), whereas SP samples from NSCLC show a trend toward lower alpha diversity (Shannon p = 0.053, Simpson p = 0.033). For fungal community, alpha diversity shows no significant difference between NSCLC and non-cancer groups in either SP (Shannon p = 0.250, Simpson p = 0.480) or BALF (Shannon p = 0.800, Simpson p = 0.700) samples. Beta diversity exhibits differences in bacterial community composition between NSCLC and non-cancer controls in both SP (p = 0.018) and BALF samples (p = 0.015), while fungal communities appear relatively stable (p = 0.611 for SP; p = 0.611 for BALF). LEfSe and Random Forest analyses identify bacterium Porphyromonas SGB2015 and fungus Psilocybe cubensis significantly enriched in BALF samples from NSCLC, whereas no species is enriched in SP samples. Cross-kingdom network indicates increased complexity and connectivity in NSCLC-associated microbial communities. Functional analysis shows the enrichment of biosynthetic pathways in SP samples and metabolic pathways in BALF samples from NSCLC.ConclusionThese findings suggest that NSCLC may be associated with compositional, structural, and functional alterations of the airway microbiome, with potentially distinct patterns between upper and lower respiratory tract.},
}

Humans
*Carcinoma, Non-Small-Cell Lung/microbiology/pathology
*Microbiota
*Lung Neoplasms/microbiology/pathology
Bronchoalveolar Lavage Fluid/microbiology
Female
Case-Control Studies
Male
Sputum/microbiology
Prospective Studies
Middle Aged
*Respiratory System/microbiology
Bacteria/isolation & purification/genetics
Aged
Fungi/isolation & purification

@article {pmid42270217,
year = {2026},
author = {An, X and Cao, Y and Zhang, Y and Zhuo, Y and Li, X and Qiu, B and Segal, E and Achmon, Y},
title = {Elucidating the effect of surface disinfection methods on strawberry microbiome composition and volatile organic compounds.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119482},
doi = {10.1016/j.foodres.2026.119482},
pmid = {42270217},
issn = {1873-7145},
mesh = {*Fragaria/microbiology ; *Volatile Organic Compounds/analysis ; *Disinfection/methods ; *Microbiota/drug effects ; *Food Microbiology/methods ; *Fruit/microbiology ; Temperature ; Fungi ; Ultraviolet Rays ; },
abstract = {Strawberries are highly perishable, with a shelf life of only a few days at room temperature. It is mostly ascribed to their susceptibility to spoilage, leading to significant postharvest losses. This study employed a unique system to examine the spoilage of strawberries through the combined perspectives of volatilomics and microbiome analysis. Three surface disinfection techniques: UV irradiation, washing with NaClO and ethanol, or with tea waste extract, were compared to untreated samples at temperatures of 4 °C, 10 °C, and 25 °C, respectively. The results indicate that certain volatile organic compounds (VOCs) were affected by the surface disinfection methods and could be correlated with the spoilage severity over time. For each experimental condition, five putative compounds were tentatively identified as key VOCs by statistical analysis, supporting the feasibility of establishing a multidimensional VOC fingerprint matrix for strawberry spoilage monitoring. The fungal microbiota's succession was strongly influenced by temperature, with key spoilage genera like Penicillium, Alternaria, and Cladosporium identified by sequencing, revealing temperature-modulated microbial dynamics. Relationships between identified potential indicators and spoilage microorganisms were elucidated by correlation analysis. The results suggested surface treatments may affect the occurrence of microbial communities, highlighting the complexity of microbial-chemical dynamics during spoilage processes, where VOC profiles appear to function both as metabolic fingerprints and ecological regulators within the spoilage microbiome. These findings provide new insights into the largely unknown metabolic processes involved in strawberry spoilage, offering new opportunities for more effective prevention strategies to reduce spoilage and waste.},
}

*Fragaria/microbiology
*Volatile Organic Compounds/analysis
*Disinfection/methods
*Microbiota/drug effects
*Food Microbiology/methods
*Fruit/microbiology
Temperature
Fungi
Ultraviolet Rays

@article {pmid42270218,
year = {2026},
author = {Li, F and Wang, S and Chen, B and He, M and Zhou, J and Duan, G and Zhu, Y and Liu, W and Tu, H},
title = {The phyllosphere as a potential microbial habitat sharing taxa with the Jiang-flavor Baijiu fermentation system: A preliminary study.},
journal = {Food research international (Ottawa, Ont.)},
volume = {239},
number = {},
pages = {119488},
doi = {10.1016/j.foodres.2026.119488},
pmid = {42270218},
issn = {1873-7145},
mesh = {*Fermentation ; *Bacteria/classification/genetics/isolation & purification ; *Fungi/classification/genetics/isolation & purification ; *Microbiota ; *Food Microbiology ; Biodiversity ; *Plant Leaves/microbiology ; Edible Grain/microbiology ; },
abstract = {Open spontaneous fermentation, a hallmark of many traditional food systems globally, relies heavily on the surrounding environment for microbial assembly. However, the role of the phyllosphere as a potential microbial habitat within the green spaces adjacent to fermentation facilities remains poorly understood. In this preliminary study, we characterized the epiphytic microbial communities of 11 dominant plant species in the vicinity of a traditional Jiang-flavor Baijiu facility. We identified a rich biodiversity comprising 5495 bacterial and 1678 fungal amplicon sequence variants (ASVs). The phyllosphere exhibited significantly higher bacterial alpha-diversity than fermented grains (Jiupei), positioning it as a highly diverse microbial habitat within the external environment. Notably, we observed extensive taxonomic sharing: 100% of the abundant and always moderate bacterial and fungal ASVs detected in Jiupei were also present on plant surfaces. Furthermore, 70.71% of conditionally rare bacterial ASVs and 68.94% of conditionally rare fungal ASVs from Jiupei were shared with the phyllosphere. These findings demonstrate that multiple microbial taxa co-occur in the phyllosphere and the fermentation system, indicating significant taxonomic sharing across the facility environment. While this exploratory survey does not establish direct microbial transfer, it highlights the phyllosphere as a potential microbial habitat that mirrors the taxonomic composition of the fermentation ecosystem, thereby informing the micro-environmental management of open fermentation systems globally.},
}

*Fermentation
*Bacteria/classification/genetics/isolation & purification
*Fungi/classification/genetics/isolation & purification
*Microbiota
*Food Microbiology
Biodiversity
*Plant Leaves/microbiology
Edible Grain/microbiology

@article {pmid42270336,
year = {2026},
author = {Ito, T},
title = {Professional Dyeing Work Enriches Dye-decolorizing Bacteria in the Fingertip Microbiome.},
journal = {Microbes and environments},
volume = {41},
number = {2},
pages = {},
doi = {10.1264/jsme2.ME26026},
pmid = {42270336},
issn = {1347-4405},
mesh = {*Bacteria/metabolism/classification/isolation & purification/genetics ; *Coloring Agents/metabolism ; Humans ; *Microbiota ; *Fingers/microbiology ; *Occupational Exposure/analysis ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Biodegradation, Environmental ; DNA, Bacterial/genetics ; },
abstract = {Individuals who regularly handle specific chemicals may harbor microorganisms capable of metabolizing those compounds. Such hands may therefore provide a practical route for obtaining functional microorganisms from easily accessible human-associated environments. In this study, we found that nearly 90% of professional dyers harbored dye-decolorizing bacteria, which were efficiently isolated from their fingertips, with 20% of isolates exhibiting decolorizing activity. These strains showed distinct genus-level profiles. These findings indicate that occupational exposure to dyes strongly enriches dye-decolorizing bacteria, suggesting that the hands of textile workers may serve as a source for isolating microorganisms with potential applications in dye bioremediation.},
}

*Bacteria/metabolism/classification/isolation & purification/genetics
*Coloring Agents/metabolism
Humans
*Microbiota
*Fingers/microbiology
*Occupational Exposure/analysis
RNA, Ribosomal, 16S/genetics
Phylogeny
Biodegradation, Environmental
DNA, Bacterial/genetics

@article {pmid42270509,
year = {2026},
author = {Samuel, TM and Samuel, SM and Varghese, E and Sreenesh, B and Büsselberg, D},
title = {Defying inflammation-driven early-onset colorectal cancer: predict, prevent, and personalize.},
journal = {Trends in cancer},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.trecan.2026.05.005},
pmid = {42270509},
issn = {2405-8025},
abstract = {Early-life exposure to both modifiable and nonmodifiable risk factors may induce chronic low-grade inflammation (CLGI), a silent threat potentially driving the rising incidence of early-onset colorectal cancer (EOCRC). Notably, CLGI could promote EOCRC by altering the proinflammatory and immune microenvironment that supports tumor growth and cancer development. In this review, we examine how risk factors disrupt immune homeostasis and contribute to CLGI in young individuals, thereby promoting the development of EOCRC. Additionally, identifying CLGI-specific biomarkers could aid in early detection and diagnosis, while targeting specific molecular pathways may enable personalized therapeutic interventions for EOCRC by reducing the chronic inflammatory threat. We also highlight the importance of lifestyle changes and interventions to reduce CLGI and address the growing health concern of EOCRC.},
}

@article {pmid42270548,
year = {2026},
author = {Carlson, N and Jurmu, JD and Dearing, MD},
title = {Gut microbes compensate for protein-deficient diets.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.05.013},
pmid = {42270548},
issn = {1878-4380},
abstract = {By coupling natural variation in carbon stable isotope signatures with amino acid-specific analysis, Mertz et al. demonstrate the substantive contribution of the gut microbiome in improving diet quality through the production of essential amino acids that are absorbed by the host (deer mouse) and incorporated into muscle tissue.},
}

@article {pmid42270571,
year = {2026},
author = {Tang, X and Shen, Z and Li, B and Yuan, J},
title = {A pilot study investigating the bacterial and fungal community shifts in facial skin in rosacea.},
journal = {The Journal of international medical research},
volume = {54},
number = {6},
pages = {3000605261454625},
pmid = {42270571},
issn = {1473-2300},
mesh = {Humans ; *Rosacea/microbiology/pathology ; Skin Microbiome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics/classification/isolation & purification ; Female ; *Skin/microbiology ; Prospective Studies ; *Face/microbiology ; Middle Aged ; *Fungi/genetics/isolation & purification/classification ; Male ; Adult ; Case-Control Studies ; Microbiota ; },
abstract = {ObjectiveThis study aimed to characterize the bacterial and fungal communities in the facial skin of patients with rosacea versus healthy controls and assess their association with skin oil content.MethodsIn this prospective observational study, facial skin samples from eight individuals (six patients with rosacea and two healthy controls) across three skin oil types were analyzed using 16S rRNA and internal transcribed spacer sequencing. Analyses included alpha/beta diversity, compositional profiling, and cross-kingdom correlations.ResultsPatients with rosacea exhibited higher bacterial diversity (Shannon index: 2.26 ± 1.12) than controls (0.71 ± 0.07). Fungal communities underwent extreme restructuring with near-complete species replacement between individuals (Bray-Curtis ∼1.0). Skin oil content was a key determinant of microbial diversity. Cross-kingdom bacteria-fungi correlations were weak and nonsignificant.ConclusionsRosacea is associated with distinctive cross-kingdom microbiome alterations, featuring increased bacterial diversity and profound fungal reorganization. These findings challenge prevailing dysbiosis paradigms and highlight the potential for therapeutic strategies targeting both bacterial and fungal elements.},
}

Humans
*Rosacea/microbiology/pathology
Skin Microbiome
Pilot Projects
RNA, Ribosomal, 16S/genetics
*Bacteria/genetics/classification/isolation & purification
Female
*Skin/microbiology
Prospective Studies
*Face/microbiology
Middle Aged
*Fungi/genetics/isolation & purification/classification
Male
Adult
Case-Control Studies
Microbiota

@article {pmid42270638,
year = {2026},
author = {Hauptmann, M and Gottschick, C and Muthukumarasamy, U and Klee, B and Strowig, T and Mikolajczyk, R and Schaible, UE},
title = {High early-life gut Bacteroides links to microbiome stability, resilience, and risk for childhood infections.},
journal = {NPJ biofilms and microbiomes},
volume = {12},
number = {1},
pages = {},
pmid = {42270638},
issn = {2055-5008},
mesh = {Humans ; *Bacteroides/isolation & purification/classification/drug effects/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/drug effects ; Anti-Bacterial Agents/therapeutic use ; Infant ; Child, Preschool ; Female ; Male ; Longitudinal Studies ; Disease Susceptibility ; Germany ; Biodiversity ; },
abstract = {Early childhood events, up to the age of two, are critical for the development of the microbiome and balanced immunity later in life. We investigated whether susceptibility to infections and microbiome resilience after antibiotic treatment are associated with key taxa in the early childhood microbiota. Therefore, we performed longitudinal microbiota analysis from stool samples of children within the German LoewenKIDS intensified subcohort. According to the exposure to antibiotic treatment, sample groups were defined as never-treated controls, 45-225 days pre-treatment (pre45-225), 0-30 days pre-treatment (pre0-30), 0-30 days post-treatment (post0-30), or >90 days post-treatment and age >540 days (post>90). 1176 stool samples of 162 children were included in our analysis, of which 49 children received antibiotics. Using generalized linear mixed models adjusted for age, we show that high abundance of Bacteroides was associated with receiving antibiotic treatment 45-225 days later, while low Bacteroides abundance before treatment was associated with low alpha diversity and increased beta diversity post treatment. Our data suggest a key role of the genus Bacteroides for the susceptibility to infections requiring antibiotic treatment and for microbiome stability and resilience in early childhood.},
}

Humans
*Bacteroides/isolation & purification/classification/drug effects/genetics
Feces/microbiology
*Gastrointestinal Microbiome/drug effects
Anti-Bacterial Agents/therapeutic use
Infant
Child, Preschool
Female
Male
Longitudinal Studies
Disease Susceptibility
Germany
Biodiversity

@article {pmid42270686,
year = {2026},
author = {Lee, S and Lee, H and Kim, JW and Kim, HJ and Lee, KJ},
title = {Quantitative evaluation of microbiome sequencing resolution under varying experimental conditions using defined mock communities.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-53382-x},
pmid = {42270686},
issn = {2045-2322},
abstract = {Objective evaluation of sequencing resolution is crucial for comparing technologies and ensuring reproducibility in microbiome analysis. Specifically, a systematic approach is necessary to quantitatively assess the effect of various platforms and experimental conditions on species-level resolution. Therefore, this study quantitatively evaluated multiple strategies, including 16S V3-V4 (16P), full-length 16S rRNA gene (16F), and whole metagenome shotgun sequencing (WMS), using a commercial DNA-based mock community (MC) and a domestically developed whole-cell MC (Korea MC [KMC]). The WMS strategy included 12 combinations of input DNA concentrations and sequencing output levels. A total of 64 WMS libraries were constructed for KMC samples, and 112 sequencing datasets were analysed. Taxonomic resolution was assessed using an adjusted F1-score integrating detection sensitivity and abundance-level reproducibility. Qualitatively examining the detected species against the expected species across platforms, WMS showed a true positive abundance ratio of over 90%, 16F was observed to have an average of 60%, and 16P was observed to have an average of less than 10%. The combination of 10 ng input and 10 gigabases output consistently yielded the highest species-level resolution. However, reduced performance was observed in some MCs under 1 ng or 100 ng DNA input conditions. Detection sensitivity varied by taxon and condition. Specifically, Streptococcus pneumoniae and Cryptococcus neoformans were detected only under high-input or -output conditions, whereas Escherichia coli exhibited optimal accuracy at intermediate inputs. Acinetobacter species demonstrated reduced resolution as input DNA increased. KMC samples showed species- and format-specific variability in DNA extraction efficiency. This study presents a quantitative evaluation of species-level resolution across sequencing conditions using defined mock communities. The results highlight how sequencing configuration and taxon-specific characteristics can influence detection performance and provide insights for interpreting microbiome sequencing results under different experimental conditions.},
}

@article {pmid42271018,
year = {2026},
author = {Mohssen, M and Zayed, AA and Kigerl, KA and Du, J and Smith, GJ and Schwab, JM and Sullivan, MB and Popovich, PG},
title = {Disruption of the spinal cord-gut axis alters microbial dynamics and carbohydrate cross-feeding in the gut.},
journal = {Communications biology},
volume = {},
number = {},
pages = {},
doi = {10.1038/s42003-026-10447-x},
pmid = {42271018},
issn = {2399-3642},
support = {890085//Craig H. Neilsen Foundation (Neilsen Foundation)/ ; ABI#2149505//National Science Foundation (NSF)/ ; DBI#2022070//National Science Foundation (NSF)/ ; },
abstract = {Spinal cord-gut communication regulates gut bacteria, yet the underlying mechanisms remain poorly understood. Previous studies relied primarily on gene markers with limited functional analysis or genome-resolved snapshots from small cohorts. Here, we assessed microbiome dynamics via genome-resolved metagenomics on 333 samples from male and female C57BL/6 mice collected before and up to six months after surgical disruption of the spinal cord-gut axis. This resulted in 6,635 microbial draft genomes as a foundation for a new "Mouse B6 Gut Catalog" that significantly expands species and strain representation for this widely used laboratory mouse strain. Sampling revealed that disrupted spinal cord-gut signaling causes persistent, lesion-severity-, sex-, and time-specific shifts in microbial community composition, with consistent depletion of Lactobacillus johnsonii. Feeding purified L. johnsonii to spinal cord-injured mice prevented metabolic defects and systemic inflammation caused by disruption of the spinal cord-gut axis. Analyses using genome-resolved and community-based metabolic profiling indicated altered carbohydrate sharing and utilization of gut microbes, potentially depleting L. johnsonii, providing a genome-inferred mechanism for future hypothesis testing. This study improves murine microbiome catalogs, illustrates how metagenome-informed microbial interventions can provide a mechanistic understanding to improve host health, and underscores the vital role of a healthy spinal cord in regulating gut ecosystem function.},
}

@article {pmid42271159,
year = {2026},
author = {Liang, X and Zhang, Y and Xie, W and Xiong, J and Lin, S and Wen, Y and Cao, Y and Yu, S and Wang, K and Deng, J and Zhao, J and Xu, J and Hu, Y and Liu, Y and Feng, Q and Zhong, Y and Gonzalez, FJ and Xie, C},
title = {Dietary fat alters goblet cell function and microbial bile acid metabolism to promote intestinal lipid absorption in mice.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42271159},
issn = {2058-5276},
support = {92557304//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82530024//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82521004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82570954//National Natural Science Foundation of China (National Science Foundation of China)/ ; },
abstract = {Dietary fat reshapes host-microbiota interactions, yet the upstream events that mediate overnutrition-driven microbiome alterations and metabolic dysfunction remain unclear. Here we compared mouse models of diet-induced and genetic obesity using multi-omics to identify the colonic mucus niche as an early, diet-sensitive driver of metabolic dysfunction. Excessive dietary lipids impaired glutamine metabolism and redox homeostasis in goblet cells, thinning the mucus layer and depleting the mucus-adapted symbiont Akkermansia muciniphila while expanding the bile-acid-transforming bacterium Clostridium scindens. Altered bile acid composition along the enterohepatic axis activates FXR-PLIN2 signalling in the small intestine and increases fat absorption. In parallel, enterocytes upregulate the PPARα-dependent uptake pathway that supports luminal lipid entry. Supplementation with glutamine restored goblet cell function and the gut microbiota-derived bile acid pool, thereby reducing intestinal FXR activation and lipid uptake. These findings reveal that dietary fat impairs colonic goblet cell function and reshapes microbial bile acid metabolism, influencing small-intestinal fat absorption.},
}

@article {pmid42271189,
year = {2026},
author = {Ojeh, N and Mohapatra, BR and O'Shea, M and Springer, D and Ward, J and Sallu, M and Paquette, N and Gooding, K and Springer, A and Peter Adams, O},
title = {Phylogenetic Profiling of the Diabetic Foot Ulcer Microbiome of an Afro-Caribbean Population.},
journal = {MicrobiologyOpen},
volume = {15},
number = {3},
pages = {e70329},
pmid = {42271189},
issn = {2045-8827},
support = {//University of the West indies/ ; },
mesh = {Humans ; *Diabetic Foot/microbiology ; *Bacteria/classification/genetics/isolation & purification ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Fungi/classification/genetics/isolation & purification ; *Phylogeny ; Male ; Female ; Middle Aged ; Pilot Projects ; Skin Microbiome ; Barbados ; Diabetes Mellitus, Type 2/complications ; Caribbean People ; Aged ; DNA, Bacterial/genetics/chemistry ; DNA, Ribosomal Spacer/genetics/chemistry ; },
abstract = {Diabetic foot ulcers (DFUs) are associated with high morbidity, amputation rates, and healthcare costs in Barbados. This pilot study compares the microbiome diversity of chronic DFUs and paired normal skin (controls) from biopsies in Afro-Caribbean patients with type 2 diabetes using Illumina amplicon sequencing targeting the 16S ribosomal RNA (rRNA) gene and the internal transcribed spacer 2 (ITS2) region. Both DFUs and controls harbored diverse bacterial and fungal communities, with differences in taxonomic composition and relative abundance profiles. The dominant bacterial genera were Corynebacterium (18.3% in DFUs, 24.3% in controls) and Staphylococcus (14.9% in DFUs, 14.1% in controls). The dominant bacterial species was Corynebacterium striatum (17.3% in DFUs, 23.8% in controls) followed by Pseudomonas aeruginosa in DFUs (8.9%) and Staphylococcus aureus in controls (13.3%). The dominant fungal genera was Densospora (12% in DFUs, 12.6% in controls). The dominant fungal species was Rhodotorula graminis in DFUs (6.18%) and Paracamarosporium leucadendri in controls (3.85%). Candida duobushaemulonii, with intrinsic resistance to antifungal agents, was detected with higher relative abundance in DFUs than in controls (4.44% vs. 2.36%). Fungal Shannon alpha diversity was significantly reduced in DFUs (p = 0.039), while beta diversity did not differ between groups for bacteria (p = 0.982) or fungi (p = 0.975). The differences in taxonomic composition and relative abundance profiles, and co-occurrence of clinically relevant bacterial and fungal taxa, highlight the potential role of polymicrobial communities in DFU chronicity in the Afro-Caribbean cohort studied, and supports future studies to evaluate implications for antimicrobial stewardship.},
}

Humans
*Diabetic Foot/microbiology
*Bacteria/classification/genetics/isolation & purification
*Microbiota
RNA, Ribosomal, 16S/genetics
*Fungi/classification/genetics/isolation & purification
*Phylogeny
Male
Female
Middle Aged
Pilot Projects
Skin Microbiome
Barbados
Diabetes Mellitus, Type 2/complications
Caribbean People
Aged
DNA, Bacterial/genetics/chemistry
DNA, Ribosomal Spacer/genetics/chemistry

@article {pmid42271199,
year = {2026},
author = {Steinert, RE and Van den Abbeele, P and Schaefer, C and Poppe, J and Vu, LD and Bajic, D},
title = {Carotenoids modulate fermentation of inulin ex vivo in IBS and overweight adult gut microbiota.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05271-6},
pmid = {42271199},
issn = {1471-2180},
abstract = {BACKGROUND: Carotenoids have direct antioxidant and anti-inflammatory health benefits. Owing to their low bioavailability, they also reach the colon, yet their microbiome interactions remain poorly characterized.

METHODS: We investigated how β-carotene (BC), lutein (LU), lycopene (LY) and zeaxanthin (ZE), at biological relevant doses (between 1 and 60 mg/d), impact composition and metabolite production of irritable bowel syndrome (IBS) and overweight (OW) adult gut microbiota using the ex vivo SIFR[®] fermentation system (systemic intestinal fermentation research). Fresh fecal samples were collected from 12 donors (n = 6 per cohort) and incubated for 24 h under anaerobic conditions, with carotenoids administered alone or in combination with prebiotic inulin (IN, tested at 2.5 g/day).

RESULTS: We observed phenotype-specific microbiota characteristics for each cohort at baseline. Carotenoids alone had only minor effects but in combination with prebiotic inulin significantly altered community composition (Bray-Curtis dissimilarity, P < 0.05) and enhanced short-chain fatty acid (SCFA) production. Most carotenoids increased butyrate production vs. inulin alone with ZE (at 2 mg/d) in IBS (+ 7.6%) and LU (at 60 mg/d) in OW (+ 8.0%) showing the strongest effects (padjusted<0.10). In contrast, LY (at 45 mg/d) uniquely increased acetate (+ 3.5%) and propionate (+ 8.0%) at the expense of butyrate (-7.5%, padjusted<0.10) when compared vs. inulin only. Changes in SCFA correlated with carotenoid- and cohort-specific shifts in the abundance of Bifidobacterium, Alistipes, Akkermansia, Faecalibacterium and Coprococcus. ZE also enhanced the effect of inulin on the health-related metabolites 3-phenyllactic acid (PLA) and 2-hydroxyisocaproic acid (HICA), particularly IBS subjects (padjusted<0.20).

CONCLUSIONS: Antioxidant carotenoids may support anaerobic gut microbes including dominant butyrate producers and counteract phenotype-specific dysbiosis, potentially offering novel dietary approaches for IBS and obesity-associated dysbiosis. As these effects were observed when carotenoids were combined with inulin, carotenoids may have greater impacts when consumed as part of a fiber-rich diet, reflecting their natural occurrence in plant-based foods.},
}

@article {pmid42271362,
year = {2026},
author = {Zhang, Z and Lu, T and Dong, B and Liu, J and Zhang, Y and Li, S and Liu, H and Li, X and Guan, T and Guo, H and Yan, Q and Lei, Z and Yu, X and Wang, L and Kang, J and Li, L and Zhao, D},
title = {Gut fungal signatures in colorectal cancer and their potential for supporting diagnosis: a multi-cohort metagenomic analysis.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08403-8},
pmid = {42271362},
issn = {1479-5876},
support = {82370563//National Natural Science Foundation of China/ ; 2024RJ018//Outstanding Young Scientific and Technological Talents Project of Dalian/ ; 2023-MSLH-032//Joint Funds of the National Natural Science Foundation of Liaoning Province/ ; },
abstract = {BACKGROUND: Colorectal cancer (CRC) is influenced by host factors and environmental exposures that shape gut microbial ecosystems. Although bacterial and viral alterations in CRC have been widely investigated, the role of gut fungi remains underexplored, partly because of their low biomass and the limited availability of well-curated fungal reference genomes.

METHODS: We conducted a large-scale metagenomic analysis across 9 publicly available cohorts comprising 1,433 fecal samples to characterize CRC-associated fungal alterations and fungal-bacterial co-abundance patterns. The predictive value of microbial signatures was assessed using LASSO and random forest models, with external validation performed in 6 independent cohorts comprising 272 samples.

RESULTS: Multi-cohort analysis revealed CRC-associated alterations in gut fungal community structure and selected diversity measures. Differential abundance analysis identified 15 fungal species with recurrent changes across cohorts. Among them, Saccharomyces cerevisiae c86 and Trichophyton rubrum c61 showed predominant enrichment in healthy controls, whereas Barnettozyma c122 and Pseudopithomyces c302 showed predominant enrichment in CRC. Fungal-only models exhibited limited standalone predictive capacity. However, integrating fungal features with bacterial biomarkers modestly improved CRC prediction performance compared with bacterial-only models. In external validation, the random forest-based fungal-bacterial model increased the mean AUC from 0.722 to 0.762, with improved AUCs in 5 of the 6 validation cohorts.

CONCLUSIONS: This study suggests that CRC is associated with gut fungal dysbiosis and supports the exploratory value of gut fungal signatures as adjunctive features in microbiome-based CRC prediction models. These findings highlight the importance of incorporating fungal communities into CRC microbiome research while emphasizing the need for prospective and mechanistic validation.},
}

@article {pmid42271469,
year = {2026},
author = {Xing, J and Jiang, Z and Jing, X and Li, Y and Guo, F and Liu, P and Liu, Z and Sun, N},
title = {Analysis of gut microbiota and intestinal mucosal neurotransmitter changes and their correlation in adolescent depression mice.},
journal = {Annals of general psychiatry},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12991-026-00686-x},
pmid = {42271469},
issn = {1744-859X},
abstract = {BACKGROUND: Adolescent depression is a major mental health disorder with increasing prevalence and substantial long-term consequences. Although growing evidence suggests that the gut-brain axis is involved in depression, the relationships among gut microbiota, intestinal mucosal neurotransmitters, and adolescent depression remain insufficiently understood. This knowledge gap limits a better understanding of the pathophysiological mechanisms underlying adolescent depression and the identification of potential microbiota-related targets. Therefore, this study aimed to investigate alterations in gut microbiota and intestinal mucosal neurotransmitters, as well as their correlations, in an adolescent mouse model of depression.

METHODS: We established an adolescent depression mouse model using chronic unpredictable mild stress (CUMS), and collected data with the Smart video tracking system. We collected intestinal contents and mucosal tissues from mice. We analyzed gut microbial composition using metagenomic sequencing and quantified mucosal neurotransmitters with liquid chromatography-tandem mass spectrometry (LC-MS/MS). We analyzed correlations among gut microbiota, intestinal mucosal neurotransmitters, and behavioral indicators.

RESULTS: Mice in the CUMS group exhibited a significantly reduced sucrose preference rate in the sucrose preference test (P < 0.001); a significantly prolonged immobility time in the forced swim test (P < 0.01); and a significantly decreased total movement distance in the open field test (P < 0.01). No significant intergroup difference was observed in the tail suspension test. Regarding the gut microbiome, the CUMS group showed significantly lower Simpson index (P = 0.018) and Pielou's evenness index (P = 0.022). Beta diversity analysis indicated a statistically significant but modest between-group difference in community structure (ANOSIM R = 0.145, P = 0.03); this finding was supported by PERMANOVA (Bray-Curtis; pseudo-F = 1.675, R² = 0.0897, P = 0.033). LEfSe (Linear discriminant analysis Effect Size) analysis suggested 27 candidate taxa with discriminatory signals between groups (nominal P < 0.05; exploratory). Neurotransmitter analysis demonstrated that levels of 5-HIAA (5-hydroxyindoleacetic acid), 5-HT (serotonin), 5-HTP (5-hydroxytryptophan), and Kyn (kynurenine) in the colon were significantly decreased in the CUMS group, whereas levels of PA (phenylethylamine) and NE (norepinephrine) were significantly elevated (P < 0.05). Spearman correlation analysis found that Lactobacillus and Lactobacillus acidophilus correlated positively with sucrose preference and negatively with immobility in the forced swim test. Lactobacillus acidophilus also showed a positive correlation with 5-HT pathway metabolites: 5-HIAA, 5-HT, 5-HTP, and Kyn.

CONCLUSION: Adolescent mice exposed to CUMS showed depression-relevant behavioral alterations, shifts in gut microbiota composition, and changes in 5-HT pathway metabolites. Gut microbiota dysbiosis was significantly associated with alterations in 5-HT pathway metabolites. Because this study is correlational, causal relationships require validation in future interventional studies.},
}

@article {pmid42271554,
year = {2026},
author = {Pons, A and Aspillaga, E and Catalán, IA and Viver, T and Arlinghaus, R and Martorell-Barceló, M and Barcelo-Serra, M and Alós, J},
title = {Social organization and habitat use shape the gut microbiome of a marine fish.},
journal = {The Journal of animal ecology},
volume = {},
number = {},
pages = {},
doi = {10.1111/1365-2656.70286},
pmid = {42271554},
issn = {1365-2656},
support = {FPI/2269/2019//FPI Predoctoral Fellowship Direcció General de Innovació i Recerca of the Balearic Islands Government/ ; PID2019‑104940GA‑I00//CLOCKS Project/ ; PID2022-139349OB-I00//METARAOR Project/ ; #033W024A//German Federal Ministry of Education and Research/ ; PD/041/2021//University of the Balearic Islands/ ; },
abstract = {The gut microbiome hosts diverse bacterial communities that significantly influence individual spatial behaviour in animal societies. However, this relationship remains understudied in marine fish due to the challenges associated with measuring behavioural traits in free-living fish and simultaneously obtaining gut microbiome composition data. In this study, we conducted a field experiment to explore the relationship between space and habitat use, social organization, and gut microbiome composition in marine fish. We used a novel high-resolution acoustic telemetry system to collect 7930 one-day-long movement trajectories from 232 individuals of Xyrichtys novacula of the same population (153 females, 79 males) near the coastline of Mallorca, Spain. A subset of these individuals was recaptured to analyse the diversity of core and non-core gut microbiome, quantified using operational phylogenetic units (OPUs) based on 16S rRNA gene amplicons through Illumina sequencing. Individuals closer to Posidonia oceanica seagrass meadow had higher non-core microbiome diversity, especially larger individuals. Multivariate analysis showed no significant differences in microbiome composition across the tested variables (i.e. body size, territory size, degree, strength, distance to the seagrass meadow, and sex), but males showed a visually greater, but non-significant, variability in core microbiome composition. Core microbiome composition was weakly associated with social harem structure. These findings indicate that gut microbiome composition is primarily shaped by local habitat conditions, while social organization may contribute weakly and indirectly, pending further experimental validation.},
}

@article {pmid42271557,
year = {2026},
author = {Wassel, MA and Makabe-Kobayashi, Y and Iqbal, MM and Huang, C and Amano, M and Shimizu, A and Mandario, MAE and Takatani, T and Sakakura, Y and Hamasaki, K},
title = {Tetrodotoxin (TTX) reshapes the functional potential of the gut microbiome in juvenile tiger pufferfish (Takifugu rubripes) across salinity gradients.},
journal = {Animal microbiome},
volume = {8},
number = {1},
pages = {},
pmid = {42271557},
issn = {2524-4671},
support = {22K05822 and 25K09271//JSPS KAKENHI/ ; No. JURCAOSIRG23-08//Interdisciplinary Collaborative Research Program of the Atmosphere and Ocean Research Institute, The University of Tokyo/ ; },
abstract = {BACKGROUND: The gut microbiota of aquatic organisms responds dynamically to environmental stressors such as salinity fluctuations. However, how microbial communities respond to combined environmental and dietary stressors, and how these interactions influence functional potential, remains incompletely understood. Here, we investigated whether dietary administration of tetrodotoxin (TTX), a neurotoxin naturally accumulated by juvenile tiger pufferfish (Takifugu rubripes), alters gut bacterial community composition and functional potential across salinity gradients.

RESULTS: Juvenile T. rubripes were reared under four salinity conditions (34.0, 17.0, 8.5, and 2.1 ppt) and fed either a control or TTX-containing diet (1.22 MU/g). Integrated 16S rRNA gene amplicon and shotgun metagenomic analyses revealed that salinity was the primary driver of gut microbiota structure, with only 5.1% of amplicon sequence variants (ASVs) shared across salinity levels. In contrast, TTX ingestion induced salinity-dependent shifts in specific bacterial taxa rather than broad community restructuring. Core taxa, including Arcobacteraceae, Mycoplasma, Brevinema, and Vibrio, were consistently detected across treatments but exhibited pronounced changes in relative abundance and functional potential under salinity and toxin stress. Metagenomic profiling indicated that Arcobacteraceae encode genetic modules for amino acid and B vitamin biosynthesis that are absent or incomplete in the host genome, suggesting metabolic complementarity. TTX ingestion reduced the genetic representation of these biosynthetic pathways at specific salinities, particularly those associated with Arcobacteraceae. Conversely, phenylalanine biosynthesis potential enriched in TTX-fed fish, primarily associated with Vibrio spp., indicating a possible microbial functional adaptation to toxin administration. Despite these microbiome and functional shifts, TTX ingestion did not affect host growth.

CONCLUSIONS: Dietary neurotoxin administration reshaped gut microbiome functional profiles in a salinity-dependent manner, highlighting microbiome plasticity and improving our understanding of host-microbiota-environment interactions relevant to aquaculture health management.},
}

@article {pmid42271576,
year = {2026},
author = {Manikandan, DC and Sathiyabama, M},
title = {Agro-nanotechnology: A comprehensive overview of its role in groundnut production.},
journal = {Journal of the science of food and agriculture},
volume = {},
number = {},
pages = {},
doi = {10.1002/jsfa.70783},
pmid = {42271576},
issn = {1097-0010},
abstract = {Groundnut (Arachis hypogaea L.) is an economically important oilseed crop cultivated worldwide for its nutritional and industrial value. However, its productivity and quality are frequently constrained by several challenges, including abiotic and biotic stresses, post-harvest losses, and aflatoxin contamination. In recent years, agro-nanotechnology has emerged as a promising approach to address these limitations by improving nutrient delivery, enhancing plant defense responses, and supporting advanced agricultural strategies. Nanoparticles have been reported to improve nodulation and rhizosphere interactions by influencing plant-microbiome dynamics, thereby contributing to enhanced crop growth and stress tolerance. However, direct evidence remains limited, and several observations are derived from related crop systems. Recent advances have highlighted the integration of nanotechnology with CRISPR-Cas genome editing systems, enabling targeted and DNA-free delivery of gene-editing components for crop improvement. It has been proposed that such approaches could contribute to improved oleic acid content, reduced allergenicity, and enhanced disease resistance in groundnut. Nano-remediation strategies have also shown potential in mitigating pesticide residues and heavy metal contamination, thereby reducing the risk of aflatoxin accumulation. Key developments in this field include nano-formulations for precise nutrient management, modulation of plant-microbiome interactions, and nanoparticle-mediated delivery systems for genome editing technologies. Nevertheless, several challenges remain, including regulatory uncertainties, potential environmental risks, nanoparticle toxicity, and the lack of standardized field-scale evaluations. Addressing these limitations through interdisciplinary research, robust risk-assessment frameworks, and crop-specific regulatory policies will be essential for the responsible implementation of agro-nanotechnology. Overall, this review highlights the emerging role of agro-nanotechnology in addressing key constraints in groundnut production, while emphasizing the need for further groundnut-specific validation and field scale applicability. © 2026 Society of Chemical Industry.},
}

@article {pmid42271632,
year = {2026},
author = {Alessandra, N and Paola, G and Anna, BC and Chiara, C and Cristina, ÁA and Ángeles, BM and Ludovica, R and Isabel, N},
title = {Compost from decentralized composting models used for improving soil quality and plant-rhizosphere microbial community response to salinity stress.},
journal = {Integrated environmental assessment and management},
volume = {},
number = {},
pages = {},
doi = {10.1093/inteam/vjag099},
pmid = {42271632},
issn = {1551-3793},
abstract = {The new EU Soil Monitoring Directive establishes the regulatory framework for assessing soil health and mitigating critical threats like salinity and contamination in degraded soils. While it promotes nature-based solutions-such as compost amendment-for soil restoration, compost efficacy remains strictly dependent on feedstock origin and processing technologies, which influence agronomic performance and potential risks of introducing emerging contaminants into soil. This study evaluated, for the first time within a holistic One Health framework, the efficiency of various composts in mitigating plant salinity stress while considering the possible spread of emerging contaminants, such as antibiotic resistance genes (ARGs) and the mobile genetic element intI1. The salinity tolerance of the Rosmarinus officinalis-microbiome system was assessed in pot experiments using degraded soil amended with four composts from various production systems: community (CC) and decentralized (DUC) urban composts, derived from the organic fraction of municipal solid waste and yard trimmings, and two agro-composts based on cattle manure and barley straw (SA) and on olive mill waste, leaves, poultry manure, and pruning residues (MA). Plant biomass, soil microbial activity and abundance were evaluated, alongside ARG dynamics. A Soil Quality Index was also calculated. Data were analysed using non-parametric ANOVA (p < 0.05). Salt stress significantly reduced plant biomass, while CC and DUC composts mitigated this effect, enhancing plant growth under this stress. Interestingly, the rhizosphere microbial community responded to salinity by increasing its activity, presumably owing to a pre-existent defence osmotic mechanism, not linked to the compost presence. However, compost type influenced microbial abundance and ARG dynamics. Notably, although salinity and composts promoted an ARG presence in soil, CC resulted more effective in improving soil quality and salt plant tolerance, including in a One Health prospective, confirming the importance of the compost production process for the use of these improvers.},
}

@article {pmid42272236,
year = {2026},
author = {van der Meulen, LWJ and Bergmans, ME and Assil, S and Klarenbeek, N and de Kam, ML and Tibboel, AJ and Brach, T and Herpers, BL and Frieling, J and de Jong, V and Freyee, B and van Doorn, MBA and Rissmann, R and Niemeyer-van der Kolk, T},
title = {S. aureus colonization and clinical symptoms remain stable upon topical XZ.700 treatment: Results of a double-blind randomized clinical trial in patients with mild to moderate atopic dermatitis.},
journal = {British journal of clinical pharmacology},
volume = {},
number = {},
pages = {},
doi = {10.1002/bcp.70630},
pmid = {42272236},
issn = {1365-2125},
support = {//Micreos Human Health B.V./ ; },
abstract = {AIM: Recovering dysbiosis may improve atopic dermatitis (AD) symptoms. XZ.700 is a recombinant chimeric endolysin that specifically targets Staphylococcus aureus and could be a new treatment option for patients with AD. The aim of this first-in-human study was to evaluate the safety, tolerability and efficacy of topical XZ.700 and explore the pharmacodynamic effects in patients with mild to moderate AD.

METHOD AND MATERIALS: This study consisted of Part A and Part B. In Part A, subjects were randomized and received XZ.700 10 μg/g, XZ.700 30 μg/g, XZ.700 100 μg/g or vehicle twice daily for 7 days on nonlesional skin and on all lesions (1% ≤ BSA ≤ 10%). In Part B, subjects received XZ.700 100 μg/g or vehicle on all lesions twice daily for 14 days (1% ≤ BSA ≤ 15%). Clinical scores and patient-reported outcomes were recorded. Pharmacodynamic measurements were taken.

RESULTS: In total, 35 patients completed the study. Tolerability of XZ.700 was acceptable. XZ.700 100 μg/g showed no evidence of effect on cultured S. aureus (estimated difference -52.9% CFU/mL; 95% CI -88.4% to 90.8%), oSCORAD (1.03; 95% CI -5.20 to 7.26) or EASI (-0.534; 95% CI -2.48 to 1.41). Furthermore, XZ.700 treatment did not result in a significant reduction in the relative abundance of S. aureus via metagenomics or other pharmacodynamic outcomes.

CONCLUSION: Tolerability and safety of short-term topical administration of XZ.700 100 μg/g for 14 days were acceptable in most participants; however, some local application-site events occurred, and one hypersensitivity reaction led to discontinuation. XZ.700 did not demonstrate target engagement or clinical benefit vs. vehicle under the tested conditions.},
}

@article {pmid42272277,
year = {2026},
author = {Mantargi, MJS and Alavudeen, SS and Easwaran, V and Goruntla, N and Afzal, M and Khan, NA and Hussein, ATM and Mohammad, AAS},
title = {Obesity-associated carcinogenesis with treatment gaps: A narrative review of updated evidence and natural products strategies.},
journal = {Journal of physiology and pharmacology : an official journal of the Polish Physiological Society},
volume = {77},
number = {2},
pages = {143-154},
doi = {10.26402/jpp.2026.2.01},
pmid = {42272277},
issn = {1899-1505},
mesh = {Humans ; *Obesity/complications/drug therapy/metabolism ; Animals ; *Biological Products/therapeutic use ; *Neoplasms/drug therapy/etiology/metabolism ; *Carcinogenesis/drug effects/metabolism ; Phytochemicals/therapeutic use ; Antineoplastic Agents/therapeutic use ; },
abstract = {Obesity contributes significantly to cancer development due to superfluous adipose tissue interfering with physiologic balance. The current narrative review outlines the molecular and physiological pathways linking obesity and cancer and highlights the role of natural products as preventive and therapeutic agents. Underlying processes intertwining obesity and cancer include chronic low-grade inflammation, insulin resistance, hormonal imbalance, adipokine dysregulation, oxidative stress, and changes in the gut microbiome. All of these are used to facilitate tumor-promoting microblood to increase tumor growth and help cancerous cells proliferate and metastasize. There are specific mediators that are important in the activation of oncogenic signalling pathways, such as tumor necrosis factor-alpha, interleukin 6, insulin-like growth factor-1, estrogen, leptin, and reactive oxygen species. Phytochemicals that have the potential to be used as natural anti-inflammatory, antioxidant, and anticancer agents include, but are not limited to, curcumin, resveratrol, epigallocatechin gallate (EGCG), quercetin, berberine, gingerol, and capsaicin. The compounds regulate major molecular pathways of the obesity-related cancers. A new method of delivery that automatically and involuntarily targets the delivery mechanism by use of nanotechnologies has demonstrated its capacity in increasing bioavailability and therapeutic effects of these bioactive agents. To reduce the burden of this impact of obesity on cancers, a strategy involving a blend of lifestyle changes, pharmacological treatment, and science-based natural solutions is required. We conclude that in order to increase the potential of natural products, there is a need to have clinical studies on oncology and public health, as well as regulatory advancement.},
}

Humans
*Obesity/complications/drug therapy/metabolism
Animals
*Biological Products/therapeutic use
*Neoplasms/drug therapy/etiology/metabolism
*Carcinogenesis/drug effects/metabolism
Phytochemicals/therapeutic use
Antineoplastic Agents/therapeutic use

@article {pmid42272345,
year = {2026},
author = {Bai, Y and Huang, H and Hang, X and Hu, S and Tong, Q and Xu, J and Jia, J and Bi, H},
title = {Multi-Targeting Carnosic Acid Kills Drug-Resistant Helicobacter pylori With Narrow-Spectrum Activity.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e76080},
doi = {10.1002/advs.76080},
pmid = {42272345},
issn = {2198-3844},
support = {82473974//National Natural Science Foundation of China/ ; 32470188//National Natural Science Foundation of China/ ; GZC20251367//Postdoctoral Fellowship Program of the China Postdoctoral Science Foundation/ ; 2025M782601//China Postdoctoral Science Foundation/ ; 326QN0613//Hainan Provincial Natural Science Foundation of China/ ; 326QN0606//Hainan Provincial Natural Science Foundation of China/ ; 2025NHCTDC12002//National Health Commission Key Laboratory of Tropical Disease Control of China/ ; 2026NHCTDC12004//National Health Commission Key Laboratory of Tropical Disease Control of China/ ; XSTS2026115//Academic Improvement Support Program of Hainan Medical University of China/ ; XSTS2026003//Academic Improvement Support Program of Hainan Medical University of China/ ; },
abstract = {Helicobacter pylori (H. pylori) is a significant global human pathogen intricately linked to gastritis, peptic ulcers, and gastric cancer. The escalating challenge of antimicrobial resistance and the adverse effects of conventional antibiotics on the gut microbiome necessitate the development of novel, targeted therapeutics. In this study, we demonstrate that carnosic acid (CA), a natural compound derived from traditional Chinese medicine, exhibits potent and specific anti-H. pylori activity in vitro, with no detectable resistance observed after prolonged serial passaging. CA also displayed enhanced antibacterial efficacy under physiologically relevant acidic conditions, correlating with its strong inhibition of urease, a key colonization factor for H. pylori. Beyond urease suppression, CA acted through multiple mechanisms, including inhibiting biofilm formation and disrupting mature biofilms, impairing bacterial motility, and compromising cell membrane integrity. In vivo, the combination of CA and omeprazole achieved superior eradication in a mouse model of multidrug-resistant H. pylori infection compared to standard triple therapy. Furthermore, CA treatment showed negligible toxicity to host tissues and minimal disruption to the diversity and composition of the gut microbiota. These findings position CA as a promising lead compound against drug-resistant H. pylori, offering a multi-targeting and microbiota-friendly strategy to combat this pathogen.},
}

@article {pmid42272754,
year = {2026},
author = {Wu, H and Shi, L and Wang, C and Liang, Y and Huang, C},
title = {Integrative metagenomic and metabolomic analysis reveals a gut microbiota-metabolite-immune axis in pediatric allergic rhinitis with functional constipation.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1779298},
pmid = {42272754},
issn = {2235-2988},
abstract = {OBJECTIVE: This study aimed to delineate the alterations in the gut microbiome and host amino acid metabolism in children with comorbid allergic rhinitis and functional constipation (ARFC), and to explore their links with clinical allergy markers.

METHODS: We performed shotgun metagenomic sequencing and amino acid-targeted metabolomics on fecal samples from 19 children with ARFC and 16 age-matched healthy controls (HC). Microbial community structure, differentially abundant taxa, and metabolic profiles were analyzed. Integrative analyzes, including correlation networks and machine learning modeling, were employed to investigate microbiota-metabolite-host interactions.

RESULTS: Significant beta-diversity distinction was found between ARFC and HC gut microbiota (PCoA R[2]=0.228, P = 0.001). ARFC children exhibited enrichment of mucin-degrading Bacteroidota (e.g., Bacteroides, Phocaeicola) and depletion of beneficial Bacillota (e.g., Bifidobacterium, Blautia). Metabolomics identified 50 differentially abundant metabolites, with widespread downregulation of immunomodulatory amino acids including L-glutamine and γ-aminobutyric acid (GABA). Enriched pathways involved mTOR and FoxO signaling, and neurotransmitter synapses. Integration revealed significant correlations between specific microbial genera (e.g., Bacteroides, Proteus) and metabolites (e.g., kynurenine), and between gut species (e.g., Bacteroides thetaiotaomicron) and serum IgE levels. A machine learning model integrating key microbial and metabolic features, evaluated under a rigorous leave-one-out cross-validation framework, demonstrated robust discriminative performance in this cohort (AUC = 0.946).

CONCLUSION: This multi-omics study unveils a distinct "gut dysbiosis-metabolite dysregulation-immune dysfunction" axis in ARFC children. The synergistic shift towards a mucolytic, pro-inflammatory microbiota alongside deficient immunomodulatory metabolite production, which correlates with clinical allergy markers, provides a novel mechanistic framework for this comorbidity and highlights potential diagnostic biomarkers for future validation.},
}

@article {pmid42272779,
year = {2026},
author = {Jain, A and Johnston, C and Zhang, Y and Oh, J and Tsung, C and Kent, E and Zhang, H},
title = {An overview of current research on exercise interventions in aging and aging-related disease.},
journal = {Frontiers in aging},
volume = {7},
number = {},
pages = {1832962},
pmid = {42272779},
issn = {2673-6217},
abstract = {Global declines in physical activity have contributed to an acceleration in immune aging, characterized by systemic inflammation (inflammaging) and impaired immune regulation (immunosenescence). This narrative review provides an overview of the evidence in both preclinical and clinical models supporting exercise as a critical intervention to counteract immune aging and its related diseases. Regular physical activity modulates systemic inflammation, reduces neutrophil extracellular trap (NET) formation, and promotes favorable shifts in immune cell populations, including T cell and natural killer (NK) cell subsets. Exercise interventions have been associated not only with maintaining immune health but also in mitigating autoimmune disease progression, improving metabolic regulation, enhancing tumor immune surveillance, and reducing neuroinflammation. Emerging studies highlight the role of exercise in promoting vascular normalization within the tumor microenvironment, alleviating tumor hypoxia and acidosis, and restoring T and NK cell function. In the elderly, appropriately prescribed multimodal exercise regimens may lower infection risk without clear evidence of immunodepression, supporting exercise as a potentially safe and effective strategy for immune rejuvenation. Furthermore, novel mechanistic insights, including the modulation of NET burden, IGF-1 signaling, kynurenine metabolism, and microbiome composition, suggest that exercise influences key biological pathways underlying age-related immune decline. While exercise offers broad clinical benefits, future research should prioritize mechanistic studies to optimize exercise prescriptions and inform the development of exercise-mimetic therapeutics. Taken together, investigating the exercise regimens employed in these studies remains a promising intervention for promoting healthy immune aging and improving resilience against chronic inflammatory, metabolic, infectious, and malignant diseases.},
}

@article {pmid42272857,
year = {2026},
author = {Kerezoudi, EN and McKay, S and Kurt, S and De Kreek, M and De Medts, J and Verstrepen, L and Ghyselinck, J and Meulebroek, LV and Calame, W and Albers, R and Mercenier, A and Brummer, RJ and Rangel, I},
title = {Dietary chicory rhamnogalacturonan-I modulates gut microbiota and immune responses in healthy adults.},
journal = {Microbiome research reports},
volume = {5},
number = {2},
pages = {11},
pmid = {42272857},
issn = {2771-5965},
abstract = {Background: Pectic rhamnogalacturonan-I (RG-I) is a dietary fiber that modulates the gut-immune axis. This study evaluates a novel variant of RG-I from chicory root (chRG-I). Methods: In a randomized, double-blind, placebo-controlled trial, 55 healthy adults were stratified by habitual fiber intake and baseline Bifidobacterium levels before receiving 500 mg/day of chRG-I or placebo for four weeks. Primary endpoints included fecal Bifidobacterium counts. Secondary outcomes assessed fecal metabolites, systemic immune cell activation markers, and gastrointestinal symptoms. To provide mechanistic insights, donor-matched fecal samples were used in in vitro fermentation and Caco-2/peripheral blood mononuclear cell co-culture gut barrier models. Results: Supplementation with chRG-I induced a statistically significant bifidogenic effect, with absolute levels peaking at week three, and lower levels of some fecal short-chain fatty acids (SCFA) compared to placebo. However, donor-matched in vitro fermentations with chRG-I confirmed robust production of SCFA and reduction of branched-chain fatty acids levels (BCFA). Systemically, chRG-I upregulated HLA-DR expression on myeloid dendritic cells. Clinically, chRG-I was well-tolerated and slightly improved stool consistency compared to placebo. In an intestinal barrier challenge model, chRG-I fermentates (a pool of metabolites including SCFA and fragments of chRG-I) protected barrier integrity, modulated the cytokine milieu away from a predominantly pro-inflammatory response, as characterized by increased IL4 and IL22 and reduced IL9, IL17A, and IL21. Conclusion: Supplementation with a low dose of chRG-I is well-tolerated, beneficially modulates the gut microbiome - which can protect the intestinal barrier, and subtly enhances systemic immune readiness, suggesting that chRG-I may have benefits as a functional food ingredient.},
}

@article {pmid42272859,
year = {2026},
author = {Fathima, S and Sarkar, T and Sharma, N and Kilgore, PE and Nguyen, HH},
title = {Immunoglobulin Y protects intestinal epithelium and modulates gut microbiota.},
journal = {Microbiome research reports},
volume = {5},
number = {2},
pages = {8},
pmid = {42272859},
issn = {2771-5965},
abstract = {Aim: This study investigated the effects of Muno-IgY®, a multi-pathogen-specific immunoglobulin Y (IgY), on microbial growth, adhesion, fermentation activity, and immune signaling using a multi-tiered in vitro approach. Methods: IgY activity was first evaluated in Caco-2 adhesion and invasion assays using adherent-invasive Escherichia coli (AIEC) at optimized concentrations, followed by assessment in a SHIME® in vitro gut model inoculated with human fecal microbiota enriched in Enterobacteriaceae. Microbial composition, fermentation markers, and metabolite production were analyzed, and downstream effects on epithelial barrier integrity and immune signaling were evaluated using a Caco-2/peripheral blood mononuclear cell (PBMC) co-culture model exposed to SHIME® effluents. Results: Muno-IgY® significantly reduced AIEC adhesion/invasion from 39.76% in controls to 13.08% and 9.13% at 3 and 6 mg/mL, respectively (P < 0.05). In the SHIME® model, IgY significantly increased acetate and propionate production (P < 0.05), alongside a marked increase in ammonium concentration (P < 0.01). Microbial biomass increased modestly, while alpha- and beta-diversity indices were not significantly altered. The compositional shifts indicated enrichment of beneficial and mucin-associated taxa and reduction of opportunistic or pathogenic species in the Muno-IgY® group. In Caco-2/PBMC co-cultures, IgY-treated effluent decreased transepithelial electrical resistance (TEER) indicating reduced barrier integrity (P < 0.05) but significantly decreased pro-inflammatory cytokines Interferon-γ (IFN-γ) and Interleukin-22 (IL-22) (P < 0.05). Conclusions: Muno-IgY® demonstrates the ability to inhibit pathogen adhesion and modulate microbial composition and immune responses in vitro. These findings support its potential as a non-antibiotic approach for microbiome-targeted interventions, although further validation in vivo is required.},
}

@article {pmid42272905,
year = {2026},
author = {Maji, M and Mandal, S and Dhali, A and Miller, LJ and Grove, J and Snowden, JA and Chakrabarti, S and Aithal, G},
title = {Role of neutropenic diet in prevention of infection and graft-versus-host disease in haematopoietic stem cell transplant recipients: systematic review and meta-analysis protocol.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1820858},
pmid = {42272905},
issn = {2296-861X},
abstract = {INTRODUCTION: Haematopoietic stem cell transplantation (HSCT) is associated with substantial early infectious risk, neutropenia, immunosuppression, and graft-versus-host disease (GVHD). Many centres continue to use neutropenic, low-microbial, low-bacterial, or protective diets to reduce dietary exposure to potential pathogens, despite variation in diet definitions and concerns regarding nutritional intake, patient experience, cost, and microbiota recovery. This protocol describes a systematic review and meta-analysis evaluating the benefits and harms of neutropenic diets compared with less restrictive, standard, or food-safety-based dietary approaches in HSCT recipients.

METHODS: We will include randomised and non-randomised comparative studies involving children or adults undergoing HSCT from any graft source and conditioning intensity. Eligible interventions will include neutropenic, low-microbial, low-bacterial, or protective diets; comparators will include unrestricted, less restrictive, standard hospital, or food-safety-based diets. MEDLINE, Embase, CENTRAL, Web of Science, CINAHL, Scopus, ClinicalTrials.gov, and the WHO ICTRP will be searched from inception without language or date restrictions, supplemented by reference screening, expert contact, grey literature, and conference proceedings. Two reviewers will independently screen studies, extract data, and assess risk of bias using RoB 2 for randomised trials and RoBANS for non-randomised studies.

RESULTS: The primary outcomes will be infection rates, acute GVHD, nutritional status, time to neutrophil recovery, and patient satisfaction or quality of life. Secondary outcomes will include overall survival, relapse, chronic GVHD, length of hospitalisation, antibiotic use to day 100, micronutrient deficiency, and cost outcomes. Where appropriate, pooled estimates will be generated using random-effects models, with subgroup and sensitivity analyses used to explore heterogeneity. Certainty of evidence will be assessed using GRADE.

DISCUSSION: This review will clarify whether neutropenic diets reduce infectious complications or GVHD after HSCT, and whether any potential benefit is offset by nutritional, patient-centred, microbiome-related, or economic harms. Findings will inform clinical practice, patient counselling, and future policy on dietary restrictions after HSCT.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251162724, identifier PROSPERO (CRD420251162724).},
}

@article {pmid42272927,
year = {2026},
author = {Sougoufara, S and Bandibabone, J and Chatterley, L and Hughes, I and Taberes, CM and Ball, J and Palliaser, T and Dhokiya, V and Heinz, E and Hughes, G and Walker, T},
title = {The presence of the wAnD strain of Wolbachia is correlated with lower levels of Plasmodium sporozoites and a less diverse microbiome in wild Anopheles demeilloni mosquito cephalothoraxes.},
journal = {Gates open research},
volume = {10},
number = {},
pages = {28},
pmid = {42272927},
issn = {2572-4754},
abstract = {BACKGROUND: The increasing insecticide resistance of malaria vectors is an urgent concern for disease control and novel vector control strategies are needed. Wolbachia are endosymbiotic bacteria that can invade mosquito populations and reduce transmission of human pathogens. Wolbachia strains in wild Anopheles (An.) malaria vectors are rare, with only two known genuine symbioses; An. moucheti with wAnM and An. demeilloni with wAnD. In this study, we set out to determine if there was a correlation between wAnD in different An. demeilloni mosquito body parts, infective stage Plasmodium (Pl.) falciparum malaria sporozoites in cephalothoraxes and the mosquito microbiome.

METHODS: We undertook a combination of quantitative PCR, 16S rRNA amplicon sequencing and sanger sequencing of the Wolbachia surface protein (wsp) gene after isolating An. demeilloni female body parts from wild caught individuals collected in 2021 and 2024 from the Sud Kivu region of Democratic Republic of Congo. Results Wolbachia prevalence rates were significantly higher in abdomens compared to cephalothoraxes and density was also significantly higher in abdomens (P<0.0001). Overall sporozoite prevalence was 1.3% (9/704) which was not significantly different between Wolbachia-positive and Wolbachia-negative cephalothoraxes (P=0.3630) despite Pl. falciparum only detected in Wolbachia-negative cephalothoraxes. However, Wolbachia-positive abdomens were associated with a lower sporozoites rate compared to Wolbachia-negative abdomens (P=0.0329). 16S rRNA amplicon sequencing revealed no significant difference in alpha/beta diversities between abdomens and cephalothoraxes but the cephalothorax microbiome composition between Wolbachia-positive and Wolbachia-negative was significantly different (P<0.05).

CONCLUSIONS: Our findings indicate a significant effect of the wAnD strain on the cephalothorax microbiome and potentially the ability of sporozoites to reach Salivary glands in mosquitoes with Wolbachia-infected abdomens. Further studies are needed to determine the mechanisms in which the wAnD strain interacts with Plasmodium sporozoites in An. demeilloni and if this strain could be used for malaria biocontrol through transinfection of major malaria vectors.},
}

@article {pmid42272967,
year = {2026},
author = {Frisch, S and Aliyazdi, S and Rehner, J and Schmartz, G and Gevaerd, C and Latta, L and Veldung, B and Becker, SL and Keller, A and Schaefer, UF and Loretz, B and Vogt, T and Lehr, CM},
title = {Staphylococcal proliferation on skin models to investigate novel anti-infective treatments against dysbiosis.},
journal = {Bioengineering & translational medicine},
volume = {11},
number = {3},
pages = {e70124},
pmid = {42272967},
issn = {2380-6761},
abstract = {Inflammatory skin conditions like Acne inversa are characterized by dysbiosis, an imbalance of commensal and pathogenic bacteria, posing challenges for specific treatments. Consequently, we investigated how biofilm formation, low-nutrition skin environments, and air interfaces influence susceptibility to anti-infective treatments in mixed bacterial cultures. To achieve this in a cost-effective and reproducible manner, we developed a simplified substrate made of gelatin, hyaluronic acid, chondroitin sulphate, and alginate (=Gel-Alg). This in vitro model simulates biofilm cultivation on skin surfaces for aerobic bacteria. We selected Staphylococcus aureus and Staphylococcus epidermidis as two clinically relevant strains, which are also abundant in Acne inversa. We tested single and mixed cultures under different conditions: (i) nutrient broth, (ii) Gel-Alg substrate, (iii) EpiDerm™ commercial skin model, and (iv) ex vivo human skin. Proliferation, measured by colony-forming units, was comparable across most conditions, except for human skin. Metabolic activity, assessed via Presto Blue staining, revealed significant differences. Dual-species cultivation and quantification by viability PMA qPCR indicated dominance of S. epidermidis over S. aureus in skin-like environments. Treatments with biofilm-dissolving rhamnolipids, the antibiotic vancomycin, and combinations thereof demonstrated varying efficacy in single and mixed cultures. While the drug combination could almost completely eradicate staphylococcal biofilms in broth, susceptibility varied in skin-like models and moreover strongly depended on temperature (37°C vs. 32°C). In conclusion, this study suggests that reductionistic models, while mimicking key features, could be valuable for early selective antimicrobial drug development for specific applications like Acne inversa therapy.},
}

@article {pmid42273048,
year = {2026},
author = {Jiao, Y and Liu, Y and Gao, Q and Song, L and Sun, F and Li, Y and Li, H and Li, S and Li, J and Du, J and Li, C and Tian, X and Liu, R},
title = {Glutamicibacter soli JF_198 stimulates the rhizosphere colonization of indigenous Paenibacillus sp. to suppress cucumber Fusarium.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1843711},
pmid = {42273048},
issn = {1664-302X},
abstract = {INTRODUCTION: Beneficial microorganisms can facilitate the formation of advantageous microbial communities in the plant rhizosphere, thereby promoting plant health. Our research indicates that Glutamicibacter soli JF_198 can mitigate the severity of cucumber Fusarium wilt caused by Fusarium oxysporum f. sp. cucumerinum. This study investigates the tripartite association among Glutamicibacter soli JF_198, the cucumber rhizosphere microbiota, and cucumber Fusarium wilt suppression.

METHODS: We evaluated JF_198-mediated disease suppression in cucumber pot experiments and analyzed rhizosphere bacterial communities by 16S rRNA amplicon sequencing. Rhizosphere transplantation, bacterial isolation, antagonistic screening, and growth, competition, and root colonization assays were performed to assess the role of candidate Paenibacillus isolates under cucumber root-exudate conditions.

RESULTS: JF_198 treatment was associated with changes in selected rhizosphere bacterial taxa, particularly an increased trend in Paenibacillus-related taxa. Rhizosphere transplantation experiments showed that JF_198-associated rhizosphere microbiota could partially transfer disease-suppressive effects to sterile soil. We identified Paenibacillus-assigned OTU1077 as a candidate indigenous beneficial taxon showing increased relative abundance under JF_198 treatment. Further investigation suggested that JF_198 treatment was associated with enhanced Paenibacillus sp. colonization under root-exudate conditions.

DISCUSSION: Our findings suggest that G. soli JF_198-mediated disease suppression under controlled pot conditions is associated with changes in selected rhizosphere bacterial taxa and increased relative abundance of indigenous biocontrol-associated bacteria. This study provides preliminary insights into microbiome-associated disease suppression under controlled pot conditions and may inform future development of microbial consortia, pending further validation under field conditions.},
}

@article {pmid42273240,
year = {2026},
author = {Meng, D and Zhang, BB and Zhao, JN},
title = {Letter to the Editor: Deciphering macrophage heterogeneity and optimizing probiotics via spatial multi-omics.},
journal = {World journal of gastrointestinal pharmacology and therapeutics},
volume = {17},
number = {2},
pages = {118195},
pmid = {42273240},
issn = {2150-5349},
abstract = {We read the paper published in World Journal of Gastroenterology by Yang et al on how Bifidobacterium species alleviate colitis by modulating deoxycholic acid (DCA) levels and macrophage polarization, which provides important insights into the microbiome-immune axis. However, the classic M1/M2 polarization model oversimplifies the plasticity of macrophages and fails to account for the spatial heterogeneity of the intestinal microenvironment. Therefore, we propose integrating spatial transcriptomics and spatial metabolomics to resolve the intricate correlations between DCA distribution and specific macrophage subsets. Building upon this, we further discuss the transition from broad-spectrum probiotic supplementation to mechanism-driven precision probiotic strategies, emphasizing the future need to develop engineered strains capable of spatial awareness and metabolic pathway remodeling. This spatial multiomics-guided precision intervention framework holds promise for advancing colitis treatment toward approaches with greater mechanistic depth.},
}

@article {pmid42273247,
year = {2026},
author = {Loktionov, A},
title = {Current approaches to disease severity and therapy effectiveness assessment in patients with inflammatory bowel disease.},
journal = {World journal of gastrointestinal pharmacology and therapeutics},
volume = {17},
number = {2},
pages = {116608},
pmid = {42273247},
issn = {2150-5349},
abstract = {Inflammatory bowel disease (IBD) is a group of chronic recurrent disorders, Crohn's disease and ulcerative colitis being its two major types. IBD patients require continuous lifetime monitoring of disease activity and effects of therapeutic interventions, achievement of stable remission being the goal of the current 'treat-to-target' strategy. This review considers a wide range of approaches applied for this purpose. Although ileocolonoscopy combined with histological evaluation and now employing modern endoscopic techniques is still regarded as the gold diagnostic standard, its inability of visualizing small intestine is a limitation. Alternative non-invasive techniques such as capsule endoscopy and, especially, cross-sectional imaging, comprising computed tomography enterography, magnetic resonance enterography, and intestinal ultrasound, are becoming increasingly popular. In addition, the use of molecular biomarkers detectable in human body fluids is a rapidly developing area, and recent rapid progress in gut microbiome research promises to add a new dimension to it. It is also anticipated that new approaches based upon multi-omics can identify new composite biomarkers useful for IBD monitoring. Artificial intelligence-driven integration of abundant information provided by various diagnostic and analytical modalities outlined in this review may help in transforming the current 'one-size-fits-all' treatment paradigm into a truly personalized model of IBD care.},
}

@article {pmid42273259,
year = {2026},
author = {Amaral, A and Piotrowska-Tomala, K and Kordowitzki, P},
title = {Editorial: Endometrial health and disease: from molecular insights to clinical advances.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1860973},
doi = {10.3389/fvets.2026.1860973},
pmid = {42273259},
issn = {2297-1769},
}

@article {pmid42273381,
year = {2026},
author = {Zhang, Y and Wang, D and Zhuang, B and Zhu, F and Tan, C and Zhang, J and Zhang, Q},
title = {The Multifaceted Roles of Gut Microbiota and Their Metabolites in Metabolic Dysfunction-associated Steatotic Liver Disease: A Literature Review.},
journal = {Journal of clinical and translational hepatology},
volume = {14},
number = {5},
pages = {554-564},
pmid = {42273381},
issn = {2310-8819},
abstract = {Metabolic dysfunction-associated steatotic liver disease (MASLD) represents a major global health concern and encompasses a spectrum ranging from hepatic steatosis and metabolic dysfunction-associated steatohepatitis to liver fibrosis, cirrhosis, and ultimately hepatocellular carcinoma. Insulin resistance, the pathogenic cornerstone of MASLD, drives enhanced peripheral lipolysis and increased hepatic de novo lipogenesis, thereby overloading the liver with lipids and inducing steatosis. Subsequent lipotoxicity, inflammation, and gut microbiota dysbiosis further exacerbate disease progression. The gut microbiota and their metabolites communicate with the liver via the gut-liver axis, forming a complex signaling network that directly or indirectly modulates hepatic metabolism, systemic immune responses, oxidative stress, and intestinal barrier integrity. In this review, we synthesize evidence for the beneficial and detrimental effects of the major human gut microbial communities and their metabolites during the course of MASLD. We delineate how these gut-derived factors regulate hepatic function through an integrated tripartite "gut-liver axis-oxidative stress-metabolic reprogramming" mechanism. These insights may inform microbiome-based precision interventions and accelerate the development of therapeutic strategies targeting MASLD.},
}

@article {pmid42273689,
year = {2026},
author = {Yang, L and Li, Z and Li, Y and Zhang, Q and Zhang, H},
title = {Synergistic antitumor and immunomodulatory effects of Bifidobacterium animalis subsp. lactis V9 combined with anti-PD-1 therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1791276},
pmid = {42273689},
issn = {1664-3224},
mesh = {Animals ; Mice ; Humans ; Female ; *Immune Checkpoint Inhibitors/pharmacology ; *Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology ; *Bifidobacterium animalis/immunology ; Cytokines/metabolism ; Cell Line, Tumor ; Immunomodulation ; Tumor Microenvironment ; *Neoplasms/therapy/immunology ; *Probiotics ; Gastrointestinal Microbiome/immunology ; },
abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) targeting PD-1/PD-L1 have revolutionized cancer immunotherapy but remain limited by low response rates, immune-related adverse events (irAEs), and reduced efficacy following antibiotic exposure. The gut microbiota critically influences ICI responsiveness, and Bifidobacterium species have emerged as potent immunomodulatory commensals. However, the mechanistic contribution of specific live biotherapeutic strains remains unclear.

METHODS: We systematically characterized Bifidobacterium animalis subsp. lactis V9 (B. lactis V9), through in-vitro cytokine assays and multiple syngeneic tumor models (CT26, MC38, 4T1). Immunophenotyping, microbiota colonization, and toxicological studies were conducted to evaluate efficacy, immune modulation, colonization stability, and safety.

RESULTS: B. lactis V9 dose-dependently induced TNF-α, IL-6, and IL-10 secretion in THP-1 macrophages, exhibiting a balanced cytokine profile distinct from LPS stimulation. In vivo, B. lactis V9 alone moderately inhibited tumor growth but synergized with αPD-1 to achieve a 50% tumor growth inhibition and extend survival in CT26 models, accompanied by increased IFN-γ[+]CD8[+] T cells and activated CD86[+]CD11c[+] dendritic cells. The synergy persisted despite antibiotic pretreatment, indicating colonization stability (8×10[8]-10[9] copies/g) and a metabolite-driven mechanism. In 4T1 models, B. lactis V9 co-therapy mitigated αPD-1-induced uterine inflammation and pulmonary hemorrhage by downregulating IL-1α, IL-1β, and IL-17A while maintaining effector cytokines. Toxicology assessments revealed no adverse findings up to 3.52×10[12] CFU/kg (acute) or 5.00×10[11] CFU/kg (90-day repeated dose), with all genotoxicity tests negative.

CONCLUSIONS: B. lactis V9 harmonizes pro- and anti-inflammatory responses through TLR2/TLR4-NF-κB/MAPK signaling, remodels the tumor microenvironment, and enhances αPD-1 efficacy without increasing toxicity. Its colonization resilience and favorable safety profile support clinical translation as a microbiome-based adjunct to immunotherapy. These results provide a mechanistic foundation for combining live biotherapeutic products with ICIs to optimize antitumor immunity.},
}

Animals
Mice
Humans
Female
*Immune Checkpoint Inhibitors/pharmacology
*Programmed Cell Death 1 Receptor/antagonists & inhibitors/immunology
*Bifidobacterium animalis/immunology
Cytokines/metabolism
Cell Line, Tumor
Immunomodulation
Tumor Microenvironment
*Neoplasms/therapy/immunology
*Probiotics
Gastrointestinal Microbiome/immunology

@article {pmid42273701,
year = {2026},
author = {Wang, Z and Bian, Q and Chu, Y and Zhu, W and Qin, Y and Zheng, J},
title = {The microbiome-inflammation-immune axis in oral squamous cell carcinoma: from mechanistic insights to therapeutic perspectives.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1842459},
pmid = {42273701},
issn = {1664-3224},
mesh = {Humans ; *Microbiota/immunology ; *Mouth Neoplasms/immunology/microbiology/therapy ; Tumor Microenvironment/immunology ; *Inflammation/immunology/microbiology ; Dysbiosis/immunology ; *Carcinoma, Squamous Cell/immunology/therapy/microbiology ; Animals ; Signal Transduction ; },
abstract = {Oral squamous cell carcinoma, the most prevalent malignancy of the head and neck, presents ongoing challenges regarding its molecular mechanisms and clinical management. Current research largely focuses on isolated signaling pathways or specific immune responses, often overlooking the potential contributing role of the microbiota in tumorigenesis. This review proposes the "microbiome-inflammation-immune axis" as an interpretive working hypothesis to elucidate how dysbiosis and microbial interactions may activate host inflammatory responses, trigger pattern recognition receptors and signaling pathways, and remodel the immune microenvironment, thereby potentially facilitating oral cancer progression. Concurrently, this paper emphasizes clinical translation by critically compiling and evaluating relevant clinical analytical indicators-such as peripheral blood inflammatory markers and salivary microbial markers-from the fields of inflammation and microbiology. This provides multidimensional reference points for future disease diagnosis and treatment.},
}

Humans
*Microbiota/immunology
*Mouth Neoplasms/immunology/microbiology/therapy
Tumor Microenvironment/immunology
*Inflammation/immunology/microbiology
Dysbiosis/immunology
*Carcinoma, Squamous Cell/immunology/therapy/microbiology
Animals
Signal Transduction

@article {pmid42273932,
year = {2026},
author = {Rezaei, F and Rollin, JA},
title = {A Microbial Formulation Perspective on Probiotic Skincare: Viability, Challenges, and Current Approaches to Maintain Probiotic Viability.},
journal = {Biotechnology and bioengineering},
volume = {},
number = {},
pages = {},
doi = {10.1002/bit.70268},
pmid = {42273932},
issn = {1097-0290},
abstract = {The human body hosts a vast and dynamic microbial ecosystem that plays essential roles in immunity, metabolism, and tissue function. Growing scientific and consumer interest in the human microbiome has accelerated innovation in topical skincare, particularly in the emerging category of probiotic, prebiotic, and postbiotic formulations. However, despite rapid market growth, most commercial products rely on non-viable microbial derivatives rather than live, strain-identified organisms, largely due to formulation, regulatory, and stability challenges. This review provides a microbial formulation perspective on probiotic skincare, beginning with an overview of the human and skin microbiomes, followed by a discussion of how beneficial microorganisms influence skin appearance and barrier function. We clarify the definitions and scientific distinctions among probiotics, prebiotics, and postbiotics and evaluate current cosmetic applications. We then explore the technical and regulatory hurdles associated with incorporating live microbes into cosmetic products, including preservative compatibility, viability, packaging, and activation requirements. Finally, we present some available strategies and technologies in an effort to keep probiotic viable until use and outline future research considerations needed to advance authentic, evidence-based probiotic skincare.},
}

@article {pmid42274211,
year = {2026},
author = {Yarkosky, EJ and Udensi, CG and Ferreira, RBR and Collins, KJR and Hotze, EM},
title = {MicrobioME: a CURE model for diverse microbiology laboratory classrooms.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0029825},
doi = {10.1128/jmbe.00298-25},
pmid = {42274211},
issn = {1935-7877},
abstract = {Undergraduate research experience (URE) positively contributes to student success, STEM identity, and STEM post-graduate careers. Despite these benefits, traditional UREs are limited, and many students encounter barriers to gaining access to these opportunities. Course-based Undergraduate Research Experiences (CUREs) increase access to UREs by incorporating authentic research projects into the course curriculum. Despite the recognized benefits of CUREs, few have been developed for introductory or upper-level microbiology courses. This scarcity largely reflects the substantial planning and financial investment required of faculty to create effective CUREs that are affordable, relevant, and align with course learning objectives. These combined demands present significant challenges to widespread adoption of CUREs in microbiology education. We considered these limitations when developing the "MicrobioME" CURE for implementation in pathogenic microbiology laboratory courses. Students participating in the MicrobioME CURE isolate and identify bacterial isolates from their own skin microbiome and investigate the impact of isolate-produced small molecules on Staphylococcus aureus biofilm production. We studied MicrobioME CURE implementation in two laboratory courses at the University of Kansas (KU) and West Virginia University (WVU) in cohorts differing in class size, research experience, meeting times, and faculty expertise in microbiome research, providing an opportunity to compare student outcomes in varied environments. Here, we report student outcomes of and provide tools for implementing the MicrobioME CURE in microbiology laboratory courses at other universities. Our results suggest that the MicrobioME CURE is scalable, affordable, and modular, making it an accessible and practical solution to increasing access to authentic research experience.},
}

@article {pmid42274249,
year = {2026},
author = {Villafuerte, NM and Stevens, EN and Sheikh, MA and Rodriguez, VH and Lin, J and Zhang, F},
title = {Natural commensal microbes induce internal hatching in C. elegans.},
journal = {Microbiology spectrum},
volume = {},
number = {},
pages = {e0403425},
doi = {10.1128/spectrum.04034-25},
pmid = {42274249},
issn = {2165-0497},
abstract = {The microbiome is increasingly recognized as a key factor of the plasticity of host life-history traits. Using the Caenorhabditis elegans model system, we examined how naturally associated bacterial strains affect internal egg hatching, a stress-adaptive reproductive strategy in this species. Among the bacterial strains tested, four strains (Ochrobactrum BH3, Lelliottia JUb66, Pantoea BIGb0393, and Enterobacter CEent1) induced high levels of internal hatching (28-57%) in C. elegans during late adulthood, compared to <5% in animals grown on E. coli OP50. These effects were accompanied by extending the reproductive window while showing a trend toward reduced total progeny and lifespan. Genetic analyses revealed that these effects are mediated through various components of the insulin signaling pathway: the α-proteobacterial strain BH3 acts via DAF-16/FOXO, whereas the three γ-proteobacterial strains act independently of DAF-16, suggesting differences in pathway dependence. Our findings demonstrate that naturally associated microbiome members can differentially interact with host endocrine signaling to shape reproductive outcomes. These results underscore the role of microbial cues in shaping life-history plasticity in animals.IMPORTANCEMicrobiome members profoundly influence host physiology, including reproductive strategies. Using the Caenorhabditis elegans natural microbiome model, we show that commensal bacteria can induce internal egg hatching, a facultative vivipary phenotype previously linked primarily to early-life starvation or pathogen exposure that severely reduces reproductive output. In contrast, commensal strains trigger this shift mainly in late adulthood, extending the reproductive window with minimal impact on overall fecundity. We further demonstrate that bacterial strains act through distinct components of the host insulin signaling pathway. More broadly, these findings highlight diverse avenues within conserved endocrine networks that are susceptible to microbial modulation and underscore the potential to leverage microbiomes to influence host life-history traits.},
}

@article {pmid42274262,
year = {2026},
author = {Guan, M and Guo, X and Kong, M and Qin, Y and Xu, H and Su, X and Wang, P and Wang, X},
title = {Potential mechanisms underlying Enterococcus faecalis-driven pancreatic cancer cell proliferation.},
journal = {mBio},
volume = {},
number = {},
pages = {e0396325},
doi = {10.1128/mbio.03963-25},
pmid = {42274262},
issn = {2150-7511},
abstract = {The development of various cancers is intricately linked with the human microbiome. Recent studies have highlighted a substantial association between pancreatic cancer and gut microbiota. However, the specific roles and underlying regulatory mechanisms of individual gut microbial species in pancreatic cancer progression remain poorly understood. Enterococcus faecalis, a common member of the human commensal microbiota, has been found to be enriched in the tumor tissues of pancreatic cancer patients. However, its functional contribution has not been clearly defined. In this study, we established a co-culture system involving E. faecalis and pancreatic cancer cells. Our results show that E. faecalis promoted the proliferation, migration, and invasion of pancreatic cancer cells. Following pre-treatment with E. faecalis, the phosphorylation level of epidermal growth factor receptor (EGFR) was markedly elevated. Inhibition of EGFR effectively suppressed the pro-proliferative effects induced by E. faecalis. Further investigation revealed that E. faecalis stimulated the production of reactive oxygen species (ROS) in pancreatic cancer cells. This ROS production might be sensed by Toll-like receptors (TLRs), leading to the activation of the EGFR signaling pathway. When cells were incubated with TLR inhibitors or ROS scavengers, both EGFR expression and its downstream pro-proliferative effects were significantly attenuated. Collectively, this study provides mechanistic insights into how E. faecalis contributes to pancreatic cancer progression and offers new perspectives for the development of diagnostic and therapeutic strategies targeting this microbial signaling pathway.IMPORTANCEA diverse microbiome is closely associated with cancer, as bacterial presence has been detected in the majority of solid tumors. However, the composition, abundance, and functional profiles of the microbiota vary significantly across different tumor types, thereby exerting distinct effects on tumorigenesis and disease progression. Recent studies have shown that pancreatic cancer hosts a variety of bacterial populations, including gut-derived bacteria that may translocate to pancreatic tissue via mesenteric venous or lymphatic drainage pathways. For example, Enterococcus and Enterobacter species have been identified in the cyst fluid of patients with pancreatic cystic neoplasms. Moreover, antibodies against Enterococcus faecalis capsular polysaccharide have been detected in the sera of patients with pancreatitis and pancreatic cancer, and E. faecalis has been observed in pancreatic ducts. Despite these observations, the precise mechanisms through which E. faecalis influences pancreatic cancer remain unclear. Our study demonstrates that E. faecalis promotes pancreatic cancer cell proliferation through the activation of the Toll-like receptor-reactive oxygen species-epidermal growth factor receptor signaling pathway.},
}

@article {pmid42274451,
year = {2026},
author = {Calvão, J and Iselin, C and Wasmayr, J and Furtmüller, C and Zeng, Z and Vadivel, CK and Gluud, M and Bataiosu-Zimmer, E and Buus, TB and Ødum, N and Gonçalo, M and Guenova, E},
title = {Pathogenesis of cutaneous T-cell lymphoma: Malignant inflammation, immune reprogramming, and microenvironmental drivers.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.03.035},
pmid = {42274451},
issn = {1523-1747},
abstract = {Cutaneous T-cell lymphomas, namely mycosis fungoides and Sézary syndrome, arise through a complex interplay of genetic alterations, epigenetic deregulation, immune imbalance, and tumor-microenvironment interactions. A progressive T helper 1-to-T helper 2 shift and chemokine-directed trafficking promote immune evasion and sustained malignant T-cell activity, whereas emerging data show subclonal diversity enabling adaptation to microenvironmental and therapeutic pressures. Skin-resident immune cells further shape disease behavior, and Staphylococcus aureus superantigens act as microenvironmental amplifiers that enhance malignant signaling and contribute to treatment resistance. A deeper understanding of how these molecular, immunological, and microbiome factors converge is essential to develop more precise, biomarker-informed therapeutic strategies.},
}

@article {pmid42274459,
year = {2026},
author = {King, D and Kalogeromitros, M and Gutama, B and Slutsky, HL and Mubang, R and Wagner, A and Kitko, CL and Lineaweaver, WC},
title = {Skin Lesion Reconstruction in Graft Versus Host Disease Using Autograft From the Bone Marrow Donor Panniculectomy Tissue.},
journal = {Annals of plastic surgery},
volume = {},
number = {},
pages = {},
pmid = {42274459},
issn = {1536-3708},
abstract = {Chronic graft-versus-host disease (cGVHD) is a common complication following hematopoietic stem cell transplant, with the skin being the most frequently affected organ. The cutaneous manifestations may be refractory to conventional wound care and skin autografts due to the complex underlying immunology. In this case report, a pediatric patient with a history of Ph-like B-cell acute lymphoblastic leukemia underwent a haploidentical bone marrow transplant from his mother. His course was complicated by cutaneous cGVHD, which failed multiple lines of immunosuppression and conservative wound management. In addition, he developed multidrug-resistant wound infections. He underwent split-thickness skin allograft transplantation from his mother's pannus, and his wounds were largely resolved within 3 months postoperatively. This report provides a review of the literature to discuss the biology behind cutaneous cGVHD, including the role of the microbiome, and the proposed mechanism for the success of this treatment. It also highlights the unique benefits of utilizing the pannus and leveraging the immunologic tolerance established by prior bone marrow transplant from the same donor. This case presents donor skin allografting in the setting of donor tolerance as a viable option for refractory cutaneous cGVHD.},
}

@article {pmid42274490,
year = {2026},
author = {Guo, Q and Niu, M and Wang, Y and Yang, S and Cai, Q and Ma, Y and Li, Y and Chen, X},
title = {Regulatory Effects of Two Ionic Liquids ([Omim]Br, [Opy]Br) on the Growth and Root Microecology of Maize Seedlings.},
journal = {Biology},
volume = {15},
number = {11},
pages = {},
pmid = {42274490},
issn = {2079-7737},
support = {No. 32272018//National Natural Science Foundation of China/ ; },
abstract = {Accumulation of ionic liquids (ILs) in soil may alter its physicochemical and biological properties. However, the current understanding of their effects on the rhizosphere microenvironment of crop plants remains limited. We examined the effects of two ILs-[Opy]Br and [Omim]Br-which differ in cation structure but share the bromide anion, on maize rhizosphere microbial communities and metabolites at a concentration of 0.6 g/kg soil. Exposure to [Opy]Br and [Omim]Br significantly impaired maize seedling development, with [Opy]Br inducing more severe growth suppression. These phytotoxic effects were also reflected in changes in rhizosphere soil properties. In bacterial communities, [Omim]Br more strongly inhibited membrane transport (e.g., ATP-binding cassette transporters), lipid synthesis, and carbon metabolism, thereby impairing bacterial nutrient uptake and energy metabolism. In fungal communities, saprophytic fungi were activated under both treatments, accelerating organic matter decomposition, whereas pathogens were suppressed, particularly under [Omim]Br treatment. Metabolomic analysis revealed widespread accumulation of amino acids in maize roots following exposure to both ILs, accompanied by significant depletion of the antioxidant glutathione. Carbohydrate metabolism was broadly suppressed, with [Omim]Br exerting a more pronounced inhibitory effect. Hormone levels were generally reduced, with [Opy]Br causing more severe depletion. Overall, both ILs induced oxidative stress, hormonal disruption, and metabolic imbalance in maize. This study provides a reference for evaluating the risks and regulatory potential of ILs in agricultural environments.},
}

@article {pmid42274506,
year = {2026},
author = {Yu, Y and Zhao, Y and He, W and Yu, Z and Yang, Y and Wang, J},
title = {Integrated 16S rRNA Sequencing and Metabolomic Analyses Reveal Gut Microbiota Dysbiosis and Metabolic Perturbations in Neonatal Dairy Calves with Bovine Rotavirus-Induced Diarrhea.},
journal = {Biology},
volume = {15},
number = {11},
pages = {},
pmid = {42274506},
issn = {2079-7737},
abstract = {Bovine rotavirus (BRV) is a major pathogen causing diarrhea in neonatal dairy calves, yet its impact on the gut microbiome and host metabolism remains incompletely understood. This study integrated 16S rRNA gene sequencing and untargeted metabolomics to characterize the fecal microbial and metabolic profiles of BRV-infected diarrheic calves compared to healthy controls. Fecal samples were collected from 16 Holstein calves (<30 days old), equally divided into a BRV-infected group (confirmed by RT-qPCR) and a healthy control group. Alpha diversity analysis revealed a significant reduction in microbial richness (Chao1, p = 0.012) in the BRV group. Beta diversity (Jaccard distance) showed distinct clustering between groups (PERMANOVA, p < 0.05). Linear discriminant analysis effect size (LEfSe) identified a significant enrichment of Escherichia (Proteobacteria) and Enterococcus (Firmicutes) in BRV calves, whereas healthy controls were enriched in Blautia and Faecalibacterium (both Firmicutes, with Faecalibacterium also commonly associated with healthy gut communities). Metabolomic analysis via UHPLC-MS/MS demonstrated a clear separation of metabolic profiles. BRV infection was associated with significant alterations in lipid metabolism pathways, notably elevated levels of lysophosphatidylcholines (LPCs) and lysophosphatidylethanolamines (LPEs). Integrated Spearman correlation analysis revealed extensive and significant associations (|ρ| > 0.6, FDR-adjusted p < 0.05) between differential bacterial genera (e.g., Enterococcus, Escherichia) and differential metabolites (e.g., glycerolipids, amino acid derivatives), suggesting a close linkage between gut microbial dysbiosis and metabolic remodeling during BRV infection. These findings provide a multi-omics perspective on the interplay between the gut microbiota and host metabolism in BRV-induced diarrhea, offering potential insights for developing microbiota-based diagnostic or therapeutic strategies.},
}

@article {pmid42274550,
year = {2026},
author = {Edkaidek, H and Dahiya, D and Nigam, PS},
title = {Epigenetic Modulators: Role of Gut Microbiome in Transformation of Nutrient Bioactives and Host Gene Regulation.},
journal = {Cells},
volume = {15},
number = {11},
pages = {},
pmid = {42274550},
issn = {2073-4409},
mesh = {Humans ; *Epigenesis, Genetic ; *Gastrointestinal Microbiome/genetics ; Animals ; DNA Methylation ; *Nutrients/metabolism ; *Gene Expression Regulation ; Polyphenols/metabolism ; },
abstract = {Biological activity of diets consisting of dietary fibers, peptides and polyphenols is largely mediated by the gut microbiota, which converts these compounds into bioactive metabolites. This review examines the microbiota-epigenome axis, highlighting gut microbiota-derived metabolites, including short-chain fatty acids (SCFAs), urolithins, and phenolic acids, that modulate host gene expression through DNA methylation, histone modifications, and non-coding RNA regulation. Current evidence from molecular and microbiome studies indicates that these metabolites influence key metabolic and inflammatory pathways, including lipid absorption via CD36, SIRT1 activation, and one-carbon metabolism involving folate and S-adenosylmethionine (SAM). Inter-individual variability in metabolic responses is associated with differences in microbial composition and metabotypes, which determine the magnitude of epigenetic regulation. Furthermore, dietary polyphenols derived from pomegranate, berries, tea, cocoa, and grapes are shown to modulate gut microbiota composition and enhance epigenetic effects. A "butyrate-polyphenol synergy" model is proposed, in which combined microbial metabolites optimize host epigenetic programming. Overall, agri-food by-products are suggested to function as modulators of the host epigenetic landscape, providing a framework for microbiome-targeted dietary strategies to improve metabolic and inflammatory health.},
}

Humans
*Epigenesis, Genetic
*Gastrointestinal Microbiome/genetics
Animals
DNA Methylation
*Nutrients/metabolism
*Gene Expression Regulation
Polyphenols/metabolism

@article {pmid42274565,
year = {2026},
author = {Khan, MS and Faizan, M and Yang, G and Kang, KS},
title = {Gut Dysbiosis-Mediated Major Depressive Disorder: A Review of Pathogenic Mechanisms and Potential Therapeutic Strategies.},
journal = {Cells},
volume = {15},
number = {11},
pages = {},
pmid = {42274565},
issn = {2073-4409},
support = {RS-2025-02263193//Bio & Medical Technology Development Program of the National Research Foundation/ ; RS-2026-25474823//National Research Foundation/ ; },
mesh = {Humans ; *Major Depressive Disorder/therapy/microbiology/etiology ; *Dysbiosis/complications/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; },
abstract = {Major depressive disorder (MDD) is a mental illness with high mortality, suicide, and relapse rates that could become the leading cause of health problems worldwide by 2030. The microbiota-gut-brain axis involves bidirectional communication between the human gut microbiota and the central nervous system (CNS). The gut microbiome is a complex ecosystem of approximately 100 trillion microorganisms, including viruses, bacteria, and fungi. The gut microbiota has recently been recognized for its impact on various diseases and health concerns. Several factors influence the composition and structure of gut microbes, ultimately affecting human physiology, with the nervous system being particularly vulnerable. The gut-brain-microbiota axis influences several important brain functions through numerous pathways, including vagus nerve signaling, gut microbial synthesis of metabolites, and immune-related chemicals. These factors can influence neurotransmitter activity, neuroinflammation, behavior, and mental health. Despite increased interest, the possibility of modifying the gut microbiota as a therapeutic approach remains unclear. Although numerous studies suggest that microbiota play an important role in many illnesses, the precise mechanisms are yet to be elucidated, and there are currently no evidence-based, microbiota-focused treatments for these illnesses. Recent research indicates that gut dysbiosis (GD) causes increased intestinal permeability (leaky gut), initiates systemic inflammation, and contaminates the blood. Opportunistic microbial metabolites cross the blood-brain barrier, triggering a neuroinflammatory cascade and apoptotic pathways while affecting neurogenesis and neurotransmitters, ultimately resulting in the development of MDD and anxiety. This review examined the factors influencing normal gut microbiota and GD-mediated MDD, as well as possible therapeutic options. The study outlines its objectives and methodological approaches, including the screening and filtering of research on GD-induced depression. Furthermore, it explored the daily use of dietary supplements, revealing new paths for clinical and preclinical research.},
}

Humans
*Major Depressive Disorder/therapy/microbiology/etiology
*Dysbiosis/complications/microbiology/therapy
*Gastrointestinal Microbiome
Animals

@article {pmid42274631,
year = {2026},
author = {Cittadini, C and Iessi, E and Vona, R and Matarrese, P},
title = {Exploring Risk Factors and Sex Differences in Colorectal Cancer: Insights from Current Evidence.},
journal = {Cells},
volume = {15},
number = {11},
pages = {},
pmid = {42274631},
issn = {2073-4409},
support = {PNRR-MAD-2022-12375679//Ministry of Health/ ; },
abstract = {Colorectal cancer (CRC) is the third most diagnosed malignancy and the second leading cause of cancer-related mortality worldwide. A consistent and epidemiologically well-documented feature of CRC is its sexual dimorphism: age-standardized incidence rates are 33-45% higher in men than in women, and mortality rates differ by 43-50%. Beyond epidemiology, biological sex influences tumor location, molecular subtype, and clinical outcome. Women more frequently develop right-sided, microsatellite-unstable tumors driven by the CpG island methylator phenotype pathway, whereas men predominantly present with left-sided, chromosomally unstable tumors harboring APC, KRAS, and TP53 mutations. Sex steroid hormones play a central modulatory role: estrogens, primarily via estrogen receptor β (ERβ), exert tumor-suppressive effects on colonic epithelium, whereas androgens promote pro-inflammatory and pro-tumorigenic signaling through androgen receptor (AR)-dependent pathways. The gut microbiome displays sex-specific compositional profiles ('microgenderome') and contributes to sex-specific CRC susceptibility through bidirectional interactions with sex hormones, shaping distinct immunological and metabolic microenvironments. Finally, sex influences the pharmacokinetics of fluoropyrimidines, the toxicity of targeted agents, and the response to immune checkpoint inhibitors. This review summarizes current evidence on sex-related differences in CRC epidemiology, molecular pathology, hormonal regulation, gut microbiota composition, and treatment outcomes, highlighting the need to systematically incorporate sex as a biological variable in CRC research and clinical practice.},
}

@article {pmid42274817,
year = {2026},
author = {Mehdizadeh, M and Omidi, A and Abideen, Z and Morya, S and Al-Taey, DKA},
title = {Impacts of microplastics on rhizosphere microbiome structure and function: a systematic review.},
journal = {Environmental monitoring and assessment},
volume = {198},
number = {7},
pages = {},
pmid = {42274817},
issn = {1573-2959},
abstract = {The pervasive contamination of agricultural soils by microplastics (MPs) represents a significant environmental stressor with potential repercussions for the rhizosphere microbiome, a critical interface for plant health and soil fertility. This systematic review synthesizes findings from 32 primary studies to evaluate MP-induced stress and its impacts on rhizosphere microbial communities. The evidence consistently demonstrates that microplastics significantly alter microbial community structure, with the majority of studies reporting substantial shifts in beta diversity. The effects on alpha diversity were context-dependent, varying with factors such as polymer type, concentration, and the presence of co-stressors; studies reported both significant decreases (a 9-10% reduction in bacterial richness with 100,000 mg kg[-1] polylactic acid (PLA) MPs) and increases. A critical finding was the marked reduction in beneficial microbial guilds; for instance, specific plant growth-promoting rhizobacteria (PGPR) genera declined significantly (p < 0.05) under combined MP and antibiotic stress. Furthermore, biodegradable microplastics (BMPs; e.g., PLA, poly(butylene adipate-co-terephthalate (PBAT)) induced equally potent or more severe disruptions than conventional polymers, often enriching copiotrophic bacteria and altering functional gene profiles for nutrient cycling. Under the high‑dose, short‑term experimental conditions reviewed, these perturbations compromise plant nutrient acquisition and stress resilience; however, whether such effects scale to environmentally realistic microplastic concentrations remains an open question, necessitating caution when extrapolating to long‑term agricultural sustainability. The review underscores the urgent need for field-relevant, long-term studies to fully understand the ecological risks posed by MPs in terrestrial ecosystems.},
}

@article {pmid42275074,
year = {2026},
author = {Yang, B and Yuen-Simović, B and Yuan, H and Degnan, BM and Degnan, SM},
title = {Early transcription factor activation distinguishes symbiotic from non-symbiotic bacteria during microbiome processing in a sponge.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag150},
pmid = {42275074},
issn = {1751-7370},
abstract = {Animals that filter-feed on environmental microbes must rapidly discriminate among captured bacteria to maintain beneficial associations while avoiding inappropriate immune activation. In innate immunity, this discrimination is executed through transcription factors (TFs), whose activation and nuclear translocation initiate effector gene expression and shape the nature of the host response. In sponges, bacteria are first physically captured by choanocytes, but the timing and cellular context in which TF-mediated immune discrimination becomes evident remains unclear. Here, we investigate the earliest detectable regulatory responses associated with discrimination between symbiotic and non-symbiotic bacteria in the marine sponge Amphimedon queenslandica. Using a feeding-based design to model post-metamorphic microbiome restructuring, we exposed juvenile sponges that already harbour vertically inherited symbionts to native (symbiont) or foreign (non-symbiont) bacterial communities and assessed early cellular processing and transcriptional responses to bacterial uptake. Symbiotic bacteria were rapidly transported across the epithelium and induced a strong, transient activation of conserved innate immune TFs, including IRF, NF-κB, and STAT, together with associated signalling pathways. IRF and NF-κB translocated to the nuclei of amoebocytes that had engulfed symbionts, indicating that discrimination becomes evident shortly after uptake and precedes downstream effector responses. In contrast, foreign bacteria were internalized more slowly, failed to induce coordinated immune TF activation or nuclear translocation, and instead elicited a xenobiotic-dominated transcriptional program. Together, these findings identify TF activation as an early regulatory checkpoint in sponge-microbe interactions and reveal key mechanisms that underpin the initial stages of symbiont discrimination.},
}

@article {pmid42275092,
year = {2026},
author = {Marsh, G and Bourquin, M and Leale, A and Bröder, L and Altshuler, I},
title = {Soil microbial diversity, succession, and greenhouse gas cycling across a Greenlandic glacial chronosequence.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag054},
pmid = {42275092},
issn = {1574-6941},
abstract = {Accelerated glacial retreat in Greenland drives increased development of glacial outwash plains. These newly exposed landscapes provide an opportunity to study microbial dynamics during soil development. We explore soil microbial diversity, community assembly, and biogeochemical cycling across the Kiattuut Sermiat glacial chronosequence (southern Greenland) via 16S rRNA gene amplicon analysis paired with microbial abundance, soil physicochemical parameters, and gas flux data. Microbial diversity varied with soil depth, with more acidic topsoils abundant in Cyanobacteriota and Armatimonadota taxa. While aerobic lower soils likely contained relatively more anoxic pore spaces, hosting aerobic nitrifiers such as Nitrospirota, low oxygen associated Planctomycetota taxa, and less characterised Gemmatimonadota. Microbial diversity varied across the chronosequence following distance-decay principles, as communities were predominately dispersal limited and shaped by heterogenous selection, with greater heterogeneous conditions further from the glacier terminus. Soil CO2 fluxes increased with distance from the glacier, following a shift from autotrophic sulfur- and iron-oxidising taxa towards heterotrophic members. CH4 fluxes demonstrated greater uptake further from the glacier and CH4-oxidation was associated with the methanotroph Methylocapsa. Considering the climatic relevancy of Greenlandic proglacial environments, we describe the largely unexplored microbial diversity and biogeochemical cycling of greenhouse gases in these developing soils.},
}

@article {pmid42275109,
year = {2026},
author = {Reich, HG and Cunningham, NR and Abramenko, AP and Adler, J and Budavari, P and Charendoff, I and Coleman, T and Crooke, S and Flint, A and Goeler-Slough, N and Houssein, A and Kwakye, B and Langer, M and Langer, M and Lennertz, H and Lin, S and McAllister, J and Mohammed, S and Morales, C and Ngochanthra, M and Noppenberger, J and Osbaldeston, R and Palacios, K and Shin, E and Sicher, E and Hillaire, TS and Sun, X and Totah, F and Villafañe, K and Wood, A and Zhao, B and Smith, M and Yoshida, O and Allen, C and Dvorak, J and Matthews, MC and Wink, HR and Richard, C and Stadtfeld, C and Smith, S and Dallmeyer-Drennen, G and Harvey, EL and Whalen, KE},
title = {Widespread siderophore production among Symbiodiniaceae-associated bacteria.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag069},
pmid = {42275109},
issn = {1574-6968},
abstract = {Nutritional exchanges fuel the evolutionary and ecological dominance of multi-partner symbioses among reef-building corals and microbial associates in oligotrophic tropical marine ecosystems. Mutualistic relationships with endosymbiotic dinoflagellates (Family Symbiodiniaceae) are central to coral holobiont metabolism, yet their metabolic contributions are sensitive to nutrient availability. Symbiodiniaceae may compensate for oligotrophic environments via metabolic exchanges with prokaryotic partners. Bacterial production of ligands with affinities for otherwise insoluble elements promotes uptake and exchanges. Bacterial secretion of small molecules with high Ferric (Fe3+) iron affinities, herein referred to as siderophore production, presents one example of microbial metabolic cooperation. We isolated 78 pure bacterial culture lines from 14 Symbiodiniaceae cultures to screen for siderophore production using a Chrome Azurol S (CAS) overlay assay. Colorimetric changes observed on CAS overlays indicated ubiquitous siderophore production across 22 bacterial genera. Many of the isolated bacterial cultures corresponded to known 'core' Symbiodiniaceae microbiome. These results suggest an avenue of bacterial metabolism may facilitate biotic iron exchange among coral holobiont partners. Future characterization of the identity siderophores secreted will inform predictions on their impacts on iron exchange within the coral holobiont. Ultimately, a greater ability to acquire iron via siderophore production may improve the coral holobiont's tolerance to environmental stressors.},
}

@article {pmid42275114,
year = {2026},
author = {Lu, TT and Isip, M and Han, CJ and Shih, HJ and Syukur, S and Trinh, LL and Perin, S and Lin, YC and Lin, PA and Ma, KW},
title = {Upregulated jasmonate signaling shifts Arabidopsis microbiota interactions and stress adaptations through a positive feedback loop.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag146},
pmid = {42275114},
issn = {1751-7370},
abstract = {The model plant Arabidopsis thaliana hosts diverse microbial communities collectively known as the microbiota. The plant microbiota is generally taxonomically structured and, in many cases, confers benefits to the plant host including plant growth promotion and enhanced stress tolerance. However, microbial imbalance can also result in deleterious effects, a phenomenon termed dysbiosis that was first coined in the gut microbiome field. To uncover the regulatory mechanism maintaining healthy plant homeostatic interactions with microbiota, we conducted screening using defined synthetic bacterial communities. We identified an Arabidopsis mutant displaying altered microbial profiles with an overall increase of microbial load and microbiota-dependent growth defects. Transcriptomic analyses combined with phytohormone quantification revealed that these phenotypes are attributed to an upregulation of the jasmonic acid (JA) signaling pathway in this mutant upon microbiota colonization. Furthermore, chemical treatment with different JA inducers reproduced similar phenotypes in wild-type plants, suggesting regulation through a positive feedback loop. Although activation of the JA pathway is typically associated with enhanced plant stress responses, our mutant exhibited reduced pathogen load at the expense of reduced plant growth and impaired salt tolerance. Together, our findings demonstrate that JA signaling not only orchestrates plant growth and defense but also plays a pivotal role in shaping plant-microbiota interactions. Controlled regulation of the JA signaling pathway is therefore essential to maintain balanced plant response to multiple environmental stressors.},
}

@article {pmid42275128,
year = {2026},
author = {Takahashi, K and Yoshikawa, Y and Chaki, T and Yamakage, M},
title = {Gut Microbiota Modulation Attenuates Myocardial Ischemia-Reperfusion Injury in Diabetic Mice.},
journal = {Shock (Augusta, Ga.)},
volume = {},
number = {},
pages = {},
doi = {10.1097/SHK.0000000000002882},
pmid = {42275128},
issn = {1540-0514},
abstract = {BACKGROUND: The gut microbiome is increasingly being recognized as a regulator of cardiometabolic health; however, whether microbiome interventions can attenuate myocardial ischemia-reperfusion injury (IRI) in diabetic hearts remains unclear. Therefore, we tested whether fecal microbiota transplantation (FMT) from lean non-diabetic donors could mitigate myocardial IRI in type 2 diabetes mellitus (T2DM) db/db mice and explored candidate taxa associated with protection.

METHODS: Male db/db mice (T2DM model) received a 14-day course of FMT from lean db/m donors or a vehicle after antibiotic pretreatment. Myocardial IRI was induced, and infarct size was quantified. The gut microbiota was evaluated by 16S rRNA gene sequencing.

RESULTS: FMT significantly reduced the infarct size as a percentage of the area at risk compared to the IRI group (38.7 ± 13.4% vs. 58.7 ± 4.3%, P = 0.003). Microbiome analysis revealed that among alpha-diversity metrics only the Simpson index differed between the donor and diabetic groups. In beta-diversity analyses, diabetic mice clustered separately from donor mice, and the microbiome intervention induced a modest but significant shift detected by the presence or absence of Unweighted UniFrac. Differential abundance analysis and exploratory LEfSe further suggested Akkermansia, particularly Akkermansia muciniphila, as a candidate taxon reduced in diabetic mice and partially restored after the FMT intervention.

CONCLUSION: A donor-derived microbiome intervention attenuated myocardial IRI in db/db mice and was accompanied by partial remodeling of the gut microbiota. Akkermansia muciniphila emerged as a candidate taxon associated with a reduced susceptibility to IRI in diabetic hearts.},
}

@article {pmid42275228,
year = {2026},
author = {Harsonowati, W and Sanjaya, LL and Krismawati, A and Rembang, JHW and Rawung, JBM and Widiyono, W and Doni, F and Iqbal, R and Ullah, S},
title = {Endophyte function in climate-stressed crops: integrating molecular regulation, metabolic trade-offs, and ecological constraints.},
journal = {Plant signaling & behavior},
volume = {21},
number = {1},
pages = {2687952},
doi = {10.1080/15592324.2026.2687952},
pmid = {42275228},
issn = {1559-2324},
mesh = {*Endophytes/physiology/metabolism ; *Stress, Physiological ; *Crops, Agricultural/microbiology/metabolism ; *Climate Change ; Reactive Oxygen Species/metabolism ; },
abstract = {Climate change increasingly exposes crops to simultaneous abiotic and biotic stresses, disrupting physiological stability and reducing agricultural productivity. Although endophytes are widely recognized for improving plant stress tolerance, their effectiveness remains inconsistent across environmental conditions. This review develops an integrative framework to explain how endophyte-mediated responses are regulated at the molecular, metabolic, and ecological levels under climate stress. We examine multi-level interactions to inform predictive deployment in varied agricultural environments. We critically synthesize recent studies on ROS-hormone signaling, carbon allocation trade-offs, metabolic reprogramming, microbiome interactions, ecological filtering, and host genotype-dependent responses. We aim to identify mechanisms that govern the stability or destabilization of plant-endophyte associations under stress conditions. The analysis indicates that endophyte-mediated beneficial traits remain effective only when redox regulation, metabolic balance, and ecological compatibility are maintained within functional physiological limits. Under severe or prolonged stress, disruption of ROS homeostasis, carbon limitation, and ecological instability progressively reduce symbiotic effectiveness, physiological stability, and plant growth performance. Potential predictive variables in this framework include ROS accumulation thresholds, antioxidant capacity, photosynthetic stability, carbon allocation balance, and ecological persistence of endophytes under fluctuating environmental conditions. These variables may enable the prediction of endophyte functional stability, stress adaptation, and growth promotion under heterogeneous climate stress conditions. Collectively, this framework advances current understanding from descriptive interpretation toward a context-dependent perspective that may support future prediction and validation of endophyte performance in climate-resilient agriculture.},
}

*Endophytes/physiology/metabolism
*Stress, Physiological
*Crops, Agricultural/microbiology/metabolism
*Climate Change
Reactive Oxygen Species/metabolism

@article {pmid42275298,
year = {2026},
author = {Majumder, A and Majumder, S and Bano, S and Sen, K and Nayak, KB},
title = {Significance of GSH and H2S regulation for cancer: an intricate interplay between diet, microbiota, metabolic reprogramming, and immune health.},
journal = {Redox report : communications in free radical research},
volume = {31},
number = {1},
pages = {2687238},
doi = {10.1080/13510002.2026.2687238},
pmid = {42275298},
issn = {1743-2928},
abstract = {Due to the proliferative nature of cancer cells, they utilize more dietary extracellular nutrients via one-carbon metabolism for the various metabolic processes, including the synthesis of antioxidants such as glutathione (GSH) and hydrogen sulfide (H2S). Indeed, several studies have found that specific cancer types produce significantly higher levels of GSH and H2S than normal healthy cells, which may serve as a protective mechanism, allowing them to resist stress, survive, and grow. This metabolic heterogeneity, driven by intrinsic and extrinsic factors, contributes to the distinct metabolic characteristics and vulnerabilities of tumor subtypes, which can be exploited to develop anticancer strategies. In this review, we summarize the fundamental roles and regulation of GSH and H2S in normal physiological systems and in the genesis and progression of cancer, their effects on the tumor microenvironment (TME), and their contribution to drug resistance. We also discuss the influences of diet and the gut microbiome on GSH and H2S production, and how cancer cells reprogram their metabolism to grow and survive in a stressful environment by overproducing GSH and H2S.},
}

@article {pmid42275736,
year = {2026},
author = {Barcan, RA and Carradori, S and Samsing, F and Nguyen, NL and He, L and Wang, Y and Barcan, AS},
title = {Machine learning in applied microbiology, from data quality to model validation and implementation.},
journal = {Microbiological research},
volume = {311},
number = {},
pages = {128588},
doi = {10.1016/j.micres.2026.128588},
pmid = {42275736},
issn = {1618-0623},
abstract = {Machine learning (ML) is now widely applied in microbiology, but its reliability varies markedly across domains. In this review, we analysed data from 254 scientific articles that evaluates ML through three linked dimensions including data readiness, model suitability, and deployment readiness across diagnostics and pathogen identification, virology, microbiome research, industrial and environmental microbial biotechnology. This framework helps distinguish robust progress from performance inflated by methodological limitations. Our review shows that pathogen identification and antimicrobial resistance prediction consistently achieve strong performance when supported by curated datasets, reliable labels, and comprehensive reference databases. However, their practical value remains limited by internal validation, lineage confounding, and uneven transfer across strains, institutions, and regions. In virological studies, predictive stability is further challenged by incomplete reference databases, changing taxonomy, and temporal drift during outbreaks. In microbiome research, ML classifiers can detect disease and environmental signals, but their generalization across cohorts remains weak because of compositional data structure, technical bias, and incomplete metadata. Industrial bioprocessing and environmental applications show promise when process data are rich and controlled, but deployment beyond laboratory or site-specific settings remains limited. Across structured microbiological datasets, classical supervised models often remain competitive with deep learning while being easier to interpret and validate. Detailed quantitative benchmarks supporting these comparisons are synthesized in the main text and summary tables. Overall, progress will depend less on algorithmic novelty than on interoperable and well-annotated datasets, representative sampling, standardized benchmarking, reproducible workflows, and prospective multi-site validation.},
}

@article {pmid42276012,
year = {2026},
author = {Budzinski, L and Beenken, AE and Sempert, T and Kang, GU and Abbas, A and Lietz, L and Maier, R and Mashreghi, MF and Chang, HD and Alexander, T},
title = {IgG4-related disease has a specific intestinal microbiota signature.},
journal = {EBioMedicine},
volume = {129},
number = {},
pages = {106326},
doi = {10.1016/j.ebiom.2026.106326},
pmid = {42276012},
issn = {2352-3964},
abstract = {BACKGROUND: While the intestinal microbiome has been implicated in Immunoglobulin-4 related disease (IgG4-RD), it remains poorly characterised. Therefore, we performed a comprehensive microbiome characterisation to identify disease-specific alterations.

METHODS: In this cross-sectional study, cryopreserved stool samples from 28 patients with IgG4-RD were characterised by 16S rRNA gene sequencing and by multiparameter microbiota flow-cytometry to determine their taxonomic composition and phenotype at the single cell level. These data were evaluated in comparison with 24 healthy controls (HC) and assessed for their potential to classify IgG4-RD using random forest classification, with an independent validation cohort (12 IgG4-RD, 12 HC).

FINDINGS: Patients with IgG4-RD exhibited reduced taxonomic diversity and disease-specific alterations in the microbiome compared to HC, characterised by significantly elevated levels of several species within the Bacillota phylum. These taxonomic alterations classified patients and HC with an AUROC of 0.87 (95% CI: 0.77-0.97) but showed reduced performance in the validation cohort (AUROC 0.58, 95% CI: 0.29-0.87). Flow cytometry revealed distinct phenotypic microbiota alterations, robustly distinguishing patients with IgG4-RD from HC in both the training (AUROC 0.9, 95% CI: 0.81-0.99) and validation cohort (AUROC 0.78, 95% CI: 0.59-0.97). The IgG4-RD microbiota were predominantly DNA-low and showed no enhanced endogenous IgG4 coating, neither natively nor after in vitro incubation with autologous serum.

INTERPRETATION: Our study revealed specific alterations in the intestinal microbiota on taxonomic and phenotypic level in IgG4-RD, which potentially reflect different mechanisms of adaptations of the gut microbiota to immune disturbances specific to IgG4-RD. We provide proof-of-concept that this "microbiota fingerprint" may be suitable to identify IgG4-RD in a machine-learning approach and may provide important insights into the complexity of intestinal microbiota alterations in IgG4-RD.

FUNDING: This work was supported by grants from Rolf M. Schwiete Foundation, DFG (German Research Foundation), Innovative Medicines Initiative 2 Joint Undertaking (3 TR), and EFRE-Project.},
}

@article {pmid42276199,
year = {2026},
author = {Bertollo, AG and Puntel, CF and Scaini, G and Quevedo, J and Barichello, T and Ignácio, ZM and Réus, GZ},
title = {The interplay between microbiota and the gut-brain axis in treatment-resistant depression.},
journal = {Progress in neuro-psychopharmacology & biological psychiatry},
volume = {},
number = {},
pages = {111782},
doi = {10.1016/j.pnpbp.2026.111782},
pmid = {42276199},
issn = {1878-4216},
abstract = {Major depressive disorder (MDD) is a common psychiatric condition, and many patients do not respond to standard antidepressant treatments, developing what is known as treatment-resistant depression (TRD). The microbiota-gut-brain axis (MGBA) encompasses the biological processes underlying MDD and TRD. This two-way communication system connects the gut microbiome, the immune system, the central nervous system, and hormone signaling. Changes in the composition and diversity of gut microorganisms can affect neurotransmitter production, blood-brain barrier (BBB) function, immune function, and metabolic processes. These changes may contribute to the development and persistence of TRD. This review describes how the MGBA may influence TRD through mechanisms including BBB function, changes in the kynurenine pathway, variations in short-chain fatty acid (SCFA) production, immune and inflammatory responses, imbalances in the hypothalamic-pituitary-adrenal (HPA) axis, and disruptions in neurotransmitter signaling. The review discusses treatment strategies, focusing on the gut microbiome, including modifications, probiotics, and other approaches.},
}

@article {pmid42276495,
year = {2026},
author = {Benedetti, F and Rahman, T and Uversky, VN and Zella, D},
title = {DnaK unmasked: Potential contributions of intrinsic disorder to the hijacking of human proteostasis by a bacterial chaperone.},
journal = {International journal of biological macromolecules},
volume = {371},
number = {},
pages = {153019},
doi = {10.1016/j.ijbiomac.2026.153019},
pmid = {42276495},
issn = {1879-0003},
abstract = {Bacteria are abundantly present through the body, and the proteins they secrete into the cellular microenvironment both interact with surface receptors and are internalized and interact with internal proteins responsible for important pathways and functions. One of these proteins is DnaK, a moonlighting bacterial chaperone interacting with many human proteins. Intrinsically disordered regions (IDRs) enable structural flexibility essential for multifunctionality, yet their role in DnaK and its interactors remains unclear. Analyzing data from our previous studies of Mycoplasma DnaK and human protein interactions, this study is the first to employ computational analysis to assess disorder in bacterial DnaK, bacterial proteomes, and human interactors, aiming to elucidate novel disorder-mediated mechanisms of bacterial pathogenesis. Results indicate that bacterial chaperones, including DnaK, are expected to be significantly more disordered than the proteome averages (∼27-42% chaperones are highly disordered vs. ∼7-10% proteome-wide highly disordered proteins). Human proteins interacting with bacterial DnaK cluster in chromatin organization and RNA processing networks. DnaK interactors are significantly more disordered than human HSP70/HSC70 interactors, as well as average human proteins, nuclear proteins, and proteins involved in RNA processing and DNA repair. Confirmed interactors, such as XRCC1 and USP10, feature long IDRs with many PTMs, have multiple disorder-based binding regions, and show high LLPS propensity, suggesting that disorder facilitates cellular pathways subversion. These findings are consistent with a model, in which DnaK, by virtue of its structural flexibility, may preferentially engage disordered host proteins, potentially influencing cellular pathways, paving the way for a hypothesis that warrants direct experimental validation.},
}

@article {pmid42276549,
year = {2026},
author = {Camus, J and Freeman, CD and Hu, X and Komnik, A and Casey, RL and Brewer, DT and Yang, S and Hines, KM and Tchoupa, AK},
title = {Extracellular wax ester biosynthesis by staphylococcal lipases detoxifies skin fatty acids and shapes interspecies competition.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag148},
pmid = {42276549},
issn = {1751-7370},
abstract = {To maintain its barrier function, human skin requires lipids, including cholesterol, ceramides, free fatty acids, and wax esters. In contrast to other skin lipids, wax esters remain largely unexplored as metabolites of the skin microbiome. Recently, we discovered that Staphylococcus aureus utilizes its lipase Lip2 to detoxify antimicrobial fatty acids (AFAs) by esterification with cholesterol. The observed promiscuity of Lip2 and the presence of similar lipases among skin staphylococci prompted the search for novel substrates and products. Here, we identify S. aureus Lip2 and Lip1, Staphylococcus simulans SsL, and Staphylococcus epidermidis GehD and GehC as lipases capable of metabolising wax esters. These lipases degraded wax esters into AFAs and fatty alcohols, and, except for GehC, shared the ability to esterify AFAs with fatty alcohols thereby generating wax esters. In monocultures of bacteria heterologously expressing staphylococcal lipases, synthesis of wax esters mirrored protection from AFAs by fatty alcohols in planktonic or biofilm settings. In pairwise cocultures, lipases secreted by lipase-proficient Staphylococcus aureus, Staphylococcus simulans, and Staphylococcus epidermidis functioned as public goods, rescuing lipase-deficient mutants. In absence of detoxifying substrates/lipases, Staphylococcus simulans or Staphylococcus epidermidis outcompeted Staphylococcus aureus when exposed to AFAs. A skin-mimicking high-salt environment increased the resistance of Staphylococcus aureus, but not Staphylococcus simulans, to AFAs, enabling Staphylococcus aureus to match or outcompete Staphylococcus simulans in the presence of AFAs or AFAs plus fatty alcohols, respectively. Collectively, our findings suggest that commensal modulation of skin lipids determines whether niche-specific communities are resilient or permissive to pathogenic invasion by Staphylococcus aureus.},
}

@article {pmid42276619,
year = {2026},
author = {Upadhyay, R and Santhosh, S and Malathi, R and Kumari, PS and Vijayanand, S and Sevanan, M},
title = {Starved synapses: Gut microbiome dysbiosis and its role in Alzheimer's glucose impairment.},
journal = {International review of neurobiology},
volume = {186},
number = {},
pages = {241-264},
doi = {10.1016/bs.irn.2026.01.010},
pmid = {42276619},
issn = {2162-5514},
mesh = {Humans ; *Alzheimer Disease/metabolism/microbiology ; Animals ; *Glucose/metabolism ; *Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; *Blood-Brain Barrier/metabolism ; *Brain/metabolism ; },
abstract = {Alzheimer's disease (AD) is increasingly recognised as a multifactorial disorder driven by metabolic, microbial, and neuroinflammatory imbalances. The study of the research results proposes that gut dysbiosis and impaired brain glucose metabolism are closely interrelated through the gut-brain metabolism axis. Changes in the intestinal microbiome may disrupt insulin sensitivity, cause systemic inflammation, and disrupt the blood-brain barrier, worsening neuronal glucose deficits and facilitating amyloid-β (Aβ) aggregation and tau phosphorylation. Alongside, neurodegenerative cascades are further enhanced by neuronal metabolic reprogramming, characterised by decreased glucose uptake, dysfunctional glycolytic enzymes, and oxidative stress. Short-chain fatty acids (SCFAs) are mainly butyrate, which have a neuroprotective effect in regulating inflammation and gut integrity, and dysbiosis causes increased pro-inflammatory cytokines and endotoxin leakage. This two-way communication network provides new therapeutic opportunities, such as probiotics, prebiotics, nutritional control, and metabolic reprogramming interventions, to regain homeostasis and prevent the advancement of AD.},
}

Humans
*Alzheimer Disease/metabolism/microbiology
Animals
*Glucose/metabolism
*Dysbiosis/metabolism
*Gastrointestinal Microbiome/physiology
*Blood-Brain Barrier/metabolism
*Brain/metabolism

@article {pmid42276744,
year = {2026},
author = {Thornton, CS and Schaupp, L and Tunney, MM and Mall, MA},
title = {Bridging the airway microbiome and targeted therapy in bronchiectasis: multi-omics insights, endotypes and emerging therapies.},
journal = {The European respiratory journal},
volume = {},
number = {},
pages = {},
doi = {10.1183/13993003.00239-2026},
pmid = {42276744},
issn = {1399-3003},
abstract = {Bronchiectasis is a heterogeneous chronic airway disease primarily driven by persistent infection, microbial dysbiosis and dysregulated host immunity. While culture-based microbiology has historically informed clinical management, advances in high-throughput sequencing and multi-omic technologies have transformed our understanding of the airway ecosystem, revealing that disease activity is shaped, not only by individual pathogens, but by complex and dynamic host-microbe interactions. Despite the breadth of descriptive microbiome data, translation into clinically actionable diagnostics or therapies has been limited. Importantly, cross-sectional correlations between microbiota and inflammation do not establish cause and effect, underscoring the need to embed host-microbiome profiling within both longitudinal and interventional therapeutic trials. In this review, we critically appraise current microbial and host multi-omics research in bronchiectasis, integrating microbiome studies with host inflammatory, proteomic and immunophenotyping data. We highlight themes emerging across cohorts, including low microbial diversity, pathogen dominance, loss of commensal networks and neutrophil-driven inflammation and discuss how these features align with biological endotypes associated with exacerbations and treatment response. Drawing on lessons from host-directed therapeutic successes, we examine translational roadblocks limiting microbiome-guided care. We further review emerging microbiome-modulating strategies such as pathogen-specific biologics, bacteriophage therapy, live biotherapeutic products, biofilm-targeting adjuncts and precision antibiotic stewardship. Finally, we propose a roadmap toward microbiome-informed precision medicine through harmonized methodologies, integration of host and microbial biomarkers into clinical trials and embedding multi-omics pipelines within large international registries. Collectively, these advances have the potential to shift bronchiectasis research and clinical management towards rationally designed, precision medicine-driven therapeutic strategies.},
}

@article {pmid42276769,
year = {2026},
author = {Fang, F and Lau, HC and Yu, J},
title = {Microbiota and metabolites modulation of cancer stem cells and chemotherapy sensitivity.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-338801},
pmid = {42276769},
issn = {1468-3288},
abstract = {Cancer stem cells (CSCs) drive tumour initiation, metastasis and therapeutic resistance through metabolic and microenvironmental adaptability. The microbiota critically modulates cancer development and treatment response, with increasing evidence linking commensal microbes and their metabolites to aberrant CSC function. In this review, we summarise the mechanistic roles of microbiota and metabolites (eg, short-chain fatty acids, bile acids) in CSC regulation, including their effects on the CSC niche via stromal cell modulation, extracellular matrix remodelling and soluble factor networks. Given the central roles of CSCs in chemoresistance, we further discuss how microbes and metabolites influence CSC-associated chemotherapy resistance and highlight microbiota-targeting and metabolite-targeting strategies including probiotics, metabolite formulations, antibiotics and nanomedicine to disrupt CSCs and enhance chemosensitivity. In summary, deeper insights into CSC-microbiota-metabolites crosstalk promise novel therapeutic targets to overcome resistance and improve patient outcomes.},
}

@article {pmid42276771,
year = {2026},
author = {Kang, G and Lam, WKJ},
title = {Beyond the virus: rethinking nasopharyngeal carcinoma through the gut microbiome.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-339135},
pmid = {42276771},
issn = {1468-3288},
}

@article {pmid42276790,
year = {2026},
author = {Gonen-Colak, B and Turan-Demirci, B and Buyuktuncer, Z},
title = {Modification of Gut Microbiome by Cereal and Pseudocereal Consumption: A Systematic Review.},
journal = {Nutrition reviews},
volume = {},
number = {},
pages = {},
doi = {10.1093/nutrit/nuag078},
pmid = {42276790},
issn = {1753-4887},
support = {20780//Hacettepe University Scientific Research Projects Coordination Unit/ ; },
abstract = {CONTEXT: Diet profoundly shapes the composition and function of the gut microbiome. Cereals and pseudocereals, as part of a healthy diet, may have significant potential in the modulation of the gut microbiome.

OBJECTIVE: This review aimed to systematically analyze the evidence from human intervention studies that examine the effects of cereal and pseudocereal consumption on the gut microbiome composition, diversity, and metabolites.

DATA SOURCES: Three electronic databases were searched from database inception to May 2025: PubMed/Medline, the Web of Science, and Cochrane. This review included randomized controlled trials with parallel and crossover designs, controlled nonrandomized intervention studies, and single-arm pre-post intervention studies. In addition, only English-language articles reporting changes in the gut microbiome and bacterial fermentation metabolites associated with dietary intake of cereal and pseudocereals in adult individuals (>18 years) were included.

DATA EXTRACTION: Basic information regarding the methodological characteristics of the included studies and the outcome measures was recorded.

DATA ANALYSIS: A total of 9670 articles were analyzed, of which 48 articles were ultimately included. The majority of the included studies (41/48) showed that cereal consumption was associated with significant changes in the gut microbiome composition. In terms of microbial diversity, only 4 of 29 studies showed significant increases in the α-diversity of the gut microbiome. Among the 28 studies analyzing short-chain fatty acid levels, 12 studies reported significant changes in the levels of short-chain fatty acids.

CONCLUSIONS: Although the importance of daily cereal consumption in modulating the gut microbiome is recognized, well-designed new studies are needed to identify the most effective types of cereal or pseudocereals, and the amount that is adequate to achieve the desired modulation.},
}

@article {pmid42276807,
year = {2026},
author = {Souza, MCDCD and de Jármy-Di Bella, ZIK and Bianchi-Ferraro, AMHM and Souza, SDL and Amanda Rafaelly Honório, M and Sobral, APT and Ribeiro, CDPV and Bussadori, SK and Fernandes, KPS and Chavantes, MC and Zamuner, SR},
title = {Effects of Erbium:YAG laser combined with vaginal estriol therapy in postmenopausal women with Genitourinary Syndrome of Menopause: protocol for a randomised, double-blind, controlled trial.},
journal = {BMJ open},
volume = {16},
number = {6},
pages = {e117269},
doi = {10.1136/bmjopen-2026-117269},
pmid = {42276807},
issn = {2044-6055},
mesh = {Humans ; Female ; *Estriol/administration & dosage/therapeutic use ; Double-Blind Method ; Middle Aged ; *Lasers, Solid-State/therapeutic use ; *Postmenopause ; *Female Urogenital Diseases/therapy/drug therapy ; Vagina ; Aged ; Syndrome ; Combined Modality Therapy ; Administration, Intravaginal ; Treatment Outcome ; Research Design ; },
abstract = {INTRODUCTION: Genitourinary syndrome of menopause (GSM) is a chronic, oestrogen-deficient condition that is frequently underdiagnosed and undertreated. Although low-dose vaginal estriol improves epithelial trophism and microbial balance, a substantial proportion of women report persistent symptoms. High-quality randomised evidence evaluating combined therapeutic strategies remains scarce. Energy-based modalities, including the erbium:YAG (Er:YAG) laser (λ=2940 nm), have been proposed as adjunctive treatments. This trial aims to assess the efficacy of Er:YAG laser therapy combined with vaginal estriol compared with estriol alone in postmenopausal women with GSM.

METHODS AND ANALYSIS: This is a single-centre, randomised, double-blind, controlled clinical trial. Postmenopausal women aged 45-70 years with vaginal pH ≥5.0 and at least one moderate GSM symptom (Visual Analogue Scale ≥4) will be eligible. Exclusion criteria include current systemic or local hormone therapy, previous vaginal energy-based treatment, abnormal cervical cytology and body mass index ≥35 kg/m[2]. All participants will receive vaginal estriol cream (0.5 mg per dose) daily for 14 days, followed by twice-weekly administration for 16 weeks. Participants will be randomised (1:1) to receive either estriol plus sham Er:YAG laser or estriol plus active Er:YAG laser. Three laser sessions will be delivered at approximately 4-week intervals. Assessments will occur at baseline, monthly during treatment and 4 months after the final session. The primary outcome is the Vulvovaginal Health Index, with the primary endpoint defined as the change from baseline to 4 months post-treatment, reflecting sustained effect. Secondary outcomes include GSM symptom severity, vaginal microbiome composition (16S rRNA sequencing), quality of life (Menopause Rating Scale) and sexual function (Female Sexual Function Index). Data will be analysed using repeated-measures analysis of variance or appropriate non-parametric tests, with significance set at p<0.05.

ETHICS AND DISSEMINATION: Ethical approval has been obtained from the Human Research Ethics Committee of UNINOVE. Written informed consent will be obtained. Findings will be disseminated via peer-reviewed journals and scientific meetings.

TRIAL REGISTRATION NUMBER: NCT06873971.},
}

Humans
Female
*Estriol/administration & dosage/therapeutic use
Double-Blind Method
Middle Aged
*Lasers, Solid-State/therapeutic use
*Postmenopause
*Female Urogenital Diseases/therapy/drug therapy
Vagina
Aged
Syndrome
Combined Modality Therapy
Administration, Intravaginal
Treatment Outcome
Research Design

@article {pmid42276920,
year = {2026},
author = {Guldan, M and Shah, E and Al-Shiab, R and Ozbek, L and Covic, A and Kanbay, M},
title = {Linking the exposome to frailty: pathways, mechanisms, clinical implications, and prevention.},
journal = {European journal of internal medicine},
volume = {},
number = {},
pages = {107006},
doi = {10.1016/j.ejim.2026.107006},
pmid = {42276920},
issn = {1879-0828},
abstract = {BACKGROUND: Frailty is a state of vulnerability that emerges from cumulative, non-genetic influences acting across the life course. This review applies an exposome lens, integrating general external exposures, specific external exposures, and internal biologic processes. We aimed to synthesize how social, environmental, behavioural, clinical, and biological exposures contribute to frailty and identify clinically actionable prevention targets.

METHODS: This structured narrative review synthesized epidemiological, clinical, environmental, and mechanistic evidence linking exposome-related exposures to frailty in older adults. Literature was identified through targeted searches of PubMed/MEDLINE, Scopus, Web of Science, and Google Scholar, supplemented by reference screening. Evidence was organized across exposome domains and narratively appraised according to study design, temporality, consistency, biological plausibility, and clinical relevance.

RESULTS: Socioeconomic disadvantages, loneliness, and social isolation are consistently associated with higher frailty risk, whereas green and walkable environments may support healthier aging through mobility and social participation. Protective factors include specific high-quality dietary patterns and physical activity, whereas ultra-processed foods, sedentary behaviour, air pollution, climate stressors, infections, and selected chemical exposures are linked to adverse outcomes. Cardiometabolic, cardiorespiratory, and neurological vulnerability further connect external exposures with frailty progression. Internal pathways, including chronic inflammation, mitochondrial dysfunction, endocrine-metabolic dysregulation, gut microbiome dysbiosis, and epigenetic aging support plausible mechanistic pathways through which exposures may contribute to frailty.

CONCLUSION: Exposome-informed frailty care should combine validated frailty assessment with brief screening for actionable risks, including social connection, diet, physical activity, pollution and temperature vulnerability, infection history, vaccination status, and chronic disease burden. Practical strategies include social prescribing, healthier dietary patterns (e.g., Mediterranean-style diets), physical activity in green and low-pollution spaces, seasonal health planning, vaccination, and cardiometabolic optimization.},
}

@article {pmid42277050,
year = {2026},
author = {Xu, J and Han, Z and Xue, Q and Wang, H and Li, Y and Song, J and Li, L and Hu, M and Wang, D},
title = {Gut commensal Odoribacter splanchnicus attenuates hyperlipidemic periodontitis via gut-oral metabolic transmission of β-GPA.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01033-4},
pmid = {42277050},
issn = {2055-5008},
support = {82470987//National Natural Science Foundation of China/ ; jcsz2025678-2//Science and Technology Project of Jilin Province Department of Finance/ ; 2024JBGS07//"Medicine+X" Interdisciplinary Innovation Project/ ; },
abstract = {Hyperlipidemic periodontitis (HPD) represents a prevalent comorbidity linking systemic metabolic dysregulation with local inflammation, yet the microbial mechanisms driving this gut-oral crosstalk remain elusive. Here, the comorbid state of HPD is linked to hyperlipidemia-associated gut microbiota changes, which are prominently accompanied by the depletion of Odoribacter splanchnicus in both patients and mice. Fecal microbiota transplantation demonstrates that this gut dysbiosis exacerbates periodontal destruction when local inflammation is present. Mechanistically, intragastric administration of live O. splanchnicus ameliorates HPD by remodeling the gut ecosystem and upregulating the metabolite β-guanidinopropionic acid (β-GPA). Notably, direct supplementation with β-GPA reproduces these protective effects. Furthermore, β-GPA is proposed as a systemic effector linking the gut and periodontal tissues, where its protective effect is associated with the suppression of the pro-inflammatory Toll-like receptor 4 (TLR4) signaling cascade. These findings highlight a link involving O. splanchnicus, β-GPA, and the modulation of TLR4 signaling, offering a potential microbiome-based therapeutic strategy for managing complex metabolic-inflammatory comorbidities.},
}

@article {pmid42277130,
year = {2026},
author = {González-Stegmaier, R and Ejsmentewicz, T and Podesta, C and Jorquera, R and Lagos, R and Barrientos, C and Aravena, E and Larrain, M and Aguilera, JP and Silva-Moreno, E and Villarroel-Espíndola, F},
title = {Gut microbiome profiles in Chilean participants with colorectal adenomas: an exploratory 16S rRNA sequencing study.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-57417-1},
pmid = {42277130},
issn = {2045-2322},
support = {LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; LMT-2020 & LMT-2021//Fundación Arturo López Pérez (FALP) Cancer Center/ ; 1221415//ANID-FONDECYT/ ; },
abstract = {Colorectal cancer (CRC) is the third most commonly diagnosed cancer globally and the second leading cause of cancer-related mortality. The disease typically progresses from premalignant adenomatous lesions. Recent studies highlight the pivotal role of the gut microbiota in colorectal carcinogenesis, suggesting a complex interplay between the microbiota and tumor development. This study analyzes gut microbiota profiles in a single-center cohort of Chilean individuals with and without adenomas, using 16S rRNA sequencing to interrogate microbial changes associated with the transition from healthy colon epithelium to precancerous lesions. The results show that the adenoma-associated microbiota is characterized by increased Proteobacteria abundance and decreased Firmicutes abundance compared with healthy controls. Participants with precancerous lesions exhibit increased abundance of Desulfovibrio, a genus of sulfate-reducing bacteria capable of producing hydrogen sulfide (H2S), a microbial metabolite that has been linked to DNA damage and epithelial stress responses. These findings provide a baseline of the microbial landscape in our population and identify biomarkers associated with premalignant lesions, highlighting microbiome analysis as a diagnostic tool for colorectal disease.},
}

@article {pmid42277260,
year = {2026},
author = {Jie, Z and Liang, W and Ding, Q and Liu, X and Zhang, Y and Chen, N and Li, S and Tong, X and Gao, H and Lu, R and Huang, X and Guo, R and Chen, J and Zhu, J and Zhang, Z and Liu, N and Xie, Z and Wang, X and Qi, L and Li, Y and Xiao, L and Zhang, S and Jin, X and Xu, X and Yang, H and Wang, J and Zhao, F and Jia, H and Kristiansen, K and Zhang, T and Hao, L and Zhu, L and Chen, C},
title = {Genomic landscape of the human vaginal microbiome is linked to host genetics and population of origin.},
journal = {Nature genetics},
volume = {},
number = {},
pages = {},
pmid = {42277260},
issn = {1546-1718},
abstract = {The vaginal microbiome is essential for women's health, yet its genomic diversity and interaction with the host remain incompletely characterized. Here we present the Global Vaginal Metagenome-assembled Genomes catalog, an extensive repository of vaginal microbial genomes generated by integrating 10,665 in-house Chinese metagenomes, with 2,967 publicly available metagenomes and 1,433 bacterial isolates. The catalog comprises 65,055 genomes from 890 prokaryotes, 11 eukaryotes and 6,590 viral taxonomic units, many not represented in public reference databases. We investigate virus-bacteria interactions, revealing conserved phages-host associations. We then identify substantial intraspecies genomic and functional variations displaying population-specific patterns. A metagenome-genome-wide association study identifies seven host genetic loci associated with vaginal species at study-wide significance and replicated in at least one independent cohort, notably connecting the gene OPRK1 with the potential pathogen Ureaplasma urealyticum. In summary, our research provides a comprehensive reference for future studies on genotype-phenotype interplay within the human vaginal microbiome.},
}

@article {pmid42277392,
year = {2026},
author = {Bugelli, V and Calabrò, F and Camatti, J and Cecchi, R and Di Paolo, M and Franceschetti, L},
title = {Artificial intelligence in forensic science: a systematic review. Part II: long-range postmortem interval estimation.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42277392},
issn = {1437-1596},
abstract = {Postmortem interval (PMI) estimation remains a major challenge in forensic medicine due to the complex and multifactorial nature of decomposition processes. In recent years, artificial intelligence (AI) and machine learning techniques have been increasingly applied to improve PMI prediction. This systematic review aimed to evaluate the current evidence on AI-based models developed for PMI estimation. A systematic literature search was conducted in PubMed/MEDLINE and Scopus from database inception to 1 March 2026, following PRISMA 2020 guidelines. Studies were included if they applied AI, machine learning, or deep learning methods to estimate PMI using real postmortem datasets. Data extraction included study characteristics, data modality, AI model architecture, validation strategy, and reported performance metrics. A total of 64 studies met the inclusion criteria. The most common approach involved microbiome-based models (n = 29), followed by metabolomics and proteomics approaches (n = 11) and imaging-based AI models (n = 11). Random Forest algorithms were the most frequently used machine learning method, particularly in microbiome studies. Reported predictive performance varied widely across studies, with several models achieving high accuracy or low prediction errors depending on the data modality and PMI range investigated. AI represents a promising tool for improving the accuracy and objectivity of PMI estimation by enabling the integration of complex forensic datasets. However, current evidence is limited by heterogeneous methodologies, small datasets, and a lack of external validation. Future research should focus on large multicenter datasets, standardized validation protocols, and multimodal AI models integrating diverse forensic data sources.},
}

@article {pmid42277393,
year = {2026},
author = {Babar, P and Babar, S and Ghate, M},
title = {Recent advances in the identification of vaginal fluid for forensic applications.},
journal = {International journal of legal medicine},
volume = {},
number = {},
pages = {},
pmid = {42277393},
issn = {1437-1596},
abstract = {Identification of body fluids in forensic investigations is important for three main reasons: first, the type of body fluid present at the crime scene may indicate the nature and context of the crime; second, one may predict the likelihood of getting quality DNA; and third, it may help to verify or discredit the statements from the victim or suspect. Vaginal fluid (VF) is a common body fluid found at the crime scene in sexual assault cases and is usually found mixed with other body fluids like semen, saliva, and blood. Methods for identifying VF are limited compared to those for blood, semen, and saliva. The existing cytochemical methods for VF detection are destructive and have low sensitivity and specificity. Examination of VF samples using spectroscopic techniques such as Fourier-transform infrared spectroscopy, fluorescence spectroscopy, and Raman spectroscopy has revealed unique spectral properties. However, identifying VF with these techniques is complicated, especially when it is mixed with other body fluids. Specific proteins unique to VF have been identified through proteomic studies. New methods to detect microbiome, DNA methylation, and RNA profiles specific to VF are being developed. Although these methods hold promise for correctly identifying VF traces at crime scenes, challenges such as high cost, complex data interpretation, and limited robustness remain. Further research to integrate chemometric algorithms, simplify workflows and develop robust methods is extremely important. Developing methods to identify and detect VF traces that are quick, reliable, non-destructive, and adaptable to existing forensic workflows is the need of the hour.},
}

@article {pmid42277400,
year = {2026},
author = {Fu, Y and Long, N and Sourn, P and Zhang, M and Tan, W and Yu, H and Yuan, J and Chen, Y and Wang, J and Zhang, X and Li, X and Wang, S and Feng, L and Wu, J and Wang, Z and Ding, W},
title = {Gardnerella enrichment in the vaginal microbiome of women with gestational diabetes mellitus is associated with lower fetal birthweight percentiles.},
journal = {Diabetologia},
volume = {},
number = {},
pages = {},
pmid = {42277400},
issn = {1432-0428},
support = {2024ZD0532100//Noncommunicable Chronic Diseases-National Science and Technology Major Project/ ; 2023BCA004//Hubei Province's Major Scientific and Technological Project/ ; },
abstract = {AIMS/HYPOTHESIS: We aimed to characterise alterations in the late-pregnancy vaginal microbiota in women with gestational diabetes mellitus (GDM), and to examine their associations with maternal glycaemic status and fetal growth.

METHODS: In this observational case-control study, women with newly diagnosed, diet-managed GDM (n=60) and healthy pregnant control participants (n=119) were recruited at a single tertiary centre. Vaginal swabs were collected in the third trimester and analysed by full-length 16S rRNA gene sequencing. Associations between vaginal microbiota composition, maternal glycaemic measures, and fetal birthweight percentile (FBW%ile) were evaluated.

RESULTS: The overall vaginal microbial composition differed between groups despite similar alpha diversity. Beta diversity analyses showed significant separation between the women with GDM and the control group (R=0.068, p=0.011 by ANOSIM). Lactobacillus-dominated communities were less frequent in women with GDM than in control participants (73.3% vs 86.6%, p=0.029), with reduced Lactobacillus abundance (79.8% vs 87.4%, nominal p=0.020) and increased Gardnerella abundance (9.7% vs 1.4%, nominal p=0.011). Within the GDM group, Gardnerella abundance correlated positively with fasting glucose levels (r=0.3617, nominal p=0.007) and inversely with FBW%ile (r=-0.2774, nominal p=0.032). Stratification by FBW%ile (<50% vs ≥50%) showed a higher proportion of non-Lactobacillus-dominated communities (44.4% vs 12.1%, p=0.001) and higher Gardnerella abundance (15.0% vs 3.2%, nominal p=0.020) in the low FBW%ile subgroup. Associations with Gardnerella were attenuated in sensitivity analyses that excluded samples with extreme Gardnerella abundance.

CONCLUSIONS/INTERPRETATION: Late-pregnancy GDM was associated with modest shifts in vaginal microbial structure, characterised by reduced Lactobacillus dominance and relative enrichment of Gardnerella. Exploratory analyses of associations of Gardnerella with maternal fasting glucose levels and fetal growth suggest that variation in the vaginal microbial environment may contribute to metabolic and fetal growth heterogeneity in women with GDM.},
}

@article {pmid42277415,
year = {2026},
author = {Prada, J and Pereira-Dias, L and Santos, JA and Santos, C},
title = {Influence of Environment and Rootstock On the Rhizosphere Bacterial Communities in Four Vineyards of the Douro Demarcated Region.},
journal = {Microbial ecology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00248-026-02798-z},
pmid = {42277415},
issn = {1432-184X},
abstract = {The Douro Demarcated Region (DDR) is a worldwide acknowledged winemaking region. Climate change is threatening the sector, as climatic shifts are expected. This work analyzed environmental and genetic traits modulating the rhizobiome of four vineyards in the DDR, focusing on understanding the hierarchy of ecological conductors for these communities. These vineyards' terroir was environmentally, genetically, and culturally characterized. Rhizosphere bacterial community composition was analyzed using 16S metabarcoding from soil samples collected between July 2022 and January 2024. Results support the hypothesis of an ecological profiling hierarchy. The soil physicochemical properties likely acted as a primary environmental modulator, determining the composition of the bacterial microbiome and contributing to the diversity and richness of the bacterial communities. The major drivers among the soil's physiochemistry were organic/inorganic profile, mainly influenced by organic matter content and pH. Rootstock genotype appears to exert a secondary selection on the microbiome, focusing on the microorganisms' functional traits. The 1103-P rootstock positively influenced the abundance of copiotrophic bacteria, compared to the R110, demonstrating that the first recruits a more versatile, exploratory, and expansionist microbiome, whilst the second focuses on attracting a highly specialized community, more focused on maximizing energy gathering and optimizing resource use. This work demonstrates that the microbial terroir is a result of multiple factors, promoting abiotic modulation and host-mediated selection, which establishes a very specific community for each scenario. The assessment of these holistic dynamics is fundamental to establishing a baseline for future precision viticulture strategies, namely bio-inoculants, to support and promote a better grapevine adaptation to climate change.},
}

@article {pmid42277556,
year = {2026},
author = {Yuan, G and Zhou, M and Xiong, C and Bai, R and Cao, F and Yuan, Y and Zhang, WH and Bai, W},
title = {Root anatomical traits modulate the assembly and nitrogen-transformation potential of root-associated microbiomes in a temperate steppe.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71342},
pmid = {42277556},
issn = {1469-8137},
support = {U2571209//National Natural Science Foundation of China/ ; 32371722//National Natural Science Foundation of China/ ; 32030075//National Natural Science Foundation of China/ ; },
abstract = {Plants have evolved numerous belowground strategies to capture nutrients. While root functional differentiation between absorption and transportation has been inferred from order-based traits, the role of microbiomes in mediating this differentiation remains unclear. We measured traits (anatomical, chemical, and morphological) of lower order (absorption-dominated) and higher order (transportation-dominated) roots of 37 herbaceous species (13 monocots and 24 dicots) in a temperate grassland. Furthermore, we employed high-throughput quantitative polymerase chain reaction and 16S rRNA gene sequencing to investigate bacterial nitrogen-transformation gene abundance, diversity, and community assembly along the soil-root continuum (rhizosphere, rhizoplane, and endosphere) and analyzed their relationships with root traits. Monocot roots exhibited greater bacterial diversity and nitrogen-transformation gene abundances than dicots. Within dicots, lower order roots showed higher bacterial diversity and nitrogen-transformation gene abundances than higher order roots, a pattern not observed in monocots. Lower order roots, characterized by higher cortex proportion, facilitated the enrichment of diverse bacteria and recruitment of nitrogen-transformation microorganisms. These patterns were associated with a decrease in homogeneous selection from lower order to higher order roots. This study reveals the mechanisms of functional differences among herbaceous root orders from a microbiome perspective, offering further insights into how root-microbe interactions underpin nitrogen-transformation potential in terrestrial ecosystems.},
}

@article {pmid42277753,
year = {2026},
author = {Pan, Y and Wang, XT and Li, Y and Wang, W and Sonne, C and Tong, YW and Ren, N and Ok, YS},
title = {Microbial communication in saline environments: quorum sensing and the future of anaerobic wastewater treatment.},
journal = {BMC biology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12915-026-02651-2},
pmid = {42277753},
issn = {1741-7007},
support = {No. 52300155, No. 52400025//the National Natural Science Foundation of China/ ; No. 2023M740917, 2024M754204//China Postdoctoral Science Foundation/ ; No. LBH-Z23177//Heilongjiang Province Postdoctoral Science Foundation funded project/ ; No. LH2024E042//Natural Science Foundation of Heilongjiang Province/ ; No. Z2024B010//Science Foundation of National Engineering Research Center for Safe Disposal and Resources Recovery of Sludge, Harbin Institute of Technology/ ; No. QA202322//Open Project of State Key Laboratory of Urban Water Resource and Environment, Harbin Institute of Technology/ ; RS-2025-00555967//National Research Foundation of Korea(NRF) grant funded by the Korea government(MSIT)/ ; RS-2021-NR060142//Basic Science Research Program through the National Research Foundation of Korea(NRF) funded by the Ministry of Education/ ; },
abstract = {Anaerobic treatment of industrial wastewater offers a sustainable and cost-effective approach to reducing environmental contamination while recovering biogas. High-salinity wastewater poses ecological risks and remains difficult to treat due to salt-induced sludge disintegration, volatile fatty acid accumulation, and reduced methane production. Quorum sensing is emerging as a key regulator of microbial activity and system stability under salt stress. This review summarizes salinity-stress inhibition mechanisms, evaluates quorum sensing-based mitigation strategies, and proposes a stage- and performance-based framework for quorum sensing application to advance resilient and efficient anaerobic treatment systems.},
}

@article {pmid42277802,
year = {2026},
author = {Guo, N and Shi, J and Zhang, X and Xu, H and Ji, T and Qiu, F and Li, K and Wu, Z and Ma, J and Weng, Q and Qiu, R and Shu, G and Chen, Z and Chen, J and Wang, X},
title = {Mesoporous catechin hydrogel for enhanced astaxanthin-based inflammatory bowel disease therapy.},
journal = {Journal of nanobiotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12951-026-04665-y},
pmid = {42277802},
issn = {1477-3155},
support = {2025KY1929//Medical and Health Science and Technology Program of Zhejiang Province (China)/ ; 2023RC309//Medical and Health Science and Technology Program of Zhejiang Province (China)/ ; },
abstract = {Inflammatory bowel disease (IBD) is a persistent intestinal inflammation driven by epithelial barrier dysfunction, immunological imbalance, and microbial dysbiosis. The restoration of gut homeostasis through biomaterial-based strategies offers a potential avenue for alleviating inflammation in IBD. Herein, an alginate-based hydrogel incorporating astaxanthin-loaded mesoporous catechin nanoparticles (AST@MCN-Gel) was designed to relieve inflammation and rebalance gut homeostasis. The mesoporous framework of MCN enabled effective encapsulation of the hydrophobic AST, thereby increasing its water solubility and bioavailability. In lipopolysaccharide-induced macrophages, AST@MCN exhibited superior ROS-scavenging capacity and anti-inflammatory activity relative to either AST or MCN. Mechanistically, AST@MCN modulated macrophage phenotype from pro-inflammatory (M1) to anti-inflammatory (M2) state through regulation of the MAPK/NF-κB pathway. On the other hand, the alginate-based hydrogel effectively enhanced the intestinal retention of AST@MCN, resulting in a marked improvement in oral therapeutic efficacy. In a DSS-induced IBD mouse model, oral administration of AST@MCN-Gel significantly alleviated the clinical symptoms and restored intestinal barrier integrity. Analysis of the gut microbiome further indicated that AST@MCN-Gel ameliorated gut dysbiosis by restoring microbial diversity and suppressing the proliferation of pathogenic species. Collectively, these underscore the potential of AST@MCN-Gel as an effective biomaterial-based therapeutic approach for restoring intestinal homeostasis and improving IBD therapy.},
}

@article {pmid42277887,
year = {2026},
author = {Mamjoud, A and Zirah, S and Rebuffat, S and Biron, É and Fliss, I},
title = {Uncovering how selected potent bacteriocins reshape the broiler chicken gut microbiome in a PolyFermS continuous in vitro model.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42277887},
issn = {1674-9782},
support = {IRCPJ 499946-15//NSERC/ ; 2014-022-C12//CRIBIQ/ ; 109048-001//IDRC-Innovet-Initiative/ ; },
abstract = {BACKGROUND: Bacteriocins are promising alternatives to antibiotics in poultry production, offering pathogen control with minimal disruption to gut microbiota and reduced risk of resistance dissemination. This study compared the impact of three bacteriocins-microcin J25, nisin Z, and pediocin PA-1-against bacitracin as a positive control, specifically evaluating their effects on gut microbiota composition and metabolic activity. The study utilized the PolyFermS continuous fermentation model to simulate chicken caecal conditions.

RESULTS: 16S rRNA sequencing revealed that bacitracin and nisin Z significantly altered the microbiota composition, reducing key families such as Lactobacillaceae and Ruminococcaceae, while microcin J25 and pediocin PA-1 had negligible effects. Short-chain fatty acid analysis revealed a significant time-dependent decrease in butyrate levels following nisin Z and bacitracin treatments, with the most pronounced reduction observed at 48 h post-injection. Conversely, microcin J25 and pediocin PA-1 maintained stable profiles. Untargeted LC-MS metabolomics indicated a marked metabolic shift under nisin Z treatment, including increased amino acids and cyclic dipeptide levels, while microcin J25 had minimal impact. Stability assays confirmed that microcin J25 remained active up to 24 h, whereas nisin Z and pediocin PA-1 lost antimicrobial activity rapidly.

CONCLUSIONS: These findings support the selective use of bacteriocins as alternatives to antibiotics in poultry farming, with microcin J25 demonstrating the most favorable profile for microbiota preservation and metabolic stability. Future research will focus on in vivo trials in broiler chickens to confirm these findings and evaluate the practical application of microcin J25 in a production environment.},
}

@article {pmid42277889,
year = {2026},
author = {Klimešová, B and Volfová, K and Hammerbauerová, I and Dulavová, K and Pajer, P and Bundilová, K and Modrý, D and Adamík, P and Votýpka, J},
title = {Bartonella transmission and gut microbiome dynamics in Ceratophyllus sciurorum fleas and their edible dormouse hosts (Glis glis).},
journal = {Parasites & vectors},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13071-026-07494-y},
pmid = {42277889},
issn = {1756-3305},
support = {284423//Grantová Agentura, Univerzita Karlova/ ; NU2305-00511//Ministerstvo Zdravotnictví Ceské Republiky/ ; },
abstract = {BACKGROUND: The genus Bartonella comprises facultative intraerythrocytic bacteria capable of causing long-lasting bacteremia in their natural hosts, with zoonotic potential across multiple species. Rodents serve as important reservoirs for a broad diversity of Bartonella spp., with blood-feeding arthropods, particularly fleas, mediating transmission. Despite their frequent association with humans, the role of edible dormice (Glis glis) and their fleas (Ceratophyllus sciurorum) in Bartonella ecology remains poorly understood.

METHODS: We combined long-term ecological and epidemiological data with gut and body microbiome analyses of C. sciurorum to investigate the prevalence, diversity, host specificity, and transmission of Bartonella across flea life stages. The study was conducted over 6 years in a natural dormouse population. Bartonella detection and characterization were performed using multilocus PCR targeting gltA, rpoB, ftsZ, and ITS loci, bacterial cultivation on selective media, and long-read nanopore sequencing. Flea gut microbiomes were assessed in pooled and individual samples to determine the impact of Bartonella infection on microbial community structure. Transmission across flea life stages was evaluated by analyzing larvae, newly emerged adult fleas, and adults directly collected from dormice.

RESULTS: We observed a consistently high prevalence of Bartonella in both dormice and their fleas. Four species were identified: B. gliris and B. grahamii subsp. shimonis dominated, each represented by multiple genotypes, whereas B. washoensis and B. bilalgolemii were each detected in a single flea. Moreover, mixed infections of B. gliris and B. grahamii subsp. shimonis were frequent in both dormice and their fleas. Detection of Bartonella DNA in flea larvae and newly emerged adults indicates possible transstadial perpetuation. Flea gut microbiomes were highly variable but consistently dominated by Bartonella in infected fleas. In contrast, uninfected fleas exhibited more diverse communities, often enriched with Staphylococcus and other environmental or host-associated taxa. We, therefore, suggest that flea populations can maintain Bartonella over extended periods, even in the absence of continuous contact with vertebrate hosts.

CONCLUSIONS: The dormouse-flea-Bartonella system represents a valuable natural model for studying flea-borne zoonoses. The high prevalence and persistent bacteremia in dormice of different ages indicate their role as suitable reservoirs for at least two Bartonella species. Flea populations are capable of sustaining Bartonella over long periods, and detections in immature life stages suggest continuity of infection across flea generations. Therefore, C. sciurorum appears to play an important role in maintaining B. grahamii subsp. shimonis and B. gliris in nature. Infection is consistently associated with pronounced restructuring of the flea gut microbiome, highlighting the ecological and microbial dimensions of vector-borne pathogen transmission. These findings underscore the importance of considering vector-associated microbial communities when evaluating disease dynamics and zoonotic risk in natural host-vector systems.},
}

@article {pmid42277905,
year = {2026},
author = {Serrano-Gómez, G and Zaida, S and Pons-Tarín, M and Mayorga, L and Maria, TC and Natalia, B and Francisco, G and Manichanh, C},
title = {Microbial, functional, and virulence biomarkers associated with familial risk of Crohn's disease and ulcerative colitis.},
journal = {Biomarker research},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40364-026-00950-y},
pmid = {42277905},
issn = {2050-7771},
support = {PI20/00130//Instituto de Salud Carlos III/ ; PID23-147387OB-100//Ministerio de Ciencia, Innovación y Universidades/ ; SGR 00459//Agència de Gestió d'Ajuts Universitaris i de Recerca/ ; },
abstract = {BACKGROUND: First-degree relatives of patients with inflammatory bowel disease (IBD) carry elevated disease risk and offer a unique window into preclinical gut microbiome alterations. We investigated whether familial IBD risk is associated with intermediate, disease-specific, or shared gut microbiome configurations in both Crohn's disease (CD) and ulcerative colitis (UC), the two main form of IBD.

METHODS: Using shotgun metagenomics, we analysed fecal samples from CD (n = 68) and UC (n = 77) patients, their healthy first-degree relatives (CD-HFDRs, n = 37; UC-HFDRs, n = 30), and unrelated healthy controls (HCs, n = 497), integrated species-level taxonomy, MetaCyc functional pathways, and virulence factor gene (VFG) profiling, with differential abundance analyses adjusted for relevant covariates.

RESULTS: HFDRs exhibited preserved alpha diversity but intermediate dysbiosis relative to patients and HCs. CD-HFDRs shared CD-associated taxonomic alterations, including depletion of Faecalibacterium prausnitzii, and enrichment of adherence- and invasion-associated VFGs, with 16 of 18 HFDR-enriched VFGs also elevated in CD patients. CD-HFDR functional pathway profiles nonetheless closely resembled those of HCs, revealing a dissociation between taxonomic and functional dysbiosis. Random forest classifiers distinguished HFDRs from HCs with strong performance: species- and VFG-based models achieved an AUCs of 0.966 in CD, and 0.946 in UC. Top predictive features were depletion of F. prausnitzii and enrichment of the E. coli adhesin gene fdeC. UC-HFDRs showed subtler alterations but comparable classifier performance.

CONCLUSIONS: IBD first-degree relatives harbour a transitional gut microbiome between health and disease, more pronounced in CD, with F. prausnitzii depletion and pathobiont virulence genes emerging as robust microbiome-based risk indicators.},
}