@article {pmid42136740,
year = {2026},
author = {Chen, Y and Li, J and Sun, Y and Yue, X and Tian, XH and Liu, F and Wang, DY and Shen, J},
title = {Biofilm-targeted liposomal curcumin delivery system for anti-caries therapy.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1808450},
pmid = {42136740},
issn = {2235-2988},
mesh = {*Biofilms/drug effects ; *Liposomes/chemistry ; *Dental Caries/drug therapy/microbiology ; Animals ; *Curcumin/administration & dosage/pharmacology ; Streptococcus mutans/drug effects ; *Anti-Bacterial Agents/pharmacology/administration & dosage ; *Drug Delivery Systems ; Rats ; Hydrogen-Ion Concentration ; Humans ; Disease Models, Animal ; },
abstract = {INTRODUCTION: Dental caries, driven by acidogenic biofilms, remains a major global health challenge. Current chemical treatments, such as chlorhexidine and fluoride, can disrupt oral microbial homeostasis and cause adverse effects, including tooth discoloration, dentin hypersensitivity, and taste disturbances. Curcumin, a natural photosensitizer, exhibits antibacterial activity and favorable biocompatibility, however, its clinical application is limited by poor stability, low aqueous solubility, and restricted biofilm penetration. There is an urgent need to develop innovative therapeutic strategies to enhance curcumin transport into acidic cariogenic biofilms.

METHODS: We developed a pH-responsive liposomal delivery system (Cur/DCPA-H2O) engineered to penetrate acidic cariogenic biofilms and enhance curcumin transport. The physicochemical characterization of Cur/DCPA-H2O was performed using a UV-1800 spectrophotometer, transmission electron microscopy (TEM), and dynamic light scattering (DLS). Biocompatibility was assessed by Cell Counting Kit-8 (CCK-8) assays, hemolysis tests, and Live/Dead cell staining. The antibacterial efficacy in vitro and ex vivo was evaluated using colony-forming unit (CFU) counting, scanning electron microscopy (SEM), confocal laser scanning microscopy (CLSM), and crystal violet (CV) staining. An in vivo caries model was established to assess the therapeutic efficacy of Cur/DCPA-H2O, using micro-computed tomography (micro-CT), Keyes' scoring, and 16S rRNA sequencing.

RESULTS: The liposomes exploit charge reversal to interact with representative caries-associated bacteria (Streptococcus mutans and the early colonizer Streptococcus sanguinis), enabling deep biofilm penetration. Upon light irradiation, Cur/DCPA-H2O was observed to generate reactive oxygen species (ROS), which may contribute to partial disruption of the biofilm matrix and reduced bacterial viability in vitro. In a rat caries model, treatment with Cur/DCPA-H2O under light irradiation reduced caries severity and decreased lesion depth by approximately 50%. It also shifted the oral microbiome composition toward a less dysbiotic profile, as confirmed by 16S rRNA sequencing.

DISCUSSION: This study demonstrates that a biofilm-targeted, pH responsive liposomal curcumin delivery system may provide a safe and effective strategy for caries prevention, highlighting the potential of natural therapeutics to modulate pathogenic biofilms with limited impact on the overall microbial community.},
}

*Biofilms/drug effects
*Liposomes/chemistry
*Dental Caries/drug therapy/microbiology
Animals
*Curcumin/administration & dosage/pharmacology
Streptococcus mutans/drug effects
*Anti-Bacterial Agents/pharmacology/administration & dosage
*Drug Delivery Systems
Rats
Hydrogen-Ion Concentration
Humans
Disease Models, Animal

@article {pmid42136780,
year = {2026},
author = {Ahmed, SH and Islam, ZS and Zaidi, SM and Khalid, T},
title = {Surgical Solution of C-Section Associated Surgical Site Infection in LMICs: A Narrative Review.},
journal = {Pakistan journal of medical sciences},
volume = {42},
number = {411AASC},
pages = {S122-S129},
pmid = {42136780},
issn = {1682-024X},
abstract = {Cesarean section (CS) is a life-saving procedure worldwide, accompanied by a substantial burden of surgical site infections (SSIs), with the most significant impact felt in low- and middle-income countries (LMICs). This review consolidates current knowledge on the surgical management of post-cesarean infections, highlighting the vaginal microbiome as a key source of infection and the physiological immunosuppression in the postpartum period. We describe the categories of deep and organ-space SSIs that require operative management, from wound debridement to laparoscopic drainage and laparotomy. The analysis also assesses proven preventive measures, such as dual-agent antibiotic prophylaxis, advanced closure techniques, and structured care bundles. It includes a standardized, context-sensitive checklist designed for LMICs, which combines pre, intra, and postoperative measures to prevent and manage SSIs, with the aim to reduce maternal morbidity and mortality in resource-limited settings.},
}

@article {pmid42136862,
year = {2026},
author = {Feng, Z and Quan, H and Li, M and He, D and Han, Y and Zou, C and Zhang, W and Chang, J and Lu, M},
title = {Distinct microbial and functional alterations across skin sites and disease severity in pediatric atopic dermatitis: a prospective study.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1805596},
pmid = {42136862},
issn = {2296-858X},
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin condition frequently associated with microbial dysbiosis.

OBJECTIVE: This study examined the diversity, composition, and functional profiles of the skin microbiome in children with varying degrees of AD in different skin regions.

METHODS: Skin samples were collected from 12 AD patients and 12 healthy controls. Genomic DNA underwent shotgun metagenomic sequencing to analyze alpha and beta diversity, taxonomic composition, and functional profiles, including the Kyoto Encyclopedia of Genes and Genomes (KEGG), Gene Ontology (GO), virulence factors and pathogen-host interactions (PHI).

RESULTS: Significant differences were observed in Shannon's diversity index and Chao1 diversity index between severity groups (p = 0.007 and 0.004). Cluster analysis revealed partial clustering by severity, with significant differences between mild and moderate groups (p = 0.042) and between moderate and severe groups (p = 0.036). Staphylococcus and Streptococcus dominated the abundance profile in AD samples. Functional analysis revealed alterations in epidermal microbial activity during AD onset and across different severity levels.

CONCLUSION: Pediatric AD involves site- and severity-specific microbial shifts. This functional dysregulation and enrichment of virulence factors may push barrier dysfunction and inflammation, suggesting that the microbiome is a critical target for future therapies.},
}

@article {pmid42136892,
year = {2026},
author = {Hu, CY and Pai, AH and Wang, YW and Lu, PC and Wu, HM and Huang, HY},
title = {Endobiota-Estrobolome Profiles in Reproductive-Aged Women With Ovarian Endometriosis.},
journal = {Reproductive medicine and biology},
volume = {25},
number = {1},
pages = {e70061},
pmid = {42136892},
issn = {1445-5781},
abstract = {PURPOSE: This case-control study investigated whether ovarian endometriosis is associated with altered estrogen metabolism and gut or urogenital microbiota by analyzing enzyme activity, bacterial composition, and variations of estrogen metabolites in fecal, vaginal, and urinary samples.

METHODS: Thirty-eight reproductive-aged women were enrolled, including 24 with pathologically confirmed ovarian endometriosis and 14 controls. Stool, urine, and vaginal samples were collected preoperatively. Gut β-glucuronidase and β-glucosidase activities were measured, estrogen and 14 metabolites were quantified using liquid chromatography-mass spectrometry, and gut and vaginal microbiota were analyzed by 16S rRNA gene sequencing. Microbial composition, diversity, and abundance were compared between groups.

RESULTS: Gut β-glucuronidase activity and overall microbial diversity were comparable between groups; however, the control group showed a higher prevalence of the genus Rothia, whereas several genera, including Megamonas and [Eubacterium] coprostanoligenes_group, were enriched in the ovarian endometriosis group. In contrast, vaginal samples from patients with ovarian endometriosis demonstrated significantly reduced bacterial abundance and diversity, accompanied by lower levels of 4-methoxyestrone, 2-methoxyestrone, and 2-hydroxyestrone-3-methyl ether.

CONCLUSIONS: Although overt dysbiosis was not observed, specific microbial shifts and altered estrogen metabolites may reflect disturbances in estrogen metabolism and urogenital-gastrointestinal microbiota in ovarian endometriosis.},
}

@article {pmid42136931,
year = {2026},
author = {Mweetwa, MN and Ahsan, K and Louis-Auguste, J and Besa, E and Posma, JM and McNulty, NP and Barratt, MJ and Gordon, JI and Kelly, P},
title = {Erratum: Intestinal microbiome changes in response to amino acid and micronutrient supplementation: secondary analysis of the AMAZE trial - CORRIGENDUM.},
journal = {Gut microbiome (Cambridge, England)},
volume = {7},
number = {},
pages = {e6},
doi = {10.1017/gmb.2026.10025},
pmid = {42136931},
issn = {2632-2897},
abstract = {[This corrects the article DOI: 10.1017/gmb.2025.10011.].},
}

@article {pmid42137127,
year = {2025},
author = {Ahmadi, N and Hossein Tehrani, MJ and Alamdary, A and Moukhah, R and Mardani, R and Shahali, M},
title = {Gut microbiome dysbiosis and inflammatory markers in severe COVID-19: links to atherosclerosis and potential therapeutic insights.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {110-120},
pmid = {42137127},
issn = {2008-2258},
abstract = {BACKGROUND: COVID-19 is implicated in the exacerbation of atherosclerosis, potentially leading to its clinical manifestations. The aim of this study was to evaluate serum biomarkers, including albumin (ALB), C-reactive protein (CRP), ferritin (FERR), CD16, CD18, NLRP3, interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α), in patients with COVID-19. In addition, assessment of microbiome profiles may provide insights into disease severity and gastrointestinal health.

METHOD: In this case-control study, serum samples were collected from 90 individuals: 30 patients with COVID-19 admitted to the intensive care unit, 30 hospitalized patients with COVID-19, and 30 healthy individuals. Concentrations of ALB, CRP, FERR, NLRP3, CD16, CD18, IL-6, and TNF-α were measured. Quantitative PCR (qPCR) was used to assess microbial diversity in stool samples.

RESULT: No significant age difference was noted between the patient (55.40 ± 10.34 years) and the control groups (58.34 ± 11.71 years). Substantial increases in CRP, CD-18, CD-16, IL-6, Alb, and TNF-α (P < 0.001) were observed in severe cases compared to non-severe cases. Microbiome analysis indicated a 40% decrease in Roseburia and a 35% reduction in Faecalibacterium in ICU patients.

CONCLUSION: Evaluating these biomarkers provides critical insights into atherosclerosis susceptibility in COVID-19 patients and reveals meaningful relationships among COVID-19, atherosclerosis, and gastrointestinal health.},
}

@article {pmid42137129,
year = {2025},
author = {Tavanaeian, S and Feizabadi, MM and Falsafi, S and Asadzadeh Aghdaei, H},
title = {Machine learning and microbiome analysis for early detection of pancreatic cancer.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {76-84},
pmid = {42137129},
issn = {2008-2258},
abstract = {AIM: To develop machine learning (ML) models integrating clinical and microbial predictors for early pancreatic cancer (PC) detection.

BACKGROUND: Pancreatic cancer is a leading cause of cancer-related mortality, with a 5-year survival rate of ~12%. Limited biomarkers and non-specific risk factors hinder early diagnosis. Emerging evidence links oral and gut microbiota, such as Fusobacterium nucleatum and Roseburia species, to PC risk, offering potential for non-invasive biomarkers.

METHODS: We analyzed a retrospective cohort of 40 participants (20 PC cases, 20 controls). Clinical (e.g., age, WBC) and microbial (e.g., Fusobacterium nucleatum, Roseburia-to-Fusobacterium ratio [RI/FN]) predictors were evaluated using five ML classifiers (logistic regression, SVM, random forest, naïve Bayes, neural network) under Leave-Group-Out Cross-Validation (LGOCV; 80/20 split, 200 repetitions). Elastic-net regularization and stability selection identified key predictors. Performance metrics included AUC, sensitivity, specificity, PPV, NPV, and accuracy. Nomograms were developed for clinical utility.

RESULTS: Age (AUC 97.4%) and microbial markers (e.g., RI/FN ratio, AUC 100%) showed excellent discrimination. Multivariable models using age and RI/FN achieved excellent performance (AUC 98-100%). Nomograms provided interpretable risk estimates.

CONCLUSIONS: Integrating clinical and microbial predictors with ML offers a promising approach for non-invasive PC detection. The RI/FN ratio and age are robust biomarkers that warrant further validation in larger cohorts. However, the small sample size limits generalizability and warrants validation in larger cohorts.},
}

@article {pmid42137133,
year = {2025},
author = {Kazemifard, N and Norouzi-Beirami, MH and Baradaran Ghavami, S and Ghanbari-Maman, L and Zali, MR and Shahrokh, S and Kavousi, K},
title = {Microbiome-microRNA interactions in inflammatory bowel disease: insights from metagenomic and transcriptomic data analysis.},
journal = {Gastroenterology and hepatology from bed to bench},
volume = {18},
number = {SI},
pages = {85-96},
pmid = {42137133},
issn = {2008-2258},
abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a chronic inflammation of the gastrointestinal tract, the precise origins of which remain not fully elucidated. This study investigates the complex relationship between gut metagenomics and host transcriptomics in IBD patients, focusing on Ulcerative Colitis (UC) and Crohn's Disease (CD).

METHOD: One proposed theory suggests that microRNAs produced by the host may significantly influence IBD development by impacting the gut microbiota. Conversely, the gut microbiome may regulate the expression of host microRNAs, leading to dysfunction in the intestinal epithelium. An enrichment analysis was conducted to pinpoint associated pathways. To unravel this intricate interplay, the study utilized data from the IBDMDB database, selecting samples from adult individuals.

RESULT: The dataset comprised 50 paired metagenomic and host transcriptomic samples, including 8 controls, 18 UCs, and 24 CDs. Computational analyses and network constructions were applied to identify relationships between bacterial species, microRNAs, and other transcripts.

CONCLUSION: This research offers valuable insights into the dynamic relationship between the gut microbiome and human transcriptomics in IBD, providing a deeper understanding of potential disease mechanisms. Furthermore, it sheds light on the complex tripartite network connecting bacterial species, microRNAs, and transcripts, contributing to a comprehension of IBD pathogenesis and the identification of novel therapeutic targets.},
}

@article {pmid42137389,
year = {2026},
author = {El Halabi, L and AlBayeh, A and Khoury, A and Katrib, M and Nasr, J and Al-Obaidi, A},
title = {Vitamins and Cancer Risk: A Comprehensive Review of Epidemiologic and Clinical Evidence.},
journal = {Kansas journal of medicine},
volume = {19},
number = {Suppl 1},
pages = {12},
doi = {10.17161/kjm.vol19.25377},
pmid = {42137389},
issn = {1948-2035},
abstract = {INTRODUCTION: Vitamin supplementation nearly is universal among patients with cancer, yet the scientific landscape is far more complex. Across decades of research, vitamins have demonstrated profound biological effects ranging from immune activation and ferroptosis modulation to paradoxical tumor promotion.

OBJECTIVE: This scoping review maps the breadth of compelling and controversial evidence surrounding vitamins A, D, E, K, C, and the B-complex in cancer prevention, treatment response, and toxicity.

METHODS: Guided by PRISMA-ScR domains, we synthesized mechanistic studies, epidemiologic cohorts, randomized trials, and therapeutic investigations addressing vitamins in the oncology context. Eligibility focused on sources examining cancer risk, progression, treatment interactions, or toxicity.

RESULTS: Several vitamins exhibit striking anticancer mechanisms: vitamin K2 triggers autophagy-driven leukemia cell death; pharmacologic vitamin C selectively kills KRAS- and BRAF-mutated colorectal cancer cells; niacin reshapes the tumor immune microenvironment; and vitamin D enhances microbiome-dependent antitumor immunity. Yet the review also identifies potential harms, including beta-carotene increasing lung cancer risk in smokers, vitamin E raising prostate cancer risk, and antioxidant supplementation potentially weakening the oxidative mechanisms essential for chemotherapy and radiotherapy efficacy. Dose-response patterns frequently are U-shaped, with both deficiency and excess linked to greater risk. High-dose intravenous vitamin C, vitamin D repletion during immunotherapy, and vitamin-targeted nanoparticles emerge as promising but unproven therapeutic strategies.

CONCLUSIONS: Across vitamins, benefits appear highly context-dependent. Routine supplementation is unsupported, while targeted correction of true deficiencies remains essential. This rapidly evolving field demands individualized decision-making and rigorously designed trials to define when vitamins act as allies, and when they become adversaries, in cancer care.},
}

@article {pmid42137425,
year = {2026},
author = {Miki, T and Ito, M and Haneda, T and Okada, N and Kim, YG},
title = {Infection strategies of SalmonellaTyphimurium for gut-lumen colonization: Overcoming host defenses, exploiting host responses, and adapting to the enteric niche.},
journal = {Gut microbes reports},
volume = {3},
number = {1},
pages = {2671472},
pmid = {42137425},
issn = {2993-3935},
abstract = {Diarrheal disease is a leading cause of child morbidity and mortality globally, largely resulting from contaminated food and water and exposure to enteric pathogens. Salmonella enterica serovar Typhimurium (STm) is an enteropathogenic bacterium that infects the gastrointestinal tract using diverse strategies that are still being elucidated. Meanwhile, the gut comprises a complex ecosystem known as the microbiome, which is densely inhabited by microbial communities. The microbiome confers colonization resistance against enteropathogenic bacteria, whereas STm can overcome these defenses to establish infection. Here, we review STm infection strategies in the gut, with a particular focus on evidence from mouse models. Understanding STm virulence mechanism and adaptation strategies may inform the development of targeted interventions to prevent and treat gastrointestinal infection.},
}

@article {pmid42137495,
year = {2026},
author = {Sekito, T and Hirakawa, H and Sadahira, T},
title = {Unraveling the vaginal microbiota-based etiology of recurrent cystitis: the potential role of Lactobacillus vaginal suppositories.},
journal = {Therapeutic advances in urology},
volume = {18},
number = {},
pages = {17562872261448600},
pmid = {42137495},
issn = {1756-2872},
abstract = {Recurrent cystitis is a common problem in women that substantially impairs quality of life and contributes to increasing healthcare costs. Traditionally regarded as an ascending infection originating from the gut, recurrent cystitis is now increasingly understood as a disorder rooted in vaginal dysbiosis, with the vagina acting as a key reservoir for uropathogenic Escherichia coli. Loss of a Lactobacillus-dominant vaginal microbiota and overgrowth of enteric and anaerobic bacteria are strongly associated with recurrent cystitis, particularly in postmenopausal women. Lactobacillus species promote vaginal health by producing lactic acid, maintaining a low pH, generating antimicrobial compounds, inhibiting pathogen adhesion, and modulating mucosal immune responses. At the same time, long-term antimicrobial prophylaxis, although effective in reducing recurrences, is limited by adverse effects and the promotion of antimicrobial resistance. These concerns have driven interest in strategies that restore the protective vaginal ecosystem rather than relying on repeated antimicrobial exposure. This narrative review summarizes current concepts linking vaginal dysbiosis to recurrent cystitis, highlights the protective role of Lactobacillus, and synthesizes clinical data on Lactobacillus vaginal suppositories, particularly Lactobacillus crispatus (L. crispatus)-based preparations, as a targeted, non-antimicrobial prophylactic option. Across pilot, phase II, and randomized trials, Lactobacillus vaginal therapy has demonstrated a generally favorable safety and tolerability profile, with preliminary evidence suggesting a potential to reduce recurrent cystitis episodes while restoring a Lactobacillus-dominant vaginal microbiota. However, larger, standardized studies are still needed. Collectively, these findings provide a rationale for investigating Lactobacillus vaginal suppositories as a microbiome-informed, non-antimicrobial strategy for the long-term prevention of recurrent cystitis, particularly in postmenopausal and other high-risk women, and highlight the importance of further research to define the role of vaginal microbiota-directed therapies in future recurrent cystitis management.},
}

@article {pmid42137543,
year = {2026},
author = {Zhang, K and Zomer, H and Potkamp, G and Salles, JF and Tieleman, BI and Dietz, MW},
title = {Seasonal Dynamics of the Gut Microbiome in Urban Feral Pigeons Are Associated With Environmental Conditions, Not With Diet Shifts.},
journal = {Ecology and evolution},
volume = {16},
number = {},
pages = {e73682},
pmid = {42137543},
issn = {2045-7758},
abstract = {Gut microbiomes play a crucial role in host physiology and seasonal adaptation. While seasonal shifts in avian gut microbiota are often attributed to seasonal diet variation, environmental factors may be equally or more important, particularly in urban ecosystems. This study aimed to determine whether seasonal variation in the gut microbiome of free-living feral pigeons (Columba livia f. domestica) inhabiting urban environments is associated with seasonal changes in diet and environmental conditions. We captured feral pigeons at three locations in Groningen, the Netherlands, during winter (January-February 2019) and summer (July-August 2019). Cloacal swabs and fecal samples were collected to assess gut microbiota via 16S rRNA sequencing and diet via DNA metabarcoding, respectively. Microbial diversity and composition showed significant seasonal variation and location effects. At Vismarkt, one of the three urban sampling sites within the city of Groningen, Firmicutes were more abundant in summer than in winter, while Actinobacteria were more abundant in winter. Dominant genera also varied seasonally, with Lactobacillus more abundant in summer. In contrast, the diet composition was dominated by Poaceae (grasses), Fabaceae (legumes), and Asteraceae (daisies) across all seasons and locations, with no detectable differences between locations or seasons. Distance-based redundancy analysis indicated that temperature was significantly associated with microbiome composition, whereas diet as measured here showed no detectable association. This suggests that seasonal microbiome variation in urban feral pigeons may be related to seasonal environmental conditions even without detectable dietary shifts, consistent with the idea that seasonal environmental conditions can contribute to microbiome seasonality in birds.},
}

@article {pmid42137790,
year = {2026},
author = {Qi, J and Zhang, K and Zhan, C and Lu, X and Chen, X and Li, X and Zhang, C and Wang, H and Tu, C and Tong, W and Dai, L and Zeng, D},
title = {Microbial and metabolic crosstalk in the rhizosphere shapes the divergent drought resilience of contrasting rice genotypes.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1788826},
pmid = {42137790},
issn = {1664-302X},
abstract = {Drought is a major constraint on rice production, yet the coordinated responses of rhizosphere microbial communities and metabolites across rice genotypes with contrasting drought tolerance remain insufficiently understood. In this study, we combined metagenomic and metabolomic analyses to investigate drought-induced changes in the rhizosphere of three rice genotypes with distinct ecological backgrounds: the drought-sensitive cultivar Bhutan, the upland rice genotype TGR78, and Oryza rufipogon K111. Field experiments were conducted under well-watered and drought conditions, and rhizosphere soil samples were collected for multi-omics profiling. Drought stress reduced plant height and panicle number in all three genotypes, but the magnitude of these effects differed among genotypes. Bhutan showed the greatest reduction in plant height (42.1%) and the largest number of differential metabolites (146), indicating a stronger drought response at both phenotypic and metabolic levels. In contrast, TGR78 and K111 displayed relatively greater phenotypic stability under drought stress. Metagenomic analysis revealed pronounced genotype-dependent shifts in rhizosphere bacterial community composition, whereas metabolomic profiling showed distinct changes in metabolite accumulation patterns among genotypes. Correlation analysis further demonstrated that drought substantially reshaped rhizosphere microbe-metabolite associations, shifting the interaction network from broadly positive and highly connected under well-watered conditions to more selective associations under drought stress. Collectively, these results indicate that rice drought adaptation is associated with genotype-dependent reorganization of the rhizosphere microbiome and metabolic profile. This study provides new insight into rhizosphere-mediated drought responses in rice and offers a basis for developing microbiome-informed strategies for drought-resilient crop improvement.},
}

@article {pmid42137793,
year = {2026},
author = {Adeleke, RA and Machailoe, TME and Malemagovha, M and Olanrewaju, OS and Alayande, KA and Obi, LU and Makinde, OM},
title = {Diversity and functional potential of bacterial and fungal endophytes in traditional food wrapping leaves reveal implications for artisanal food safety and quality.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1641069},
pmid = {42137793},
issn = {1664-302X},
abstract = {Plant leaves are widely utilised globally for the packaging and serving of traditionally prepared foods. The microbial communities associated with these wrapping leaves, particularly endophytes, are recognised to potentially influence food quality, safety, and preservation. Specifically, certain endophytes can enhance sensory attributes and nutritional value through fermentative processes, while the presence of harmful microorganisms may lead to spoilage and pose a risk of foodborne illness. This study utilised 16S rRNA, ITS metabarcoding and metagenomic functional analysis (PICRUSt2) to comprehensively investigate the composition and infer the putative functional potential of putative endophytic bacterial and fungal communities present in 53 samples of four different food wrapping leaves. The leaves examined included Thaumatococcus daniellii (n = 10), Alstonia macrophylla (n = 18), Theobroma species (n = 14), and Megaphrynium macrostachyum (n = 11). Distinct microbial community profiles were observed across the different leaf types. Highest bacterial species richness and community variability were detected in A. macrophylla samples, reflected by Principal Coordinates Analysis (PCoA) values (PCoA1 = 43.97%; PCoA2 = 10.68%). Conversely, M. macrostachyum exhibited the greatest fungal species richness and variability (PCoA1 = 20.08%; PCoA2 = 8.72%). Taxonomic analysis identified Proteobacteria as the dominant bacterial phylum and Stenotrophomonas as the dominant bacterial genus. Other notable bacterial taxa included the phyla Bacteroidota and Firmicutes, and genera such as Pseudomonas, Faecalibacterium, and Bacteroides. For fungal communities, Ascomycota was the dominant phylum. Additional fungal taxa included the phylum Basidiomycota and genera Cryptococcus, Candida, and Meyerozyma. A core microbiome analysis revealed that 42 bacterial (notably Stenotrophomonas and Chryseobacterium) and 7 fungal taxa (notably Pleosporaceae and Ascomycota) were shared across all examined wrapping leaves. The identified microbial communities (e.g., Lactobacillus and Geotrichum) encompass taxa with potential beneficial roles, such as enhancing food fermentation and potentially contributing to human gut health upon consumption of the packaged food. However, the detection of potentially pathogenic and toxigenic bacterial taxa highlights a possible public health risk associated with the use of these leaves. Further investigation into the specific functionalities of these associated bacteria and fungi is essential to maximise their beneficial applications while simultaneously mitigating potential health risks posed by harmful strains.},
}

@article {pmid42137801,
year = {2026},
author = {D'Amico-Willman, KM and Joglekar, P and Turner, D and Flaherty, M and Ritchie, DF and Huerta, AI},
title = {Four decades of genomic stability and adaptive divergence in Xanthomonas phages: defining Duraznoxanthovirus arenicola and its evolutionary framework.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1779411},
pmid = {42137801},
issn = {1664-302X},
abstract = {Bacteriophages (phages) are abundant and ecologically significant, yet their diversity and roles in plant-associated ecosystems remain poorly understood, limiting their application in sustainable disease management. To address this gap, we characterized 15 phages infecting Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot on peach, has been isolated for over four decades from North Carolina orchards. Comparative genomic and phylogenetic analyses revealed two temporally distinct clades with >95% nucleotide identity and 63 conserved core genes, forming a new genus and species, Duraznoxanthovirus arenicola. These findings challenge assumptions of pervasive genomic mosaicism, highlighting remarkable genomic stability alongside localized variability in accessory loci. Beyond genus-level characterization, our analyses support a broader taxonomic restructuring within the family Anamaviridae, introducing a new subfamily (Terravirinae) and two new genera (Duraznoxanthovirus and Ralstopathovirus). This work provides the a family-level framework for phages exclusively infecting plant-associated bacteria, offering evolutionary insights and a foundation for ecological studies and management strategies.},
}

@article {pmid42137803,
year = {2026},
author = {Liu, Y and Chen, C and Gao, J},
title = {Topological characteristics and longitudinal dynamics of co-abundance networks involving beneficial commensal bacteria in the pig gut microbiome and its association with average daily gain.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1818141},
pmid = {42137803},
issn = {1664-302X},
abstract = {Microorganisms are intricately interrelated with each other in the gut microecosystem, which influences the colonization and functional roles of probiotics. However, how these interactions dynamically change during host development and whether their topological features influence host phenotypes, such as average daily gain (ADG), remain poorly understood. In this study, we performed metagenome analysis for 2,311 fecal samples collected from a specifically designed eight genetically divergent breed intercrossed mosaic F6 and F7 population, at three developmental ages of 25 days (D25), 120 days (D120), and 240 days (D240) of each individual, covering pre-weaning to market. By constructing their microbiota co-abundance networks, we systematically characterized dynamic changes in beneficial commensal bacteria involved co-abundance networks in the pig gut microbiome across three ages. We elucidated conserved and variable co-abundance features involving these bacteria across developmental stages. We observed that the cross-age stable co-abundance correlations of beneficial commensal bacteria were maintained by a large set of weak correlations. A subset of age-shared co-abundance correlations remained variable across different ages in correlation strength and direction. Topological analysis revealed that beneficial commensal bacteria involved co-abundance networks were highly age-specific. Among the three age stages sampled in this study, the D120 stage represented a critical window for the structural and functional reorganization of gut microbiota. Using metagenomic sequencing data at the D120, we identified two guilds that were significantly associated with ADG from D120 to D240. Guild 1 included short chain fatty acid-producing taxa and was positively associated with ADG, whereas Guild 2 tended to self-utilization of energy and was negatively associated with ADG. We also inferred the ecological interaction mechanisms of ADG-associated microbial communities using genome-scale metabolic models. These findings provided a theoretical basis for stage-specific intervention in the pig gut microbiome using probiotics to improve production traits.},
}

@article {pmid42137813,
year = {2026},
author = {Chiuta, NE and Pofu, KM and Mashela, PW},
title = {Short-term crop rotation interactive effects on soil microbial communities and potato yield under field conditions.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1807765},
pmid = {42137813},
issn = {1664-302X},
abstract = {INTRODUCTION: The inclusion of plant-parasitic nematode (Meloidogyne species) non-host crops in potato (Solanum tuberosum L.) -based cropping systems can sustainably manage the pest and reduce the application of greenhouse gas-emitting agro-chemicals. Nevertheless, there exists a research gap on how these cropping systems interact with soil microbiome.

METHODS: A 2-year field study was conducted at the University of Limpopo and the Agricultural Research Council to investigate the effects of potato monoculture, Cucumis africanus-potato, sorghum-potato and potato (Velum)-potato cropping sequences on soil health and tuber yield. The treatment crops, namely, sweet stem sorghum (Sorghum bicolor) cv. 'Ndendane-X1', C. africanus, potato cv. 'Mondial G3' and potato cv. 'Mondial G3'-velum (control), were assigned to 4 m[2] subplots in Sequence 1, in a randomized complete block design, with six replicates. The successor potato crop was planted in Sequence 2. Crop arrangement in Sequences 3 and 4 was as in Sequences 1 and 2, respectively. Soil organic carbon content, enzyme activity, nematode and bacterial functional diversity data were collected from Sequences 1 to 4. Final potato tuber yield was recorded in Sequence 4.

RESULTS: Based on the results, nematode indices revealed disturbed agroecosystems dominated with bacterial decomposition pathways, which is a common occurrence in intensively managed soils. High soil organic carbon content, microbial diversity and enzyme activity were observed in sorghum-potato and C. africanus-potato compared to potato monoculture (with or without velum), at both locations. In addition, sorghum-potato improved soil structure over time based on the nematode faunal results, thereby depicting its ability to promote soil health compared to other cropping systems. Tuber yield mass significantly varied (p ≤ 0.05) among cropping sequences at both locations with potato (Velum)-potato and C. africanus-potato sequences recording higher yields than potato monoculture or sorghum-potato.

DISCUSSION: Crop diversification increased soil organic carbon content, microbial diversity and enzyme activity. Overall, sorghum-potato effectively improved soil health and soil structure over time, better than the other cropping systems.},
}

@article {pmid42137817,
year = {2026},
author = {Farmakioti, I and Tegopoulos, K and Stylianopoulou, E and Siskos, N and Angelopoulou, L and Vasileiou, AR and Karagianni, E and Kandylas, D and Fragkiskatou, F and Pavlatou, C and Tsaroucha, A and Ypsilantis, P and Kourkoutas, Y and Kolovos, P and Skavdis, G and Grigoriou, ME},
title = {Genomic characterization and preclinical evaluation of the candidate probiotic strain Lactococcus cremoris FBMS_5810.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1812433},
pmid = {42137817},
issn = {1664-302X},
abstract = {This study presents a comprehensive genomic and preclinical evaluation of Lactococcus cremoris FBMS_5810, establishing its taxonomic identity, genomic uniqueness, and safety profile. Genomic analyses identified strain-specific genes linked to adhesion, colonization, and pathogen exclusion, aligning with previously observed in vitro probiotic properties. In vivo studies in healthy mice demonstrated that Lactococcus cremoris FBMS_5810 modulates gut microbiota composition. Specifically, the relative abundance of Muribaculaceae, Erysipelotrichaceae, and Streptococcaceae was significantly increased in the probiotic-treated group, whereas the relative abundance of Ruminococcaceae, Bacteroidaceae, Porphyromonadaceae, and Dehalobacteriaceae was decreased. Administration of Lactococcus cremoris FBMS_5810 was also associated with changes in intestinal gene expression: in the ileum, Tnf and Il1b expression increased, while in the cecum, Zo1 expression was elevated. These findings may indicate a role in supporting intestinal homeostasis and could be linked to reduced susceptibility to diet- and inflammation-related disorders. Overall, these results suggest that Lactococcus cremoris FBMS_5810 may be a useful candidate for further investigation in the development of health-oriented microbial products. By integrating genomic characterization with preclinical evaluation, this study not only highlights Lactococcus cremoris FBMS_5810 as a promising candidate but also provides a systematic approach for the identification and validation of probiotics, advancing both fundamental understanding and translational applications in molecular microbiology.},
}

@article {pmid42137872,
year = {2026},
author = {Parrino, J and Sunshine, J and Tripp, K and Shaffer, M and Sughra, U and Procházková, N and Jara, M and Moll, JM and Noble, R and Muir, L and McIntyre, E and Guduk, E and Zachariah, D and Vernochet, C and Frahm, N and Schmidt, AC},
title = {Impact of Bifidobacterium infantis supplementation on growth, health outcomes, and gut microbiome features in underweight infants from Pakistan.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783141},
pmid = {42137872},
issn = {2296-861X},
abstract = {BACKGROUND: Alterations in the gut microbiome are implicated in infant malnutrition. Bifidobacterium longum subspecies infantis (B. infantis), a commensal common in breastfed infants, has been shown to have reduced abundance in malnourished infants. This trial (NCT05952076) evaluated if B. infantis strain Bi-26 supplementation could improve growth and health outcomes in underweight infants in Pakistan.

METHODS: In this double-blind, randomized, placebo-controlled trial, 40 infants aged 30-120 days (d) with a weight-for-age Z score (WAZ) below -2 received daily oral Bi-26 or placebo for 28d, with follow-up to d90 for safety. The primary endpoint was change in WAZ from baseline to d56. The intended sample size was 396 infants but study was terminated early due to operational delays. Total B. infantis levels microbiome, metabolome, and cytokine profiles were assessed.

RESULTS: Bi-26 supplementation increased fecal B. infantis levels at d28 (p = 0.001) and d56 (p = 0.03) but did not result in significant change in WAZ (p = 0.69) or weight gain (p = 0.56) compared to placebo. Fewer adverse events (AEs) occurred in the Bi-26 group compared to placebo (40% vs. 80% of infants; 17 vs. 49 events). Probiotic engraftment was impacted by presence of baseline endogenous B. infantis, suggesting that Bi-26 complemented rather than outcompeted endogenous strains. Bi-26 altered microbiome composition with transient alterations in function and metabolite abundance that reverted to baseline by d56, without cytokine differences between groups. B. infantis levels and Bifidobacterium-community types were associated with fewer AEs but not changes in WAZ or weight.

DISCUSSION: Bi-26 supplementation had an acceptable safety profile but did not improve growth. The findings of this trial support further evaluation of B. infantis strains in larger studies of underweight infants across diverse LMIC settings. Future trials should determine whether sustained metabolic and functional remodeling can translate into measurable improvements in growth and health outcomes.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov/study/NCT05952076, NCT05952076.},
}

@article {pmid42138066,
year = {2026},
author = {Allwang, M and Wipplinger, M and Akbarimoghaddam, P and Alonso-Roman, R and Cseresnyes, Z and Dietschmann, A and Wegner, V and Feile, A and Bachelot, Y and Warschinke, M and Hassan, MIA and Mittag, S and Huber, O and Hube, B and Gresnigt, MS and Figge, MT and Mosig, AS},
title = {Human Colitis-on-Chip Model Reveals Dual Roles of Butyrate in Epithelial and Macrophage Defense Against Candida albicans Tissue Invasion.},
journal = {Small (Weinheim an der Bergstrasse, Germany)},
volume = {},
number = {},
pages = {e00074},
doi = {10.1002/smll.202600074},
pmid = {42138066},
issn = {1613-6829},
support = {434385622/GR 5617/1-1//German Research Foundation/ ; //Exploration Grant of the Boehringer Ingelheim Foundation (BIS)/ ; //Free State of Thuringia and co-funded by the European Union/ ; 390713860//DFG Cluster of Excellence "Balance of the Microverse"/ ; FKZ: 13N15713 13N15716//DFG Cluster of Excellence "Balance of the Microverse"/ ; //Collaborative Research Center "PolyTarget"/ ; //Scholarship from the Interdisciplinary Center of Clinical Research of the Jena University Hospital/ ; },
abstract = {Microbial dysbiosis in inflammatory bowel disease (IBD) reduces intestinal butyrate levels, compromising epithelial barrier integrity and enabling overgrowth of opportunistic pathogens such as Candida albicans. Here, we present a human immunocompetent colitis-on-chip model (CooC) that mimics key features of inflamed gut mucosa, including DSS-induced epithelial damage and C. albicans tissue invasion. Using this model, we uncover dual protective roles of microbiota-derived butyrate: (i) stabilization of epithelial adherens junctions and promotion of epithelial renewal, thereby restricting fungal invasion; and (ii) modulation of macrophage function to enhance antifungal activity while attenuating inflammasome-mediated inflammation. Butyrate pretreatment preserves barrier function, limits fungal translocation, and promotes macrophage viability through the inhibition of histone deacetylase (HDAC) and the suppression of NLRP3 inflammasome activation. These findings position butyrate as a key metabolite in orchestrating epithelial-immune defense against fungal exacerbation in colitis, supporting its therapeutic and preventive potential in restoring mucosal resilience in IBD.},
}

@article {pmid42138097,
year = {2026},
author = {Kozajda, A and Miśkiewicz, E and Gawor, J and Gromadka, R},
title = {Bacteria and associated antibiotic resistance in air filter-derived biological material from utility vehicles at mechanical-biological treatment plants.},
journal = {International journal of occupational medicine and environmental health},
volume = {},
number = {},
pages = {},
doi = {10.13075/ijomeh.1896.02785},
pmid = {42138097},
issn = {1896-494X},
abstract = {OBJECTIVES: The study objective was to assess occupational exposure to bacteria and antimicrobial resistance genes (ARGs) present on air filters of utility vehicles used in the working environment of mechanical-biological treatment (MBT) facilities, in the context of workers health risks.

MATERIAL AND METHODS: The study was conducted in summer 2024 in 9 air filters from utility vehicles used in MBT plants in Poland. External filters were removed from the vehicle's ventilation system, packed and shipped according to instructions. From the duplicate filters samples DNA was isolated and high-throughput next-generation sequencing (NGS) was carried out. Bioinformatic data analysis was conducted to detect bacteria and ARGs in air filters' surfaces.

RESULTS: Totally, 34 bacterial taxa were detected in relative abundance ≥0.5%. The genera most frequently present at the highest relative abundances: Saccharomonospora, Thermobifida, Nocardiopsis, Pectobacterium, Aerococcus, Thermoactinomyces, Novibacillus and Streptomyces. Across all bacteria isolated from the analyzed filters, regardless of their relative abundance, a total of 91 taxa were classified into risk groups 2 or 3 (86 and 5 taxa, respectively). The most frequently detected ARGs were those encoding resistance to a single class of antibiotics (AAC(3)-VIIa, aadA2, ANT(6)-Ia, APH(3'')-Ia, APH(3'')-Ib, APH(6)-Id, cml, cmx, lnuA, lnuD, novA, parY, sul2, vanHF, vanJ, vanRA, vanRI, vanRO - each at least on 4 air filters). Antimicrobial resistance genes encoding multi antibiotic resistance were also detected: CRP, emtA, erm(34), erm(36), ermA, ermC, ermF, ermG, ermT, ermX, ernB, H-NS, mel, msrA, msrE, mtrA, optrA, ramA, ykkD - each at least on 1 air filter.

CONCLUSIONS: Despite the limited number of analyzed filters, the study demonstrated a high bacterial species diversity in the MBT plant environment. The MBT workers are exposed to bacteria with high pathogenic potential and to ARGs encoding resistance to antibiotics used exclusively in human medicine, used in human and veterinary medicine, and not intended for human use. Int J Occup Med Environ Health. 2026;39(2).},
}

@article {pmid42138193,
year = {2026},
author = {Ma, X and Zhao, Y},
title = {Gut‑brain axis in anesthesia and critical illness: Molecular crosstalk and its impact on delirium and outcome (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {1},
pages = {},
doi = {10.3892/ijmm.2026.5859},
pmid = {42138193},
issn = {1791-244X},
mesh = {Humans ; Critical Illness ; *Delirium/etiology/metabolism ; *Gastrointestinal Microbiome ; *Brain/metabolism ; *Anesthesia/adverse effects ; Animals ; },
abstract = {The gut‑brain axis (GBA) has emerged as a critical mediator of acute brain dysfunction, particularly postoperative delirium and sepsis‑associated encephalopathy, in surgical and critically ill patients. Anesthesia, surgical stress, and critical illness collectively disrupt gut microbiota composition and intestinal barrier integrity, leading to increased systemic translocation of microbial products. This process triggers neuroinflammation and compromises blood‑brain barrier function through defined molecular pathways, including alterations in microbe‑derived short‑chain fatty acids, tryptophan metabolites, and potent neuroimmune signaling via the LPS‑TLR4‑NF‑κB axis. The present review synthesizes current evidence on the molecular crosstalk within the GBA, highlighting how perioperative and intensive care interventions drive dysbiosis and subsequent neurological sequelae. Furthermore, it evaluates promising GBA‑targeted therapeutic strategies, including dietary modulation, biotherapeutics and pharmacological interventions, are evaluated for their potential to mitigate delirium and improve long‑term cognitive outcomes. A deeper understanding of these mechanisms is essential for developing novel preventive and therapeutic approaches in vulnerable patient populations.},
}

Humans
Critical Illness
*Delirium/etiology/metabolism
*Gastrointestinal Microbiome
*Brain/metabolism
*Anesthesia/adverse effects
Animals

@article {pmid42138225,
year = {2026},
author = {Jamieson, PE and Gu, I and Reichart, NJ and Maier, CS and Ho, E and Sharpton, TJ and Metz, TO and Bradley, R and Stevens, JF},
title = {Modulation of Microbiota-Derived Bile Acids Linked to Symptom Amelioration in Crohn's Disease: Insights From a Randomized Clinical Trial With Xanthohumol Supplementation.},
journal = {Molecular nutrition & food research},
volume = {70},
number = {10},
pages = {e70501},
doi = {10.1002/mnfr.70501},
pmid = {42138225},
issn = {1613-4133},
support = {R01 AT010271/NH/NIH HHS/United States ; R01 AT010271-02S1/NH/NIH HHS/United States ; S10OD026922/NH/NIH HHS/United States ; },
mesh = {Humans ; *Flavonoids/pharmacology/therapeutic use ; *Crohn Disease/drug therapy/microbiology ; *Bile Acids and Salts/metabolism ; *Propiophenones/pharmacology/therapeutic use ; Male ; Female ; *Gastrointestinal Microbiome/drug effects ; Adult ; Dietary Supplements ; Middle Aged ; Feces/microbiology/chemistry ; Interleukin-10/blood ; Young Adult ; Humulus/chemistry ; },
abstract = {Xanthohumol (XN), a dietary flavonoid from hops (Humulus lupulus), possesses anti-inflammatory and microbiome-modulatory properties with potential therapeutic benefits for Crohn's disease (CD). To investigate the effects of XN on the gut environment in CD, we conducted a randomized, placebo-controlled clinical trial-the XN Microbiome and Signature (XMaS) trial (NCT4590508). 19 participants with clinically active CD completed the study. They were randomized to receive 24 mg/day of XN or placebo for 8 weeks, with clinical assessments at baseline and every 2 weeks. We assessed changes to Crohn's disease activity index (CDAI) scores, systemic inflammation, gut barrier function, profiling of microbial metabolism of XN, and gut microbiota composition and metabolism. Integration analysis of gut microbiota abundance, fecal metabolites, and inflammatory markers with CDAI scores revealed a pattern in which reductions in secondary bile acids and increases in IL-10 were associated with improved CDAI score in XN-treated individuals. These findings suggest that XN beneficially modulates the gut environment in CD by influencing microbial bile acid metabolism and host inflammatory response, thereby improving symptoms in individuals with severe innate immune activation.},
}

Humans
*Flavonoids/pharmacology/therapeutic use
*Crohn Disease/drug therapy/microbiology
*Bile Acids and Salts/metabolism
*Propiophenones/pharmacology/therapeutic use
Male
Female
*Gastrointestinal Microbiome/drug effects
Adult
Dietary Supplements
Middle Aged
Feces/microbiology/chemistry
Interleukin-10/blood
Young Adult
Humulus/chemistry

@article {pmid42138268,
year = {2026},
author = {Camps-Massa, P and Pérez-Mormeneu, J and Guevara-Nuñez, D and Saiz-Escobedo, L and Calatayud, L and González-Díaz, A and Sanllorente, A and Vicens-Zygmunt, V and Santos, S and Morros, R and Salvador-González, B and Domínguez, MÁ and Martí, S and , },
title = {Gut microbiome shift in long COVID: impact of disease and montelukast treatment.},
journal = {Journal of global health},
volume = {16},
number = {},
pages = {04164},
pmid = {42138268},
issn = {2047-2986},
mesh = {Humans ; *Cyclopropanes/therapeutic use ; *Sulfides/therapeutic use ; *Quinolines/therapeutic use ; *Gastrointestinal Microbiome/drug effects ; *Acetates/therapeutic use ; *COVID-19/microbiology/complications ; Male ; Female ; Cross-Sectional Studies ; Middle Aged ; SARS-CoV-2 ; Feces/microbiology ; Adult ; Aged ; Longitudinal Studies ; *COVID-19 Drug Treatment ; },
abstract = {BACKGROUND: Long COVID-19 is a post-infectious syndrome with persistent symptoms that can involve multiple organ systems. Evidence suggests that SARS-CoV-2 infection may disrupt gut microbiome composition, potentially contributing to long-term effects. As treatment remains symptom-based, interest has grown in repurposing drugs like montelukast. However, non-antibiotic medications may also alter gut microbial communities, raising questions about their impact. Here, we compare gut microbiota between long COVID patients and healthy controls and examine how montelukast treatment affects microbial composition.

METHODS: We analysed stool samples from long COVID patients and healthy controls using 16S rRNA gene sequencing (Illumina MiSeq). We evaluate alpha (Shannon) and beta (Bray-Curtis) diversity, followed by relative abundance and linear discriminant effect size analysis, to identify differentially abundant taxa. This proof-of-concept study included a cross-sectional comparison and a longitudinal analysis of montelukast-treated patients vs. placebo.

RESULTS: Cross-sectional analysis revealed a significant structural reorganisation of the gut microbial community in long COVID patients, although overall species richness was largely maintained. Linear discriminant effect size analysis revealed that this architectural shift was driven by an enrichment of Firmicutes (Agathobacter and Faecalibacterium genera) in the long COVID group, while healthy controls were characterised by higher abundances of the phyla Verrucomicrobiota and Actinobacteriota, as well as genera Alistipes and Akkermansia. Longitudinal analysis demonstrated that the broader community structure remained stable in both groups; however, montelukast treatment led to a specific enrichment of the genus Dialister, suggesting targeted and potentially transient effects without disrupting the overall microbial landscape.

CONCLUSIONS: Long COVID is characterised by a significant restructure of the gut ecosystem. This qualitative dysbiosis reflects a shift in homeostatic balance, where the core microbial community remains present, but its proportions are altered. Short-term montelukast treatment shows a minimal impact on the microbial landscape, suggesting treatment does not further destabilise the gut environment. These findings highlight the specific and targeted nature of gastrointestinal involvement in long COVID.},
}

Humans
*Cyclopropanes/therapeutic use
*Sulfides/therapeutic use
*Quinolines/therapeutic use
*Gastrointestinal Microbiome/drug effects
*Acetates/therapeutic use
*COVID-19/microbiology/complications
Male
Female
Cross-Sectional Studies
Middle Aged
SARS-CoV-2
Feces/microbiology
Adult
Aged
Longitudinal Studies
*COVID-19 Drug Treatment

@article {pmid42138670,
year = {2026},
author = {Khanna, S and Allegretti, JR and Hashash, JG and Feuerstadt, P},
title = {AGA Clinical Practice Update on Management of Clostridioides difficile Infection in Inflammatory Bowel Disease: Expert Review.},
journal = {Gastroenterology},
volume = {},
number = {},
pages = {},
doi = {10.1053/j.gastro.2026.03.008},
pmid = {42138670},
issn = {1528-0012},
abstract = {DESCRIPTION: Clostridioides difficile infection (CDI) remains a significant driver of disease flares and poor outcomes in patients with inflammatory bowel disease (IBD), leading to increased hospitalization, intensified or failed therapy, and higher surgical rates. Compared with the non-IBD population, patients with IBD face greater CDI risk and severity and higher recurrence risk, creating clinical dilemmas when considering antibiotic selection and the timing or necessity of IBD-related therapy adjustments. Emerging evidence highlights microbiota-based therapies such as unapproved fecal microbiota transplantation or US Food and Drug Administration-approved donor-derived therapies as a promising therapeutic avenue for recurrent CDI in patients with IBD, reflecting a growing emphasis on microbiome-directed interventions. This review examines the evolving literature, considering the diagnosis and management strategies and offering pragmatic guidance to optimize outcomes for patients with IBD challenged by concomitant CDI and recurrent CDI.

METHODS: This Expert Review was commissioned and approved by the American Gastroenterological Association (AGA) Institute Clinical Practice Updates Committee and the AGA Governing Board to provide timely guidance on a topic of high clinical importance to the AGA membership and underwent internal peer review by the Clinical Practice Updates Committee and external peer review through standard procedures of Gastroenterology. These practical Best Practice Advice statements were drawn from a review of the best available published evidence, including existing clinical studies, systematic reviews and practice guidelines, and expert opinion. Because a formal systematic review was not performed, these Best Practice Advice statements do not carry formal ratings of the quality of evidence or strength of the presented considerations. The focus is on the management of both CDI and IBD in patients with underlying IBD who develop CDI. Best Practice Advice Statements BEST PRACTICE ADVICE 1: In patients with IBD who have new or worsening diarrhea, CDI should be excluded, especially among those with colonic involvement, as they are at increased risk of CDI. Clinicians should consider and treat CDI in patients with end ileostomy or ileo-anal pouch anastomosis with worsening diarrhea. BEST PRACTICE ADVICE 2: In patients with IBD and suspected CDI, a multistep toxin-based assay should be used for diagnostic evaluation. BEST PRACTICE ADVICE 3: In patients with IBD and recent CDI who have been treated successfully with antibiotics, recurrent diarrhea should prompt retesting for CDI. BEST PRACTICE ADVICE 4: In patients with IBD who develop an initial episode of CDI, clinicians should preferentially use fidaxomicin or use vancomycin if fidaxomicin is unavailable or cost-prohibitive. Metronidazole should not be used. BEST PRACTICE ADVICE 5: Clinicians should strongly consider hospitalization for patients with IBD and CDI who demonstrate features of severe colitis or systemic toxicity (eg, more than 6 bowel movements per day, severe abdominal pain, marked leukocytosis, hemodynamic instability, or other evidence of sepsis). BEST PRACTICE ADVICE 6: When selecting an immunosuppressive therapy to treat IBD, no class or mechanism of action has a differential risk of CDI and, therefore, clinicians should choose the therapy that is best to treat the IBD. BEST PRACTICE ADVICE 7: In patients with IBD and acute CDI, concurrent treatment of IBD is critical and clinicians should continue therapy with the required immunosuppressive therapies (ie, immunomodulators, biologics, or small molecules). Steroids can also be used if deemed necessary while CDI is treated with antibiotics. BEST PRACTICE ADVICE 8: Clinicians should consider endoscopic evaluation for IBD activity and exclusion of concomitant cytomegalovirus infection if symptoms persist 48-72 hours after initiation of treatment for CDI. BEST PRACTICE ADVICE 9: Clinicians may consider loperamide in patients with improving inflammation and infection but ongoing diarrhea. BEST PRACTICE ADVICE 10: Clinicians should offer microbiome-based therapies (eg, fecal microbiota, live-jslm, fecal microbiota spores, live-brpk, or unapproved fecal microbiota transplantation) to patients with IBD with at least 1 recurrence of CDI to prevent future infection. BEST PRACTICE ADVICE 11: In patients with IBD, clinicians should not advise probiotics for primary or secondary prevention of CDI. BEST PRACTICE ADVICE 12: In patients with IBD and a history of CDI who are receiving systemic antibiotics, clinicians may consider oral vancomycin prophylaxis as secondary prevention.},
}

@article {pmid42138705,
year = {2026},
author = {Zhu, L and Wang, M and Zhang, X and Dou, T and Hua, H and Tang, X and Niu, X and Kou, Q and Chen, Y and Pan, M and Ma, B},
title = {Early supplemental feeding improves post-weaning growth restriction in lambs via the gastrointestinal-metabolic axis.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0242125},
doi = {10.1128/aem.02421-25},
pmid = {42138705},
issn = {1098-5336},
abstract = {The weaning period often induces growth restriction in lambs due to gastrointestinal immaturity and dietary transition. Although early supplemental feeding (ESF) shows promise, its systemic mechanisms via the rumen microbiota-gut-metabolism axis remain incompletely understood. Sixty Tan lambs were assigned to a control group (suckling only), Trial Group I (free-access ESF from 10 days), and Trial Group II (free-access + forced isolation from 15 days). Growth performance, rumen fermentation, intestinal morphology, serum metabolites, and rumen microbiota were comprehensively analyzed. The supplemental feeding regimen in Trial Group I significantly improved body weight, average daily gain, and body size before and after weaning. Rumen butyrate and acetate concentrations increased markedly, with enrichment of beneficial microbiota (Bifidobacteriaceae and Sharpea). Intestinal villus height and villus-to-crypt ratio were enhanced in the jejunum and ileum. Regarding serum metabolism, lambs in both supplemental feeding groups showed significantly increased levels of albumin and urea and decreased total cholesterol. The activities of antioxidant enzymes (catalase, superoxide dismutase, and glutathione peroxidase) and the levels of oxidative products (malondialdehyde and hydrogen peroxide) in the serum of lambs from both supplemental feeding groups were significantly higher than those in the control group. Correlation analysis revealed positive associations between beneficial microbiota, fermentation parameters, intestinal development, and growth performance. ESF alleviates post-weaning growth restriction by remodeling the rumen microbiota, enhancing volatile fatty acid production, improving intestinal development, and optimizing host nutrient utilization. The free-access ESF regimen is recommended for efficient lamb production.IMPORTANCEThis study reveals that different regimens of early supplemental feeding differentially alleviate post-weaning growth restriction in lambs by distinctly remodeling the host's "rumen microbiota-gut-metabolism axis." The optimized regimen enriches beneficial rumen microbiota (e.g., Bifidobacteriaceae and Sharpea), increases key metabolite production (e.g., butyrate), and synergistically improves intestinal development and host protein/lipid metabolism, thereby elucidating the mechanism of growth promotion via microbe-host interactions. These findings advance the understanding of "nutrition-microbe-host" crosstalk in young ruminants and provide a theoretical framework for precision nutrition through microbiome modulation. The identified key microbes and metabolic functions offer potential targets for developing eco-friendly feed additives, aiding in reducing antibiotic reliance and promoting sustainable lamb production.},
}

@article {pmid42138826,
year = {2026},
author = {Chen, X and Shen, M and Zhang, R and Huang, Z and Niu, H and Yu, Q and Chen, Y and Pan, X and Rong, L and Wen, H and Yang, J and Xie, J},
title = {Sulfated Cyclocarya Paliurus Polysaccharide Sorchestrates the Gut Microbiome to Mobilize a Host-Derived 12-HEPE Against Ulcerative Colitis.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e75681},
doi = {10.1002/advs.75681},
pmid = {42138826},
issn = {2198-3844},
support = {2023YFF1104001//National Key Research and Development Program of China/ ; 82460642//National Natural Science Foundation of China/ ; },
abstract = {Despite extensive evidence supporting the therapeutic potential of natural product-derived compounds in Ulcerative colitis (UC), their precise mechanisms have yet to be fully elucidated. In this study, structurally modified Cyclocarya paliurus polysaccharide (CP) derivatives were evaluated in a dextran sulfate sodium (DSS)-induced UC mouse model. Among the variants tested, sulfated Cyclocarya paliurus polysaccharide (SCP) emerged as the most therapeutically potent. SCP administration markedly attenuated colitis severity, as evidenced by relieved disease symptoms and reinforced intestinal barrier function. Mechanistically, SCP restored gut microbial homeostasis by enriching beneficial Bacteroidetes and enhancing short-chain fatty acids (SCFAs) production. This remodeled microbial ecosystem orchestrates the upregulation of host-derived 12-hydroxyeicosapentaenoic acid (12-HEPE), which exerts anti-inflammatory effects via direct inhibition of Toll-like receptor 4 (TLR4) signaling. The gut microbiota's functional relevance was substantiated by fecal microbiota transplantation and antibiotic-mediated exhaustion studies. Notably, the therapeutic benefits of 12-HEPE were abrogated upon co-administration of a TLR4 agonist, confirming its target specificity. Elevated serum 12-HEPE levels were observed in a human UC cohort, implying a potential compensatory immunoregulatory response. Our findings elucidate a novel microbiota-host interaction axis wherein SCP alleviates UC by modulating the gut microbiota to enhance endogenous 12-HEPE production, thereby suppressing TLR4-mediated inflammation.},
}

@article {pmid42138982,
year = {2026},
author = {Pereira, VH and Cassiano, GH and Ferreira, PHN and Abreu, LGF and Sousa, JES and Carazzolle, MF and Pereira, GAG and Silva, NV},
title = {An integrated microbiological analysis of the soil and rhizosphere of Agave spp. under minimum technological input farming systems.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {5},
pages = {},
pmid = {42138982},
issn = {1465-2080},
mesh = {*Agave/microbiology/growth & development ; *Rhizosphere ; *Soil Microbiology ; *Soil/chemistry ; Microbiota ; Agriculture/methods ; Bacteria/classification/isolation & purification/genetics ; Crops, Agricultural/microbiology ; },
abstract = {The expansion of arid and semi-arid regions, consequent to the intensification of desertification processes attributable to global warming, exerts a deleterious effect on the agricultural production of energy crops, with current estimates indicating that a further 23% of global agricultural areas will suffer from desertification by 2100, precipitating crises in these sectors. Agave species have the capacity to thrive in these marginal environments characterized by aridity and elevated temperatures. These plants can serve as a source of biomass for the production of biofuels, a process that mitigates the environmental impacts of the transport sector while promoting the utilization of drylands, thereby eliminating competition with food crops. Given the paucity of knowledge regarding the soil microbiota and rhizosphere in minimal technological input Agave plantations, the objective of this study was to evaluate the microbiological and chemical soil properties of Agave sisalana and Agave hybrids (H11648 and H400f) farming systems. The analyses, which were carried out using microbial quantification, enzyme stoichiometry and enzymatic vector calculations, demonstrated that the microbiome of these plants is active and well-structured in terms of nutritional acquisition. It was observed that the Agave fields' microbiome is very similar to that of the native vegetation. This finding suggests that the soil and rhizosphere microbiota are healthy and stable in the Agave fields evaluated, even with the implementation of agronomic exploitation models, as the chemical analysis of the soil reveals that all measured parameters are consistent with those of soils suitable for crop production. These observations persist even in long-established Agave plantations of varying ages that have never received any type of implement or soil correction. Thus, the integration of the chemical and biological data through principal component analysis, redundancy analysis and Permutational Multivariate Analysis of Variance (PERMANOVA) enabled the differentiation of the soil among the three Agave species, which shows the influence of the plant genotype on its microbiota.},
}

*Agave/microbiology/growth & development
*Rhizosphere
*Soil Microbiology
*Soil/chemistry
Microbiota
Agriculture/methods
Bacteria/classification/isolation & purification/genetics
Crops, Agricultural/microbiology

@article {pmid42139081,
year = {2026},
author = {Shen, H and Song, J and Li, J and Hu, Y and Peng, N and Zhao, S},
title = {Dietary Niches Drive Microbial Community Assembly, Network Reorganization, and Symbiont Evolution in Freshwater Fish Gut Microbiomes.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag125},
pmid = {42139081},
issn = {1751-7370},
abstract = {Host diet is a fundamental ecological factor shaping the assembly and evolution of host-associated microbiomes, yet how dietary niches influence the structure of microbial associations and functional adaptation in freshwater fish remains poorly understood. This study selected five dominant farmed freshwater fish species in China with distinct feeding habits (herbivory, omnivory, filter-feeding, and carnivory) and systematically investigated the adaptive mechanisms of their gut microbiomes by integrating metagenomics, targeted cultivation, comparative genomics, and in vitro assays. We show that dietary niches exert a strong deterministic effect on microbial community assembly, leading to pronounced differences in ecological network topology, including connectivity, modularity, and keystone taxa. Cetobacterium was detected in all five fish species but exhibited a higher relative abundance in omnivorous (16.0%) compared to carnivorous fish (5.4%), suggesting that it may be a core genus within the gut microbiota of freshwater fish. Comparative genomics further revealed that Cetobacterium symbionts exhibit streamlined genome architectures and conserved core metabolic functions, indicative of adaptive evolution toward stable host-associated lifestyles. Guided by metagenomic insights, we isolated multiple Cetobacterium strains displaying host-adapted functional traits, linking community-level ecological patterns to cultivable symbiont resources. In summary, our findings demonstrate that freshwater fish guts function as ecological niches that deterministically structure microbial community assembly and drive symbiont evolution, providing a conceptual framework for understanding host-microbiome co-adaptation in aquatic ecosystems.},
}

@article {pmid42139085,
year = {2026},
author = {Sidhom, J and Balla, SB and Tadakamadla, SK and Tadakamadla, J},
title = {The Association Between Self-Reported Nicotine Vaping and the Human Oral Microbiome: A Systematic Review.},
journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco},
volume = {},
number = {},
pages = {},
doi = {10.1093/ntr/ntag103},
pmid = {42139085},
issn = {1469-994X},
abstract = {INTRODUCTION: Nicotine Vapes have experienced a rise in their popularity, and our understanding of how vapes affect our oral microbiome remains to be reviewed. This systematic review explores whether the use of vapes is associated with measurable alterations in the diversity and taxonomic composition of the oral microbiome compared to non-vapers or conventional cigarette smokers.

METHODS: A comprehensive and systematic search of 6 databases was meticulously conducted, covering published literature up to the end of August 2024. The data was then extracted and underwent a qualitative analysis. Studies' risk of bias was assess using Newcastle Ottawa Scale Eligible studies needed to have a comparison group of either non-smokers or tobacco users or both and a group of sole e-cigarette users.

RESULTS: The search yielded 18 articles, with sixteen being cross-sectional and the remaining two were cohort studies. There were 1418 participants across the studies, ranging from 30-125 participants in each study. Majority of the included literature indicated e-cigarettes can alter the taxonomic composition and diversity of their user's oral microbiome.

CONCLUSIONS: Vaping was found to be associated with changes in oral microbiome. Since, the majority of the existing literature relied on self-reporting to see if participants were sole vapers, and mainly focused on bacterial genera, the exact impact of these changes are difficult to ascertain. However, the existing literature demonstrates a relationship in a few bacterial genera associated with periodontal disease among e-cigarette users, highlighting the need for further comprehensive studies with sound methodological approach to recruit sole e-cigarette users.

IMPLICATIONS: This study concludes that nicotine vapes do have a demonstratable impact on the oral microbiome that is unique to vapes. E-cigarette use may be associated with an increase periodontal pathogens which may predispose e-cigarette users to worse periodontal disease, however, further research is required.},
}

@article {pmid42139269,
year = {2026},
author = {Wein, H and Iglesias-Moreno, P and Apostolov, A and Salumets, A and Muzzio, DO and Sola-Leyva, A},
title = {Bacterial Extracellular Vesicles: New Hype or Hope to Explain Reproductive Host-Microbiota Interactions.},
journal = {Journal of extracellular vesicles},
volume = {15},
number = {5},
pages = {e70296},
pmid = {42139269},
issn = {2001-3078},
support = {PSG1082//Estonian Research Council/ ; PRG1076//Estonian Research Council/ ; 2024-02530//Vetenskapsrådet/ ; 101236395//Horizon Europe / Marie Skłodowska-Curie Staff Exchange/ ; TK214//Estonian Ministry of Education and Research/ ; 101120075//HORIZON EUROPE Health/ ; NNF24OC0092384//Novo Nordisk Fonden/ ; MU 4404/3-1//Deutsche Forschungsgemeinschaft/ ; },
mesh = {Humans ; *Extracellular Vesicles/metabolism ; Female ; Pregnancy ; *Microbiota ; *Host Microbial Interactions ; Animals ; *Reproduction ; *Bacteria/metabolism ; },
abstract = {Rapid advances in microbiome research are transforming our understanding of human health and disease, with growing focus on the female reproductive tract as a critical but understudied niche. Evidence for a local microbiome largely derives from bacterial nucleic acid detection; however, the biological relevance of these signals remains debated, with whether they reflect viable microbial communities, transient colonisation, or mere microbial remnants with immunomodulatory effects. Bacterial extracellular vesicles (BEVs) have emerged as pivotal mediators of host-microbiota crosstalk. Their small size enables them to traverse tissue barriers, enter systemic circulation and access barrier-protected anatomical sites like the placenta, thereby extending their biological reach beyond the site of origin. Although BEVs have been extensively characterised in the context of gastrointestinal, respiratory and systemic diseases, their relevance within the reproductive tract remains insufficiently defined. Understanding whether BEVs contribute to processes such as endometrial receptivity, gamete interaction, embryo implantation and immune tolerance in early pregnancy may reveal novel mechanisms of reproductive physiology and pathology. Furthermore, unravelling the role of BEVs could help resolve the ongoing debate regarding the existence of a functional upper reproductive tract (URT) microbiota, reframing it in terms of microbial activity rather than microbial presence alone. This review synthesises the limited but growing body of evidence on BEVs in the reproductive tract, with a particular emphasis on their potential influence on female fertility and early pregnancy outcomes. We also outline the major methodological challenges, including the discrimination of BEVs from host-derived extracellular vesicles (EVs), the technical limitations of current detection approaches and the risk of contamination in low-biomass environments that complicate research in this field. Finally, we highlight conceptual frameworks and future research directions needed to establish BEVs as important players in reproductive biology and to harness their diagnostic and therapeutic potential in reproductive medicine.},
}

Humans
*Extracellular Vesicles/metabolism
Female
Pregnancy
*Microbiota
*Host Microbial Interactions
Animals
*Reproduction
*Bacteria/metabolism

@article {pmid42139619,
year = {2026},
author = {Dorohavtseva, HA and Dorofieiev, AE and Myroshnychenko, MS},
title = {Clinical, endoscopic, morphological and microbiological characteristics of diverticular disease in patients with metabolic disorders.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {4},
pages = {803-810},
doi = {10.36740/WLek/220666},
pmid = {42139619},
issn = {0043-5147},
mesh = {Humans ; Male ; Female ; Middle Aged ; *Gastrointestinal Microbiome ; Colonoscopy ; Aged ; *Diverticular Diseases/microbiology/pathology/complications ; *Obesity/complications ; Adult ; Intestinal Mucosa/pathology/microbiology ; *Metabolic Diseases/complications ; Overweight/complications ; },
abstract = {OBJECTIVE: Aim: The aim of the study was to identify the clinical course and endoscopic activity features in patients with uncomplicated diverticular disease (UDD) associated with diabetes mellitus (DM), overweight, and obesity and perform an analysis of the gut microbiome and morphological characteristics of the colonic mucosa in such patients.

PATIENTS AND METHODS: Materials and Methods: 259 patients with UDD, hospitalized in the Department of Gastroenterology of Feofaniya Clinical Hospital of the State Administration of Affairs during the period of 2020-2024, were included in the study. Among all patients with DD included in the study, 43 had no metabolic disorders (MD) (DM, overweight, obesity), while 216 presented with varying degrees of MD. All patients underwent total colonoscopy with assessment of endoscopic activity of diverticular inflammation using the Diverticular Inflammation and Complication Assessment (DICA) score. The clinical course of DD was evaluated according to the classification proposed by the German Society of Gastroenterology, Digestive and Metabolic Diseases and the German Society of General and Visceral Surgery in 2021. The microbiome analysis was conducted only in 172 patients who had the financial means to undergo this test. During endoscopic examination of the colon in all patients, mucosal biopsies were obtained from the diverticular orifice. Histological, histochemical, and immunohistochemical methods were used. The obtained digital indicators in the groups were analyzed using statistical methods.

RESULTS: Results: This study evaluated clinical, endoscopic, morphological, and microbiological characteristics of DD in patients with metabolic disorders. A recurrent course of diverticular inflammation was observed more frequently in patients with metabolic dysfunctions. Endoscopic assessment of inflammatory activity correlated with histological changes of colon mucosa and alterations in mucin expression (MUC2 and MUC4). Microbiological analysis revealed a reduction in butyrate-producing flora (Akkermansia muciniphila, Faecalibacterium prausnitzii) with predominance of Bacteroidetes in metabolic disorder patients.

CONCLUSION: Conclusions: The clinical, morphological, microbiological and endoscopic features of DD identified by the authors highlight pathophysiological links between metabolic dysfunction (DM, overweight, obesity) and DD progression.},
}

Humans
Male
Female
Middle Aged
*Gastrointestinal Microbiome
Colonoscopy
Aged
*Diverticular Diseases/microbiology/pathology/complications
*Obesity/complications
Adult
Intestinal Mucosa/pathology/microbiology
*Metabolic Diseases/complications
Overweight/complications

@article {pmid42139623,
year = {2026},
author = {Khudhair, HM and Alhamdani, ASH and Al Tameemi, AMH},
title = {Microbiology of dental decay and periodontal disease: A review.},
journal = {Wiadomosci lekarskie (Warsaw, Poland : 1960)},
volume = {79},
number = {4},
pages = {829-846},
doi = {10.36740/WLek/216932},
pmid = {42139623},
issn = {0043-5147},
mesh = {Humans ; *Periodontal Diseases/microbiology/therapy ; *Dental Caries/microbiology/therapy ; Biofilms ; Porphyromonas gingivalis/pathogenicity ; Mouth/microbiology ; },
abstract = {OBJECTIVE: Aim: This review attempts to examine the microbiology, pathogenesis and current therapeutic approaches of dental caries and periodontal diseases with a special focus on the role of polymicrobial biofilms, the host-microbe interaction and the major pathogenic species involved in disease progression.

PATIENTS AND METHODS: Materials and Methods: A thorough literature review was performed using major scientific databases such as PubMed, Scopus, Web of Science and Google Scholar. Studies that were published between 2000 and 2025 were included. Relevant experimental, clinical and review articles that focused on the etiology, microbial composition, virulence mechanisms, host immune responses and therapeutic approaches of dental caries and periodontal disease were analyzed.

CONCLUSION: Conclusions: The oral cavity harbors over 700-800 bacterial species, of which the primary cariogenic pathogen is Streptococcus mutans and Porphyromonas gingivalis has been implicated as a major cause of periodontal disease. Dental caries progression is mostly attributed to acid production and demineralization of enamel, whereas periodontal disease is a result of dysbiotic shift in the subgingival microbiome with destructive host inflammatory responses. The "red complex" (P. gingivalis, Treponema denticola and Tannerella forsythia) has a high degree of synergistic virulence in advanced periodontitis. Biofilm formation, production of extracellular polysaccharide (EPS) matrix, quorum sensing and immune components (neutrophils, macrophages and matrix metalloproteinases or MMPs) are all factors that contribute to disease formation. Prevention strategies include oral hygiene measures, fluoride exposure, dietary modification, and antimicrobial agents, whereas treatment measures include mechanical debridement, systemic antibiotics, antimicrobial peptides, probiotics, and photodynamic therapy. Dental caries and periodontal diseases are the result of complex interactions between polymicrobial biofilms and immune responses by the host. A better understanding of the microbial ecology, virulence pathways and host-pathogen interactions is crucial in the process of improving prevention and treatment. Advances in targeted antimicrobial therapies and innovative therapeutic approaches hold promise for enhancing global oral health outcomes.},
}

Humans
*Periodontal Diseases/microbiology/therapy
*Dental Caries/microbiology/therapy
Biofilms
Porphyromonas gingivalis/pathogenicity
Mouth/microbiology

@article {pmid42139793,
year = {2026},
author = {Jibril, AH and Alencar, ALF and Olsen, JE and Hounmanou, YMG},
title = {Effect of age, severity of diarrhoea, number of pathogens present and blooming of E. coli on metagenomic characteristics of stools from Danish dairy calves with diarrhoea.},
journal = {Veterinary microbiology},
volume = {319},
number = {},
pages = {111070},
doi = {10.1016/j.vetmic.2026.111070},
pmid = {42139793},
issn = {1873-2542},
abstract = {BACKGROUND: Calf diarrhoea causes substantial welfare and economic losses, and it is one of the major drivers of antimicrobial use. This study aimed to characterize the faecal microbiome of diarrhoeic calves, with a specific focus on Escherichia coli, and to assess whether microbial profiles vary with age, diarrhoea severity, and high E. coli abundance in the absence of other detectable enteric pathogens.

METHODS: Stool samples from Danish diary calves (n = 32) below 4 weeks of age were collected from 11 herds and were analysed using direct long-read sequencing (mgt) as well as analyses of a subset of samples by swiping microbiota from faecal samples grown on McConkey agar plates (plate-swipe). Metagenomes were analysed to characterise community structure (Shannon α-diversity; Bray-Curtis PCoA with PERMANOVA) and to assess differential abundance at the species level while adjusting for sample type (mgt/plate swipe), herd, age, number of other pathogens detected by qPCR (rotavirus, coronavirus, Cryptosporidium parvum, Salmonella Dublin, Clostridium perfringens A, B, C, Eimeria and Escherichia coli F5) and recorded as presence/absence and summarised into infection classes (None/Mono/Co-2/Co-3 +). Binning was performed to build metagenome assembled genomes (MAGs) of E. coli.

RESULTS: Microbiome structure was dominated by methodological and contextual factors: sample type (direct metagenomic vs plate swipe) and herd explained far more variation than clinical severity and age. Metagenomic species profiles from plate swabs were comparatively homogeneous and E. coli-rich, whereas direct metagenomes captured higher diversity. Differential abundance identified species enriched with increasing diarrhoea severity and with infection classes, while pathogen-specific contrasts (e.g., C. perfringens A-positive vs negative) revealed discrete sets of bacterial co-occurrences. Classical pathotype markers (virulence-genes) were uncommon among E. coli MAGs.

CONCLUSIONS: Long-read metagenomics revealed insignificant influence of severity of diarrhoea, age below 4 weeks and number of pathogens detected in stool samples on diversity and microbial communities in diarrheic dairy calves. In contrast, large variation was observed between herds. On average, E. coli constituted about half of the microbiota. MAGs generated by binning indicated non-specific blooming of strains without particular virulence genes.},
}

@article {pmid42140024,
year = {2026},
author = {Mu, Y and Zhang, H and Pan, Y and Tian, Z and Huang, Y and Yang, L and Zhang, C and Zhao, C and Li, D and Liu, X and Jiang, L},
title = {Deciphering the mechanisms underlying regional heterogeneity of high-temperature Daqu through integrated electronic sensory, volatilome, and microbiome analysis.},
journal = {International journal of food microbiology},
volume = {457},
number = {},
pages = {111847},
doi = {10.1016/j.ijfoodmicro.2026.111847},
pmid = {42140024},
issn = {1879-3460},
abstract = {High-temperature Daqu (HTD) is crucial for shaping the style of Moutai-flavor Baijiu, but its quality characteristics exhibit geographical and spatial heterogeneity, resulting in diminished typicity of products from non-core production regions. Therefore, this study employed multiphase detection techniques to analyze HTD samples from the typical region (Guizhou) and emerging region (Shandong), along with their surface and inner layers. Guizhou HTD possessed superior biochemical activity (especially on the surface) and higher response values for W1W, W2W, umami, and salty sensors. It also showed higher concentrations of key flavor compounds, such as pyrazines, acids, and alcohols. Targeted amplicon sequencing showed Kroppenstedtia, Thermoascus, and Thermomyces dominated all samples, but Guizhou HTD had greater microbial diversity and richness. Metagenomics indicated a higher proportion of bacteria in Guizhou HTD, represented by Kroppenstedtia eburnea and Oceanobacillus indicireducens, whereas fungi were more prevalent in Shandong HTD, with Paecilomyces varioti, Aspergillus chevalieri, and Rasamsonia emersonii as the dominant species. Functional annotation demonstrated that carbohydrate metabolism and amino acid metabolism were core biological functions of HTD, with gene abundances showing Guizhou > Shandong and inner > surface. Furthermore, species-enzyme contribution and metagenome-assembled genomes analyses confirmed that HTD exhibited functional redundancy at the ecological scale, yet the species responsible for these functions displayed regional specificity, explaining the phenotypic heterogeneity between Guizhou HTD and Shandong HTD. These findings highlight the pivotal role of the production region in HTD quality and offer insights for improving Moutai-flavor Baijiu flavor in non-core regions.},
}

@article {pmid42140124,
year = {2026},
author = {Lu, Y and Wu, Y and Zhang, H and Gao, D and Xie, H and Fu, S and Wang, H and Li, X},
title = {Multi-omics and in silico assessment of ecological risks posed by agrochemical coatings: Disruption of rhizosphere stress signaling and induction of bulb rot in Fritillaria cirrhosa.},
journal = {Ecotoxicology and environmental safety},
volume = {318},
number = {},
pages = {120276},
doi = {10.1016/j.ecoenv.2026.120276},
pmid = {42140124},
issn = {1090-2414},
abstract = {Agrochemical seed coatings are widely used to control soil-borne pathogens. However, their unintended ecological effects on rhizosphere interactions and plant health remain unclear. Here, we combined a field transplantation trial, multi-omics analyses, and molecular docking to investigate the effects of fungicide-based seed coatings on the rhizosphere microecology of Fritillaria cirrhosa.The field trial showed that coating treatment unexpectedly increased bulb rot incidence by 2.8-fold compared with untreated controls (P < 0.001). Multi-omics analyses further indicated that coating application disrupted rhizosphere microecology, as evidenced by a 25.1% decline in bacterial diversity, reduced network complexity, and enrichment of pathogenic Fusarium species. Metabolomic analysis revealed the accumulation of exogenous xenobiotics along with downregulation of pyrimidine metabolism pathway, suggesting altered plant-microbe chemical communication. Stress-related metabolites, including salicylic acid (SA), L-carnitine, and ethylmalonate, accumulated, whereas key signaling molecules, such as adenosine, monoacylglycerol (18:3), Lysophosphatidylethanolamine 15:1 were depleted (0.03-fold) in the treatment group. Moreover, the decrease in jasmonic acid coupled with an increase in SA suggests immune hijacking associated with necrotrophic pathogens such as Fusarium, a pathological cascade further supported by the accumulation of mycotoxins such as T-2 triol. Cross-domain network and molecular docking analyses further clarified interactions between hub metabolites and the microbial community. Notably, adenosine exhibited strong binding affinities (< -6.0 kcal/mol) to both plant defense-related proteins (JOX2 and CotA laccase) and fungal pathogenicity targets, indicating a key role for endogenous plant defense signals in maintaining rhizosphere ecological balance. Collectively, these findings provide robust correlative evidence linking agrochemical seed coatings to rhizosphere microecological dysbiosis, characterized by reduced metabolite-mediated recruitment of beneficial microbiota and disrupted interkingdom signaling. This pathogen-favoring environment highlights the often-overlooked ecological impacts of seed coatings and underscores the urgent need for microbiome-compatible disease management strategies in perennial bulbous crop production.},
}

@article {pmid42140291,
year = {2026},
author = {Ojeda-Martinez, D and Boter, M and Ortego, F and Santamaria, ME},
title = {Unveiling CAZyme modularity patterns: Comparative genomics links domain architecture to arthropod diets and life histories.},
journal = {International journal of biological macromolecules},
volume = {},
number = {},
pages = {152547},
doi = {10.1016/j.ijbiomac.2026.152547},
pmid = {42140291},
issn = {1879-0003},
abstract = {Carbohydrate-active enzymes (CAZymes) are proteins that assemble, remodel, and depolymerize complex carbohydrates. They are ubiquitous across the tree of life, underpinning energy capture, cell-wall architecture, microbiome interactions, and host-pathogen dynamics. CAZymes are modular in structure and function, being tightly related to the overall enzyme architecture. Domain architecture constrains folding, substrate range, and integration into metabolic pathways. Arthropods, the most species-rich animal phylum, offer a powerful system to study enzymatic modularity because their enzymatic machineries must function in extremely diverse ranges of diet, niche, and abiotic conditions. Here we built a genome-scale framework to characterize CAZyme modular organization across Arthropoda and to test how domain architecture is influenced by diets, life histories and clades while revealing emergent functional relationships. We find that unimodular architectures dominate CAZyme repertoires, while multimodular and class-exclusive arrangements remain rare but highly variable. We identify herbivory as responsible for the discrimination on three CAZyme structural strategies (saprophagous, leaf-stem-root, and pollen-nectar feeders) differing in class composition, modular complexity, and catalytic emphasis. Correlation and co-occurrence analyses at genomic and protein levels show that expansions of glycosyltransferases, glycoside hydrolases, carbohydrate-binding modules, and auxiliary activities are tightly coupled, especially in myriapods and crustaceans, and that intra-protein networks of CAZyme families are denser in hexapods, holometabolans, and herbivores. Within these networks, GT2 and hydrolytic domains occupy central positions in co-occurrence clusters. Together, our findings indicate that arthropod CAZymes evolve as integrated macromolecular systems whose modularity and class balance track ecological demands, providing a scalable framework for engineering CAZyme networks for biotechnological and pest-management applications.},
}

@article {pmid42140378,
year = {2026},
author = {Tan, MW and Clister, D and Chandra, QM and Wangsa, CE and Simone, CN and Umaya, C and Choi, J and Park, S and Rani, A and Akter, S and Kim, B and Kim, SH and de Azambuja Ribeiro, RIM and Syahputra, RA},
title = {Circulating microbial metabolites and the gut-prostate axis in prostate cancer: Implications for laboratory biomarkers and therapeutic response.},
journal = {Clinica chimica acta; international journal of clinical chemistry},
volume = {590},
number = {},
pages = {121086},
doi = {10.1016/j.cca.2026.121086},
pmid = {42140378},
issn = {1873-3492},
abstract = {Prostate cancer progression and treatment response are influenced not only by tumor genomics and androgen receptor signaling but also by systemic host-microbiome interactions along the gut-prostate axis. Increasing evidence indicates that gut microbial metabolism produces bioactive compounds that circulate in human body fluids and can influence immune regulation, hormone metabolism, and therapeutic outcomes. This review synthesizes current evidence on microbiome-derived metabolites that may serve as measurable biomarkers relevant to prostate cancer biology and clinical laboratory diagnostics. Microbial metabolism of dietary substrates generates circulating molecules-including short-chain fatty acids, secondary bile acids, indole derivatives, polyamines, and endotoxin-associated signals-that can modulate inflammation, epithelial barrier integrity, and systemic immune responses involved in tumor progression. In addition, intestinal microbes participate in steroid transformation and enterohepatic cycling of hormones, potentially influencing circulating androgen and estrogen levels that contribute to androgen-driven prostate cancer development and adaptation under androgen deprivation therapy. Importantly, many of these microbial metabolites are detectable in serum or plasma using validated analytical platforms such as liquid chromatography-mass spectrometry and gas chromatography-mass spectrometry, supporting their potential integration into laboratory biomarker panels. Emerging multi-omics approaches combining metagenomics, metabolomics, host transcriptomics, and immune profiling are beginning to clarify mechanistic links between microbial activity and therapy response, including variability in outcomes with androgen-targeted agents, chemotherapy, radiotherapy, and immune checkpoint inhibitors. From a clinical chemistry perspective, characterization of circulating microbiome-derived metabolites may enhance the diagnostic and prognostic performance of established biomarkers such as prostate-specific antigen while providing new opportunities for non-invasive monitoring of disease progression and treatment response. Establishing reproducible microbial metabolic signatures across diverse patient populations will be essential to translate microbiome-informed biomarkers into next-generation diagnostic and prognostic tools in prostate cancer management.},
}

@article {pmid42140385,
year = {2026},
author = {Li, Y and Zhang, J and Liu, H and Noman, M and Rizwan, MA and Isiaka, ID and Chen, H and Li, W and Zhao, N and Li, Y and Sun, Y and Lu, X and Liu, D and Yan, Y},
title = {Age-related pharyngeal microbiome and host transcriptomic signatures underlying fever responses in RSV bronchiolitis.},
journal = {Virologica Sinica},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.virs.2026.05.002},
pmid = {42140385},
issn = {1995-820X},
abstract = {Respiratory syncytial virus (RSV) bronchiolitis is the leading cause of hospitalization in infancy and exhibits pronounced age-dependent clinical heterogeneity. Fever becomes increasingly prevalent with age, yet whether febrile representation reflects a uniform inflammatory and immune phenotype across infancy remains unclear. In this prospective cohort of infants hospitalized with RSV bronchiolitis, we performed an integrated analysis of clinical features, pharyngeal microbiome composition, host transcriptomic profiles, and host-microbe interaction networks, with particular attention to age-related variation in fever-associated patterns. Clinically, fever prevalence exhibited a strong age-dependent increase across infancy. Correspondingly, canonical correspondence analysis identified age and fever as dominant gradients related to variation in both pharyngeal microbiome composition and host gene expression. Although no significant age-dependent correlations were observed at the global microbial and host transcriptomic levels in the fever-age interaction model, distinct patterns of microbial and host responses related to fever were observed across different age groups. Specifically, ranked gene set enrichment analysis indicated that febrile infants in early infancy showed relative attenuation of host defense-related programs, whereas older infants showed stronger enrichment of antiviral and inflammatory effector pathways, with more selective regulatory and signaling-associated patterns in late infancy. Integrated host-microbe network analysis further delineated a coherent developmental trajectory of fever-associated interaction architectures, evolving from densely interconnected regulatory networks in early infancy to modular, selectively coupled, host-centered configurations with advancing age. Together, febrile responses in RSV bronchiolitis should not be interpreted as a uniform biological phenotype across infancy and support age-aware interpretation of fever in pediatric RSV infection.},
}

@article {pmid42140394,
year = {2026},
author = {Linton, S and Sjaarda, C and Hossenbaccus, L and Davis, A and Greenlaw, J and Douchant, K and Thiele, J and Garvey, S and Botting, H and Steacy, LM and Sheth, PM and Ellis, AK},
title = {Characterizing the Nasal Microbiome Using a Nasal Allergen Challenge Model.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.05.003},
pmid = {42140394},
issn = {1097-6825},
abstract = {BACKGROUND: The role of the nasal microbiome in allergic rhinitis (AR), particularly following direct allergen exposure using a controlled model, remains incompletely understood. Understanding microbiome dynamics after allergen challenge could provide insights into AR pathophysiology.

OBJECTIVE: To evaluate nasal microbiome changes following a nasal allergen challenge (NAC) with ragweed pollen extract in individuals with ragweed-induced AR compared to non-allergic controls.

METHODS: Nineteen ragweed-allergic and twelve non-allergic participants completed an out-of-season NAC. Middle meatus and the adjacent nasal cavity secretions were collected at baseline and 6, 24, and 48 hours post-challenge. Microbial composition was characterized using 16S rRNA sequencing. Alpha diversity was assessed using Shannon and Chao1 indices, and beta diversity using Bray-Curtis dissimilarity with principal coordinate analysis. Ragweed-specific IgE (sIgE), total IgE (tIgE), and Staphylococcus aureus nasal carriage were also evaluated.

RESULTS: Nasal microbial community composition differed according to biological sex (beta diversity P = 0.001) and S. aureus carriage (P = 0.015). However, allergic status and NAC exposure had no significant effect on alpha or beta diversity over time. Genus-level differences between allergic and non-allergic participants emerged at 24 and 48 hours post-challenge (P = 0.028 and P = 0.0062), with greater relative abundance of Streptococcus and Veillonella observed in non-allergic individuals. Stratification by sIgE demonstrated significant differences in microbial community structure (P = 0.001), with higher sIgE levels associated with increased relative abundance of Streptococcus, Rothia, and Neisseria. Higher tIgE levels were also associated with distinct microbial community profiles and reduced Shannon diversity.

CONCLUSION: The nasal microbiome remained stable following acute allergen exposure despite clinical responses, while host factors including IgE levels, sex, and S. aureus carriage were associated with differences in microbial community composition.},
}

@article {pmid42140492,
year = {2026},
author = {Corcione, S and Benech, N and Kuijper, E and , },
title = {Microbiome science at a turning point: from descriptive ecology to clinical decision-making in infectious diseases.},
journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.cmi.2026.05.017},
pmid = {42140492},
issn = {1469-0691},
}

@article {pmid42140743,
year = {2026},
author = {Lee, JB and Baek, S and Kim, DK and Kwon, BE and Ahn, JS and Nagasaka, M and Davar, D and Park, H and Kim, H and Im, J and Yang, J and Yang, E and Shin, GH and Choi, S and Kwon, JE and Kim, JM and Kang, SY and Kim, Y and Park, SY and Kim, JH and Oh, HS and Chalita, M and Min, A and Cho, BC},
title = {Phase I trial of CJRB-101 plus pembrolizumab in patients with metastatic non-small cell lung cancer, head and neck squamous cell carcinoma and melanoma.},
journal = {Journal for immunotherapy of cancer},
volume = {14},
number = {5},
pages = {},
doi = {10.1136/jitc-2025-014702},
pmid = {42140743},
issn = {2051-1426},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use ; Female ; Male ; Middle Aged ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; Aged ; *Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology ; *Melanoma/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Mice ; *Head and Neck Neoplasms/drug therapy/pathology ; *Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology ; Animals ; Adult ; },
abstract = {BACKGROUND: Dysbiosis of gut microbiome leads to resistance to immunotherapy in various advanced solid tumors. CJRB-101 is a live biotherapeutic product consisting of a novel strain belonging to the species Leuconostoc mesenteroides. To modulate the tumor microenvironment, CJRB-101 was combined with pembrolizumab.

METHODS: Preclinical efficacy and mechanistic studies were performed using humanized non-small cell lung cancer (NSCLC) patient-derived xenograft (PDX) models. This is a multicenter, first-in-human, two-part, phase I, open-label study of CJRB-101 (1×10[11] or 4×10[11] colony forming unit (CFU)/day) plus pembrolizumab (200 mg every three weeks (Q3W)) in advanced NSCLC, melanoma, and head and neck squamous cell carcinoma in both immune checkpoint inhibitor (ICI)-naive and ICI-refractory settings. The primary endpoint was to assess the dose-limiting toxicities (DLTs), adverse events, and preliminary activity of the combination treatment. Exploratory endpoints included stool metagenomics analysis and pharmacodynamics parameters.

RESULTS: In four PDX models, CJRB-101 with pembrolizumab demonstrated enhanced antitumor efficacy, showing a tumor growth inhibition (TGI) of 77.3% in the CJRB-101 monotherapy group and 61.9% in the combination group, which was significantly improved compared with pembrolizumab alone. A distinct M2-to-M1 repolarization was observed and validated in vitro. Notably, increased activation of cytotoxic T cells was observed, suggesting an immune-mediated antitumor mechanism of CJRB-101. A total of 42 patients were enrolled in the low-dose cohort (one capsule once a day; n=6) and high-dose cohort (two capsules two times a day, n=36). Metastatic NSCLC accounted for 86% (n=36) and 67% (n=28) of the patients were refractory to ICIs. None of the patients experienced DLT. In ICI-naïve NSCLC (n=12) with programmed death-ligand 1 (PD-L1) >50%, the overall response rate (ORR) and disease control rate (DCR) were 58% and 75%, respectively. The ORR was 5% and DCR was 41% in the ICI-refractory NSCLC (n=22) with an ORR of 5% and DCR of 41%. After a median follow-up of 15.6 months and 8.9 months for ICI-naïve and ICI-refractory NSCLC, the median progression-free survival was 9 months (95% CI 5.6 to not reached) and 1.8 months (95% CI 1.6 to 4.3), respectively. CJRB-101 plus pembrolizumab was well-tolerated, and none of the patients experienced grade >3 treatment-related adverse events.

CONCLUSIONS: Early clinical data show encouraging antitumor response of CJRB-101 plus pembrolizumab in ICI-naïve metastatic NSCLC with PD-L1 >50%.

TRIAL REGISTRATION NUMBER: NCT05877430.},
}

Humans
*Antibodies, Monoclonal, Humanized/pharmacology/therapeutic use
Female
Male
Middle Aged
*Carcinoma, Non-Small-Cell Lung/drug therapy/pathology
Aged
*Squamous Cell Carcinoma of Head and Neck/drug therapy/pathology
*Melanoma/drug therapy/pathology
*Lung Neoplasms/drug therapy/pathology
Mice
*Head and Neck Neoplasms/drug therapy/pathology
*Antineoplastic Combined Chemotherapy Protocols/therapeutic use/pharmacology
Animals
Adult

@article {pmid42140787,
year = {2026},
author = {Singh, N and Srivastav, M},
title = {Comment on "Distinct gut microbiota signatures and predicted lipid metabolism pathways in Taiwanese patients with acute versus chronic coronary syndromes".},
journal = {Journal of the Formosan Medical Association = Taiwan yi zhi},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jfma.2026.05.046},
pmid = {42140787},
issn = {0929-6646},
}

@article {pmid42140850,
year = {2026},
author = {Fagundes, D and Costa, LMS and Cagliari, A and de Vargas, DP and Rieger, A},
title = {Microbial Community Shifts and Plant Performance Improvements Driven by Bacillus firmus in Pampa Agroecosystems.},
journal = {Environmental microbiology reports},
volume = {18},
number = {3},
pages = {e70315},
pmid = {42140850},
issn = {1758-2229},
mesh = {*Bacillus/physiology ; *Soil Microbiology ; *Microbiota ; Rhizosphere ; *Glycine max/growth & development/microbiology/parasitology ; Plant Roots/growth & development/microbiology ; Animals ; Fungi/classification/genetics/isolation & purification ; Bacteria/classification/genetics/isolation & purification ; Nematoda ; Ecosystem ; Soil ; },
abstract = {The impact of Bacillus firmus-based bionematicides on rhizosphere microbiota and plant performance remains poorly understood in complex agroecosystems. This study evaluated the effects of B. firmus application on soil microbial communities, nematode dynamics, and soybean productivity in the Pampa biome. Our results demonstrate that B. firmus significantly modulates the composition and diversity of soil microbiota, with effects varying across locations and over time. Treated areas exhibited shifts in bacterial communities, including increased abundance of beneficial taxa, while fungal diversity tended to decrease, likely due to the combined effect of the fungicide used in seed treatment. Despite persistent populations of target nematodes such as Pratylenchus brachyurus and Heterodera glycines, treated areas showed reduced root infestation in specific stages and locations. Importantly, the application of B. firmus consistently enhanced soybean shoot and root growth, resulting in productivity gains of 6%-7% across all sites. These findings reveal that B. firmus not only contributes to plant growth promotion but also induces significant, yet context-dependent, shifts in rhizosphere microbial communities. The study highlights the ecological complexity of microbial responses to biocontrol agents and underscores the importance of integrating microbiome dynamics into sustainable nematode management strategies in agroecosystems.},
}

*Bacillus/physiology
*Soil Microbiology
*Microbiota
Rhizosphere
*Glycine max/growth & development/microbiology/parasitology
Plant Roots/growth & development/microbiology
Animals
Fungi/classification/genetics/isolation & purification
Bacteria/classification/genetics/isolation & purification
Nematoda
Ecosystem
Soil

@article {pmid42140946,
year = {2026},
author = {Zheng, R and Li, Y and Shang, P and Shen, Y and Nan, Z and Duan, T},
title = {Anthracnose drives assembly of phyllosphere epiphytic bacterial communities to increase disease resistance.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00991-z},
pmid = {42140946},
issn = {2055-5008},
support = {grant no. 2023-NK-147//the Fundamental Research Funds for the Leading Scientist Project of Qinghai Province/ ; },
abstract = {The phyllosphere microbiome plays crucial roles in plant health, but evidence of 'cry for help' strategy in the face of pathogen attack in the phyllosphere remains limited, particularly for the microbiomes of distinct leaf ecological niches. We investigated whether foliar pathogen anthracnose (Colletotrichum lentis) influenced the assembly and functions of microbiomes in epiphytic and endophytic niches of the phyllosphere of common vetch (Vicia sativa) leaves. We also evaluated synthetic microbial communities (SynComs), including representatives of disease-associated strains, for pathogen protection. Anthracnose mediated the deterministic assembly process of epiphytic bacterial and endophytic fungal communities, and increased the complexity of bacterial co-occurrence networks. Iron competition and antifungal genes were also enriched in the epiphytic bacteria, which produce siderophores and degrade fungal cell walls to counteract pathogens. SynComs of beneficial epiphytic bacteria partially protect hosts by regulating bacterial interactions and inducing host immune responses. These findings suggest that disease drives the deterministic assembly of distinct phyllosphere microbiomes, their diversity and their function. Moreover, SynComs from the epiphytic niche can confer host plant disease resistance.},
}

@article {pmid42140950,
year = {2026},
author = {Garrido-Castro, AC and Graham, N and Li, KX and Bi, L and Crowdis, J and Bi, K and Park, J and Pastorello, R and Li, Y and Gupta, H and Kuntz, T and Petry, R and Pasquina, LW and Patel, A and Lange, P and DiLullo, M and Attaya, V and Frey, AM and Childress, MA and Wesolowski, R and Sinclair, N and Sinclair, S and Lo, S and Tung, N and Faggen, M and Kaufman, PA and Block, CC and Walsh, J and Toke, M and Chen, W and Wucherpfennig, KW and Tian, Y and Williams, AJ and Mukhopadhyay, S and Dasgupta, T and Schnitt, S and Cherniack, AD and Barroso, R and Ligibel, J and Lin, NU and Mittendorf, EA and Tayob, N and Van Allen, E and Tolaney, SM},
title = {Carboplatin with or without nivolumab in metastatic triple-negative breast cancer: a randomized phase II trial.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73085-1},
pmid = {42140950},
issn = {2041-1723},
abstract = {This multi-institutional randomized phase II clinical trial (NCT03414684) investigated the efficacy and safety of carboplatin plus nivolumab compared to carboplatin in metastatic triple-negative breast cancer (mTNBC). The primary endpoint was progression-free survival (PFS) in a modified intention-to-treat (mITT) population of patients with chemotherapy-naïve (i.e., first-line) mTNBC. Secondary endpoints included overall survival (OS), confirmed objective response rate, confirmed clinical benefit rate, time to and duration of confirmed objective response, safety, and tolerability. Clinical outcomes were evaluated in the PD-L1-positive subgroup (≥ 1% immune cells; SP142 clone) per central review. Biospecimens were collected for correlative analyses. 75 patients were enrolled and treated between 2/2018-9/2020. Among the mITT population (n = 62), median PFS was 4.2 months with carboplatin plus nivolumab vs 5.5 months with carboplatin. Median OS did not significantly differ between arms (16.8 vs 11.1 months, respectively). In PD-L1-positive mTNBC patients (n = 24), median PFS was 8.3 vs 4.7 months; median OS was 17.6 vs 10.7 months. Grade ≥3 adverse events occurred in 56.8% of patients in the combination arm and 65.8% in the carboplatin arm. Carboplatin plus nivolumab did not significantly improve PFS compared to carboplatin in patients overall; however, a trend toward improved outcomes was observed in PD-L1-positive mTNBC patients. High mutational burden, interferon-gamma signaling, early circulating tumor DNA reduction, low baseline serum thymidine kinase activity, and urea cycle dysregulation in the microbiome emerged as potential predictors of response to immune checkpoint inhibitors with platinum.},
}

@article {pmid42141277,
year = {2026},
author = {Jiao, S and Pan, H and García-Palacios, P and Tu, H and Zhang, Y and Liu, Y and Gao, H and Chen, B and Peng, Z and Chen, S and Qi, J and Liang, C and Li, X and Wang, Y and Jin, C and Gao, M and Liu, J and Wang, Y and Zhao, J and Jiang, L and Romero, F and Banerjee, S and Yang, Y and Lu, Y and Delgado-Baquerizo, M and van der Heijden, MGA and Wei, G},
title = {Agricultural soil microbiomes are structurally and functionally more resistant to warming than adjacent natural ecosystems.},
journal = {Nature food},
volume = {},
number = {},
pages = {},
pmid = {42141277},
issn = {2662-1355},
abstract = {Agricultural soil microbiomes experience frequent disturbance from intensive management and may therefore be better equipped to withstand climate warming than microbiomes in undisturbed natural soils. Here we test this by combining a continental-scale warming microcosm experiment across 100 paired agricultural-natural sites with a global meta-analysis and three microbiome manipulation experiments (microbial suspensions, cross-inoculation and synthetic communities). Agricultural soils showed a higher resistance of soil multifunctionality to warming than natural soils, consistent across the meta-analysis. Resistance of microbial community composition was the strongest predictor of functional resistance and was confirmed in artificial soils inoculated with agricultural versus natural microbial suspensions. Introducing soil microbiomes from agricultural ecosystems into previously undisturbed natural soils enhanced functional resistance to warming. Metagenomic analysis revealed that microbial life-history strategies play a crucial role in regulating the resistance of soil microbial community to warming, with communities dominated by stress-tolerant strategies conferring significantly stronger resistance. Our work highlights the potential of microbiome engineering to strengthen ecosystem functioning under climate change.},
}

@article {pmid42141284,
year = {2026},
author = {},
title = {Even mild blows to the head disrupt the microbiome.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42141284},
issn = {1476-4687},
}

@article {pmid42141351,
year = {2026},
author = {Sarkar, S and Roy, S and Choudhury, L},
title = {Importance of the inflammasome in gut-brain axis: from pathological driver to therapeutic target.},
journal = {Inflammopharmacology},
volume = {},
number = {},
pages = {},
pmid = {42141351},
issn = {1568-5608},
abstract = {The inflammasome, a supramolecular complex, plays important role in the gut-brain axis (GBA), acting as a sensor of cellular stress and danger signals. It activates inflammatory responses, and its dysregulation has been implicated in neurological diseases. Various inflammasomes, such as NLRP3, NLRC4, and AIM2, contribute to disease progression by promoting inflammation, tissue damage, and oxidative stress. These inflammasomes recognize and get activated by different stimuli, such as ATP, fluctuations in ion fluxes, nucleic acids, and molecular signatures associated with pathogens, eventually releasing inflammatory cytokines, and triggering inflammatory responses. Although the inflammatory response is orchestrated, sometimes it might happen that its dysregulation causes excessive and sustained inflammation leading to cellular damage and tissue injuries. Inhibiting or modulating these inflammasomes can therefore, provide therapeutic benefits. Targeting NLRP3, like MCC950, has shown promise in reducing inflammation. Some natural compounds have also been found to inhibit NLRP3 and other inflammasomes. Interestingly, regulating the gut microbiome can impact inflammasome activation, and reduce unsolicited inflammation. This review explores the bidirectional communication network between the gut and brain, and emphasizes the importance of understanding the role of inflammasomes in the GBA which can lead to novel therapeutic strategies for neurological diseases like Multiple Sclerosis, Parkinson's, and Alzheimer's.},
}

@article {pmid42141362,
year = {2026},
author = {Baeuerle, E and Semwal, MK and Nie, J and Zhang, N and Liang, H and Ganapathy, V and Sathavarodom, N and Fernandez, R and Wang, CP and Espinoza, S and Dong, Q and Gao, X and Yang, Z and Kostic, A and Musi, N},
title = {Effect of Sevelamer and B. longum on Insulin Sensitivity in Participants With Obesity: A Randomized Clinical Trial.},
journal = {Obesity (Silver Spring, Md.)},
volume = {},
number = {},
pages = {},
doi = {10.1002/oby.70224},
pmid = {42141362},
issn = {1930-739X},
support = {7-13-GSK-01//American Diabetes Association/ ; R01DK080157//Foundation for the National Institutes of Health/ ; P30AG044271//Foundation for the National Institutes of Health/ ; P30AG094848//Foundation for the National Institutes of Health/ ; U01AR071130//Foundation for the National Institutes of Health/ ; R01AG075684//Foundation for the National Institutes of Health/ ; U54AG075941//Foundation for the National Institutes of Health/ ; T32GM113896//Foundation for the National Institutes of Health/ ; //South Texas MSTP/ ; },
abstract = {OBJECTIVE: This study evaluated whether two interventions with putative lipopolysaccharide (LPS)-lowering properties, the phosphate binder sevelamer or a synbiotic, improve insulin sensitivity in humans.

METHODS: We conducted a randomized, double-blind, placebo-controlled, three-arm parallel-group trial. Twenty-two lean and twenty-eight participants with obesity completed the trial. Participants were randomized to: (1) sevelamer; (2) synbiotic (oligofructose plus Bifidobacterium longum Rosell-175); or (3) placebo, three times a day for 4 weeks. The primary outcome was change in peripheral insulin sensitivity (M) assessed by hyperinsulinemic (60 mU/m[2] min) euglycemic clamp versus placebo.

RESULTS: In participants with obesity, sevelamer improved the M (+2.176 [0.314, 4.038] mg/kg min vs. placebo; p = 0.022) and lowered LDL-C (-29.675 [-53.794, -5.556] mg/dL vs. placebo; p = 0.016). Synbiotic had no effect on insulin sensitivity or lipids in either group. No changes in markers of endotoxemia were observed with any intervention. Sevelamer increased plasma levels of metabolites linked to improved glucose and lipid metabolism, such as bile acids, amino acids (citrulline, betaine), NAD+ precursors (trigonelline), and xenobiotics (genistein, umbelliferone).

CONCLUSIONS: Sevelamer improves insulin sensitivity and LDL-C in participants with obesity. Further investigation is warranted to elucidate sevelamer's metabolic mechanisms, potentially involving the mediation of bile acids and other host-microbiome-derived metabolites.

TRIAL REGISTRATION: ClinicialTrials.gov NCT02127125.},
}

@article {pmid42141481,
year = {2026},
author = {Roslund, MI and Uimonen, L and Kummola, L and Cerrone, D and Ojala, A and Luukkonen, A and Holopainen, E and Korhonen, A and Penttilä, R and Saarenpää, M and Venäläinen, M and Haveri, H and Rajaniemi, J and Laitinen, OH and Sinkkonen, A and Group, TBR},
title = {Neighborhood deadwood and yard rewilding modulate commensal microbiomes and inflammatory signals among urbanites.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02413-w},
pmid = {42141481},
issn = {2049-2618},
support = {346136//Strategic Research Council/ ; 346137//Strategic Research Council/ ; 346138//Strategic Research Council/ ; },
abstract = {BACKGROUND: Urbanization and biodiversity loss reduce human exposure to diverse microbiomes. Current evidence suggests that the vanishing microbiomes in industrialized populations are a central factor in the rising prevalence of non-communicable immune-mediated diseases. Rewilding has been proposed as an approach to diversify urban microbial communities and promote immunological resilience.

RESULTS: We rewilded 21 urban private yards with deadwood, vegetation, and microbially rich soil. Control yards (15) were analyzed for comparison. We analyzed skin bacteria and oral microbiomes and used vegetation and deadwood inventories, satellite data, and questionnaires to determine the effects of rewilding, living environment, and lifestyle factors on skin and oral microbiota, functional gene pathways, and cytokine levels (IL-6, IL-10). Neighborhood deadwood within 200-m radii around home yards was used as an indicator of environmental biodiversity. Samples were collected before the rewilding in summer and three months later in autumn. Skin microbial diversity stayed constant and was associated with plant richness in the rewilding group, despite the normal seasonal decline and reduced outdoor time in autumn. Rewilding was associated with a decrease in tetrahydrofolate biosynthesis and salvage, and L-histidine degradation gene pathways and other changes in oral microbiota. In the rewilding group in autumn, picking of berries and fruits was directly associated with immunoregulatory IL-10 and pleiotropic IL-6 in saliva, and neighborhood deadwood abundance with the fatty acid biosynthesis superpathway in oral microbiomes. When groups were analyzed jointly, the diversity of oral microbial functional gene pathways was negatively correlated with IL-6 levels, and neighborhood deadwood abundance was directly linked to skin Gammaproteobacterial taxa, and typically soil-derived Cytobacillus sp. CY-G and Streptomyces sp. HSG2 in saliva.

CONCLUSIONS: Our findings are consistent with the biodiversity hypothesis, suggesting that biodiversity exposure may influence commensal microbiomes and biological pathways involved in host-microbe interactions. Our results suggest that the amount of decaying deadwood in the neighborhood, in addition to conventional measures of greenness and vegetation diversity, may provide advantageous information in studies examining human-environment microbiome interactions. This may inform biodiversity-related ecosystem services related to impacts on human health. Our findings provide an incentive for future studies and strategic investments for rewilding urban microbiomes to support planetary health. Video Abstract.},
}

@article {pmid42141512,
year = {2026},
author = {Li, Y and Sun, J and Dai, Z and Jin, LN and Chen, Z and Lin, D and Zhu, L},
title = {Antibiotic Metabolites Are an Overlooked Driver of Resistance Dissemination in Plant Systems.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.6c04146},
pmid = {42141512},
issn = {1520-5851},
abstract = {Antibiotic pollution in agroecosystems is widely recognized, yet the risks posed by their metabolites remain insufficiently addressed. Using lettuce as a model, we investigated how tetracycline (TC) and its metabolites, anhydrotetracycline (ATC) and epitetracycline (ETC), contribute to the dissemination of antibiotic resistance genes (ARGs). TC primarily accumulated in roots and declined during translocation, whereas ATC exhibited greater persistence and became the predominant residue through in planta transformation. At environmentally relevant concentrations (≤0.1 mg·L[-1]), ATC more effectively expanded the mobilizable resistome than the parent compound by inducing reactive oxygen species, activating the SOS response, increasing membrane permeability, and promoting RP4 plasmid conjugative transfer. These processes facilitated the acquisition of multidrug resistance and the colonization of plant tissues by human pathogens, including Stenotrophomonas maltophilia and Pseudomonas aeruginosa, thereby increasing ARG burdens in both rhizosphere and phyllosphere compartments. Metagenomic analysis further confirmed the coselection of nontetracycline ARGs, such as aph3'-I and catB, and the enrichment of efflux systems (acr/emr) in pathogenic bacteria. Our findings challenge the parent-compound-centered paradigm of antibiotic risk assessment by identifying ATC as a key high-risk driver of ARG dissemination in food plants and highlighting the need to incorporate transformation products into future management strategies.},
}

@article {pmid42141788,
year = {2026},
author = {Garcia-Godos, C and Jauhal, MK and Khan, MA and Mendoza-Cozatl, DG},
title = {Plant-microbiome interactions provide novel insights into the regulation of iron-sulfur metabolism in plants.},
journal = {Journal of experimental botany},
volume = {},
number = {},
pages = {},
doi = {10.1093/jxb/erag224},
pmid = {42141788},
issn = {1460-2431},
abstract = {Iron-sulfur (Fe-S) clusters are at the core of photosynthesis, respiration, and redox homeostasis, yet their biogenesis and stability are highly sensitive to fluctuations in iron (Fe) and sulfur (S) availability. Although the molecular players of Fe and S assimilation pathways are well characterized, the mechanisms mediating the crosstalk between these nutrient networks remain largely unknown, particularly within the context of plant-microbiome interactions. Recent work has revealed that plant-associated microbial communities play active roles in shaping Fe-S metabolism through metabolite exchange, hormonal modulation, and redox signaling. Here we discuss recent research demonstrating how root-associated microbes and synthetic microbial communities (SynComs) can influence Fe and S homeostasis, including the reprograming of plant transcriptional and metabolic networks to preserve photosynthesis under nutrient limitation. We also highlight key microbial strategies, including siderophore-mediated Fe mobilization, S-containing metabolites release, and microbial modulation of hormonal pathways that collectively enhance Fe and S use efficiency. Finally, we discuss future directions for AI-driven trait-based design of SynComs, multi-omics integration, and field-level validation to translate these novel insights into agricultural solutions. Harnessing the power of plant-microbe interactions to improve Fe-S metabolism offers a promising path toward sustainable agriculture and crop productivity under stress and challenging environments.},
}

@article {pmid42141942,
year = {2026},
author = {Ebersole, JL and Gonzalez, OA},
title = {Characteristics of the Health-Associated Oral Microbiome in Young Nonhuman Primates.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.70033},
pmid = {42141942},
issn = {2041-1014},
support = {R56DE029954//The National Institutes of Health/ ; P40RR03640//Caribbean Primate Research Center/ ; //Microarray Core of the University of Kentucky/ ; },
abstract = {Nonhuman primates have been shown to develop periodontitis with clinical and demographic features similar to humans. This preclinical disease model is well-positioned to advance the elucidation of novel biologic-based preventive and therapeutic approaches to controlling periodontitis, a chronic infection and immunoinflammatory disease. In this analysis, the oral microbiomes of younger (10-19 human years; n = 30) nonhuman primates are compared for matriline (an indicator of heritability), sex, and age variations. A holistic assessment of the microbiome similarities/differences suggested two primary conclusions in this younger group of orally healthy nonhuman primates. First, at the microbiome level of phyla, orders, and families, the ecology was relatively similar across sexes, matrilines, and age groups. However, at the genus level, matriline, sex, or age differences were observed. Of interest was that the principal differential genus proportions with matriline and age were similar, but somewhat unique with the sex comparison. These genus differences encompassed microorganisms generally considered as human commensals, albeit Fusobacterium, Tannerella, and Treponema genera did show some variation. The second, broader observation was the rather extensive species variation across these nonhuman primates. Nevertheless, the data could define a "core microbial species" pattern that included species across the Actinobiota, Bacteroidota, Desulfobacterota, Firmicutes/Bacillota, Fusobacteriota, Proteobacteriota, and Spirochaetota phyla. The results provide seminal details of the oral microbiome in this disease model and underpin the ability to elucidate specific microbial changes that can occur related to early-life oral environmental stimuli that may presage a greater risk for periodontitis in adulthood.},
}

@article {pmid42142239,
year = {2026},
author = {Khattab, R},
title = {Artificial Sweeteners and Gut Microbiota: Mechanistic Insights and Implications for Metabolic Health.},
journal = {Current nutrition reports},
volume = {15},
number = {1},
pages = {},
pmid = {42142239},
issn = {2161-3311},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; *Sweetening Agents/pharmacology/adverse effects ; Energy Metabolism/drug effects ; Animals ; Insulin Resistance ; Fatty Acids, Volatile/metabolism ; Signal Transduction/drug effects ; Aspartame/pharmacology ; },
abstract = {PURPOSE OF REVIEW: Artificial sweeteners (ASs) are widely used as sugar substitutes to reduce caloric intake. Emerging evidence indicates that these compounds are not metabolically inert and can alter gut microbiota composition and downstream metabolic regulation. This review synthesizes recent mechanistic and clinical evidence on how commonly used ASs-particularly sucralose, saccharin, acesulfame-K, aspartame, and steviol glycosides-modulate intestinal microbiota.

RECENT FINDINGS: Experimental and human studies show that AS exposure is associated with alterations in microbial diversity, short-chain fatty acid (SCFA) production, and gut barrier integrity. These alterations are linked to changes in glucose homeostasis, insulin sensitivity, and energy metabolism. Proposed mechanisms include modulation of nutrient-sensing G-protein-coupled receptors, interference with bile acid metabolism, and receptor-independent activation of intracellular signaling pathways such as PI3K/Akt and mTORC1. Notably, responses in human studies appear highly individualized and dose-dependent, highlighting substantial interindividual variability. This review integrates microbiome, metabolic, and mechanistic perspectives to identify areas of emerging consensus, conflicting results, and critical research gaps in AS-microbiota-metabolism interactions. Current evidence suggests that ASs can modulate host metabolism through both microbiota-dependent and independent mechanisms. These findings have direct implications for clinical dietary guidance and risk stratification, particularly among individuals with obesity, insulin resistance, or other metabolic disorders.},
}

Humans
*Gastrointestinal Microbiome/drug effects
*Sweetening Agents/pharmacology/adverse effects
Energy Metabolism/drug effects
Animals
Insulin Resistance
Fatty Acids, Volatile/metabolism
Signal Transduction/drug effects
Aspartame/pharmacology

@article {pmid42142240,
year = {2026},
author = {Xiang, W and Yang, Q and Ji, J and Qiao, H and Khan, A and Salama, ES and Mao, C and Wu, Y and Li, X},
title = {Food-Derived Limosilactobacillus fermentum GR-3 Enhances Anti-PD-1 Immunotherapy Efficacy.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42142240},
issn = {1867-1314},
support = {GZC20251840//The Postdoctoral Fellowship Program of CPSF/ ; 32370110//National Natural Science Foundation of China/ ; 24ZDWA005//Gansu Province Science and Technology Major Project/ ; },
abstract = {Immune checkpoint blockade (ICB) has improved the cancer treatment, its application remains constrained by heterogeneous response rates and immune-related adverse events. While gut microbiome modulation represents a promising avenue to optimize ICB, rationally selected probiotics with defined mechanistic actions are critically lacking. Here, we selected Lactobacillus fermentum GR-3 (L. fermentum GR-3), a food-derived strain pre-screened for exceptional gastrointestinal resilience (maintaining > 10[7] CFU/mL), antioxidant activity (87.4% DPPH-Scavenging efficiency), and immunomodulatory potential, as an oral combination strategy to enhance anti-PD-1 therapy. In the MC38 murine colorectal cancer model, oral L. fermentum GR-3 synergistically enhanced ICB efficacy, yielding significantly greater tumor suppression than anti-PD-1 monotherapy (51.7% volume reduction vs. untreated controls), while attenuating therapy-associated weight loss. Locally within the tumor microenvironment (TME), the combination therapy promoted dendritic cell maturation (MHC-II[+] DCs reaching 56.0%), favored pro-inflammatory macrophage polarization (M1 increased to 20.8%, while M2 reduced to 2.57%), and suppressed regulatory T cell infiltration (Tregs decreased to 2.32%). These shifts strongly correlated with enhanced cytotoxic responses, with Granzyme B[+] CD8[+] T cells reaching 40.4% (doubling the effect of PD-1 monotherapy). Mechanistically, L. fermentum GR-3 colonization partially reversed tumor-associated gut dysbiosis, enriching short-chain fatty acid (SCFA)-producing consortia (e.g., Lachnospiraceae and Bacteroides) and increasing intestinal SCFA concentrations (e.g., propionic and butyric acids recovering to 70.13 and 26.07 μM/g, respectively)). This microbial-metabolic shift was accompanied by upregulated expression of mucosal tight junction genes (ZO-1, Occludin). Furthermore, L. fermentum GR-3 facilitated a balanced immune response. Systemically, it alleviated oxidative stress and buffered peripheral inflammatory signals, contributing to immune homeostasis in non-tumor tissues (spleen and colon). Collectively, these findings position L. fermentum GR-3 as a grounded, translatable strategy to simultaneously enhance ICB efficacy and improve therapeutic tolerability.},
}

@article {pmid42142274,
year = {2026},
author = {Mari, PV and Carriera, L and Saviano, A and Ricci, A and Coppola, A and Ielo, S and Lipsi, R and Dodaj, M and Gennari, F and Gullà, M and Stivalini, D and Pellegrino, MG and Migneco, A and De Corso, E and Ojetti, V},
title = {Impact of IL-4/IL-13 Blockade with Dupilumab on the Microbiome in Type 2 Inflammatory Diseases: A Systematic Review.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42142274},
issn = {1534-6315},
mesh = {Humans ; *Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology ; *Microbiota/drug effects ; *Interleukin-13/antagonists & inhibitors ; *Interleukin-4/antagonists & inhibitors ; Skin/microbiology ; *Inflammation/drug therapy ; *Dermatitis, Atopic/drug therapy/microbiology ; Gastrointestinal Microbiome/drug effects ; Sinusitis/drug therapy/microbiology ; },
abstract = {PURPOSE OF REVIEW: To systematically review current evidence on microbiota changes associated with dupilumab treatment across different anatomical sites in type 2 inflammatory diseases.

RECENT FINDINGS: Fifteen studies were included, comprising two randomized trials and thirteen observational studies, mostly in atopic dermatitis, with fewer data in chronic rhinosinusitis with nasal polyps and NSAID-exacerbated respiratory disease. The skin was the most frequently investigated site, followed by the sinonasal tract and gut. Across skin studies, dupilumab was consistently associated with reduced Staphylococcus aureus, increased microbial diversity, and enrichment of commensal taxa. Sinonasal studies suggested shifts toward more eubiotic microbial communities. Gut evidence was limited, although one study suggested modulation of tryptophan metabolism-related pathways.  Dupilumab appears to exert compartment-specific and disease-dependent effects on the microbiome. The strongest evidence concerns the skin and sinonasal compartments, whereas gut microbiota changes remain poorly defined. Further prospective studies are needed to assess microbiota signatures as potential biomarkers of response.},
}

Humans
*Antibodies, Monoclonal, Humanized/therapeutic use/pharmacology
*Microbiota/drug effects
*Interleukin-13/antagonists & inhibitors
*Interleukin-4/antagonists & inhibitors
Skin/microbiology
*Inflammation/drug therapy
*Dermatitis, Atopic/drug therapy/microbiology
Gastrointestinal Microbiome/drug effects
Sinusitis/drug therapy/microbiology

@article {pmid42142639,
year = {2026},
author = {Afresham, S and Khan, MK and Mughal, MAS and Bashir, M and Mehmood, MS and Ali, S and Abbas, Z and Azeem, A and Latif, M},
title = {Ecological and Biomedical Functions of Parasitofauna: Mechanistic and Evolutionary Perspectives.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108561},
doi = {10.1016/j.micpath.2026.108561},
pmid = {42142639},
issn = {1096-1208},
abstract = {Parasites have traditionally been viewed primarily as pathogenic organisms associated with disease and economic burden. However, growing evidence indicates that parasitofauna-the diverse assemblage of parasitic organisms across ecosystems-plays fundamental roles in ecological regulation, host evolution, and biomedical innovation. Despite increasing recognition of these functions, existing literature largely treats ecological, immunological, and translational aspects of parasitism in isolation, lacking an integrated mechanistic framework that links these domains across biological scales. This review synthesizes current knowledge to provide a cross-disciplinary perspective on the ecological and biomedical functions of parasitofauna. Ecologically, parasites act as regulators of host population dynamics, modulators of biodiversity, and contributors to nutrient cycling and ecosystem stability. Evolutionarily, they impose strong selective pressures that shape host genetic diversity, immune system architecture, and behavioral adaptations through mechanisms such as allele frequency shifts and fitness trade-offs. From a biomedical standpoint, parasite-derived molecules demonstrate promising immunomodulatory, anti-inflammatory, and anticancer properties, with evidence derived primarily from in vitro studies and preclinical animal models, and limited support from early-phase clinical trials. In addition, interactions between parasites and the gut microbiome highlight their role in immune regulation and potential implications for inflammatory and metabolic disorders. By integrating ecological theory, evolutionary biology, and translational research, this review proposes a unified conceptual model of parasitofauna as multi-level regulators rather than solely pathogenic agents. This perspective supports a shift toward evidence-based parasite management strategies that balance disease control with ecological and therapeutic considerations. The synthesis also identifies key knowledge gaps and emphasizes the need for mechanistic, multi-system studies to better understand context-dependent outcomes of host-parasite interactions.},
}

@article {pmid42142662,
year = {2026},
author = {Montenegro, J and Oliveira, CLP and Nguyen, NK and Armet, AM and Berg, A and Sharma, AM and Mereu, L and Cominetti, C and Ghosh, S and Cani, PD and Richard, C and Walter, J and Prado, CM},
title = {The effects of a powdered meal replacement intake on inflammation, gut microbiota, and metabolism compared to habitual diet in people with excess body weight - results from a randomized controlled trial.},
journal = {The Journal of nutrition},
volume = {},
number = {},
pages = {101595},
doi = {10.1016/j.tjnut.2026.101595},
pmid = {42142662},
issn = {1541-6100},
abstract = {BACKGROUND: Excess body weight is associated with chronic low-grade inflammation and metabolic abnormalities, such as insulin resistance, and dyslipidemia.

OBJECTIVE: This study aimed to assess the impact of a soy protein-yogurt-honey powdered meal replacement (PMR) on inflammation, gut microbiota, and metabolism in individuals with excess body weight and in weight-stable conditions.

METHODS: The Premium Study was a 12-week, parallel-arm, randomized controlled trial. Participants (body mass index 25-37 kg/m[2]) were randomized into either control (CON; usual diet, n=34) or PMR (two daily doses added to usual diet, n=29) groups, maintaining a stable body weight. Assessments occurred at baseline, week 6, and week 12, and included inflammation markers (primary outcome: interleukin-6 [IL-6]), gut microbiota diversity and composition (secondary outcome), metabolic blood markers (glucose and lipid profile), body composition (via dual-energy X-ray absorptiometry), and dietary intake. Data of completers was analyzed by two-way repeated measures analysis of variance or generalized estimating equations with Bonferroni-corrected post-hoc tests. Between-group differences in changes over time are expressed as mean and 95% confidence intervals.

RESULTS: Adherence to PMR was 98% of total doses, which increased protein intake (6.53 [5.04, 8.02]%, p<0.001) and decreased fat intake (-5.23 [-7.10, -3.35]%, p<0.001) compared to CON. By design, body weight remained stable. There were no changes in IL-6 (0.01 [-0.47, 0.45] pg/mL, p=0.412, with a low statistical power of 13.7%). Minor changes in gut microbiota composition included an increase in relative abundance of Subdoligranulum (0.72 Log2 fold-change, q=0.002). In exploratory outcomes, PMR increased lean soft tissue (LST; 0.57 [0.12, 1.02] kg, p=0.014) and reduced total cholesterol (-0.33 [-0.58, -0.08] mmol/L, p=0.01) and low-density lipoprotein cholesterol (-0.28 [-0.46, -0.10] mmol/L, p=0.003).

CONCLUSIONS: In this population, PMR intake did not improve chronic low-grade inflammation and had limited effects on gut microbiota. Improvements in LST and lipid profile warrant further exploration.

CLINICAL TRIAL REGISTRY: Number NCT03235804 registered on August 1[st], 2017: https://clinicaltrials.gov/study/NCT03235804.},
}

@article {pmid42142668,
year = {2026},
author = {Keber, C and Schmitt, M and Visekruna, A and Brichkina, A and von Strandmann, EP and Bartsch, JW and Huber, M and Bauer, UM and Gress, TM and Lauth, M},
title = {Emerging concepts, hot topics, and open questions in today's pancreatic cancer research.},
journal = {Biochimica et biophysica acta. Reviews on cancer},
volume = {},
number = {},
pages = {189614},
doi = {10.1016/j.bbcan.2026.189614},
pmid = {42142668},
issn = {1879-2561},
abstract = {Despite intense research, pancreatic ductal adenocarcinoma (PDAC) remains one of the most lethal malignancies to date. The low 5-year survival rate of currently 8-10% has only marginally improved over the last years, necessitating novel approaches and a thinking "outside the box". We as translational basic and medical scientists working in a clinical research unit on tumor-stroma interactions in PDAC (the DFG-funded CRU325) have sought to identify emerging concepts in current pancreatic cancer research. We have addressed recent developments and open questions, covering a wide spectrum of topics, including clinical treatment, lifestyle, the tumor microenvironment, drug targeting, vaccination, and the microbiome. This selection of topics is highly personal and does not claim to be complete, yet it represents those areas that we believe may contribute to relevant developments in the near future. In our review, we not only briefly describe the state of the art but also pinpoint the potential of recent advances, while not ignoring current contradictions or uncertainties. Taken together, we provide our subjective view on upcoming topics in today's PDAC research landscape.},
}

@article {pmid42142727,
year = {2026},
author = {Li, M and Liu, T and Yue, Y and Bae, S},
title = {Gut Microbiome and Metabolic Responses of Adult Zebrafish (Danio rerio) to the Co-exposure of Polyethylene Microplastics and Levofloxacin.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {128358},
doi = {10.1016/j.envpol.2026.128358},
pmid = {42142727},
issn = {1873-6424},
abstract = {The co-occurrence of microplastics (MPs) and antibiotics in aquatic environments poses complex ecological risks. This study investigated the combined toxicity of polyethylene microplastics (PE MPs) and levofloxacin (LEV) in zebrafish using integrated untargeted metabolomics and gut microbiome profiling. Zebrafish were exposed to environmentally relevant concentrations of LEV (0.1 μg/L, 1 μg/L, 100 μg/L), PE (1 mg/L), and their combinations for 96 hours. LEV exposure produced concentration-dependent metabolic toxicity, progressing from energy conservation at 0.1 μg/L to inflammatory activation at 1 μg/L, and ultimately to system-wide metabolic perturbation at 100 μg/L. PE independently disrupted oxidative stress and membrane integrity pathways. Co-exposure generated emergent interactive effects exceeding additive predictions, with PE+LEV 0.1 μg/L affecting 387 metabolites versus 245 for LEV alone. Crucially, co-exposure elicited synergistic toxicity with unique metabolic fingerprints-including neuroendocrine activation (dynorphin B) and mTOR signaling modulation-that were absent in individual treatments. Conversely, microbiome analysis revealed an antagonistic interaction; while LEV alone caused significant dysbiosis and enrichment of resistant taxa, co-exposure stabilized microbial diversity and composition, likely due to LEV adsorption onto PE particles reducing luminal bioavailability. These findings highlight a "microbiome-host interaction paradox": PE mitigates antibiotic-induced gut dysbiosis yet exacerbates host systemic toxicity through mechanisms of epithelial barrier disruption and pharmacokinetic modulation. This study demonstrates that microbiome stability does not reliably predict host physiological health under multi-stressor conditions, underscores the importance of integrative, multi-omics approaches to assess the emergent risks of complex environmental mixtures.},
}

@article {pmid42142802,
year = {2026},
author = {Stalder, M and Raurich, S and Finzel, A and Schlifke, A and Ghanbari, M and Campiche, R and Pagac, MP},
title = {3-Dimensional Facial Skin Microbiome Mapping: An Integrated Technology for Continuous Visualization of Absolute Microbial Densities.},
journal = {The Journal of investigative dermatology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jid.2026.04.037},
pmid = {42142802},
issn = {1523-1747},
}

@article {pmid42142804,
year = {2026},
author = {Zheng, F and Gao, J and Han, X and Kang, S and Zhou, T and Zhu, D and Neilson, R and Zhang, Z and Chen, B},
title = {Nematode gut microbiota confers cadmium tolerance through microbial-dependent activation of detoxification and innate immune pathways.},
journal = {Journal of advanced research},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jare.2026.05.035},
pmid = {42142804},
issn = {2090-1224},
abstract = {INTRODUCTION: Soil heavy metal pollution, especially cadmium (Cd) contamination, represents a serious threat to ecosystem health and agricultural sustainability. Understanding how soil organisms and their associated microbiota respond to such stress is crucial for developing bioremediation strategies.

OBJECTIVES: This study aimed to investigate the response of the gut microbiota in the model soil nematodeCaenorhabditis elegansunder Cd(II) stress, identify key bacterial taxa involved in metal detoxification, and elucidate the underlying mechanisms of microbe-mediated host resistance.

METHODS: We employed an integrated multi-omics approach, combining 16S rRNA gene sequencing, metatranscriptomics, and culturomics. The structural and functional differences between the nematode gut microbiome and the soil microbial community were compared. A core Cd(II)-tolerant gut bacterium was isolated and used for colonization experiments inC. elegansunder Cd(II) exposure. Host responses were assessed via transcriptomic analysis, antioxidant enzyme activity assays, and physiological fitness measurements.

RESULTS: Nematode gut microbiota exhibited lower diversity but higher compositional stability compared to soil communities, with deterministic host selection (R[2] = 0.480) overriding stochastic assembly. The gut community was dominated by Proteobacteria, particularly Pseudomonadaceae and Sphingomonadaceae, which maintained conserved abundances across cadmium gradients. Phenotype prediction and functional analysis revealed enhanced stress tolerance and enrichment of glutathione S-transferase (GST) in the gut microbiota. From 100 isolated colonies, we identified Brucella pseudogrignonensis (formerly Ochrobactrum) as a core gut symbiont with high Cd(II) tolerance. B. pseudogrignonensis successfully colonized the C. elegans gut, significantly improving host survival, reproduction, and growth under Cd(II) exposure. Transcriptomic analysis identified 1929 bacteria-Cd(II) interaction genes, with significant enrichment in glutathione metabolism, cytochrome P450 pathways, and lysosome function. Mechanistically, live bacteria primed host immunity (e.g., clec-67, lys-2) and activated a two-phase defense program: Phase I involved lysosome pathway activation and basal immune priming; Phase II featured GST-mediated detoxification (gst-4, gst-5, and gst-6) coordinated by transcription factors DAF-16 and SKN-1, with GSH-Px activity increasing 213% under Cd(II) stress while maintaining stable ROS levels.

CONCLUSION: Using C. elegans as a model system, we demonstrate that the gut bacterium B. pseudogrignonensis enhances host Cd(II) resistance through synergistic activation of detoxification and immune pathways. These findings provide mechanistic insights into microbe-mediated heavy metal tolerance in soil fauna and identify B. pseudogrignonensis as a promising microbial candidate for developing bioremediation strategies for cadmium contaminated soils.},
}

@article {pmid42143007,
year = {2026},
author = {Zhang, XD and Shen, XN and Liu, CX and Liu, ZH and Ao, X and Che, TY and Ran, TJ and Li, HL and Zhang, Y and Zhou, CH and Zou, DW},
title = {Analysis of gut microbiome dynamics in patients with type 1 autoimmune pancreatitis before and after glucocorticoid treatment.},
journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.pan.2026.05.002},
pmid = {42143007},
issn = {1424-3911},
abstract = {BACKGROUND: Type 1 autoimmune pancreatitis (AIP) is a rare inflammatory pancreatic disease. Emerging evidence suggests that gut microbiota dysbiosis may contribute to the pathogenesis of type 1 AIP. However, no study has systematically characterized gut microbiota alterations before and after glucocorticoid treatment in patients with type 1 AIP.

METHODS: Fecal samples were collected from 45 healthy controls (HC), 61 patients with type 1 AIP before glucocorticoid treatment, and 27 patients after glucocorticoid treatment for metagenomic sequencing. To investigate the potential role of Streptococcus anginosus in the development of type 1 AIP, heat-killed Streptococcus anginosus was administered by oral gavage in an AIP mouse model.

RESULTS: Significant differences in both α-diversity and β-diversity were observed among HC and the pre- and post-treatment groups. Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus, Streptococcus anginosus, and Streptococcus salivarius, along with decreased abundances of Blautia and Dorea formicigenerans. Moreover, the abundances of Streptococcus and Streptococcus anginosus were reduced in the post-treatment group. In the AIP mouse model, oral gavage with heat-killed Streptococcus anginosus significantly increased the pancreatic pathological injury score.

CONCLUSIONS: Compared with the HC group, the pre-treatment group showed increased abundances of Streptococcus and Streptococcus anginosus, which were reduced in the post-treatment group. In addition, heat-killed Streptococcus anginosus exacerbated pancreatic injury in the AIP mouse model.},
}

@article {pmid42143054,
year = {2026},
author = {Eom, JA and Park, IG and Hyun, JY and Lee, NY and Kwon, GH and Yoon, SJ and Won, SM and Ham, YL and Lee, KJ and Han, SH and Yang, DH and Kim, DJ and Suk, KT},
title = {Pharmabiotics, Phocaeicola dorei, ameliorates cholestatic liver fibrosis by alleviating macrophage efferocytosis of neutrophils.},
journal = {Nature communications},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41467-026-73166-1},
pmid = {42143054},
issn = {2041-1723},
support = {NRF-2020R1I1A3073530 and NRF-2020R1A6A1A03043026//National Research Foundation of Korea (NRF)/ ; },
abstract = {Phocaeicola dorei has been reported to ameliorate metabolic diseases. Its role in liver fibrosis remains unclear. We evaluated the hepatoprotective effect of P. dorei in liver fibrosis. Fecal samples were collected from healthy controls and patients (n = 285) to assess the clinical relevance of P. dorei. In male mice models (3,5-diethoxycarbonyl-1.4-dihydrocollidine [DDC] diet), P. dorei (10[9] CFU/g twice/week) was orally administered. Primary HSCs, LX-2, THP-1, and HL-60 cell lines were used for mechanical validation. The relative abundance of P. dorei increased with worsing liver disease in human. P. dorei administration significantly reduced neutrophil degranulation and efferocytosis pathways (Ly6g and F4/80). The dysregulated expression of neutrophil-associated chemokines (Cx3cl1 and Cx3cr1) was restored by P. dorei. P. dorei culture supernatant inhibited macrophage-mediated efferocytosis. P. dorei attenuates liver fibrosis by suppressing neutrophil and macrophage infiltration and disrupting efferocytosis. Our results identify P. dorei as a potential microbiome-based therapeutic candidate for cholestatic liver fibrosis.},
}

@article {pmid42143215,
year = {2026},
author = {Martínez, S and Cerdeiras, MP and Douterelo, I and Ijaz, UZ},
title = {Biofilm and sediment phases as key components of microbial community dynamics within secondary drinking water distribution systems.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05149-7},
pmid = {42143215},
issn = {1471-2180},
support = {EP/V030515/1//Engineering and Physical Sciences Research Council/ ; },
abstract = {BACKGROUND: Secondary drinking water distribution systems (SDWDS), particularly rooftop storage tanks, are critical components of water supply infrastructure in many regions, yet the ecological processes governing microbial community development within these systems remain poorly characterized. Here we present a year-long, phase-resolved metagenomic study of an operational full-scale SDWDS in Uruguay to assess how environmental conditions and surface materials are associated with microbiome dynamics across bulk water, biofilm and sediment phases. We integrated amplicon sequencing, whole-genome sequencing (WGS) metagenomics, culture-based microbiology and physicochemical analyses over a one-year period.

RESULTS: Microbial communities associated with biofilm and sediment phases consistently exhibited higher richness and diversity than bulk water, with marked seasonal variation. Biofilms formed on concrete and polyethylene surfaces followed distinct successional trajectories, indicating material-associated patterns in community development. Seasonal increases in temperature were associated with greater similarity in community composition across phases, while functional richness remained comparatively stable over time. Functional pathways related to energy production, stress response, and antibiotic resistance showed phase- and time-dependent enrichment, particularly in mature biofilms. Across the system, Proteobacteria, Actinobacteriota, and Bacteroidota were persistent taxa. Temperature and pH were the primary variables associated with temporal shifts in water-phase microbial communities, with chlorine residuals contributing to additional variation.

CONCLUSIONS: Together, these findings provide in situ ecological insight into microbial succession and phase-specific community dynamics in drinking water storage systems, highlighting the importance of long-term observations in real-world engineered environments.},
}

@article {pmid42143340,
year = {2026},
author = {Yu, C and Lin, Y and Cui, X and Huang, X and Zhang, Y and Kang, M and Lu, J},
title = {Characteristics of gut microbiota changes in patients with nasopharyngeal carcinoma during radiotherapy.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08265-0},
pmid = {42143340},
issn = {1479-5876},
support = {GXHL202305//the Scientifc research project of Guangxi Nursing Society/ ; Excellent nursing talent 202202//"Nursing Talents" Research and Innovation Ability Training Program of the First Affiliated Hospital of Guangxi Medical University/ ; No. 2021KY0126//Adolph C. and Mary Sprague Miller Institute for Basic Research in Science, University of California Berkeley/ ; Key No: S2023075//Health Promotion Administration, Ministry of Health and Welfare/ ; },
abstract = {BACKGROUND: This study aimed to characterize the longitudinal and dynamic changes of gut microbiota in patients with nasopharyngeal carcinoma (NPC) during radiotherapy, to inform the development of strategies for maintaining gut microbiota homeostasis.

METHODS: Thirty-one newly diagnosed NPC patients were recruited from the Department of Radiotherapy, First Affiliated Hospital of Guangxi Medical University, and 31 age-matched healthy controls from the same Hospital Physical Examination Center between August and December 2023. Fecal samples were collected from NPC patients at three key time points, including days 1-3 pre-radiotherapy (T0), days 14-18 of mid-radiotherapy (T1), and days 28-32 at end of radiotherapy (T2). Meanwhile, fecal samples from healthy controls were collected on the morning of their physical examination. 16S rDNA sequencing, combined with bioinformatics and statistical analyses, was used to compare the structural characteristics and dynamic changes of gut microbiota in NPC patients during radiotherapy.

RESULTS: Alpha diversity analysis showed significantly lower Shannon and Chao1 indices in NPC patients compared with healthy controls. Beta diversity analysis based on the Bray-Curtis distance revealed distinct gut microbial community structures between NPC patients and healthy controls. In this intergroup comparison, a total of 16 core differentially abundant taxa were consistently identified by two complementary analytical methods (LEfSe and ALDEx2). Linear mixed-effects models demonstrated that the Chao1 index at T0 was significantly lower than at T1 and T2 in NPC patients. Following adjustment for multiple confounding variables, mucositis grade was the only factor significantly associated with gut microbiota alpha diversity during radiotherapy. Radiotherapy time points, treatment regimen, and most clinical and demographic variables showed no such association. Beta diversity analyses based on the Bray-Curtis and unweighted Unifrac distances revealed significant compositional and structural differences linked to radiotherapy time points (T0/T1/T2) in the gut microbiota of NPC patients. This temporal variation was abrogated by stratification according to chemotherapy regimen. Beta diversity based on Bray-Curtis distance showed no significant differentiation across time points in either the concurrent chemotherapy (CCRT) alone cohort or the induction chemotherapy plus CCRT cohort. LEfSe and ALDEx2 concordantly identified seven core differentially abundant taxa across all NPC patients in the longitudinal T0 vs. T1 vs. T2 analysis. Stratification by chemotherapy regimen revealed such core taxa in the CCRT alone cohort, whereas no core differentially abundant taxa were detected by either method in the induction chemotherapy plus CCRT cohort.

CONCLUSION: Our findings demonstrate that NPC patients exhibit significant gut microbial dysbiosis compared with healthy controls, characterized by reduced alpha diversity and altered genus-level composition. Longitudinal analyses further revealed that radiotherapy is associated with dynamic alterations in gut microbial diversity, composition, and structure in NPC patients. Notably, these temporal shifts in the gut microbiota are strongly stratified by chemotherapy regimen, with pronounced changes observed in patients receiving CCRT alone but a stable microbial profile in those receiving induction chemotherapy followed by CCRT. Collectively, these results highlight the profound impact of oncological treatment on the gut microbiome in NPC patients and identify treatment regimen as a critical modifier of microbial dynamics during radiotherapy.},
}

@article {pmid42143365,
year = {2026},
author = {ChenLiu, Z and Tang, D},
title = {Neuron-tumor interplay in colorectal cancer: from mechanisms of onset and progression to targeted therapies.},
journal = {Cell communication and signaling : CCS},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12964-026-02938-5},
pmid = {42143365},
issn = {1478-811X},
support = {SJCX22_1816//the Graduate Research- Innovation Project in Jiangsu province/ ; },
abstract = {Colorectal cancer (CRC) is a major cause of cancer-related mortality worldwide, traditionally attributed to genetic mutations and epigenetic alterations. However, with the emergence of cancer neuroscience, a paradigm shift has occurred, revealing the central role of the nervous system in the initiation, progression, and metastasis of CRC. The gastrointestinal tract, being the only organ in the body with an independent peripheral nervous system - the enteric nervous system (ENS) - provides a unique anatomical and functional basis for neuro-tumor interactions. This review systematically explores the mechanisms by which the nervous system regulates CRC cell proliferation, invasion, and immune microenvironment remodeling through neurotransmitters (such as norepinephrine and acetylcholine) and neurotrophic factors (including NGF and BDNF). We also delve into the role of the brain-gut-microbiome axis, particularly its influence on tumor progression through metabolic reprogramming and neuroimmune crosstalk. Finally, we discuss novel therapeutic strategies based on the bidirectional communication between the nervous system and CRC, offering new perspectives for precise interventions in CRC.},
}

@article {pmid42143575,
year = {2026},
author = {Zhang, P and Zhao, M and Cheng, Z and Ding, Y and Xia, S and Guo, J},
title = {Bile acid metabolism dysregulation following Helicobacter pylori eradication promotes plasmid-mediated antimicrobial resistance in the gut microbiome.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag126},
pmid = {42143575},
issn = {1751-7370},
abstract = {Antimicrobial resistance (AMR) transmission within the gut microbiome poses a major health risk during antibiotic exposure, primarily via horizontal gene transfer (HGT). However, how antibiotic-induced metabolic remodeling of the intestinal environment modulates plasmid-mediated AMR dissemination remains unclear. Herein, integrating metagenomics, metabolomics, in vitro conjugation assays, and in vivo mouse models, we show that Helicobacter pylori eradication therapy reshapes gut metabolism in ways that enhance transfer of antibiotic resistance genes (ARGs). Metagenomic analysis revealed the expansion of Escherichia populations and the enrichment of plasmid-borne ARGs after H. pylori eradication. Fecal filtrates from treated individuals significantly increased conjugation frequencies of the broad-host-range plasmid RP4 in E. coli. Metabolomic profiling identified a pronounced accumulation of primary bile acids, including glycocholic acid, taurocholic acid, glycochenodeoxycholic acid, and taurochenodeoxycholic acids, which could increase bacterial membrane permeability, induce the SOS response, and upregulate conjugation and pilus assembly genes, thereby accelerating ARG transfer. Molecular docking further suggested these bile acids may likely participates in interacting with global plasmid repressors KorA/KorB, derepressing conjugation operons. In mice, H. pylori eradication therapy elevated fecal primary bile acid levels and significantly promoted in vivo plasmid transfer, with the critical role of bile acids further confirmed through interventions using the bile acid sequestrant cholestyramine or glycocholic acid. Together, these findings demonstrate that dysregulation of bile acid metabolism due to H. pylori eradication creates a permissive gut niche for plasmid-mediated ARG dissemination, providing mechanistic insight into how clinical antibiotic regimens can unintentionally promote microbiome-associated AMR risk.},
}

@article {pmid42143576,
year = {2026},
author = {Xu, X and Tan, Y and Xiecun, S and Wang, J and Zhao, W and Wang, L and Dai, R and Tang, L and Li, X and Jin, D and Fan, Y},
title = {Galactosaminogalactan orchestrates Verticillium dahliae virulence and rhizosphere microbial ecology through multi-partite interactions.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag123},
pmid = {42143576},
issn = {1751-7370},
abstract = {The infection of plants by soil-borne fungal pathogens is a complex process and depends on their adhere ability to host surfaces and interactions with the rhizosphere bacteria. In this study, we identify galactosaminogalactan (GAG) as a pivotal virulence determinant in the pathogenesis of Verticillium dahliae. By characterizing the VdGAG biosynthetic gene cluster, we show that the glycosyltransferase VdGtb is essential for GAG synthesis. The knockout of GAG increased fungal sensitivity to the cell wall-perturbing agent calcofluor white (CFW) and reduced mycelial ball formation in liquid culture. The absence of GAG polysaccharides reduced root-binding capacity by 50% and increased cotton immune responses 1 day post fungal infection. The ΔVdGtb mutant exhibited a significant 30.5% decrease in the pathogenicity toward cotton seedlings compared with the wild type V991. Microbiome and bacterial enrichment analysis indicate that the GAG polysaccharides promote the enrichment of soil bacteria and alter the bacterial community structure in the plant rhizosphere. Several bacteria enriched by GAG-contained fungal cells, including Achromobacter animicus, Pseudomonas aeruginosa, and Acinetobacter pittii exhibited strong growth-inhibitory effects against V. dahliae and showed distinct effects on fungal virulence in a GAG-dependent manner. Together, these results reveal that GAG is not merely a cell wall component but a multi-functional molecule that orchestrates fungal protection, host infection, and inter-kingdom microbial communication.},
}

@article {pmid42143583,
year = {2026},
author = {Kim, J and Kim, WI and Lee, K and Kim, N and Hwang, AY and Suh, DH and Cho, D and Ji, Y and Kang, H and Jung, ES},
title = {Systems-level restoration of vaginal and gut microbiota by lactobacillus helveticus 20 838 alleviates Gardnerella vaginalis-induced dysbiosis.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag118},
pmid = {42143583},
issn = {1751-7370},
abstract = {Bacterial vaginosis (BV), often driven by Gardnerella vaginalis overgrowth, is characterized by epithelial disruption, inflammation, and microbiome dysbiosis across the vaginal and gut ecosystems. Affecting a majority of women during their reproductive years, BV increases the risk of infection and reproductive complications. Here, we identify a novel probiotic strain, Lactobacillus helveticus 20 838, exhibiting potent antagonistic activity against G. vaginalis and evaluate its ecological and immunological effects in a murine model of vaginitis. Comparative genomics revealed distinct adaptive and antimicrobial traits of L. helveticus 20 838 relatives to the reference strain DPC4571. Both oral and intravaginal administration reduced G. vaginalis colonization, suppressed Tnf-α and Il-1β expression in vaginal tissue, and prevented pathological epithelial thickening. Multi-omics profiling of fecal and vaginal samples demonstrated restoration of microbial alpha and beta diversity disrupted by infection. The L. helveticus 20 838 reduced dysbiosis-associated taxa such as Staphylococcaceae whereas enriching protective Lactobacillus species, with intravaginal delivery achieving superior local recolonization of Lactobacillaceae. Collectively, these findings identify L. helveticus 20 838 as a next-generation probiotic that alleviates G. vaginalis-induced dysbiosis by restoring microbial and immune homeostasis across interconnected mucosal niches, providing a systems-level framework for microbiota-targeted therapy in women's health.},
}

@article {pmid42143599,
year = {2026},
author = {Dong, A and Paju, S and Leskelä, J and Manzoor, M and Putaala, J and Ylikotila, P and Könönen, E and Pussinen, P and Zaric, S},
title = {Microbial burden of periodontal diseases and its clinical application: The stage, grade, and furcation matter.},
journal = {Journal of periodontology},
volume = {},
number = {},
pages = {},
doi = {10.1002/jper.70140},
pmid = {42143599},
issn = {1943-3670},
support = {SGL023/1035/AMS_/Academy of Medical Sciences/United Kingdom ; //Medical Research Council Impact Acceleration Account/ ; 202108410182//Engineering and Physical Sciences Research Council/ ; //Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences/ ; //Revealing the Etiology/ ; //Sigrid Jusélius Foundation/ ; TYH2014407//Helsinki and Uusimaa Hospital District/ ; TYH2018318//Helsinki and Uusimaa Hospital District/ ; //Finnish Medical Foundation/ ; //Finnish Dental Society Apollonia/ ; //King's-China Scholarship Council/ ; },
abstract = {BACKGROUND: Periodontal diseases are associated with dysbiotic oral microbial communities, but clinically applicable measures that reflect microbial burden across disease severity and progression remain limited. This study aimed to assess the oral microbial burden of periodontal diseases by evaluating salivary and subgingival lipopolysaccharide (LPS) activity and lipoteichoic acid (LTA) levels, to explore their relationships with microbial dysbiosis and clinical periodontal parameters in individuals with periodontal health (n = 52), gingivitis (n = 194), and periodontitis of varying stages, grades, and furcation involvement (n = 78), and to assess their diagnostic potential.

METHODS: Saliva and subgingival plaque samples from 324 SECRETO cohort participants were analyzed for microbial virulence factors using a recombinant Factor C assay for LPS and enzyme-linked immunosorbent assay (ELISA) for LTA. Microbial dysbiosis was assessed using a sequencing-derived, simplified dysbiosis index, calculated from subgingival 16S rRNA gene sequencing and salivary shotgun metagenomic profiles, based on the relative abundances of health-associated and periodontitis-associated taxa.

RESULTS: Subgingival LPS activity was significantly higher in periodontitis patients compared to healthy individuals and increased progressively across disease stages and grades. Salivary LPS activity differed only by periodontal diagnosis and correlated with full-mouth bleeding score (FMBS). LTA levels showed no statistical variations across periodontal conditions. Subgingival LPS activity and LPS/LTA ratio were strongly associated with simplified dysbiosis index. Salivary dysbiosis index was significantly higher in patients with furcation involvement. Receiver operating characteristic (ROC) analyses identified subgingival LPS, salivary LPS, and simplified dysbiosis index as diagnostic biomarkers with good clinical utility (area under the curve [AUC] 0.59-0.87).

CONCLUSIONS: This study highlights the importance of periodontitis diagnoses, stages and grades of periodontitis and furcation involvement as determining factors for increased salivary and subgingival bioburden. In addition, LPS activity could be used as a reliable periodontal biomarker, while the LPS/LTA ratio is an indirect indicator of microbial dysbiosis.

TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT01934725.

PLAIN LANGUAGE SUMMARY: Periodontitis is a common inflammatory disease that affects the tissues supporting the teeth and can lead to tooth loss and broader health consequences if not properly managed. This study explored whether measures of oral microbial burden, particularly bacterial components such as lipopolysaccharide (LPS) and lipoteichoic acid (LTA), could help explain differences in periodontal disease severity and progression. Saliva and subgingival plaque samples were analyzed from individuals with periodontal health, gingivitis, and different stages and grades of periodontitis. We found that microbial burden, especially subgingival LPS activity, increased consistently with more severe and rapidly progressing forms of periodontitis and was closely associated with clinical signs of inflammation. In contrast, LTA levels showed limited variation across disease categories. Importantly, LPS-related measures demonstrated good ability to distinguish periodontal health from disease. These findings suggest that assessing microbial burden, particularly LPS activity, may provide clinically useful information beyond traditional periodontal assessments and could support improved disease classification, risk assessment, and the development of more personalized periodontal care strategies.},
}

@article {pmid42143685,
year = {2026},
author = {T, K and T, B and M S, K and T, S},
title = {Simulating the impacts of ocean deoxygenation on coral reef resilience using adaptive ecosystem modeling.},
journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering},
volume = {},
number = {},
pages = {1-15},
doi = {10.1080/10934529.2026.2664333},
pmid = {42143685},
issn = {1532-4117},
abstract = {Adaptive ecosystem modeling provides a proactive approach to mitigating ocean deoxygenation and enhancing coral reef resilience. This study proposes an integrative framework that combines machine-learned dissolved oxygen (DO) reconstructions with a multispecies reef ecosystem model, augmented by Bayesian uncertainty quantification to identify intervention strategies that maximize ecological recovery. By explicitly linking oxygen dynamics with biological feedbacks and management actions, the framework addresses critical gaps in current hypoxia mitigation research. The approach is applied to the central Great Barrier Reef using long-term in situ measurements and satellite observations for model calibration. Simulation results indicate that targeted aeration, watershed nutrient reduction, and microbiome manipulation can reduce cumulative hypoxic stress by up to 43% over two decades, while increasing live coral cover by 28% relative to baseline projections. Sensitivity analyses reveal that model outcomes are particularly influenced by microbial acclimation rates and seasonal DO minima, highlighting the importance of fine-scale biogeochemical monitoring. Overall, the findings demonstrate the value of an adaptive, data-driven decision-support framework that integrates ecological processes, high-resolution environmental data, and management interventions, offering scalable guidance for hypoxia resilience planning in threatened coral reef systems.},
}

@article {pmid42143767,
year = {2026},
author = {Zhang, Y and Zhang, X and Wang, S and Xu, Z and Wei, Q and Hua, S},
title = {Intestinal Alkaline Phosphatase Alleviates Ruminal Acidosis in Dairy Cows Fed High-Concentrate Diets Improves Their Overall Health.},
journal = {Journal of animal physiology and animal nutrition},
volume = {},
number = {},
pages = {},
doi = {10.1111/jpn.70073},
pmid = {42143767},
issn = {1439-0396},
abstract = {The pursuit of high milk yields via high-concentrate diets risks ruminal acidosis and microbial dysbiosis, triggering lipopolysaccharide (LPS) release, subacute ruminal acidosis (SARA) incidence, and substantial economic losses. This study evaluated the efficacy of the dietary intestinal alkaline phosphatase (IAP) against high-concentrate feeding effects, hypothesizing it prevents SARA by degrading LPS, modulating microbiota, stabilizing ruminal pH, and improving gut health. Thirty-six lactating cows were stratified into three groups (n = 12): a high-concentrate diet group (HC, 5:5 concentrate:forage), an HC group supplemented with IAP (HC + IAP), and a low-concentrate control group (LC, 3:7). Key biomarkers such as ruminal pH, ruminal and fecal LPS, inflammatory cytokines (IL-6, IL-1β), and acute-phase proteins (SAA, LBP)--were monitored at 30-day intervals from calving through lactation. SARA status was defined by ruminal pH: < 5.6 (SARA), 5.6-5.8 (at-risk), and ≥ 5.8 (healthy). Fecal microbiome analysis was conducted on HC and HC + IAP cows at 90 days in milk (DIM). The HC group exhibited a high incidence of SARA, peaking between 90 and 120 DIM. In stark contrast, dietary supplementation with IAP (0.5 kg per 1000 kg of concentrate feed) effectively stabilized ruminal fluid pH, thereby completely preventing the incidence of SARA throughout the entire lactation period. This prophylactic effect was associated with significantly reduced systemic concentrations of SAA, LBP, IL-6, and IL-1β. Moreover, IAP treatment markedly enhanced gut microbial diversity and the relative abundance of beneficial bacteria. Therefore, IAP acted primarily in the rumen to detoxify LPS, thereby stabilizing pH and preventing the occurrence of SARA, while also entering the intestine to regulate the structure of gut microbiota, thereby maintaining the health of dairy cows under high-concentrate feeding conditions.},
}

@article {pmid42135082,
year = {2026},
author = {Saranya, RG and Ramesh Babu, K and Viswanathan, P},
title = {Corrigendum to "Investigating gut microbiome dysbiosis in adults with chronic kidney disease: Diabetes-induced alterations via metagenomics and qPCR" [Life Sci. 393 (2026) 124336].},
journal = {Life sciences},
volume = {},
number = {},
pages = {124457},
doi = {10.1016/j.lfs.2026.124457},
pmid = {42135082},
issn = {1879-0631},
}

@article {pmid42135208,
year = {2026},
author = {He, F and Lin, Q and Tan, Y and Yan, Z and He, H and Lin, L},
title = {Drug-Induced Alterations of Mouse Aorta Lipidome and Their Potential Correlations with the Gut Ecosystem.},
journal = {Journal of proteome research},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.jproteome.6c00103},
pmid = {42135208},
issn = {1535-3907},
abstract = {Drug-induced cardiovascular risk is one of the primary concerns in drug development and clinical practice. Meanwhile, drugs can also alter the gut microbiome, the disturbance of which is correlated with cardiovascular diseases. However, the detailed molecular information underlying these associations is still unclear. Here, we comprehensively investigated the impact of 33 commonly used drugs on the mouse aorta lipidome and gut metaproteome, revealing that 6 out of 8 (75.0%) anticancer drugs and 2 out of 16 (12.5%) cardiovascular drugs significantly altered the aorta lipids, with the majority being downregulated. Drugs triggered a greater increase in phosphatidylethanolamine (PE) with longer fatty acyl chains and higher degrees of unsaturation rather than hydrophobicity. Drugs also tend to suppress gut microbial producers of short-chain fatty acids. Antibiotic pretreatment and conventional mouse models revealed potential drug-host-microbe interactions on the gut-vascular axis. This study provides a deeper insight into the pharmacological actions of the studied drugs with a molecular basis for the management of cancer treatment-related cardiovascular diseases.},
}

@article {pmid42135319,
year = {2026},
author = {Chuanjian, L and Hao, Z and Xinyang, L and Wenjin, G and Yang, Z and Qianyu, W and Hongmingxiu, F and Zhihui, L},
title = {Naringin alleviates periodontitis via direct AMPK/Nrf2 activation and NLRP3 inhibition, amplified by gut microbiota/Arg-Gln modulation.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01007-6},
pmid = {42135319},
issn = {2055-5008},
support = {82370934//National Natural Science Foundation of China/ ; YDZJ202401160ZYTS//Jilin Provincial Natural Science Foundation/ ; },
abstract = {Periodontitis, driven by oral-gut microbiota dysbiosis and NLRP3 inflammasome activation, lacks effective natural therapeutic strategies. This study investigated naringin (Nar), a grapefruit peel flavonoid, using ligature-induced periodontitis in rats and LPS-stimulated RAW264.7 cells. Nar treatment significantly reduced alveolar bone loss, inhibited NLRP3 inflammasome activation (NLRP3, IL-1β), and suppressed inflammatory mediators (COX2, iNOS, IL-6, TNF-α) while improving collagen organisation. Microbiome analysis revealed that Nar suppressed pathogenic bacteria (Veillonella orally, Escherichia-Shigella in the gut) and enriched beneficial Lactobacillus. Metabolomics analysis revealed a significant decrease in the abundance of arginyl-glutamine (arg-gln) in the intestines of rats with periodontitis. Both Nar and arg-gln activated the AMPK/Nrf2 pathway, suppressing NLRP3 activation. FMT from Nar-treated donors had similar anti-inflammatory effects. In conclusion, Nar alleviates periodontitis primarily by directly activating the AMPK/Nrf2 pathway and inhibiting NLRP3 inflammasome activation in periodontal tissues. Additionally, Nar reshapes the gut microbiota to elevate arg-gln levels, which further amplifies AMPK activation and contributes to inflammation control, but is not sufficient alone to drive structural repair. These findings provide a novel theoretical basis for natural compound-mediated microbiota and inflammatory regulation in periodontitis treatment.},
}

@article {pmid42135323,
year = {2026},
author = {Park, JH and Kim, SY and Lim, HS and Kim, HJ and Lee, JY and Chung, J and Na, HS},
title = {A cross-sectional study of supragingival microbiome depending on age in Korean population.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47336-6},
pmid = {42135323},
issn = {2045-2322},
support = {NRF-RS-2024-00349457//National Research Foundation of Korea/ ; NRF-RS-2024-00349457//National Research Foundation of Korea/ ; NRF-RS-2024-00349457//National Research Foundation of Korea/ ; },
abstract = {Age is a key factor influencing the composition of the oral microbiome, but its age-related dynamics remain unclear as most studies focus on specific age groups or disease-related changes. The objective of this study was to characterize age-related differences in the supragingival microbiome. Supragingival plaque samples were collected from 533 participants across four age groups including Child (3 ~ 5 year), Young adult (18 ~ 34 year), Mid-age (35 ~ 65 year) and Elder (over 65 year) groups. Microbial DNA was extracted and analyzed using 16S rRNA gene sequencing. Alpha and beta diversity were assessed. Taxonomic classification was performed using a Naïve Bayes classifier trained on the eHOMD database. Differential abundance analysis was conducted using LEfSe, and microbial network interactions were examined using SparCC. Alpha diversity differed among age groups, and beta diversity also showed significant differences among groups, except between the Mid-age and Elder groups. The relative abundance of Firmicutes and Proteobacteria was lower in the Mid-age and Elder groups, whereas Bacteroidetes and Fusobacteria were more abundant. Early colonizers such as Streptococcus, Veillonella, and Haemophilus were less abundant in these groups, while periodontopathogens including Porphyromonas, Fusobacterium, and Treponema were more abundant. Core microbiome analysis revealed Streptococcus dominance in the Child group, the presence of Rothia and Actinomyces in the Young adult group, and more pathogen-enriched microbiome in the Mid-age and Elder groups. Microbial network complexity also differed across age groups, with denser and more pathogen-centered networks observed in the older groups. Distinct age-related differences in the oral microbiome were observed in this cross-sectional study, with microbial diversity, taxonomic composition, and microbial interaction patterns. These findings suggest that understanding age-related microbial variation may be important for long-term oral health.},
}

@article {pmid42135341,
year = {2026},
author = {Huang, Y and Hong, L and Li, S and Zhang, L and Guo, X and Han, J and Yu, W and Chen, H and Luo, N and Chen, J and Peng, W and Zhou, Y and Hong, S and Yan, W and Jiang, S and Cao, Y},
title = {Neonatal intensive care unit exposures reprogram microbiome-metabolome trajectories and modulate host calprotectin in preterm infants: a longitudinal multi-omics study.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-01008-5},
pmid = {42135341},
issn = {2055-5008},
support = {82402017//National Key Research and Development Program of China/ ; 82402017//National Key Research and Development Program of China/ ; },
abstract = {Early-life gut microbiota development is critical for orchestrating mucosal barrier function and immune priming, as disruptions in this process can increase susceptibility to life-threatening diseases such as necrotizing enterocolitis (NEC) and sepsis. This longitudinal multi-omics study of 186 preterm infants (<32 weeks of gestation or <1500 g birth weight) explores the impact of early-life exposures in the neonatal intensive care units (NICUs) on gut microbiota, metabolism, and immune responses. We analyzed 1153 stool samples using quantitative microbial profiling, untargeted metabolomics, and fecal S100A8/A9 (calprotectin) levels. Antibiotic exposure suppressed anaerobic colonization and microbial diversity in a cumulative exposure-dependent manner, with breastmilk feeding partially mitigating these effects. The stool metabolome correlated with microbial colonization, showing antibiotic-driven disruptions in polyamine metabolism linked to anaerobe abundance. Host calprotectin levels followed a biphasic pattern, correlating with microbial diversity and polyamine metabolites. Mediation analysis identified anaerobe suppression and polyamine depletion as key drivers of antibiotic-associated reductions in calprotectin. This study reveals that NICU interventions, particularly antibiotics, reprogram the preterm gut ecosystem and immune response, with anaerobes and polyamines being key mediators linking microbial ecology to immune maturation during early life.},
}

@article {pmid42135536,
year = {2026},
author = {Adedire, DE and Onilude, AA and Odeniyi, OA and Nash, O and Semenya, K and Unuofin, JO},
title = {Snapshot reflection of the seasonal resilience and diversity of fungal phylotypes in the tropical Ikogosi spring.},
journal = {Environmental science and pollution research international},
volume = {},
number = {},
pages = {},
pmid = {42135536},
issn = {1614-7499},
abstract = {Freshwater ecosystems like rivers, streams, and springs harbour diverse microbial communities, including fungal and bacterial phylotypes. These communities are an important part of the aquatic ecosystem, playing key roles in biogeochemical cycles. However, research on the seasonal differences concerning the fungal diversity of Ikogosi Warm Spring's sediments and water has been lacking. In this pilot study, we aimed to bridge this gap by employing high-throughput DNA sequencing to examine the fungal microbiome of this spring during the wet and dry seasons. Metagenomic DNA was extracted from water and sediment samples from different locations of the spring, and the fungal ITS1 region was sequenced using Illumina HiSeq technology. Sequences were processed with the DADA2 pipeline in R, enabling comprehensive taxonomic and diversity analyses. In addition, the spring's sediment and water physicochemical characteristics were assessed, and the impact of environmental variables on fungal communities was examined using redundancy analysis. Taxonomic analysis revealed that the spring was dominated by Ascomycota and Basidiomycota, irrespective of seasonal differences. In water samples, Ascomycota represented 62.0% (wet season) and 89.0% (dry season), while Basidiomycota accounted for 37.7% and 10.7%, respectively. Sediments exhibited a similar dominance, with Ascomycota comprising 65.1% in both seasons and Basidiomycota contributing 34.8% (wet season) and 33.5% (dry season). Alpha diversity indices indicated that fungal diversity was higher during the dry season than in the wet season, with no significant difference at p < 0.05. Redundancy analysis showed that some physicochemical factors, such as potassium and sulphate ions in water samples, were associated with seasonal patterns. These factors also influenced fungal communities in the spring, such as Cladosporium, Trichosporon, and Meyerozyma.},
}

@article {pmid42135574,
year = {2026},
author = {Yang, Y and Vega, A and Holck, J and Planas, A and Biarnés, X and Zeuner, B},
title = {Computationally guided enzyme engineering for regioselective synthesis of fucosylated human milk oligosaccharides.},
journal = {Applied microbiology and biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1007/s00253-026-13860-8},
pmid = {42135574},
issn = {1432-0614},
abstract = {Human milk oligosaccharides (HMOs) are key bioactive components of human milk that support infant health and microbiome development. Prevalent HMOs include the internally fucosylated pentasaccharides lacto-N-fucopentaose II (LNFP II) and lacto-N-fucopentaose III (LNFP III), which are absent from infant formula. Their enzymatic synthesis from simpler HMOs such as 3-fucosyllactose (3FL), lacto-N-tetraose (LNT) and lacto-N-neotetraose (LNnT) represents an important step towards bridging this gap, especially now that these simpler HMOs are available on an industrial scale. We evaluated the use of the GH29B α-1,3/4-L-fucosidase SpGH29[C] from Streptococcus pneumoniae for transfucosylation at equimolar donor-to-acceptor ratio and applied the computational pipeline BindScan to design variants with reduced hydrolytic activity to avoid undesirable product hydrolysis. Guided by these predictions, we generated and tested 21 variants of SpGH29[C], achieving significantly reduced hydrolysis and enhanced transglycosylation yields. Variants W264F and D257N reached LNFP II yields of up to 73% and 68%, respectively, while A173H improved LNFP III formation to 53%. Importantly, the product levels remained stable over 24 h as the variants displayed significantly decreased product hydrolysis as intended. Further binding analyses with BindScan enabled rational targeting of regioselectivity, identifying W211 as a key position influencing branched vs. linear product formation for LNFP II synthesis, while F202 and D257 variants improved regioselectivity in LNFP III synthesis. This study demonstrates that computationally guided protein engineering can optimize glycosidase-catalyzed transglycosylation and provides a framework for designing regioselective biocatalysts for complex oligosaccharides synthesis. KEY POINTS: • BindScan designs fucosidase variants with improved transglycosylation performance • SpGH29[C] variants efficiently synthesize LNFP II and LNFP III with low hydrolysis • SpGH29[C] positions W211, F202 and D257 influence regioselectivity.},
}

@article {pmid42135633,
year = {2026},
author = {Basu, U and Ahanger, SA and Song, T and Gai, X and Hu, X},
title = {Ecological and genomic dynamics of the soil microbiome under sustained pressure from Phytophthora nicotianae, the causal agent of tobacco black shank disease.},
journal = {BMC microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12866-026-05137-x},
pmid = {42135633},
issn = {1471-2180},
support = {202405AD350100, 2023530000241003/YNDG202302XJ02//Yunnan Applied Fundamental Research Projects and the Yunnan Provincial Tobacco Monopoly Bureau/ ; },
abstract = {BACKGROUND: Soil-borne pathogens threaten global agriculture, yet soil microbiome adaptation to persistent pathogen pressure is poorly understood. This study characterized the ecological and genomic long-term shifts in a tobacco field soil microbiome under sustained Phytophthora nicotianae pressure. We conducted a six-year longitudinal metagenomic study in a field with a documented history of tobacco black shank disease. Comparative analysis of the rhizosphere microbiome from Year_1 and Year_6 was performed using shotgun sequencing, non-redundant gene catalog construction, and functional annotation against specialized databases.

RESULTS: Our analysis revealed a profound genetic remodelling, with 45.6% (116,529) of 255,258 genes showing significant differences in abundance (p < 0.05, |log2FC| ≥ 1). This restructuring was systematic, characterized by significant enrichment of the soil antibiotic resistome, where 45.88% of antibiotic resistance genes were differentially abundant and showed a distinct trend toward increased abundance. The functional potential for carbohydrate metabolism was reorganized, with 53.2% of CAZymes (Carbohydrate-Active enZYmes) genes showing differential abundance and a predominant depletion. Analysis of COG (Clusters of Orthologous Groups) revealed a strategic functional trade-off, with significant enrichment of defense-related categories like secondary metabolite biosynthesis (+ 52.9%) alongside a reduction in growth-related processes. Such functional changes were ultimately driven by an taxonomically homogenized community, as indicated by a major reduction in species level alpha diversity (Shannon index: 5.52 to 5.31) that coexisted with a 14.8% significant increase in species level abundance, which showed a selective enrichment of a subset of dominant taxa.

CONCLUSION: Sustained pathogen pressure triggers a coordinated, multi-level adaptive succession, reshaping the genetic, functional, and taxonomic structure of the soil microbiome into a more defended and specialized state.},
}

@article {pmid42135724,
year = {2026},
author = {Jiang, S and Shang, G and Ning, W and Liu, D and Huang, J and Lan, X and Bai, Y and Hao, Y and Wang, H and Zhang, H},
title = {Lactobacillus-derived indole-3-lactic acid suppresses meningioma malignant phenotypes by direct anti-proliferative effects and macrophage reprogramming.},
journal = {Journal of translational medicine},
volume = {},
number = {},
pages = {},
doi = {10.1186/s12967-026-08222-x},
pmid = {42135724},
issn = {1479-5876},
abstract = {BACKGROUND: The intratumoral microbiome influences cancer progression, but its role in meningiomas is unknown. We characterized the meningioma intratumoral microbiome and investigated its functional significance.

METHODS: 16 S rRNA sequencing was performed on 80 meningioma specimens (44 benign, 36 non-benign). Microbial findings were validated via fluorescence in situ hybridization (FISH) and transmission electron microscopy. Among differentially abundant genera, Lactobacillus was identified as the core genus due to its 100% detection rate and significant enrichment in benign tumors, and was thus selected for functional interrogation. We employed in vitro assays (proliferation, migration), non-targeted metabolomics, RNA sequencing, and co-culture systems with primary human macrophages derived from peripheral blood mononuclear cells (PBMCs) and THP-1 cells to dissect microbial-metabolite-immune interactions.

RESULTS: Meningiomas harbor a distinct intratumoral microbiome dominated by Firmicutes and Bacteroidota, with beta diversity revealing significant compositional differences between benign and non-benign tumors. The Lactobacillus genus was identified as a core genus enriched in benign tumors, and its abundance negatively correlated with the Ki-67 proliferation index. Logistic regression analysis further indicated an association between Lactobacillus abundance and low-aggressiveness tumor phenotypes (benign histology and low Ki-67 index); however, this association was not independent after adjusting for key clinical confounders. Functionally, the supernatant from cultured Lactobacillus intestinalis (putative L. intestinalis, a species belonging to the Lactobacillus genus that showed a differential abundance pattern between benign and non-benign meningiomas) suppressed IOMM-Lee cell proliferation and migration. Non-targeted metabolomics identified indole-3-lactic acid (ILA) and niacin as the predominant metabolites in the bacterial supernatant. ILA was established as the primary effector, recapitulating the direct antitumor effects and skewing human macrophages towards an M1-polarized phenotype with enhanced secretion of IL-12 and IL-6. While niacin also promoted M1 cytokine secretion, it lacked direct antiproliferative activity. Transcriptomic profiling of ILA-treated tumor cells confirmed the suppression of multiple oncogenic pathways.

CONCLUSION: This study characterizes the intratumoral microbiome of meningiomas and reveals that the Lactobacillus genus may serve as a potential microbial marker for a low-proliferation, low-necrosis tumor microenvironment. Furthermore, we uncover a tumor-suppressive mechanism mediated by Lactobacillus, identifying its metabolite, indole-3-lactic acid (ILA), as a key effector. As an exogenous compound, ILA exerts dual anti-tumor activity through direct anti-proliferative effects and immunomodulation in vitro experiments. While these findings are preliminary and require further validation in vivo, they suggest ILA as a potential preclinical candidate for informing future therapeutic strategies.},
}

@article {pmid42135886,
year = {2026},
author = {Wang, X and Song, F and Zhang, L and Jiang, L and Li, D and Huang, Z},
title = {Advances in Protein-Based Delivery Systems: From Structural Design to Smart Responses and Intestinal Microbiome Modulation.},
journal = {Comprehensive reviews in food science and food safety},
volume = {25},
number = {3},
pages = {e70504},
doi = {10.1111/1541-4337.70504},
pmid = {42135886},
issn = {1541-4337},
support = {ZDYF2025XDNY084//Hainan Province Science and Technology/ ; ZDYF2025XDNY065//Hainan Province Science and Technology/ ; GHYF2025001//International Science & Technology Cooperation Program of Hainan Province/ ; },
mesh = {*Gastrointestinal Microbiome/drug effects ; Humans ; *Drug Delivery Systems ; *Proteins/chemistry/administration & dosage ; },
abstract = {While bioactive compounds hold significant potential for health promotion, their application is severely constrained by issues such as poor stability, low oral bioavailability, and susceptibility to degradation in the gastrointestinal environment. Protein-based delivery systems (PBDS), as novel carriers, demonstrate the potential to overcome these challenges through encapsulation and targeted release technologies. This paper provides a systematic review of the latest research advances in various PBDS systems, including Pickering emulsions, protein-small molecule complexes, protein-polysaccharide complexes, nanogels, nanoparticles, core-shell microcapsules, self-assembled nanotubes, and nanofibers, along with their performance and characteristics in encapsulation, protection, and controlled release. PBDS enables smart stimulus-responsive release through pH, temperature, enzymatic reactions, redox reactions, and receptor recognition, thereby enhancing targeted delivery and controlled release efficiency. Furthermore, PBDS interacts with the gut microbiota to modulate microbial composition and strengthen intestinal barrier function, positively impacting systemic metabolic health. In summary, PBDS offers a solution for developing next-generation functional foods with improved nutritional properties, sensory qualities, and storage performance. Future research should focus on novel protein sources, multi-stimulus response design, scalable preparation processes, and in-depth exploration of PBDS-microbiome interaction mechanisms to advance personalized nutrition and smart food applications.},
}

*Gastrointestinal Microbiome/drug effects
Humans
*Drug Delivery Systems
*Proteins/chemistry/administration & dosage

@article {pmid42136241,
year = {2026},
author = {Singh, R and Monika, and Mazumder, R and Mazumder, A and Singh, M and Majee, C and Padhi, S and Das, S},
title = {Chronic Inflammation (A Silent Killer) - Molecular Mechanisms and Emerging Therapeutic Approaches.},
journal = {Current drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113894501450885260409050432},
pmid = {42136241},
issn = {1873-5592},
abstract = {Chronic inflammation is a dysregulated and persistent immune response that underlies numerous serious health conditions, like heart problems, diabetes, nerve damage, cancer, or conditions where the body attacks itself. Recently, scientists have gained a better understanding of how molecules such as cytokines and chemokines, along with dysregulated immune cells, contribute to excessive oxidative stress and impaired healing processes. New tools now help identify this condition as early as possible through biomarkers, advanced laboratory techniques, integrated data approaches, and smart sensors that track biological changes in real time. However, despite this knowledge, effective strategies for early prevention and long-term treatment remain limited. Daily habits, particularly anti-inflammatory dietary patterns, regular physical activity, and stress management, play a critical role in reducing the risk of disease. Emerging therapies, including inflammasome inhibitors, cytokine-targeted biologics, immunometabolic modulators, and specialized pro-resolving mediators, may restore immune homeostasis rather than merely suppressing symptoms. Additionally, microbiome-targeted interventions-such as probiotics, prebiotics, bacteriophage therapy, and fecal microbiota transplantation-are increasingly being recognized as potential strategies to modulate systemic inflammation. Daily habits, especially eating patterns that fight inflammation, walking regularly, or handling stress, are critically important for lowering the chances of illness. Chronic inflammation is a complex, multifactorial process; therefore, its effective management requires integrated efforts in basic research, therapeutic innovation, and population- level healthcare strategies. Innovations in personalized medicine, AI-based analytics, digital health technologies, and microbiome science are poised to significantly enhance diagnostic and therapeutic approaches. Sustained cross-disciplinary collaboration will be critical in mitigating the worldwide impact of chronic inflammatory disorders and improving long-term health outcomes.},
}

@article {pmid42136267,
year = {2026},
author = {Saraswati, BD and Wicaksono, AW and Valles, SL and Poeggeler, B and Singh, SK},
title = {Exploring the Gut Microbiome as a Promising Frontier in Alzheimer's Disease Therapy.},
journal = {Current neuropharmacology},
volume = {},
number = {},
pages = {},
doi = {10.2174/011570159X444975260408044214},
pmid = {42136267},
issn = {1875-6190},
abstract = {Alzheimer's Disease (AD) is a major global health challenge, particularly in ageing populations, and current therapies offer limited modification of disease progression. Emerging evidence indicates that the gut microbiome contributes to AD pathogenesis through metabolic, immune, and neuroendocrine mechanisms. Microbial metabolites, including Short-Chain Fatty Acids (SCFAs), bile acids, and trimethylamine-N-oxide (TMAO), regulate neuronal signalling and blood-brain barrier integrity, and dysbiosis has been linked to amyloid-β (Aβ) accumulation, tau hyperphosphorylation, chronic neuroinflammation, oxidative stress, and synaptic dysfunction. Host genetic factors, particularly APOE ε4 and immune-regulatory variants such as TREM2 and CD33, further influence microbial composition and susceptibility to metabolite-driven pathology. This review provides a deeper synthesis of current evidence by integrating findings across multi-omics studies and identifying key unresolved issues in the microbiome-AD field. The discussion evaluates whether microbiome alterations act as early initiators or downstream consequences of neurodegeneration, examines sources of heterogeneity in microbiome-targeted interventions, and considers how inter-individual variability in host genetics and microbial ecology may inform precision therapeutics. Conceptual frameworks presented here, including a two-phase dysbiosis trajectory and a metabolite "tipping-point" network, aim to reconcile conflicting results and support the development of testable mechanistic hypotheses. Microbiome-directed strategies, such as probiotics, prebiotics, dietary modulation, faecal microbiota transplantation, and antiviral therapies, demonstrate promise but require rigorous mechanistic validation and methodological standardisation. Continued advancement in longitudinal, genotype-stratified, and multi-omics research will be essential for translating microbiome science into clinically actionable approaches. Overall, current evidence positions the gut microbiome as a compelling frontier for the development of personalised, diseasemodifying strategies in AD.},
}

@article {pmid42136277,
year = {2026},
author = {Saxena, V and Singh, V and Sanskriti, },
title = {Translational Perspectives on Anti-Inflammatory Interventions for Neurodegenerative Disorders: Evidence from Gut-Brain Axis.},
journal = {Central nervous system agents in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715249430752260407050033},
pmid = {42136277},
issn = {1875-6166},
abstract = {The Gut-Brain Axis (GBA) has a complex role in chronic neuroinflammation, which is increasingly connected to neurodegenerative diseases (NDDs) such as Multiple Sclerosis (MS), Parkinson's Disease (PD), and Alzheimer's Disease (AD). Through neuronal, endocrine, and immunological pathways, the GBA enables twoway communication between the gastrointestinal tract and the central nervous system. According to recent research, the pathophysiology of neuroinflammatory responses in NDDs may be significantly influenced by gut dysbiosis, increased intestinal permeability, and modified microbial metabolites, such as Short-Chain Fatty Acids (SCFAs) and polyphenols. This study summarizes preclinical and clinical data supporting several anti- inflammatory approaches targeting GBA. Probiotics and fecal microbiota transplantation are two examples of microbiota-based treatments that have demonstrated promise in reducing neuroinflammatory responses and enhancing cognitive performance. Mediterranean and polyphenol-rich diets are among the dietary therapies that show promise in modifying the composition of microorganisms, lowering pro-inflammatory signaling, and enhancing neuroprotection. Through microbiota regulation, pharmacological substances such as curcumin, resveratrol, and SCFA mimetics also have anti-neuroinflammatory benefits. However, a number of translational challenges still exist, including limitations in animal models, a lack of standardized therapies, and inter-individual microbiome heterogeneity. In order to provide precise, GBA-targeted therapies, future views place a strong emphasis on integrating multi-omics, artificial intelligence, and personalized medicine. This study highlights a new therapeutic approach to treating neurodegeneration by examining the translational potential of anti- inflammatory therapies targeting GBA. It also emphasizes the necessity of strong clinical studies to confirm these findings.},
}

@article {pmid42136303,
year = {2026},
author = {Rahimkhani, M and Hosseini, M},
title = {From Microbes to Minds: The Impact of Gut Bacteria on Infant Cognitive Growth.},
journal = {CNS & neurological disorders drug targets},
volume = {},
number = {},
pages = {},
doi = {10.2174/0118715273391751251125075624},
pmid = {42136303},
issn = {1996-3181},
abstract = {Recent advances underscore the pivotal role of the gut microbiota in shaping infant brain development, emphasizing how the diversity and function of microbial communities regulate neurodevelopmental processes. This review synthesizes current literature on how maternal and early-life microbial exposures influence the infant gut ecosystem, producing cascading effects on cognitive and behavioral outcomes. Perturbations in gut microbial composition during sensitive developmental windows may increase the risk of conditions such as autism spectrum disorder (ASD) and attention- deficit/hyperactivity disorder (ADHD). Furthermore, research highlights the significance of the gut-brain axis, particularly the impact of nutrition and environmental factors on both microbiome composition and neurodevelopment. This review aims to provide an integrated overview of current evidence and to outline future directions for microbiota-targeted interventions that may enhance cognitive and neurological outcomes in children.},
}

@article {pmid42136370,
year = {2026},
author = {Wu, C and Liu, H and Carvalhais, LC and Guo, J and Cai, P and Zhong, J and Zhang, H and Jin, B and Li, G and Yang, J and Chen, J and Ge, T},
title = {Root exudate-associated microbiome assembly contributes to viral disease resistance in wheat.},
journal = {The New phytologist},
volume = {},
number = {},
pages = {},
doi = {10.1111/nph.71254},
pmid = {42136370},
issn = {1469-8137},
support = {CARS-08-G09//China Agriculture Research System from the Ministry of Agriculture of P.R. China/ ; U24A20404//National Science Foundation of China/ ; 42477341//National Science Foundation of China/ ; 2022YFD1400700//National Key Research and Development Program of China/ ; 2022YFA1304401//National Key Research and Development Program of China/ ; 2024YFC3406003//National Key Research and Development Program of China/ ; //K.C. Wong Magna Fund of Ningbo University/ ; YLS-2025-ZY01012//Yuelushan Laboratory Breeding Program/ ; },
abstract = {Early mutualistic interactions between host plants and their rhizosphere microbes have the potential to provide soil-borne disease resistance. However, it remains unclear how the early rhizosphere microbiome protects against viral diseases such as wheat yellow mosaic virus, which is a major threat to global wheat production. We combined field trials with microbiome transplantation experiments to investigate the role of early rhizosphere microbiomes in suppressing wheat yellow mosaic disease. To uncover the underlying mechanisms, we further performed integrated multi-omics analyses of microbial communities, functional genes, and metabolic profiles. Disease-resistant wheat cultivars were consistently associated with distinct seedling rhizosphere microbiome assembly, including a lower Polymyxa graminis abundance, lower community compositional variation, and enrichment of beneficial taxa such as Bacillus, Pseudomonas, and Trichoderma. Resistant cultivars also exhibited distinct rhizosphere metabolite profiles, including higher levels of glyceraldehyde and N-acetyltryptophan, which were positively associated with keystone microbial taxa and stimulated representative isolates in vitro. Isolate-based and synthetic community validation further supported the functional relevance of these taxa, while microbial inoculation was associated with reduced vector abundance, lower virus accumulation, and activation of host defense-related pathways. Our findings showed that early cultivar-dependent rhizosphere microbiome assembly was closely linked to resistance against soil-borne viral disease in wheat.},
}

@article {pmid42136372,
year = {2026},
author = {Mawer, CMA and Stanel, SC and Ward, EM and Smith, DJF and Hull, RC and Mehta, P},
title = {A framework for translational research in interstitial lung disease (ILD) using bronchoalveolar lavage (bal).},
journal = {Expert review of clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1080/1744666X.2026.2675640},
pmid = {42136372},
issn = {1744-8409},
abstract = {INTRODUCTION: Bronchoalveolar lavage (BAL) offers a minimally invasive window into the distal airspaces and is an important tool in the study of interstitial lung disease (ILD). As chest imaging has obviated the need for diagnostic surgical biopsies, research tissue is increasingly limited, strengthening the rationale for BAL. By sampling the epithelial lining fluid, BAL captures cellular and acellular host- and microbe-derived signals relevant to inflammation and fibrogenesis, enabling multi-omic mechanistic and biomarker studies. However, variation in technique, dilution, and pre-analytical handling limits reproducibility and cross-center comparability.

AREAS COVERED: Here, we summarize key biological insights gained from BAL fluid-based studies, divided into cellular, acellular and microbiome compartments. We highlight current guidance, methodological challenges, and outline standardized frameworks to maximize translational scientific yield and multi-center validation.

EXPERT OPINION: Standardized protocols will maximize the value of BAL samples. Paired multi-compartment analysis can expand actionable readouts: multimodal cellular pipelines combining single-cell RNA and protein profiling, aligned with clinical annotation, may define ILD endotypes and prognostic/predictive biomarkers. Acellular BALF bioassays coupled to transcriptional and proteomic signatures can support mechanistic validation and pharmacological targeting, while microbiome profiling integrated with host multi-omics may improve risk stratification. Ultimately, these data could inform clinical decision-making and regulatory endpoints.},
}

@article {pmid42136474,
year = {2026},
author = {Javadi, B},
title = {The Modulating Effects of Alkaloids on Gut Microbiota: Insights and Implications for Parkinson's Disease Management.},
journal = {Mini reviews in medicinal chemistry},
volume = {},
number = {},
pages = {},
doi = {10.2174/0113895575413113251031045342},
pmid = {42136474},
issn = {1875-5607},
abstract = {Parkinson's Disease (PD) is a neurodegenerative disorder characterized by the selective degeneration of dopaminergic neurons in the substantia nigra, leading to motor and non-motor symptoms. Recent research highlights the importance of the microbiome-Gut-Brain Axis (GBA) in PD pathogenesis, particularly the role of gut microbiota dysbiosis and inflammation. This review aims to explore the potential of alkaloids, a diverse group of naturally occurring compounds, in modulating gut microbiota and their implications for PD management. We evaluated studies that investigated the effects of various alkaloids on gut microbial composition, neuroinflammation, and dopaminergic neuron health using PubMed, Scopus, Web of Science, and Google Scholar databases. The search strategy combined Medical Subject Headings (MeSH) and free-text keywords. The primary search terms included: "Parkinson's disease" OR "PD", "gut-brain axis" OR "gut microbiota" OR "intestinal dysbiosis", "alkaloids" OR specific compound names (e.g., "berberine," "harmine," "galantamine," "nicotine," etc.). Evidence suggests that alkaloids such as berberine, protopine, and palmatine, matrin, etc., can restore microbial balance, reduce inflammation, and enhance neuroprotective effects, potentially mitigating both gastrointestinal and neurological symptoms associated with PD. This review underscores the need for further research, particularly human clinical trials, to validate the therapeutic efficacy and safety of alkaloids in the context of PD. By elucidating the mechanisms through which alkaloids influence the GBA, we can pave the way for innovative treatment strategies that enhance the quality of life for PD patients.},
}

@article {pmid42136577,
year = {2026},
author = {Serdo, DF and Németh, Z},
title = {The Integrative Imperatives of Locust Phase Polyphenism Research: A Bibliometric Analysis.},
journal = {Integrative organismal biology (Oxford, England)},
volume = {8},
number = {1},
pages = {obag018},
pmid = {42136577},
issn = {2517-4843},
abstract = {Locust phase polyphenism, a classic example of phenotypic plasticity, has been studied for over a century, generating an extensive body of literature. However, a quantitative synthesis of the field's structure, evolution, and disparities has been lacking. Here, we present the first comprehensive bibliometric analysis of locust phase polyphenism research, quantitatively mapping its intellectual structure, collaborative networks, and thematic evolution. Analyzing 400 peer-reviewed primary studies published from 1921 through February 2025, we reveal a field at a critical inflection point. Publication trends demonstrate robust growth since the 1990s, reflecting the refinement of classical methods and the emergence of molecular and neurobiological approaches. However, this expansion rests upon a narrow foundation: research concentrates almost exclusively on two model species-Schistocerca gregaria and Locusta migratoria-while ecologically important non-model taxa remain critically understudied. Co-authorship network analysis exposes significant geographical disparities: research leadership concentrates in a small number of countries (UK, China, Japan, Belgium, Israel, Kenya, Germany, and USA), while most other locust-affected regions across the Sahel, the Horn of Africa, and the Middle East remain peripherally integrated. Keyword co-occurrence mapping identifies critical thematic blind spots within the phase polyphenism literature, including a complete absence of explicit climate change framing and limited representation of socioeconomic dimensions and non-model species. The field thus exhibits a notable disconnect: deep mechanistic knowledge of how phase change occurs exists alongside limited understanding of when and why outbreaks occur under changing environmental conditions. Transformative advances require strategic reorientation: from model-organism focus to comparative ecology, from episodic collaboration to equitable partnership with range-state scientists, from descriptive mechanism to functional validation, and from neglected frontiers (microbiome, epigenetics, and climate) to systematic investigation. This bibliometric mapping provides an evidence-based framework to guide future research toward greater impact on global food security.},
}

@article {pmid42136643,
year = {2026},
author = {Wan, Y and Zheng, M and Fu, W and Zhu, H and Li, Y and Lin, H and Chen, J and Li, J and Mo, Q and Tai, W and Yang, J},
title = {Research trends on autoimmune liver diseases and gut microbiota (1989-2025): a bibliometric and visualization analysis based on the web of science core collection database.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1785064},
pmid = {42136643},
issn = {1664-3224},
mesh = {*Gastrointestinal Microbiome/immunology ; Humans ; Bibliometrics ; *Hepatitis, Autoimmune/microbiology/immunology/epidemiology ; Cholangitis, Sclerosing/microbiology/immunology ; *Autoimmune Diseases/microbiology ; *Biomedical Research/trends ; *Liver Diseases/immunology/microbiology ; Databases, Factual ; },
abstract = {Autoimmune liver diseases (AILD) encompass autoimmune hepatitis (AIH), primary biliary cholangitis (PBC), primary sclerosing cholangitis (PSC), and IgG4-related sclerosing cholangitis (IgG4-SC), with both incidence and prevalence showing an upward trend in recent years. Increasing evidence indicates that the onset and progression of AILD are inextricably linked to the gut microbiota. So far, no comprehensive and objective bibliometric study on AILD and gut microbiota has been conducted. This study retrieved literature from the Web of Science Core Collection (WoSCC) and Scopus database up to October 13, 2025, for analysis and validation respectively. VOSviewer, CiteSpace, R, Bibliometrix, SciExplorer, and WPS Office analysis tools were employed to systematically evaluate research trends, hot topics, and knowledge structures in the field. Our analysis indicates a growing research trend in AILD-gut microbiota interactions, involving 58 countries, 981 institutions, and 3,528 authors. Influential journals in this field include Frontiers in Immunology, GUT, and World Journal of Gastroenterology. Gershwin M. Eric stands as an authoritative author in this domain. Hot topics include "Mendelian randomization","primary sclerosing cholangitis", "primary biliary cholangitis", "bile acids", and the "gut-liver axis". Exploring therapeutic targets in AILD patients through the gut microbiome and its metabolites may emerge as a key future research direction. In summary, this study employed bibliometric methods to evaluate the application and development of gut microbiota in the field of AILD. Research in this area has experienced rapid growth in recent years, progressively focusing on the mechanisms of the gut-liver axis and genetics. Future efforts should further explore the potential of gut microbiota modulation in AILD treatment.},
}

*Gastrointestinal Microbiome/immunology
Humans
Bibliometrics
*Hepatitis, Autoimmune/microbiology/immunology/epidemiology
Cholangitis, Sclerosing/microbiology/immunology
*Autoimmune Diseases/microbiology
*Biomedical Research/trends
*Liver Diseases/immunology/microbiology
Databases, Factual

@article {pmid42136650,
year = {2026},
author = {Shao, M and Zhang, Y and Tang, H and Zhou, Z and Zhai, M and Zhou, X and Bi, X and Liao, J and Zhang, C and Jiang, L},
title = {Multi-omics insights into immune tolerance at the maternal-fetal interface in recurrent pregnancy loss: mechanisms, integration challenges, and translational perspectives.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1811970},
pmid = {42136650},
issn = {1664-3224},
mesh = {Humans ; Female ; Pregnancy ; *Abortion, Habitual/immunology/metabolism/genetics/etiology ; *Immune Tolerance ; Translational Research, Biomedical ; Animals ; Metabolomics ; Proteomics ; Genomics/methods ; *Maternal-Fetal Exchange/immunology ; Multiomics ; },
abstract = {Recurrent pregnancy loss (RPL) is a heterogeneous reproductive disorder in which dysregulation of maternal-fetal immune tolerance, aberrant decidual immune remodeling, and altered inflammasome signaling have been implicated within a complex multi-omics landscape. Multi-omics profiling (genomics, epigenomics, single-cell/spatial transcriptomics, proteomics, metabolomics, microbiome analyses, and immunomics) is increasingly being used to characterize mechanistic heterogeneity in RPL and to support biomarker discovery and immune-informed stratification. Genomic studies have associated chromosomal abnormalities and pathogenic variants with early embryonic developmental failure, while epigenomic profiling has highlighted aberrant methylation patterns and imprinting disturbances. Single-cell and spatial transcriptomics have revealed altered cellular composition and disrupted communication among decidual stromal cells, uterine natural killer (uNK) cells, macrophages, regulatory T cells (Treg), T helper 17 (Th17) cells, and trophoblast lineages. Proteomic and metabolomic studies have further identified immune-metabolic signatures associated with impaired trophoblast function and vascular remodeling, while emerging microbiome studies suggest a gut-reproductive axis that may modulate systemic immune homeostasis. Integration of multi-omics datasets with computational frameworks (e.g., weighted gene co-expression network analysis (WGCNA), multi-omics factor analysis (MOFA), and deep-learning models may improve RPL subtype classification, risk prediction, and the identification of potentially actionable pathways. However, current studies remain limited by small cohort sizes, especially in single-cell datasets, cross-platform heterogeneity, insufficient longitudinal validation, and a lack of multicenter reproducibility. Future work should prioritize standardized multi-omics pipelines, clearer evidence stratification, and immune-centric analytical frameworks to improve the robustness and translational relevance of RPL research. These advances may ultimately support immune-informed risk assessment and contribute to the gradual development of more individualized management strategies for RPL.},
}

Humans
Female
Pregnancy
*Abortion, Habitual/immunology/metabolism/genetics/etiology
*Immune Tolerance
Translational Research, Biomedical
Animals
Metabolomics
Proteomics
Genomics/methods
*Maternal-Fetal Exchange/immunology
Multiomics

@article {pmid42136651,
year = {2026},
author = {Jin, W and Tang, L and Yang, J and Hu, X and Guo, W and Ai, H and Zuo, Y and Jin, Z},
title = {The oral - X axis: from periodontal dysbiosis to systemic disease.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1806445},
pmid = {42136651},
issn = {1664-3224},
mesh = {Humans ; *Dysbiosis/immunology/microbiology ; *Mouth/microbiology/immunology ; *Periodontitis/microbiology/immunology ; Animals ; Microbiota ; },
abstract = {Chronic oral inflammatory diseases, particularly periodontitis, are increasingly recognized as important contributors to the onset and progression of systemic disorders. Accumulating epidemiological, clinical, and mechanistic evidence indicates that the oral cavity is not an isolated organ, but rather a critical hub and early window for systemic disease development. Through microbial translocation, chronic low-grade inflammation, immune dysregulation, oxidative stress, and epigenetic reprogramming, oral diseases engage in bidirectional communication with distant organs.We conceptualize this integrated network as the "oral-X axis, " encompassing the oral-cardiovascular, oral-metabolic, oral-respiratory, oral-gastrointestinal, oral-oncologic, oral-immune, oral-brain, and other systemic axes. At the core of these interactions lies periodontitis-associated microbial dysbiosis dominated by key pathogens such as Porphyromonas gingivalis, Fusobacterium nucleatum, and Aggregatibacter actinomycetemcomitans. The ensuing inflammatory response compromises periodontal barrier integrity, facilitating the dissemination of bacteria, virulence factors, and inflammatory mediators into the systemic circulation. These processes promote endothelial dysfunction, insulin resistance, breakdown of immune tolerance, neuroinflammation, and the formation of pro-tumorigenic microenvironments, thereby mechanistically linking oral inflammation to a broad spectrum of systemic diseases. This review systematically summarizes the current evidence supporting the oral-X axis, with a particular focus on epidemiological associations and underlying molecular and cellular mechanisms. In addition, we discuss periodontal interventions and oral microbiome modulation as potential strategies for the prevention and treatment of systemic diseases. A deeper understanding of the oral-X axis may provide novel insights into integrated oral-systemic healthcare and precision medicine.},
}

Humans
*Dysbiosis/immunology/microbiology
*Mouth/microbiology/immunology
*Periodontitis/microbiology/immunology
Animals
Microbiota

@article {pmid42136652,
year = {2026},
author = {Hou, Y and Chen, C and Chen, X},
title = {Advancing precision immuno-oncology in melanoma: the synergistic convergence of personalized neoantigen vaccines and multi-omics biomarker profiling.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1831047},
pmid = {42136652},
issn = {1664-3224},
mesh = {Humans ; *Melanoma/immunology/therapy/genetics ; *Cancer Vaccines/immunology/therapeutic use ; *Precision Medicine/methods ; *Antigens, Neoplasm/immunology ; *Biomarkers, Tumor/genetics/immunology ; Tumor Microenvironment/immunology ; *Immunotherapy/methods ; Genomics/methods ; *Skin Neoplasms/therapy/immunology/genetics ; Proteomics ; Multiomics ; },
abstract = {Cutaneous melanoma represents a paradigm of immunological complexity, where multifactorial primary and acquired resistance often undermine the clinical efficacy of conventional immune checkpoint blockades and targeted therapies. This review provides a comprehensive analysis of the strategic shift toward precision immuno-oncology, focusing on the mechanistic synergy between personalized neoantigen-directed vaccines and integrated multi-omics profiling. Rather than viewing these as independent pillars, we propose an integrated framework where multi-omics data functions as the indispensable 'operating system' that drives the entire lifecycle of neoantigen vaccines. By targeting patient-specific somatic mutations, bespoke vaccines are capable of orchestrating de novo, high-avidity T-cell responses with superior specificity and minimal off-target toxicity. We evaluate the clinical evolution and immunological foundations of advanced vaccine platforms-including mRNA, synthetic long peptides (SLPs), and engineered exosome-based systems-highlighting their transformative potential in the neoadjuvant and adjuvant settings. Central to this paradigm is the deployment of a robust multi-omics ecosystem (encompassing genomics, transcriptomics, epigenomics, proteomics, and the host microbiome) to decipher the dynamic landscape of the melanoma tumor microenvironment (TME). Facilitated by artificial intelligence (AI) and real-time liquid biopsy monitoring, this framework enables an iterative, biologically informed feedback loop for adaptive clinical management. We emphasize that the integration of personalized vaccines with immune checkpoint inhibitors (ICIs) and MAPK pathway inhibitors is essential to dismantle resistance barriers, providing a definitive roadmap for achieving durable clinical remission and curative outcomes in the era of personalized oncology.},
}

Humans
*Melanoma/immunology/therapy/genetics
*Cancer Vaccines/immunology/therapeutic use
*Precision Medicine/methods
*Antigens, Neoplasm/immunology
*Biomarkers, Tumor/genetics/immunology
Tumor Microenvironment/immunology
*Immunotherapy/methods
Genomics/methods
*Skin Neoplasms/therapy/immunology/genetics
Proteomics
Multiomics

@article {pmid42136670,
year = {2026},
author = {Gidaro, A and Guarino, MD and Arcoleo, F and Bignardi, D and D'Antonio, C and Brussino, L and Accardo, P and Nicola, S and Pucci, S and Cognigni, M and Popescu Janu, V and Cogliati, C and Bizzi, E and Cancian, M},
title = {Probiotic supplementation to mitigate berotralstat gastrointestinal side effects: a multicenter case series from the ITACA network.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1790199},
pmid = {42136670},
issn = {1664-3224},
mesh = {Humans ; *Probiotics/therapeutic use/administration & dosage ; Female ; Male ; Middle Aged ; Adolescent ; Adult ; Aged ; Child ; Young Adult ; Aged, 80 and over ; *Gastrointestinal Diseases/chemically induced/prevention & control ; *Angioedemas, Hereditary/drug therapy ; Pilot Projects ; },
abstract = {INTRODUCTION: Berotralstat, the first oral plasma kallikrein inhibitor approved for hereditary angioedema (HAE) prophylaxis, may be associated with gastrointestinal (GI) side effects, particularly during the first three months of therapy. Probiotics have been shown to reduce GI disturbances in several conditions. This pilot study described GI tolerability in patients receiving initiation-phase probiotic co-administration alongside berotralstat and explored whether this supportive strategy merits further controlled evaluation.

MATERIALS AND METHODS: We analyzed 25 adolescents and adults with HAE treated with berotralstat across six Italian centers (December 2023-November 2025). All patients received probiotics during the early treatment phase. Demographic and clinical data, side effects, and monthly HAE attack rates were collected. Severity of complaints was graded using the Common Terminology Criteria for Adverse Events (CTCAE).

RESULTS: Participants were 60% females, and the mean age for the cohort was 45 years (range 12-82). The most common probiotics were Lacteol[®] , Codex[®] , and Lactoflorene Plus[®] . GI complaints occurred in 5/25 patients (20%); only 3/25 (12%) experienced GI side effects while receiving probiotics. 2/25 GI complaints occurred after probiotic discontinuation. No serious side effects were reported. Mean monthly attack rate decreased from 2.6 to 0.8 attacks per month, ~3.3-fold reduction from baseline.

CONCLUSION: Probiotic co-administration during early berotralstat therapy was accompanied by a low incidence of GI side effects, while clinical effectiveness was maintained. These preliminary findings support further controlled studies to validate probiotics as a supportive strategy for improving the tolerability of berotralstat.},
}

Humans
*Probiotics/therapeutic use/administration & dosage
Female
Male
Middle Aged
Adolescent
Adult
Aged
Child
Young Adult
Aged, 80 and over
*Gastrointestinal Diseases/chemically induced/prevention & control
*Angioedemas, Hereditary/drug therapy
Pilot Projects

@article {pmid42134890,
year = {2026},
author = {Mohan, S and Selvam, PK and Vasudevan, K},
title = {Advances in immunomodulation: From dietary influence to computational precision.},
journal = {Advances in protein chemistry and structural biology},
volume = {151},
number = {},
pages = {29-44},
doi = {10.1016/bs.apcsb.2025.10.004},
pmid = {42134890},
issn = {1876-1631},
mesh = {Humans ; *Diet ; *Immunomodulation/drug effects ; Machine Learning ; Gastrointestinal Microbiome/immunology ; Animals ; *Immunologic Factors/therapeutic use/pharmacology ; },
abstract = {Immunomodulators are bioactive agents that play a crucial role in modulating immune responses, making them essential for managing autoimmune disorders, infections, and cancers. This chapter provides a thorough examination of immunomodulators, highlighting their clinical importance and therapeutic potential. It begins with an overview of immunomodulators and their applications, followed by a detailed classification into two primary categories: immunosuppressants and immunostimulants. Additionally, the chapter explores the influence of dietary and lifestyle factors on immunomodulation, emphasizing how specific nutritional components can enhance or suppress immune function, ultimately affecting health outcomes. The integration of computational approaches in immunomodulation is discussed, particularly focusing on the interactions between immunomodulators and the gut microbiome. This section underscores the significance of computational modeling and data analytics, including Artificial Intelligence (AI) and Machine Learning (ML), for predicting therapeutic efficacy and optimizing treatment strategies. Challenges and limitations are critically assessed, addressing the complexities of immune system interactions and the variability in individual responses to immunomodulatory therapies. The chapter concludes with future directions in the field, advocating for continued research to fully unlock the potential of immunotherapeutic interventions. This comprehensive review aims to clarify the interplay between dietary factors, computational advancements, and immunological strategies, ultimately contributing to the development of more effective and personalized therapeutic approaches in immunomodulation.},
}

Humans
*Diet
*Immunomodulation/drug effects
Machine Learning
Gastrointestinal Microbiome/immunology
Animals
*Immunologic Factors/therapeutic use/pharmacology

@article {pmid42134973,
year = {2026},
author = {Nagamine, T},
title = {The Gut-Muscle Axis in Sarcopenia: From Parallel Aging to a Self-Perpetuating Vicious Cycle.},
journal = {Geriatrics & gerontology international},
volume = {26},
number = {5},
pages = {e70538},
doi = {10.1111/ggi.70538},
pmid = {42134973},
issn = {1447-0594},
mesh = {*Sarcopenia/physiopathology/microbiology/metabolism ; Humans ; *Gastrointestinal Microbiome/physiology ; *Dysbiosis/complications ; *Muscle, Skeletal/metabolism ; *Aging/physiology ; Aged ; },
abstract = {Sarcopenia and gut dysbiosis form a bidirectional vicious cycle where microbial changes drive systemic inflammation and muscle loss. Conversely, declining muscle metabolism further disrupts the microbiome. While "bottom-up" microbial interventions show promise in restoring muscle integrity, more research is needed on "top-down" muscle rejuvenation to fully confirm this interaction.},
}

*Sarcopenia/physiopathology/microbiology/metabolism
Humans
*Gastrointestinal Microbiome/physiology
*Dysbiosis/complications
*Muscle, Skeletal/metabolism
*Aging/physiology
Aged

@article {pmid42127905,
year = {2026},
author = {Shen, J and Sun, Z and Song, H and Pu, Y and Wang, P and Hailili, G and Huang, Y and Mei, Z and Chen, H and Huang, L and Yuan, C and Wang, X and Zheng, Y},
title = {Healthful plant-based diet, gut enterotype, and cognition in a rural Chinese elderly cohort: A longitudinal multi-omics study.},
journal = {Cell reports. Medicine},
volume = {},
number = {},
pages = {102797},
doi = {10.1016/j.xcrm.2026.102797},
pmid = {42127905},
issn = {2666-3791},
abstract = {The gut microbiome may shape how diet influences cognitive aging, but population-based evidence remains limited. In 784 older adults living in rural China (70-98 years old) with fecal metagenomics and structured dietary assessment, a modified healthful plant-based diet index (mHPDI) is associated with distinct gut microbial structure and taxonomic shifts (15 species, 17 genera). Among participants with repeated cognitive measurements, higher mHPDI is associated with better global cognition, with stronger benefits in participants with non-Prevotella-dominant enterotypes (highest versus lowest tertile β = 0.34, 95% confidence interval [CI], 0.16 to 0.52) than in those with a Prevotella-dominant enterotype (0.04, -0.22 to 0.29; p interaction = 0.04). Enterotype-associated differences in microbial metabolic pathways, including preQ0 and L-isoleucine biosynthesis, parallel this heterogeneity. Moreover, 12 circulating microbiota-related metabolites (primarily amino acids and short-chain fatty acids) are linked to mHPDI. A composite score comprising these metabolites mediates 11.0% of the mHPDI-cognition association (p mediation = 0.02), with branched-chain amino acids as major contributors. These findings suggest that gut microbial context may shape diet-cognition associations.},
}