@article {pmid42623301,
year = {2026},
author = {Pareek, S and Wright, RD and Ballarò, R and Xue, C and Bartelli, TF and Chandra, V and Li, L and Ortiz, J and Lam, T and Patel, H and Lee, J and Shrestha, P and Savage, H and Le Roux, O and Liu, H and Vallejo-Schmidt, T and De Maleki, R and Putluri, V and Putluri, N and Petrosino, JF and Burks, JK and Gomez, JA and Guarnerio, J and Katz, MHG and Ngo-Huang, A and Prakash, LR and Parker, NH and Petzel, MQB and Tan, L and Baydogan, S and McAllister, F and Schadler, KL},
title = {Exercise Modulates Microbial Metabolites and Induces Stromal Remodeling in Pancreatic Cancer.},
journal = {Cancer research},
volume = {},
number = {},
pages = {OF1-OF17},
pmid = {42623301},
issn = {1538-7445},
support = {P30 CA125123/CA/NCI NIH HHS/United States ; R01 CA282786/CA/NCI NIH HHS/United States ; R21 CA218732/CA/NCI NIH HHS/United States ; R37 CA237384/CA/NCI NIH HHS/United States ; },
abstract = {UNLABELLED: Exercise induces a variety of changes in the tumor microenvironment, with beneficial effects in several tumor types. However, a better understanding of the clinical effects of exercise and mediating mechanisms is needed to maximize the utility of exercise for patients. In this study, we analyzed tumors from patients with pancreatic ductal adenocarcinoma (PDAC) in the PancFit trial and identified an exercise-induced reduction in cells expressing α-smooth muscle actin (αSMA). Interrogation of changes in tumor stromal composition with exercise in a murine PDAC model revealed a microbially influenced reduction in αSMA+ cells and Il6-expressing inflammatory cancer-associated fibroblasts (iCAF). Cholic acid, a microbial bile acid, was increased in both patients and murine models with exercise, as a potential mediator of exercise-induced reduction in iCAFs. Consistent with these findings, patients that exercised more also exhibited fewer iCAFs and lower tumor IL6 expression, supporting a stromal remodeling effect of physical activity. In summary, this study demonstrates that the antitumor effect of exercise includes stromal remodeling, which is affected by microbial metabolites.

SIGNIFICANCE: Exercise-induced changes in cancer associated fibroblasts vary with microbiome composition, which may explain the heterogeneity in tumor responses to exercise and could guide future exercise trials in cancer patients.},
}

@article {pmid42828327,
year = {2026},
author = {Moody, ZK and Joseph, AT and Gill, R and Persaud, R and Gurreri, A and Manikkuttiyil, C and Ahmed, A and Golakoti, S and Villamil, S and Ghotra, R and Scripa, I},
title = {Exploring the Effect of Nutrition on Fetal Development in Pregnant Patients With Inflammatory Gut Diseases: A Scoping Review.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e115649},
pmid = {42828327},
issn = {2168-8184},
abstract = {Inflammatory gut diseases (IGDs) are increasing in prevalence and pose unique challenges during pregnancy. Poorly controlled IGDs in pregnant women are linked to adverse fetal outcomes such as low birth weight, preterm birth, and impaired gut microbiome development. Nutritional deficiencies, particularly in magnesium, folate, and vitamin B12, exacerbate these risks due to both inadequate intake and malabsorption. This scoping review aimed to evaluate the role of nutrition in fetal development among pregnant women with IGDs, highlighting dietary strategies that may enhance maternal gastrointestinal health and optimize fetal outcomes. This study was designed as a scoping review to examine the relationship between IGDs, pregnancy, and nutrition. Following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for scoping review (PRISMA-ScR) guidelines, a search was conducted for peer-reviewed literature using the databases Embase, Web of Science, Ovid MEDLINE, and CINAHL. The search was restricted to studies published in English within the last ten years and that focused on pregnant or postpartum patients and fetuses in the context of nutrition and IGDs. The search strategy used predefined terms in multiple combinations with Boolean operators: "inflammatory bowel disease", "pregnancy", "fetus development", "nutritional deficiency", "diet restriction", and "vitamin supplementation". The search identified 1,589 records, of which 728 remained after duplicate removal. Following title and abstract screening, 103 full-text reports were sought for retrieval, 98 were assessed for eligibility, and five studies met the final inclusion criteria. The included studies suggest that multidisciplinary antenatal care, maintenance of disease remission, and attention to maternal nutritional status may support favorable maternal and neonatal outcomes. However, the available evidence is limited, consists primarily of observational studies, and no included study directly evaluated nutritional interventions and fetal outcomes. Research on fetal outcomes remains limited and warrants future investigations exploring long-term fetal outcomes, the impact of maternal nutritional deficiencies, and dietary interventions to improve treatment protocols. Advancements in this research can ultimately improve maternal and neonatal outcomes in IGD-affected pregnancies.},
}

@article {pmid42828346,
year = {2026},
author = {Zamfirescu, M and Chirila, SI and Gurgas, L and Gheorghe, E and Hangan, T},
title = {Ultraviolet Radiation and the Skin Microbiome: Dose-Dependent Effects and Consequences for Epidermal Barrier Integrity.},
journal = {Clinical, cosmetic and investigational dermatology},
volume = {19},
number = {},
pages = {630891},
pmid = {42828346},
issn = {1178-7015},
abstract = {The skin microbiome is continuously exposed to solar ultraviolet radiation (UVR), but the magnitude, direction and clinical meaning of the associated microbial changes remain uncertain. This narrative review critically evaluates evidence from controlled human, environmental, phototherapy, animal and in vitro studies linking UVA/UVB exposure to changes in skin microbial composition or function and to epidermal barrier outcomes. The available evidence indicates that UVA and UVB can alter community composition within minutes to days. However, these effects vary according to dose, wavelength, body site, host and sampling time, and may partly recover. The evidence does not support a universal pattern of decreased Cutibacterium acnes and increased Staphylococcus aureus. Dose is central to this relationship: repeated very-low or suberythemal exposure can induce antimicrobial peptides and adaptive responses, whereas single high exposures are more likely to cause inflammation, barrier injury and immunosuppression. Microbiome-dependent mechanisms include changes in tryptophan metabolites and AhR signaling, short-chain fatty acids, extracellular DNA and modulation of cytokine responses. Evidence from phototherapy studies shows that microbial remodeling can accompany clinical improvement, while sunscreen studies suggest that some formulations preserve microbial features without measurably disrupting dominant resident taxa. Because the available studies differ substantially in exposure, site, platform and endpoint, quantitative pooling is not currently defensible. Numerical results are therefore summarized in a structured evidence table Broad-spectrum photoprotection remains foundational. Microbiome-compatible formulations and microbial or metabolite adjuncts are promising but still require randomized, dose-resolved, multi-omic clinical validation.},
}

@article {pmid42828397,
year = {2026},
author = {Cai, P and Zhao, F and Zhao, Z and Zhang, X and Wu, C},
title = {Synthetic microbial communities for plant growth promotion and soil-borne disease suppression: design principles, mechanisms, and translational challenges.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1942488},
pmid = {42828397},
issn = {1664-302X},
abstract = {Declining soil health and soil-borne diseases threaten sustainable crop production, while single-strain inoculants often perform inconsistently in the field due to poor establishment, limited persistence, and narrow functional capacity within resident microbiomes. Synthetic microbial communities (SynComs), assembled from defined and functionally characterized microorganisms, offer a tractable strategy to improve plant growth and suppress disease through complementary and redundant functions. This review critically examines recent advances in plant-associated SynComs, emphasizing rational design over empirical strain mixing. We compare construction strategies based on core microbiome mining, trait-based screening, microbial interaction networks, host and niche adaptation, and multi-omics- or model-guided assembly. Available available evidence suggests that no single SynCom construction strategy is universally superior; rather, robust design requires an integrated, context-specific approach combining host- or core-microbiome-guided candidate selection, trait validation, interaction-informed assembly, and model-guided optimization. We synthesize direct and plant-mediated mechanisms, including nutrient mobilization, phytohormone modulation, stress alleviation, niche pre-emption, resource competition, antibiosis, rhizosphere restructuring, and immune priming. Evidence from representative crop-pathogen systems is evaluated based on mechanistic support, community stability, and validation under non-sterile greenhouse and field conditions. Major barriers to deployment include context-dependent efficacy, instability of community composition and function, formulation and delivery constraints, quality control, ecological safety, and regulatory uncertainty. We propose a design-to-deployment framework linking community assembly with ecological validation, formulation engineering, and multi-environment testing, providing a plant-centered roadmap for developing reliable SynCom-based biofertilizers as well as biocontrol products.},
}

@article {pmid42828409,
year = {2026},
author = {Song, Y and Xing, Y and Liu, Y and Zhang, X},
title = {Forensic applications of the skin microbiome: a structured narrative review of donor association, contact inference, and crime-scene reconstruction.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1947173},
pmid = {42828409},
issn = {1664-302X},
abstract = {BACKGROUND: Skin-associated microbial communities are individualized, anatomically structured, temporally dynamic, and readily transferred to contacted surfaces. These properties have generated interest in the skin microbiome as complementary forensic evidence when conventional human DNA or fingerprint evidence is limited.

METHODS: We conducted a structured narrative review guided by the Scale for the Assessment of Narrative Review Articles (SANRA). PubMed/MEDLINE was searched from database inception through 2 August 2026, and reference lists of eligible studies and recent reviews were examined. Peer-reviewed studies were evaluated for relevance to skin microbial individuality, temporal stability, touch transfer, donor or source inference, postmortem interval estimation, analytical standardization, and legal or ethical interpretation. Evidence was synthesized according to study realism, analytical resolution, validation design, and proximity to forensic casework.

RESULTS: The biological basis for forensic use is supported by reproducible inter-individual and body-site variation, including persistent strain- and gene-level features. Controlled studies show that skin-associated communities can be recovered from touched objects and clothing and can support donor differentiation, particularly when targeted markers, microbial single-nucleotide polymorphisms, or metagenomic features are used. Nevertheless, performance estimates are strongly affected by cohort size, body site, substrate, time since deposition, environmental background, contamination, and machine-learning design. Evidence for body-site and biological-trace source inference is promising, whereas postmortem interval estimation, chronological contact reconstruction, and spatial trajectory inference remain exploratory.

CONCLUSION: Skin microbiome profiling should currently be regarded as a source of investigative intelligence and potentially complementary evidence rather than a replacement for human DNA profiling. Translation into practice requires harmonized protocols, realistic multicenter validation, open and representative reference datasets, explicit error-rate reporting, likelihood-based interpretation, and proportionate ethical and legal safeguards.},
}

@article {pmid42828627,
year = {2026},
author = {Alabi, A and Ngwese, MM and Essone, PN and Mbouna, AV and Kabwende, AL and Lotola-Mougeni, F and Mahmoudou, S and Kokou, K and Esen, M and Lell, B and Adegnika, AA and Ramharter, M and Grobusch, MP and Ley, RE and Kremsner, PG and Agnandji, ST},
title = {Gut resilience and clinical homeostasis following administration of neomycin and albendazole in soil-transmitted helminth-infected adults living in Lambaréné, Gabon.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42828627},
issn = {1439-0973},
abstract = {PURPOSE: Gut resilience and systemic homeostasis are interrelated dynamic functions. A gut that fails to regulate intestinal barrier integrity, metabolite production, and immune regulation will lead to systemic pathogenic invasion and susceptibility to infections. Gut resilience withstands stressors that can induce gut failure, and even when disturbances occur, it quickly restores its composition and functions. There is a paucity of data on the microbiome of people living in low- and middle-income settings. We therefore assessed the local and systemic conditions of gut resilience following neomycin treatment in individuals with intestinal soil-transmitted helminth infections.

METHODS: A randomised, placebo-controlled, participant-blinded study was conducted in adults up to 40 years with known soil-transmitted helminth infections (STH) living in Lambaréné, Gabon. Participants were randomly assigned to the intervention or placebo groups. The intervention group received neomycin 2000 mg per os (p.o) three times daily for 10 days and fluconazole 150 mg p.o once weekly for two weeks. On day 90, all study participants were treated with 400 mg of albendazole for three days. Outcome measures included egg counts of Ascaris lumbricoides, Necator americanus and Trichuris trichiura, a dual marker of gut barrier permeability and metabolite production (FABP2), incidence of adverse events, and assessment of pathogen proliferation.

RESULTS: Thirty-eight participants were enrolled and followed up for 180 days. At the gut level, the intestinal STH egg counts decreased on day 7 after neomycin administration. From day 14 onward, intestinal STH egg counts began to increase, reaching the initial counts by day 90. There was no difference in FABP2 marker concentration between the two groups. Adverse events occurred more frequently in the intervention group, most commonly side effects of neomycin and fluconazole. There was no pathogen proliferation.

CONCLUSION: Broad-spectrum antibiotic-induced changes in laying of STH helminth eggs in STH-infected adults, which occurred at the peak of the drug concentration observed in the blood, corresponding to a high availability in the gut. These changes support that the antibiotic-induced changes were transient and did not induce occurrence of clinical peripheral changes. The local resilience of the gut translated into peripheral-maintained homeostasis.

TRIAL REGISTRATION: The study was registered at the Pan African Clinical Trial Registry (https//pactr.samrc.ac.za/) database with identification numberPACTR201707002361207.},
}

@article {pmid42828629,
year = {2026},
author = {Alkhanafsa, M and Wafi, J and Deek, S},
title = {Oral tebipenem pivoxil for complicated urinary tract infections: evidence, potential role in IV-to-oral transition, and antimicrobial stewardship.},
journal = {Infection},
volume = {},
number = {},
pages = {},
pmid = {42828629},
issn = {1439-0973},
abstract = {Complicated urinary tract infections (cUTIs), including pyelonephritis, are increasingly challenging when resistant Enterobacterales eliminate conventional oral treatment options. Tebipenem pivoxil (UTEBZI), approved by the US Food and Drug Administration in June 2026, is the first oral carbapenem approved in the United States for selected adults with cUTI. This review evaluates its pharmacology, microbiological activity, efficacy, safety, and potential role in intravenous (IV)-to-oral treatment and antimicrobial stewardship METHODS: A structured narrative review of PubMed/MEDLINE, regulatory documents, clinical-trial reports, guidelines, pharmacokinetic/pharmacodynamic studies, microbiological studies, and relevant oral step-down literature was conducted through 12 August 2026. Priority was given to randomized phase 3 trials, FDA prescribing information, and IDSA guidance RESULTS: ADAPT-PO and PIVOT-PO demonstrated noninferiority of complete oral tebipenem regimens to IV ertapenem and IV imipenem-cilastatin, respectively, with high clinical cure rates. Tebipenem retains activity against many ESBL- and AmpC-producing Enterobacterales but lacks reliable activity against major carbapenemases. Neither phase 3 trial randomized clinically improving patients after initial IV therapy; therefore, direct randomized evidence for a formal tebipenem step-down strategy is lacking. Important uncertainties include limited bacteremia data, every-six-hour adherence, optimal post-IV duration, cost-effectiveness, microbiome effects, and resistance selection CONCLUSION: Tebipenem is an important culture-directed oral option for selected adults with cUTI when narrower effective oral agents are unavailable. Its most defensible early role is replacement of otherwise necessary continued IV carbapenem therapy in carefully selected patients, with source control, susceptibility confirmation, renal doseadjustment, safety screening, duration planning, and stewardship oversight. Dedicated switch, bacteremia, implementation, and resistance-surveillance studies remain needed.},
}

@article {pmid42828642,
year = {2026},
author = {Balabat, MTJ and Loquero, EJ and Amer, NB and Coñado, JC and Cabolbol, HJB and Romarate, RA and Mabuhay-Omar, J and Watanabe, K and Chien, MF and Bacosa, HP},
title = {Urban Road Dust as a Microbial Hotspot: Spatial Variation of Bacterial Communities and Metal Associations in the Philippines.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828642},
issn = {1573-0972},
mesh = {*Bacteria/classification/genetics/isolation & purification ; RNA, Ribosomal, 16S/genetics ; Philippines ; *Dust/analysis ; Cities ; *Metals/analysis ; *Microbiota ; Biodiversity ; DNA, Bacterial/genetics ; Environmental Monitoring ; Phylogeny ; Soil Microbiology ; },
abstract = {Urban road dust is a reservoir and transport medium for diverse microorganisms, yet its bacterial communities in tropical environments remain poorly understood. This study examined the spatial variation of road dust bacterial communities across three Philippine metropolitan areas: Metro Manila, Metro Cebu, and Metro Cagayan de Oro, spanning the country's three principal island groups. Dust from nine sites was analyzed using 16 S rRNA gene metabarcoding (V3-V4), with community composition, diversity, predicted functional potential (PICRUSt2), and metal associations evaluated; contamination was assessed using pollution indices (PLI, degree of contamination, and ecological risk). Proteobacteria and Actinobacteria dominated all sites, and a small core of genera: Paracoccus, Acinetobacter, Kocuria, and Deinococcus, was consistently detected. Alpha diversity did not differ among cities (Kruskal-Wallis, p > 0.05), whereas community composition did (PERMANOVA: R[2] = 0.466, p = 0.004), with distinct metropolitan clustering. This decoupling indicates that local conditions shape which taxa dominate rather than overall diversity, consistent with environmental filtering of a shared regional pool. Alkanindiges reached its highest relative abundance at Metro Cebu's commercial core. In Metro Cagayan de Oro, Paracoccus increased toward the most trace-metal-laden site (D3) and correlated positively with cobalt and nickel; with elevated predicted denitrification in this area, this points to a possible pollution-responsive signal. Metro Cagayan de Oro also showed a pronounced higher relative abundance of Chloroflexi, marking it as a distinctive, transitional urban environment. Pollution indices indicated baseline-to-moderate contamination across the sampled roadsides. Predicted function paralleled taxonomy (R[2] = 0.467). These findings establish a baseline for tropical road-dust microbiota and support integrating microbial assessment into urban environmental monitoring.},
}

*Bacteria/classification/genetics/isolation & purification
RNA, Ribosomal, 16S/genetics
Philippines
*Dust/analysis
Cities
*Metals/analysis
*Microbiota
Biodiversity
DNA, Bacterial/genetics
Environmental Monitoring
Phylogeny
Soil Microbiology

@article {pmid42828644,
year = {2026},
author = {Kaur, M and Mishra, AK},
title = {Next-generation probiotics and microbiome-based therapeutics highlighting Akkermansia muciniphila and Amuc_1100.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42828644},
issn = {1573-0972},
mesh = {*Probiotics/therapeutic use/pharmacology ; Humans ; *Gastrointestinal Microbiome ; Animals ; Akkermansia ; Verrucomicrobia ; *Bacterial Proteins ; Intestinal Mucosa/microbiology ; },
abstract = {The gut microbiota is pivotal in regulating host metabolism, immune signaling, and the integrity of the mucosal barrier, thus serving as a critical factor in various metabolic, inflammatory, and gastrointestinal disorders. Traditional probiotics, primarily comprising Lacticaseibacillus and Bifidobacterium species, have been utilized to enhance gut health; however, the strain-dependent effects and variable clinical outcomes associated with these probiotics have prompted increased interest in next-generation probiotics (NGPs). Akkermansia muciniphila, a commensal organism that degrades mucin and resides at the mucosal interface, has emerged as a prominent NGP owing to its ability to reinforce epithelial integrity, modulate immune responses, and foster metabolic homeostasis. Of particular significance is its surface protein, Amuc_1100, which acts as a parabiotic molecule. This protein engages host pattern-recognition pathways, bolsters tight-junction proteins, and alleviates low-grade inflammation. In contrast to live bacterial formulations, purified Amuc_1100 presents advantages concerning stability, safety, and regulatory compliance. This review aims to synthesize contemporary insights into gut microbiome functionality while comparing traditional probiotics with next-generation alternatives. Additionally, it delineates the therapeutic potential of A. muciniphila and Amuc_1100. The discussion further encompasses clinical advancements, regulatory frameworks, and formulation considerations that are propelling the shift towards mechanism-based microbiome therapeutics.},
}

*Probiotics/therapeutic use/pharmacology
Humans
*Gastrointestinal Microbiome
Animals
Akkermansia
Verrucomicrobia
*Bacterial Proteins
Intestinal Mucosa/microbiology

@article {pmid42828686,
year = {2026},
author = {Kazarina, A and Vaškevica, A and Senkāne, DE and Zayakin, P and Hušča, S and Vīksne, K and Pirsko, V and Sokolovska, L and Sergejeva, N and Nakurte, I and Pastare, L and Ruhl, S},
title = {Salivary microbiome responses to chlorhexidine and Coriandrum sativum essential oil mouthwashes in patients with periodontitis in a randomized 2-week clinical trial.},
journal = {Clinical oral investigations},
volume = {30},
number = {10},
pages = {},
pmid = {42828686},
issn = {1436-3771},
mesh = {Humans ; *Mouthwashes/pharmacology ; *Saliva/microbiology ; *Chlorhexidine/pharmacology ; *Microbiota/drug effects ; *Oils, Volatile/pharmacology ; Female ; Male ; *Periodontitis/drug therapy/microbiology ; *Coriandrum/chemistry ; Adult ; Middle Aged ; Porphyromonas gingivalis/drug effects ; },
abstract = {OBJECTIVES: To compare the short-term salivary microbiome effects of a Coriandrum sativum essential oil (CSEO) mouthwash, chlorhexidine (CHX) as a benchmark comparator, and water in patients with periodontitis.

MATERIALS AND METHODS: In this randomized three-arm trial, participants with periodontitis rinsed twice daily for 14 days with water, CSEO, or 0.12% CHX. Preclinical anti-Porphyromonas gingivalis and fibroblast cytotoxicity assays informed CSEO concentration selection. Shotgun metagenomic sequencing was performed on 54 saliva libraries, two per participant, from 27 participants sampled at baseline and week 2 (H2O n = 9, CSEO n = 8, CHX n = 10). Alpha diversity, within-subject Bray-Curtis change, and differential abundance were analysed longitudinally.

RESULTS: Both active agents inhibited P. gingivalis in vitro, with CHX showing greater potency. In the clinical trial, no statistically detectable difference between CSEO and water was observed for the primary species-level Bray-Curtis outcome (q = 0.413), alpha diversity (all q ≥ 0.259), or differential abundance. CHX showed greater species-level Bray-Curtis change than water (q = 0.020), lower species-level Simpson diversity (q = 0.014), and broad taxonomic restructuring.

CONCLUSIONS: Under the tested formulation and exposure conditions, CSEO did not produce a statistically detectable group-level salivary microbiome shift relative to water. CHX provided a benchmark for broad ecological perturbation. The CSEO null finding does not exclude modest or heterogeneous effects in a larger cohort.

CLINICAL RELEVANCE: No clinical benefit can be inferred from the absence of a detectable CSEO-associated microbiome shift. Larger studies integrating clinical, inflammatory, and direct functional outcomes are needed.

TRIAL REGISTRATION: ISRCTN79156900, retrospectively registered on 11 May 2026.},
}

Humans
*Mouthwashes/pharmacology
*Saliva/microbiology
*Chlorhexidine/pharmacology
*Microbiota/drug effects
*Oils, Volatile/pharmacology
Female
Male
*Periodontitis/drug therapy/microbiology
*Coriandrum/chemistry
Adult
Middle Aged
Porphyromonas gingivalis/drug effects

@article {pmid42828720,
year = {2026},
author = {Naveed, M and Yang, T and Togliatti, O and Joe, B and Hill, JW},
title = {Gut dysbiosis, blood pressure regulation, and cardiometabolic risk in polyendocrine metabolic ovarian syndrome (PMOS).},
journal = {Reviews in endocrine & metabolic disorders},
volume = {},
number = {},
pages = {},
pmid = {42828720},
issn = {1573-2606},
abstract = {Polyendocrine metabolic ovarian syndrome (PMOS), formerly known as polycystic ovary syndrome (PCOS), is a common endocrine-metabolic disorder associated with increased hypertension and cardiometabolic risk. Gut dysbiosis is also frequently reported in affected women, raising the question of whether microbiome-linked pathways contribute to blood pressure elevation or vascular risk in this syndrome. To evaluate and synthesize the available evidence linking gut dysbiosis, gut microbial function, and microbiome-related mechanisms to hypertension, blood pressure regulation, and cardiovascular risk in women with PMOS, we conducted a narrative review of the literature in PubMed, Scopus, Web of Science, Google Scholar, and citation tracking. Search terms included PCOS, PMOS, gut microbiota, gut dysbiosis, hypertension, blood pressure, cardiovascular risk, microbial metabolites, bile acids, intestinal permeability, inflammation, renin-angiotensin signaling, renal sodium handling, and autonomic regulation. Human studies, animal models, interventional studies, and mechanistic investigations relevant to PMOS and hypertension were reviewed according to predefined inclusion and exclusion criteria. Eligible publications were preclinical studies, human studies, English language, adult females, and peer-reviewed original or review articles. Clarifying whether gut dysbiosis contributes to hypertension in PMOS may improve understanding of the mechanisms underlying cardiometabolic risk in affected women and inform the development of microbiome-targeted diagnostic and therapeutic strategies. Achieving this goal will require well-phenotyped clinical studies integrating PMOS, blood pressure and vascular assessments with functional microbiome analyses.},
}

@article {pmid42828814,
year = {2026},
author = {Shah, AM and Li, Z and Chen, L and Zhao, Y and Jiang, J and Ma, Y and Wang, W},
title = {Dietary date (Phoenix dactylifera) modulates antioxidant defenses, immune function, and cecal microbiota to improve performance in Muscovy ducks.},
journal = {Poultry science},
volume = {105},
number = {12},
pages = {107852},
doi = {10.1016/j.psj.2026.107852},
pmid = {42828814},
issn = {1525-3171},
abstract = {Phytogenic feed additives from agro-industrial byproducts are increasingly explored as antibiotic alternatives in poultry, yet their efficacy in Muscovy ducks remains poorly documented. This study investigated the effects of dietary date (Phoenix dactylifera) fruit supplementation at 0% (control), 5% (D1), and 10% (D2) on growth performance, blood biochemistry, antioxidant status, immune function, meat quality, intestinal morphology, and cecal microbiota in Muscovy ducks over a 42-day feeding trial. Date fruit supplementation dose-dependently improved final body weight, average daily gain, and feed conversion ratio (p < 0.05) without affecting feed intake. Serum antioxidant capacity was markedly enhanced, with elevated T-SOD, GSH-Px, and T-AOC alongside reduced MDA in both treated groups (p < 0.05). Immunologically, date significantly increased IgA and IgG while decreasing TNF-α and IL-6 (p < 0.05). Intestinal histomorphometry revealed improved ileal villus height, width, and crypt depth (p < 0.05). Cecal microbiome analysis showed increased alpha diversity, phylum-level shifts favoring Bacillota and Actinomycetota, and genus-level enrichments correlated with enhanced performance and immunity. Meat quality remained largely unaffected, with only reduced leg muscle redness. Correlation analyses linked specific beneficial genera to improved antioxidant and immune indices. Collectively, these findings provide the first systematic evidence that 10% whole date fruit inclusion is a safe, effective functional additive for Muscovy ducks, enhancing productivity through antioxidant, immunomodulatory, and microbiome-modulating mechanisms and offering a sustainable nutritional strategy to reduce reliance on synthetic additives in duck production systems.},
}

@article {pmid42829048,
year = {2026},
author = {Hashem, MA and Kayesh, MEH and Kohara, M and Tsukiyama-Kohara, K},
title = {Combining antiviral therapy with cancer treatment in HBV-associated HCC: A translational approach.},
journal = {Virus research},
volume = {373},
number = {},
pages = {199812},
doi = {10.1016/j.virusres.2026.199812},
pmid = {42829048},
issn = {1872-7492},
abstract = {Hepatitis B virus (HBV) infection remains a major global health concern and is a leading cause of hepatocellular carcinoma (HCC). Despite advances in antiviral therapy and cancer treatment, HBV-related HCC (HBV-HCC) continues to pose significant challenges due to its complex pathogenesis involving chronic inflammation, viral persistence, and liver fibrosis. Current antiviral therapies reduce viral load and liver inflammation but often fail to eliminate integrated viral DNA or prevent carcinogenesis. On the other hand, cancer therapies such as surgery, ablation, immunotherapy, and targeted therapy have limited success when used in isolation, especially in patients with active HBV replication. This review examines the emerging concept of combining antiviral and anticancer strategies to improve clinical outcomes in HBV-HCC. We discuss the molecular mechanisms linking HBV infection to HCC, the role of antiviral therapy in reducing recurrence post-HCC treatment, and the impact of HBV reactivation during cancer therapy. In addition, we explore emerging biomarkers for early detection and prognosis, the therapeutic implications of HBV DNA integration, and the potential of gene-editing technologies targeting viral reservoirs. We further review the influence of HBV-induced immune dysregulation on immunotherapy outcomes, the relevance of host-microbiome interactions in liver carcinogenesis, and the utility of precision medicine approaches in guiding treatment. We highlight recent translational studies, clinical trials, and future directions that support a dual-modality approach, aiming for long-term remission and improved survival in patients with HBV-HCC.},
}

@article {pmid42829191,
year = {2026},
author = {Schaefer, HR and Frankenfeld, CL and Wikoff, D},
title = {Low- and No-Calorie Sweeteners Lack Shared Target Organs or Modes of Action Required for Cumulative Risk Assessment.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {},
number = {},
pages = {116424},
doi = {10.1016/j.fct.2026.116424},
pmid = {42829191},
issn = {1873-6351},
abstract = {BACKGROUND AND OBJECTIVE: The safety of individual low- and no-calorie sweeteners (LNCS) has been well established over decades, yet interest has grown in potential combined effects from concurrent exposure. This study evaluated (a) whether existing cumulative risk assessment (CRA) frameworks are appropriate for LNCS and (b) their applicability to aspartame, saccharin, sucralose, acesulfame-K, steviol glycosides, and cyclamate.

METHODS: Regulatory CRA guidance and safety evaluations for each LNCS were reviewed. Toxicological data from repeat-dose and reproductive/developmental studies were synthesized by organ system and effect thresholds. A structured review of human microbiome studies was also conducted. Evidence was assessed for shared structure, target organ toxicity, and mode of action relevant to CRA frameworks.

RESULTS: Existing frameworks rely on grouping chemicals with shared structure or mode of action; however, LNCS lack common structural features, toxicological profiles, and target organ effects. Kidney findings observed at high doses were inconsistent, species-specific, and considered toxicologically insignificant. Microbiome effects were variable, sweetener-specific, and not indicative of cumulative impact.

CONCLUSIONS: LNCS do not exhibit properties necessary for cumulative assessment under established CRA methods. Evidence supports no cumulative effects at typical intake levels, reinforcing the adequacy of individual acceptable daily intakes (ADIs) for safety evaluation.},
}

@article {pmid42829202,
year = {2026},
author = {Zhang, J and Jiang, X and Lin, Z and Li, H and Jiang, S},
title = {Clinical Landscape of Microbiome Modulators in Gynecological Tumor Treatment: From Pre-Clinical to Clinical Trials.},
journal = {Biomedical journal},
volume = {},
number = {},
pages = {101043},
doi = {10.1016/j.bj.2026.101043},
pmid = {42829202},
issn = {2320-2890},
abstract = {Intestinal microbiota dysbiosis is linked to gynecological tumors (endometrial, ovarian, cervical cancers), and microbiome modulators show therapeutic potential by regulating gut microbiota. This Perspective analyzes the field from pre-clinical to clinical stages. Pre-clinically, a Web of Science bibliometric analysis (2010-2025, 114 articles, 86 reviews) revealed focus on "epithelial ovarian cancer," "estrogen," and "mechanism," with key studies by Baker et al. (2017, gut microbiota-estrogen-endometrial cancer link) and Kopustinskiene et al. (2020, flavonoids' anti-tumor effect via gut flora). Clinically, 4 INFORMA-database trials (2 closed, 1 completed, 1 planning) targeted ovarian/endometrial cancer (no cervical cancer trials), using live microorganisms/faecal modulators mainly for immuno-oncology therapy; bacteriophages (e.g., M13) also emerged as potential modulators. Challenges include unclear optimal combination therapies, lack of cervical cancer trials, and limited modulator types. This analysis offers a field overview and future research directions. The intestinal microbiota constitutes a complex ecological community that influences the normal physiological and pathological processes of distal organs through its metabolic activities. Previous research has demonstrated that dysbiosis of the intestinal microbiota can contribute to the development of endometrial cancer, ovarian cancer, and cervical cancer [1-3]. Microbiome modulators enhance host health by regulating the intestinal microbiota and hold potential as therapeutic agents for gynecological tumors [4]. Consequently, it is imperative to analyze the landscape of clinical trials investigating the efficacy of microbiome modulators in the treatment of gynecological tumors.},
}

@article {pmid42829336,
year = {2026},
author = {Merecz, K and Jarząbek, J and Fichna, J},
title = {Recent developments in the role of oxidative stress in pathogenesis and treatment of inflammatory bowel diseases.},
journal = {Expert review of gastroenterology & hepatology},
volume = {},
number = {},
pages = {},
doi = {10.1080/17474124.2026.2744666},
pmid = {42829336},
issn = {1747-4132},
abstract = {INTRODUCTION: Inflammatory bowel disease (IBD) is a chronic and relapsing disorder of the gastrointestinal tract. Its prevalence has risen rapidly, and nowadays it is a global health concern. Currently available medications reduce inflammation and alleviate the symptoms, but do not cure the disease. Recent findings suggest that dysregulated redox homeostasis may contribute to IBD progression, positioning oxidative stress as one of the primary mechanisms driving inflammation.

AREAS COVERED: Data for this review were identified through a comprehensive search of PubMed and Google Scholar for the period from February 2013 to September 2026. This review aims to describe recent approaches focused on oxidative stress and IBD, including the use of oxidative stress biomarkers, treatment options employing neutrophils and nanoparticles, the emerging role of the Nrf2 signaling pathway, ferroptosis suppression, and oxidative stress-related changes in the microbiome. Furthermore, inflammaging and dietary interventions are discussed in the context of oxidative stress, as they modulate redox homeostasis and influence inflammatory pathways.

EXPERT OPINION: A better understanding of the interplay between ROS, inflammation, microbiome, and dietary interventions may provide valuable insights into mechanisms underlying IBD pathology, while targeting these pathways may facilitate the development of novel, adjunctive therapeutic approaches in IBD management.},
}

@article {pmid42829422,
year = {2026},
author = {Xie, SS and Hu, J and Zhou, W and Ge, XL and Luo, YY and Liu, ZG},
title = {Microbiome signatures and mechanistic pathways in pediatric obesity: from early-life risk to precision interventions.},
journal = {World journal of pediatrics : WJP},
volume = {},
number = {},
pages = {},
pmid = {42829422},
issn = {1867-0687},
support = {82470544//National Natural Science Foundation of China/ ; },
abstract = {BACKGROUND: The gut microbiota is increasingly recognized as a modulator of metabolic health in children, influencing nutrient absorption, immune tone, epithelial barrier function, and energy homeostasis. This review summarizes current evidence on microbial signatures and mechanistic pathways associated with pediatric obesity and evaluates microbiota-targeted strategies for prevention and intervention.

DATA SOURCES: Relevant studies published between January 2000 and February 2026 were identified through searches of PubMed, Embase, and Web of Science using keywords related to pediatric obesity, gut microbiota, microbial metabolites, and microbiota-based interventions. Human studies and mechanistic animal models examining host-microbe metabolic interactions were included.

RESULTS: Pediatric obesity is associated with shifts in gut microbial composition, although taxonomic findings are heterogeneous across studies and should not be interpreted as universal biomarkers. Relatively consistent patterns include reduced Bifidobacterium and Akkermansia muciniphila, whereas associations involving Faecalibacterium, Blautia, and lactobacilli are context-, species-, and strain-dependent. Functional alterations include changes in short-chain fatty acid production, bile acid signaling, microbial branched-chain and aromatic amino acid metabolism, and endotoxin-related inflammatory pathways. The enrichment of Gram-negative taxa such as Enterobacteriaceae may contribute to impaired epithelial barrier integrity, lipopolysaccharide translocation, toll-like receptor 4 signaling, chronic low-grade inflammation, and insulin resistance. Early-life exposures, including cesarean delivery, formula feeding, and antibiotic use, are repeatedly associated with altered microbial succession and later obesity risk, although causality remains incompletely defined. Interventional studies indicate that dietary fiber enrichment and selected probiotic strains can improve microbial and metabolic outcomes in some settings, but efficacy remains strain-specific and clinically heterogeneous.

CONCLUSIONS: Microbial and metabolic signatures are associated with pediatric obesity, converging on pathways of energy harvest, epithelial barrier dysfunction, inflammation, and disrupted host-microbe signaling. Integrative multi-omic and longitudinal studies are required to establish causality and guide the development of personalized, microbiota-based interventions for obesity prevention and treatment in children.},
}

@article {pmid42829460,
year = {2026},
author = {Salman, A and Salman, MA and Abdallah, A and Elewa, A and Marwan, A},
title = {Microbiology and antimicrobial resistance in biliary tract infections including acute and post-ERCP cholangitis: a systematic review and meta-analysis.},
journal = {Annals of Saudi medicine},
volume = {46},
number = {5},
pages = {388-403},
pmid = {42829460},
issn = {0975-4466},
mesh = {Humans ; *Cholangitis/microbiology/drug therapy ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial ; Bile/microbiology ; *Cholangiopancreatography, Endoscopic Retrograde/adverse effects ; *Biliary Tract Diseases/microbiology ; Acute Disease ; },
abstract = {BACKGROUND: Organisms cultured from bile in biliary tract infection, and their resistance, vary widely between settings, and pooled estimates to guide empirical therapy are lacking.

OBJECTIVE: Estimate bile-culture yield, organism distribution, and resistance.

DESIGN: Systematic review and random-effects meta-analysis of PubMed and reference lists.

SETTING: Reports spanned nine countries across Asia, Europe, Africa, and North America.

METHODS: We extracted ductal-bile culture data from observational studies published from 2015 to 2025 of biliary infection/cholangitis; noninfectious, gall bladder-only, microbiome-only, and nonextractable reports were excluded. DerSimonian-Laird models, subgroup analysis, and JBI appraisal were used.

MAIN OUTCOME MEASURE: Culture yield; secondary organism proportions and resistance.

SAMPLE SIZE: 5147 patients (97% retrospective; 3% prospective); organisms: 35 267 observations.

RESULTS: Yield was 77.3% (95% CI, 67.8-84.6); Gram-negative organisms 69.8% (65.6-73.7), E. coli, 27.4% (23.5-31.7), K. pneumoniae, 14.1% (12.3-16.2).

HETEROGENEITY: I[2]=86.0%-97.7%; all P<.001.

RISK OF BIAS: Fourteen reports were low risk, two moderate; exclusions minimally changed estimates.

CONCLUSION: Bile-culture yield was high and Gram-negative organisms, particularly E. coli and K. pneumoniae, predominated, but estimates were highly heterogeneous and resistance could not be pooled; culture-directed therapy guided by local antibiograms is therefore preferable to a universal empirical regimen.

LIMITATIONS: PubMed-only/open-access search, retrospective designs, inconsistent definitions, one dominant dataset.

REGISTRATION: Retrospectively registered on OSF (89wqs; DOI: 10.17605/OSF.IO/89WQS).},
}

Humans
*Cholangitis/microbiology/drug therapy
*Anti-Bacterial Agents/pharmacology
*Drug Resistance, Bacterial
Bile/microbiology
*Cholangiopancreatography, Endoscopic Retrograde/adverse effects
*Biliary Tract Diseases/microbiology
Acute Disease

@article {pmid42829701,
year = {2026},
author = {Métris, KL and Métris, J},
title = {Fungus above us: exploring the atmospheric mycobiome by aircraft.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21746},
pmid = {42829701},
issn = {2167-8359},
mesh = {*Fungi/classification/isolation & purification/genetics ; *Air Microbiology ; *Aircraft ; *Mycobiome ; *Atmosphere ; Seasons ; Biodiversity ; Ecosystem ; Environmental Monitoring/methods ; },
abstract = {Fungi play a key role in ecosystems, influencing the global bioaerosol budget and pollution dynamics even when metabolically inactive. Despite this, diversity and transport of fungi in the atmosphere are not well explored. This study shows that the atmosphere contains diverse fungi with varied ecological classifications and recruitment patterns reflecting underlying terrestrial habitats. Abundant genera include Neoascochyta, Cladosporium, Alternaria, Coniothyrium, Penicillium, Hymenochaetopsis, Lachnum, and Fonsecazyma. The atmospheric mycobiome is dominated by decomposers and pathogens; over 40% of the sampled airborne fungi are putative plant or animal pathogens. Using aircraft surveys from 2022 to 2023 in distinct seasons alongside comprehensive environmental datasets, airborne fungal diversity was found to decline with altitude and increasing vegetation productivity. Patterns of diversity in atmospheric fungal communities are shaped by vegetation productivity and meteorology. Remote sensing and meteorological data provide valuable insight into this diversity and reinforce the role of local or regional phenology as an important determinant of atmospheric biodiversity. Additionally, the proportional composition of functional guilds in the atmosphere shifts with vegetation productivity and surface winds, suggesting that seasonal transport dynamics may contribute to shaping assembly of the atmospheric mycobiome. This work demonstrates how integrated genomic and environmental datasets acquired by aircraft and satellite data could be leveraged in future to clarify aerobiology questions and contribute to a unified view of fungal ecology.},
}

*Fungi/classification/isolation & purification/genetics
*Air Microbiology
*Aircraft
*Mycobiome
*Atmosphere
Seasons
Biodiversity
Ecosystem
Environmental Monitoring/methods

@article {pmid42830139,
year = {2026},
author = {Hayashi-Okamura, Y and Shintani, T and Obayashi, N and Morihara, N and Oki, Y and Yoshimoto, T and Ando, T and Suzuki, M and Kataoka, N and Yasuda, G and Kobayashi, Y and Miyata, R and Kajiya, M},
title = {Age-related shifts in the salivary microbiome linked to cariogenic changes: A cross-sectional study.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {107091},
doi = {10.1016/j.jdent.2026.107091},
pmid = {42830139},
issn = {1879-176X},
abstract = {INTRODUCTION: Although the prevalence of dental caries in older individuals is increasing, there are limited reports on the dental health of this population. In this cross-sectional study, we compared caries risk assessed using saliva and microbiome components between older and younger individuals.

METHODS: Between February 2022 and September 2025, 229 younger people (12-35 years) and 111 older people (≥50 years) underwent caries risk testing and oral bacterial count measurement using stimulated saliva at the Oral Examination Center of Hiroshima University Hospital. Caries risk was assessed using salivary secretion volume, salivary pH, buffering capacity, and cultures of Mutans streptococci (MS), Lactobacillus, and Candida species. The DMFT index and plaque control record were obtained from medical records. Bacterial DNA was extracted from a randomly selected subset of 30 younger-group samples and 58 older-group samples. The diversity and composition of the microbiome were analyzed by 16S rRNA sequencing. Data were compared between the two groups using univariate and multivariate analyses.

RESULTS: MS levels and salivary buffering capacity were significantly higher in the older group compared to the younger group (p < 0.05). Microbial diversity was lower in the older group. Prevotellaceae and Actinomycetota were among the most prevalent bacteria in the older group. Kyoto Encyclopedia of Genes and Genomes pathway analysis showed elevated expression of genes involved in anaerobic metabolism and glucose metabolism in the older group compared to the younger group.

CONCLUSION: These findings suggest that age-related ecological shifts in the oral microbiome may increase the risk of dental caries.},
}

@article {pmid42830277,
year = {2026},
author = {Feng, T and Shang, J and Ma, Y and Li, J and Qin, Y and Zhang, J and Cheng, S and Zhang, G and Xie, H},
title = {Metagenomic analysis of rhizosphere soil microbiota in wild and cultivated Notopterygium incisum, an umbelliferae medicinal herb.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {42830277},
issn = {1471-2180},
mesh = {*Rhizosphere ; *Soil Microbiology ; *Metagenomics/methods ; *Apiaceae/microbiology/growth & development ; *Plants, Medicinal/microbiology/growth & development ; *Microbiota/genetics ; *Bacteria/classification/genetics/isolation & purification ; },
abstract = {Notopterygium incisum is not only a traditional Chinese medicine but also an endemic herb. Artificial domestication and large-scale cultivation are crucial for resolving the crisis of wild resources and the supply-demand imbalance of N. incisum, yet current techniques have failed to stably provide the herb medicine in good quality. Metagenomic analyses revealed significant differences in the rhizomicrobiota between wild and cultivated N. incisum, particularly in microbial composition, gene functions, and community assembly. The rhizomicrobiota of the wild N. incisum from 3 different sites with an altitude drop over 1400 m had a similar composition when being compared with the cultivated samples. The wild N. incisum had higher abundances of beneficial microbes, particularly Hyphomicrobiales (Rhizobiales) (21.27% on average). In contrast, the rhizosphere microbial communities of the cultivated N. incisum showed a high prevalence of functional genes involved in the pathways of DNA repair and recombination proteins, replication and repair, peptidases and inhibitors, DNA replication proteins, and transfer RNA biogenesis. The co-occurrence networks analysis indicated that the stability of the wild samples' network remained significantly more robust when nodes were proportionally removed, as the wild samples' network had approximately the same positive and negative links while the cultivated samples' network had nearly all positive links and many fewer connectors. This is related to the conclusion that wild N. incisum exhibits superior efficacy, as reported in previous studies. Additionally, it can be observed from the sampling images that the root surface of wild N. incisum has more pronounced tiny protrusions, which may be associated with rhizobial attachment, thereby enhancing the nitrogen fixation process. Importantly, the observed shifts in rhizosphere microbial communities, particularly the enrichment of beneficial rhizobia in wild plants, are closely linked to enhanced accumulation of bioactive secondary metabolites such as coumarins and volatile oils. These microbiome-driven differences are likely associated with the superior medicinal quality of wild N. incisum compared to cultivated counterparts, highlighting the pivotal role of rhizosphere microbes in shaping therapeutic efficacy.},
}

*Rhizosphere
*Soil Microbiology
*Metagenomics/methods
*Apiaceae/microbiology/growth & development
*Plants, Medicinal/microbiology/growth & development
*Microbiota/genetics
*Bacteria/classification/genetics/isolation & purification

@article {pmid42830393,
year = {2026},
author = {Gao, YY and Xu, JJ and Wu, YX and Xu, HM and Wang, GZ and Zhou, GB},
title = {Air pollution and early-onset lung cancer: from environmental carcinogenesis to early intervention strategies.},
journal = {Carcinogenesis},
volume = {},
number = {},
pages = {},
doi = {10.1093/carcin/bgag070},
pmid = {42830393},
issn = {1460-2180},
abstract = {Air pollution remains a global public health challenge, with nearly the global population (99%) breathing air that exceeds World Health Organization (WHO) guideline limits-annual means of 5 μg/m3 for PM2.5 and 15 μg/m3 for PM10. Both household and ambient air pollution are classified as Group 1 carcinogens and contain hazardous components, including polycyclic aromatic hydrocarbons (PAHs), heavy metals, and volatile organic compounds. Exposure contributes to a broad spectrum of systemic diseases and is responsible for more than 14% of global lung cancer deaths, while also elevating risks for breast, gastrointestinal, and brain cancers. Mechanistically, air pollutants drive early lung carcinogenesis through intrinsic genomic instability, manifesting as DNA damage, telomere dysfunction, mitochondrial impairment, and specific mutational signatures, alongside epigenetic dysregulation. Concurrently, they foster a tumor-promoting niche via chronic inflammation mediated by CXCL13 and IL-1β and facilitate early immune evasion through activation of the PD-L1 and CD47-SIRPα axes. In addition, air pollution disrupts the respiratory-gut microbiome, reducing microbial diversity and promoting pathogenic enrichment. A range of early biomarkers-including genomic, epigenomic, inflammatory, and microbiome profiles-have been validated for preventive interventions, with multi-marker combinations demonstrating improved efficacy. Multiple chemopreventive targets have also been identified to counteract oxidative stress, inflammation, and immune evasion. Looking ahead, research priorities should include exploring gene-environment interactions, clinically validating biomarkers and therapeutic targets, translating basic discoveries into clinical practice, and developing precision prevention strategies for high-risk populations. Ultimately, integrating biomarker-guided early detection with multi-target chemoprevention will be essential to reducing the global burden of air pollution-induced early-onset lung cancer.},
}

@article {pmid42830658,
year = {2026},
author = {AlRamadneh, TN and Jyothi-S, R and Priyadarshini-Nayak, P and Nanda, A and Al-Hasnaawei, S and Bhatt, A and Singh-Chauhan, A and Singla, S and Mishra, MK},
title = {The Microbiome in Glioblastoma: Mechanisms, Tumor-Immune Interactions, and Translational Perspectives.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70431},
doi = {10.1002/mbo3.70431},
pmid = {42830658},
issn = {2045-8827},
mesh = {Humans ; *Glioblastoma/immunology/microbiology ; Animals ; *Brain Neoplasms/microbiology/immunology ; *Gastrointestinal Microbiome/immunology ; *Microbiota ; Translational Research, Biomedical ; },
abstract = {Despite multimodal treatment, glioblastoma (GBM) remains difficult to control because of diffuse invasion, tumor heterogeneity, immune dysfunction, and frequent recurrence. Increasing attention has focused on whether intestinal microbial communities and their products can modify systemic and central nervous system processes relevant to GBM. This narrative review critically evaluates current evidence linking microbial communities, microbial metabolites, tumor-associated microbial signals, and host immune responses with GBM biology and clinical translation. PubMed, Scopus, Web of Science, and Google Scholar were searched for English-language studies published from January 2019 through August 2026, with earlier foundational studies included when necessary. Human cohorts, tumor-tissue studies, glioma models, microbiota-transfer experiments, and mechanistic investigations were considered. Preclinical evidence supports several plausible pathways, including changes in short-chain fatty acid availability, microglial and macrophage states, blood-brain barrier regulation, systemic immunity, and tryptophan-related signaling. However, many relevant metabolites may originate from microbial, host, immune, or tumor sources. Human studies remain limited and vulnerable to confounding, reverse causation, treatment effects, and geographic variation. Bacterial nucleic acids and bacteria-associated HLA-bound peptides have been detected in brain tumors, but these findings do not establish viable colonization or a gut origin. Low microbial biomass also necessitates rigorous contamination control and orthogonal validation. Microbial influences are biologically plausible modifiers of GBM rather than established drivers. Clinical translation requires longitudinal human studies, source-resolved analyzes, standardized low-biomass methods, mechanistic validation, and independent replication. No microbiome-based biomarker or microbiome-directed therapy is currently validated for routine GBM care or patient stratification in clinical practice.},
}

Humans
*Glioblastoma/immunology/microbiology
Animals
*Brain Neoplasms/microbiology/immunology
*Gastrointestinal Microbiome/immunology
*Microbiota
Translational Research, Biomedical

@article {pmid42830770,
year = {2026},
author = {Gopinath, D and Selvakumar, B and Sekar, P and Mohammed, MM and Li, Z},
title = {Metabolic effects of periodontal pathogens Fusobacterium nucleatum and Porphyromonas gingivalis in colorectal cancer cells.},
journal = {Journal of Taibah University Medical Sciences},
volume = {21},
number = {5},
pages = {998-1006},
pmid = {42830770},
issn = {1658-3612},
abstract = {BACKGROUND: Periodontal pathogens are increasingly recognized as key regulators of cancer biology. However, their roles in modulating metabolism-related gene expression in colorectal cancer remain poorly understood.

METHODS: Human colorectal cancer (HCT)116 cells were exposed to Fusobacterium nucleatum and Porphyromonas gingivalis for 6 h and 24 h. Expression levels of genes involved in lipid metabolism (ACAT1 and PLD2), amino acid metabolism (PAH), polyamine synthesis (SMS), kynurenine pathway (KYNU), and detoxification (ALDH2) were evaluated using quantitative real-time PCR (qPCR). The expression profiles of these genes were also compared between colorectal tumor and normal tissues using The Cancer Genome Atlas (TCGA) RNA-seq data.

RESULTS: F. nucleatum and P. gingivalis induced distinct, time-dependent metabolic changes in HCT116 cells. At 6 h, F. nucleatum upregulated KYNU, PLD2, and ACAT1 , whereas P. gingivalis broadly suppressed SMS, PAH, KYNU, ACAT1, and ALDH2. At 24 h, F. nucleatum and P. gingivalis maintained predominantly suppressive effects on KYNU, SMS, and PAH. mRNA expression analysis indicated the downregulation of ACAT1 and ALDH2, and upregulation of KYNU, PLD2, PAH, and SMS in colorectal cancer, and partial overlap with F. nucleatum-induced changes.

CONCLUSION: The distinct impacts of the two bacterial species demonstrated the complexity of colorectal cancer host-microbiome interactions. These findings suggest that microbial species may influence tumor biology through different metabolic processes, leading to diverse rather than uniform metabolic changes in colorectal cancer cells.},
}

@article {pmid42830840,
year = {2026},
author = {Rizvi, M and Mufarji, AA and Shizawi, NA and Jabri, ZA and Haque, OI and Haider, M and Sami, H and Malehi, AA and Mohammad, R and Masters, K and Khan, F and Mamari, AA and Bahlani, SA and Mohamed, O and Stepanskyi, D and Khan, M and Shaukat, A and Gautam, A and M Luthfee, N and Malhotra, S and Agarwal, J and Gur, R and Siddiqui, AH and Devi, S and Thakuria, B and Princess, I and Gupta, A and Sultan, A and Jitendranath, A and G S, B and Kalita, JB and Jain, M and Singh, NP and Mohapatra, S and Farooq, S and Jankhwala, MS and Devi, VRY and Sen, M and Al-Hattali, H and Al-Ghussaini, HS and Ghafari, MSHA and Jardani, AA},
title = {Public perceptions on antibiotic use and resistance: a social media-based multicountry survey during WAAW 2022.},
journal = {IJID regions},
volume = {21},
number = {},
pages = {100975},
pmid = {42830840},
issn = {2772-7076},
abstract = {OBJECTIVES: This study aimed to assess the global public's knowledge, attitudes, and practices concerning antibiotic use and antimicrobial resistance (AMR) during World Antimicrobial Awareness Week 2022 because public engagement is crucial in promoting responsible antibiotic use.

METHODS: A validated trilingual questionnaire (Cronbach α 0.78) created in Google Forms was disseminated via the social media platforms of the Diagnostic and Antimicrobial Stewardship to Protect Antibiotics study group, yielding 766 responses from 30 countries. The survey explored the respondents' sociodemographic data, antibiotic knowledge, AMR awareness, and behavioral intentions in common clinical scenarios. Statistical analysis evaluated knowledge, attitudes, and practices scores by education level, academic background, and geographic region.

RESULTS: Respondents were predominantly from Asia and Africa. Higher education levels overall and a science background in particular were strongly associated with higher knowledge and more positive attitudes (P < 0.001). However, only 38% knew that antibiotics treat bacterial infections. Over half expected antibiotics for cold or flu symptoms; 31% would question why doctors were not prescribing them, and 18.5% would seek a second opinion. Awareness of the impact of antibiotics on the gut microbiome and fetal health was linked to reduced antibiotic-seeking behavior.

CONCLUSION: The findings primarily reflect engagement from the Middle East and the Indian subcontinent. The critical gaps in the public's understanding of appropriate antibiotic use support the need for school- and university-based AMR curricula, greater community engagement, and strategic use of digital platforms to foster responsible antibiotic practices.},
}

@article {pmid42831109,
year = {2026},
author = {Luo, H and Zhao, C and Yu, S and Zhou, C and Wei, D and Lin, W and Wang, X and Gong, Z and Xie, K},
title = {Ecological assembly of activated sludge microbiomes under contrasting process configurations and influent regimes.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1912780},
pmid = {42831109},
issn = {2296-4185},
abstract = {Activated sludge microbial communities are central to pollutant removal and operational stability in petrochemical wastewater treatment plants (PWWTPs). However, in full-scale systems, the relative associations of process configuration and influent composition with microbial community organization and treatment performance remain difficult to disentangle. This study investigated four full-scale PWWTPs in Northeast China, including three oxic systems and one anoxic/oxic system receiving different proportions of petrochemical, mixed industrial, and domestic wastewater inputs. We combined 16S rRNA gene sequencing, phylogenetic bin-based null model analysis (iCAMP), and partial least squares path modeling (PLS-PM) to evaluate microbial community structure, inferred assembly patterns, and their associations with influent characteristics, effluent quality, and chemical oxygen demand (COD) removal. The oxic systems showed higher alpha diversity than the anoxic/oxic system, although this comparison was potentially influenced by differences in influent composition and site-specific operational conditions. Community composition differed among influent types, with Proteobacteria, Bacteroidota, Acidobacteriota, and Planctomycetota showing contrasting enrichment patterns. iCAMP indicated a predominance of stochastic assembly patterns in the oxic systems and deterministic assembly in the anoxic/oxic system. Core zOTUs, including members of Rhodocyclaceae, Pseudomonadaceae, and Candidatus Berkiella, were associated with COD and nitrogen removal, supporting their potential as ecological indicators of treatment performance. Within the PLS-PM, influent characteristics showed stronger direct statistical associations with COD removal than process configuration, whereas process-related associations were represented mainly by indirect paths through microbial community composition. These findings highlight the joint influence of influent composition and process configuration on activated sludge microbial communities and treatment performance while providing an ecological basis for future microbiome-informed monitoring and process diagnosis in PWWTPs.},
}

@article {pmid42831379,
year = {2026},
author = {Huang, S and Tang, Y and Wang, Z and Li, D},
title = {Biofilm-associated microbial risks in a mega water diversion project: distribution of putative pathogen-associated taxa and concrete biocorrosion potential in the Middle Route canal of the South-to-North water diversion project.},
journal = {Biofouling},
volume = {},
number = {},
pages = {1-16},
doi = {10.1080/08927014.2026.2742367},
pmid = {42831379},
issn = {1029-2454},
abstract = {The ecological assembly of putative pathogen-associated taxa and the biogeochemical potential related to concrete biocorrosion have rarely been examined within an integrated framework in large freshwater diversion systems. We conducted quarterly biofilm sampling at eight stations along the Middle Route canal of the South-to-North Water Diversion Project, and combined 16S rRNA gene amplicon sequencing with shotgun metagenomics to characterize longitudinal and seasonal microbial patterns. Taxonomy-based screening identified 279 putative pathogen-associated ASVs with a mean relative abundance of 3.40%, primarily affiliated with Bacillus and Brevundimonas. Their relative abundance was lowest in the middle reaches, where higher flow velocity and dissolved oxygen may reduce biofilm-associated retention. Total nitrogen accounted for the largest individual contribution among the measured environmental variables (6.13%), whereas normalized stochasticity ratios indicated that stochastic processes predominated in overall community assembly. Metagenomic analysis further revealed spatially structured nitrogen- and sulfur-cycling potential, including biocorrosion-associated taxa such as Thiobacillus and Desulfovibrio, with several related functional pathways showing comparatively higher abundances in upstream biofilms. These findings establish an integrated ecological framework in which stochastic assembly, nutrient-associated selection, and hydrodynamic modulation jointly shape biofilm-associated microbial risks. The study provides critical insights for safeguarding both water-quality monitoring and century-scale infrastructure performance in mega water diversion systems.},
}

@article {pmid42831621,
year = {2026},
author = {Espinoza, JL and Phillips, AJ and Dupont, CL},
title = {Leviathan: fast, memory-efficient, and scalable taxonomic and pathway profiling for (pan)genome-resolved metagenomics and metatranscriptomics.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0097026},
doi = {10.1128/msystems.00970-26},
pmid = {42831621},
issn = {2379-5077},
abstract = {Functional profiling of meta-omics is essential for understanding microbial communities, yet support for custom genome-resolved reference databases is limited. We introduce Leviathan for integrated taxonomic and functional profiling at both genome and pangenome resolution. Leviathan combines Sylph for ultrafast alignment-free taxonomic profiling with Salmon for pseudo-alignment-based read quantification in DNA space against (pan)genome-resolved gene catalogs, producing dual metrics per (pan)genome: pathway abundance and graph-based pathway coverage. Benchmarking alignment backends on synthetic metagenomes, we show that DNA-space pseudo-alignments retain competitive (pan)genome-level classification performance compared to traditional alignment, reducing resource requirements, while translated searches in protein space lose classification resolution from ambiguous mapping events. Leviathan's utility is demonstrated through two case studies: a marine plastisphere metagenomics data set analyzing metabolic shifts between early and mature biofilm communities, and a dental caries metatranscriptomics data set where co-expression network analysis identified organism-specific transcriptional patterns diagnostic of health and disease states. Leviathan is available at https://github.com/jolespin/leviathan.IMPORTANCEUnderstanding what microbes can do, not just which ones are present, is central to translating microbiome research into actionable insight. Existing functional profiling tools either rely on fixed reference databases or require complex multi-step pipelines when applied to custom genome collections, and none natively compute per-(pan)genome pathway abundance and graph-based pathway completeness in a single workflow. This limits the ability for researchers to directly compare functional profiles to tangential analyses on their specific genome catalogs. Leviathan addresses this gap with integrated taxonomic and functional profiling against user-defined (pan)genome-resolved references using pseudo-alignment, achieving competitive classification accuracy, with lower resource requirements compared to current methods. Native pangenome support enables routine quantification of metabolic potential and transcriptional activity at both genome and pangenome resolution, revealing functional variation across related strains that single-genome or community-level analyses obscure.},
}

@article {pmid42831644,
year = {2026},
author = {Beck, CW and Younge, SN and Gerardo, NM and Blumer, LS},
title = {Implementation and continuation in a network CURE: insights from the Bean Beetle Microbiome Project.},
journal = {Journal of microbiology & biology education},
volume = {},
number = {},
pages = {e0022226},
doi = {10.1128/jmbe.00222-26},
pmid = {42831644},
issn = {1935-7877},
abstract = {The positive impact of course-based undergraduate research experiences (CUREs) on student outcomes is widely acknowledged. Yet, barriers to initial and then continued implementation of CUREs limit their use. In this Perspective, we expand on previous research on why faculty do (or do not) implement CUREs by exploring patterns and reasons for CURE implementation and continuation in the context of a network CURE that provided intensive faculty professional development, and curricular and financial resources. The compatibility of the CURE to existing curricula, the complexity of the CURE from the perspective of both instructors and students, and changes in faculty positions or the courses they were teaching were the biggest barriers to both initial and continued implementation. In contrast, in-person, hands-on faculty professional development, and flexibility in the duration of implementation were the biggest facilitators of implementation and continuation. We propose the following recommendations to encourage even broader implementation and continuation of CUREs: (i) in-person hands-on faculty development workshops, (ii) implementation flexibility, allowing for either full-semester or half-semester implementations or modular activities with core modules and then a selection of add-ons, (iii) maximize learning-teaching innovation compatibility with already existing courses and curriculum by focusing on foundational skills and knowledge, (iv) implement CUREs in core courses with multiple sections and instructors to increase implementation success and foster systemic change, and (v) give faculty resources and support to lead students in a CURE for which the faculty are not experts, and the outcome is unknown.},
}

@article {pmid42831655,
year = {2026},
author = {Fulcher, JA and Newman, KP and Pham, BT and Li, F and Cho, GD and Elliott, J and Tobin, NH and Shoptaw, S and Gorbach, PM and Aldrovandi, GM},
title = {Comparison of oral and gut microbiome highlights the role of oral bacteria in systemic inflammation in HIV.},
journal = {mSphere},
volume = {},
number = {},
pages = {e0038426},
doi = {10.1128/msphere.00384-26},
pmid = {42831655},
issn = {2379-5042},
abstract = {UNLABELLED: Chronic HIV-1 infection is associated with increased inflammation-related comorbidities, despite effective viral suppression with antiretroviral therapy. While the role of the gut microbiome in inflammation is well studied, the contribution of the oral microbiome remains less clear. This study investigates the relationship between the oral and gut microbiomes in driving systemic inflammation in persons with HIV. This cross-sectional study utilized archived samples from 198 participants (99 with HIV and 99 without HIV). Oral and gut microbiome composition was analyzed via 16S rRNA sequencing, and systemic inflammatory biomarkers were measured using multiplex assays. Bacterial inflammatory potential was assessed through in vitro co-culture and epithelial barrier permeability assays. The oral microbiome in HIV was characterized by increased Veillonella, Capnocytophaga, and Megasphaera, and several decreased genera including Fusobacterium. Using permutational multivariate analysis of variance, we found that the oral microbiome was a significant driver of cytokine variation in HIV compared to the gut microbiome and identified specific associations with oral Veillonella and Megasphaera. We found no differences in anti-Veillonella parvula serum IgG by HIV status, but IgG titers did correlate with microbial translocation markers sCD14 and LBP in HIV. In vitro studies demonstrated that Veillonella parvula increased oral epithelial barrier permeability and induced monocyte activation. These studies suggest that the oral microbiome, particularly Veillonella parvula, may contribute to systemic inflammation in HIV through mechanisms involving epithelial barrier disruption, oral translocation, and monocyte activation.

IMPORTANCE: In HIV, persistent inflammation contributes to the elevated risk of cardiovascular disease, metabolic disorders, and other non-AIDS comorbidities. Alterations in the gut microbiome and resultant microbial translocation are contributors to this ongoing inflammation. Most microbiome research has focused on the gut compartment, though there is increasing appreciation for the role of the oral microbiome in chronic inflammatory diseases. Few studies have systematically compared the oral and gut compartments in HIV-associated inflammation. In this study, we identify Veillonella parvula as a plausible oral driver of epithelial barrier disruption and immune activation, expanding current understanding of microbial contributors to persistent inflammation in HIV.},
}

@article {pmid42831995,
year = {2026},
author = {Biswas, A and Ghosh, B and Kumari, P and Rangra, A and Chowdhury, KR and Kumar, A},
title = {Pharmacomicrobiomics-driven targeted drug delivery for precision microbiome modulation.},
journal = {Daru : journal of Faculty of Pharmacy, Tehran University of Medical Sciences},
volume = {34},
number = {2},
pages = {},
pmid = {42831995},
issn = {2008-2231},
mesh = {Humans ; *Drug Delivery Systems/methods ; *Microbiota ; Probiotics/administration & dosage ; Precision Medicine/methods ; Multiomics ; Prebiotics ; Animals ; },
abstract = {BACKGROUND: The human microbiome can actively influence how drugs are handled and processed in our body. More knowledge of host-microbiome-drug interactions has shifted drug delivery from current approaches to precision therapeutics.

OBJECTIVES: The review is to evaluate various targeted strategies and mechanisms of drug delivery systems (DDS) driven by pharmacomicrobiomics. Moreover, the pharmacomicrobiomics-based DDS will also be discussed in terms of their therapeutic applications, translation, and new technologies for microbiome precision.

METHODS: Assessment on the latest development on microbiome-drug interactions and microbiome-based drug delivery strategies, including microbial enzyme activated prodrugs, nano- and micro-particle systems, probiotics, prebiotics, postbiotics, bacteriophages, genetically modified microorganisms, smart materials, and niche-selective delivery systems. The researchers also investigated clinical evidence, security, regulatory issues, Pharmacoeconomics and new emerging multi-omics and AI based strategies.

RESULTS: Microbiome-targeted DDS enable localized drug activation, site-specific delivery, and reduced systemic exposure. Enzyme-responsive systems achieved up to a 3-fold increase in local drug concentration, while SER-109 (VOWST) reduced CDI recurrence to 12% versus 40% with placebo at 8 weeks. FMT combined with pembrolizumab achieved objective responses in 40% (6/15) of previously non-responsive melanoma patients. Engineered microbial therapeutics, including SYNB1618 and AG013, further demonstrate the growing translational potential of programmable microbiome-based therapies.

CONCLUSION: Pharmacymicrobiomics-driven drug delivery systems (DDS) represent an innovative approach to precision therapeutics utilizing microbes. However, challenges such as individual microbiome variability, unvalidated biomarkers, safety concerns, intricate regulatory hurdles, and inconsistent translational outcomes from preclinical studies persist. A comprehensive integration of omics data and interdisciplinary collaboration is essential to enhance the predictability of microbiome therapies. Future efforts should focus on microbiome profiling, validating mechanism-based biomarkers, scalable manufacturing, and conducting clinical studies to define patient selection, ensure therapeutic consistency, and confirm long-term benefits.},
}

Humans
*Drug Delivery Systems/methods
*Microbiota
Probiotics/administration & dosage
Precision Medicine/methods
Multiomics
Prebiotics
Animals

@article {pmid42832042,
year = {2026},
author = {Cihan, E and Campbell, PM and Wu, Y and Ledder, RG and Summers, AM and Augustine, T and Knight, CG and McBain, AJ},
title = {Taxon-specific oral mycobiome differences and bacterial-fungal associations in kidney transplant recipients and donors.},
journal = {Journal of applied microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1093/jambio/lxag247},
pmid = {42832042},
issn = {1365-2672},
abstract = {AIMS: This study characterised the pre-transplant salivary mycobiome of kidney transplant recipients and living donors and investigated cross-kingdom associations with the bacteriome.

METHODS AND RESULTS: Mycobiome profiling was performed using ITS sequencing of donor and recipient samples, while paired bacteriome data were obtained from our previous study. No significant differences in fungal or bacterial alpha diversity or beta diversity were detected between recipients and donors, indicating an absence of broad community-level separation. Malassezia and Candida were the dominant fungal genera in both groups. Differential abundance analyses using ANCOM-BC2 and DESeq2 consistently identified lower Malassezia abundance in recipients, alongside predominantly lower abundance of several bacterial taxa. Cross-kingdom network analysis showed low Jaccard similarity in highly central taxa between donors and recipients, despite no significant differences in global network properties. This pattern persisted across most sample-size-matched subsamples.

CONCLUSIONS: These findings suggest that oral microbiome differences between kidney transplant recipients and donors are more apparent in specific taxonomic changes, particularly the reduction in Malassezia, and in the relative organisation of central community members than in broad shifts in overall microbial composition.},
}

@article {pmid42828250,
year = {2026},
author = {Snelling, TJ and Johnson, CA and Warren, HE and Taylor-Pickard, J and Huntington, JA and Sinclair, LA},
title = {Correction: Modulation of the rumen microbiome and metabolism in dairy cows by altering the concentrate feeding pattern and the inclusion of Saccharomyces cerevisiae yeast.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1965017},
doi = {10.3389/frmbi.2026.1965017},
pmid = {42828250},
issn = {2813-4338},
abstract = {[This corrects the article DOI: 10.3389/frmbi.2026.1884444.].},
}

@article {pmid42828283,
year = {2026},
author = {Doshier, J and Anderson, B and Yang, F and Stewart, SD and Calapa, KA and Cooper, R and Wilson-Robles, H and Embree, M and Khanna, C},
title = {Correction: Pilot study evaluating tolerability and changes in fecal microbiota associated with novel probiotic administration to dogs with diarrhea.},
journal = {Frontiers in veterinary science},
volume = {13},
number = {},
pages = {1981863},
doi = {10.3389/fvets.2026.1981863},
pmid = {42828283},
issn = {2297-1769},
abstract = {[This corrects the article DOI: 10.3389/fvets.2025.1720932.].},
}

@article {pmid42828306,
year = {2026},
author = {Wayah, SB and Arakawa, K and Philip, K},
title = {From predicted bacteriocins to ecological function.},
journal = {Current research in microbial sciences},
volume = {11},
number = {},
pages = {100662},
pmid = {42828306},
issn = {2666-5174},
abstract = {Genome and metagenome mining have uncovered large repertoires of predicted bacteriocin loci, but ecological interpretation has lagged behind discovery. This review uses bacteriocins as a focused model for a broader problem in antimicrobial gene prediction: sequence identifies encoded potential, but it does not establish expression, product deployment, target engagement, or community-level consequence. We distinguish four forms of bacteriocin "silence": transcriptional silence, where loci are not detectably expressed under tested conditions; conditional silence, where expression or activity emerges only under specific environmental or social cues; phenotypic silence, where expression or product formation does not yield detectable activity in routine assays; and ecological silence, where activity is observed but its consequences for coexistence, exclusion, colonization, or community assembly remain unresolved. We also clarify how this framework extends previous reviews of bacteriocin diversity and microbiome-shaping roles by providing an inference-centered taxonomy that separates encoded potential from demonstrated ecological function. Finally, we propose a function-first roadmap for bacteriocin research, including condition-resolved transcriptomics and proteomics, promoter and cue-dissection experiments, expanded target panels, spatially structured assays, defined consortia and microcosms, producer/non-producer comparisons, and explicit tests of resistance, immunity, and fitness consequences. Treating predicted bacteriocin loci as hypotheses rather than conclusions will improve how the field moves from gene catalogs to causal ecological understanding.},
}

@article {pmid42828326,
year = {2026},
author = {Kinyua, WN and Munyiri, SW and Wagacha, JM and Mwaura, MN and Njage, PMK},
title = {Agroecological drivers of aflatoxin contamination in maize-based systems: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1802402},
pmid = {42828326},
issn = {1664-462X},
abstract = {Aflatoxin contamination of maize remains a global food safety and public health challenge, particularly because it is a dietary staple food and feed ingredient produced across diverse agroecological zones. Although numerous mitigation strategies have been developed, contamination levels remain variable. This reflects complex interactions among climate, soil properties, crop management practices, plant physiological stress and rhizosphere microbial communities. This review synthesizes evidence on key agroecological drivers of aflatoxin contamination in maize, highlighting climate variability, soil properties, crop and nutrient management, cropping systems, and rhizosphere microbial communities as primary determinants. We examine how these factors influence Aspergillus population dynamics, microbial interactions and aflatoxin biosynthesis across contrasting production environments. Evidence synthesized in this review indicates that inconsistent outcomes of existing management including biological control strategies largely arise from insufficient consideration of soil-plant-microbe interactions and spatial heterogeneity. We identify climatic stress, soil properties and crop management strategies as the dominant determinants of aflatoxin risk, acting through biological mediators such as plant physiological status, rhizosphere microbial communities and fungal population. The review argues that effective and scalable aflatoxin mitigation requires integrated, context-specific and systems-based approaches. We conclude that incorporating agroecological heterogeneity into research design, predictive models and management frameworks is essential for improving risk prediction and developing aflatoxin control strategies in maize-based cropping systems.},
}

@article {pmid42824926,
year = {2026},
author = {Zhao, N and Leng, Z and Li, Q and Wei, S and Li, M and Zhang, Y and Wang, C},
title = {Renal tissue microbiota and metabolite profiling reveal dysregulated signatures in diabetic kidney disease.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1898177},
pmid = {42824926},
issn = {1664-302X},
abstract = {INTRODUCTION: Diabetic kidney disease (DKD) has become the main cause of end-stage renal disease in China. Mounting evidence links microecological disorders to DKD progression. However, the composition and the functional characteristics of the renal microecology in DKD patients remain poorly defined. This study characterized renal tissue microbiota and metabolite profiles in DKD patients, aiming to provide insights for novel diagnostic strategies for DKD.

METHODS: Renal tissue microbiome was analyzed in 42 DKD patients and 10 controls via 16S ribosomal DNA sequencing. Renal metabolomics was performed in 20 DKD patients and 10 controls using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Spearman correlation analysis clarified associations of clinical parameters with renal microbiome and metabolites. Biomarkers were identified by multi-omics integration.

RESULTS: IHC, IF and TEM reveals the presence of bacteria in both glomeruli and renal tubules. A significant separation in microbial community composition was observed between DKD patients and controls (p < 0.05). The relative abundance of Acidobacteriota, Acinetobacter and Afipia genus were significantly elevated in DKD group, whereas Ralstonia genus was decreased. Notably, the genus Acinetobacter demonstrated a significant negative correlation with the eGFR, while Afipia genus exhibited a significant positive correlation with blood glucose levels. Renal microbiota resembled urinary microbiota more closely than gut microbiota. Metabolomic analysis revealed significant difference in renal tissue metabolites between DKD patients and healthy controls. Lactate, hypoxanthine and phosphorylcholine were significantly positively correlated with the eGFR. Comprehensive multivariate analyses identified the genus Ralstonia as a crucial biomarker associated with renal fibrotic injury in DKD, consistent across urinary and gut microbiomes. Decreased serum levels of stearylcarnitine (Car18:0), oleylcarnitine (Car18:1) and tryptophan were closely associated with renal injury, whereas decreased urinary serine and tyramine levels reflected the change of renal metabolites in DKD.

CONCLUSION: Our finding confirms the existence of microbiota within renal tissue and demonstrates that its structure and composition are significantly altered in DKD. These disruptions in renal microecology are closely associated with the progression of DKD. Multi-omics analysis further identified a panel of candidate markers for evaluation of DKDs.},
}

@article {pmid42825108,
year = {2026},
author = {Knoll, RL and Rossow, V and Rössler, J and Hilbert, K and Jarquín-Díaz, VH and Bartolomaeus, TUP and Nitsche, O and Essex, M and Löber, U and Meng, C and Kleigrewe, K and Gehring, S and Forslund-Startceva, SK and Poplawska, K},
title = {A longitudinal multi-omic dataset of pediatric cystic fibrosis patients receiving lumacaftor/ivacaftor therapy: clinical, microbiome, inflammatory and metabolomic measurements collected over 24 months.},
journal = {Data in brief},
volume = {69},
number = {},
pages = {113237},
pmid = {42825108},
issn = {2352-3409},
abstract = {This article describes a longitudinal multiomic dataset generated within a prospective phase IV pilot study of eight children with cystic fibrosis homozygous for the F508del mutation who initiated lumacaftor/ivacaftor therapy. Participants were followed for up to 24 months with repeated collection of clinical metadata, anthropometric measurements, sweat chloride concentrations, lung function assessments, inflammatory markers, conventional microbiology results, stool samples, respiratory samples, and serum metabolomics. The resulting dataset links host phenotypes, microbiome composition, inflammatory parameters, and metabolomic measurements across multiple body sites and time points. Microbiome data were generated from stool, sputum and throat swab samples using 16S rRNA gene sequencing, while serum metabolomics was assessed using untargeted mass spectrometry. The dataset is publicly available through SRA, MassIVE and GitHub repositories and may support future studies of longitudinal host-microbiome interactions, biomarker discovery, methodological benchmarking and comparative analyses across CFTR modulator eras.},
}

@article {pmid42825194,
year = {2026},
author = {Prasad, SS and Singh, A and Ramteke, P and Veres, C and Büchner, R and Vágvölgyi, C},
title = {Symbiotic interactions of plant microbiota in alleviating stress: a review.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1892395},
pmid = {42825194},
issn = {1664-462X},
abstract = {Plants continuously encounter a wide range of biotic and abiotic stresses that adversely affect their growth, development, and productivity. Because they are sessile, plants cannot escape these unfavorable conditions and therefore rely on a diverse array of morpho-physiological, biochemical, and molecular adaptations to survive. Among these adaptive strategies, symbiotic associations with beneficial microorganisms have emerged as a crucial mechanism for enhancing stress tolerance. These plant-microbe interactions are mediated by intricate chemical signaling networks that regulate nutrient exchange, defense responses, and stress adaptation. Despite their immense potential for sustainable agriculture, the large-scale application of beneficial microbes remains limited owing to poor microbial establishment under field conditions and an incomplete understanding of the complex mechanisms governing plant-microbe mutualism. Deciphering these interactions is particularly challenging because they are highly dynamic and involve continuous communication between plants and diverse microbial communities. Recent advances in omics technologies, synthetic biology, and nanotechnology provide unprecedented opportunities to unravel these complex relationships at the molecular and systems levels. This review summarizes plant adaptive strategies under biotic and abiotic stresses, examines the role of microbial symbiosis in stress alleviation, and highlights emerging approaches, including multi-omics integration, synthetic microbial consortia, engineered quorum-sensing circuits, holobiont-level analyses, and nanoparticle-mediated modulation of the rhizosphere microbiome, for understanding and engineering beneficial plant-microbe interactions. Collectively, these advances offer new insights into symbiotic crosstalk and provide a foundation for developing resilient and sustainable agricultural systems.},
}

@article {pmid42825217,
year = {2026},
author = {Zhu, Y and Zhang, J and Wei, Y and Zhou, S and Qin, X},
title = {Biochar application alters soil properties and microbial gene profiles in a continuous cassava cropping system.},
journal = {PeerJ},
volume = {14},
number = {},
pages = {e21731},
pmid = {42825217},
issn = {2167-8359},
mesh = {*Manihot/growth & development ; *Soil Microbiology ; Rhizosphere ; *Charcoal/pharmacology ; *Soil/chemistry ; Nitrogen/metabolism ; Metagenome ; *Microbiota/genetics ; Nitrogen Cycle ; },
abstract = {Continuous cassava cropping can lead to soil degradation and disturbances in soil microbial functions, threatening the sustainability of cassava production systems. To address these challenges, this study examined the effects of biochar on soil physicochemical properties and microbial functional profiles in a continuous cassava cropping system. Two biochar application rates (0 and 3 Mg ha[-1]) were applied, and metagenomic sequencing was conducted to evaluate microbial community composition and functional genes related to carbon and nitrogen cycling in rhizosphere and bulk soils. The results demonstrated that biochar was associated with higher soil pH, soil organic matter, and available nutrient content, with a stronger effect in rhizosphere soil. Biochar application altered the genetic potential of microbial communities, particularly in the rhizosphere soil. In terms of functional categories, biochar was related to higher gene abundances in "homologous recombination" and "DNA replication" categories (Kyoto Encyclopedia of Genes and Genomes (KEGG) database), as well as the "replication, recombination, and repair" category (evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) database) in rhizosphere soil. Biochar also affected the abundance of carbon cycling genes, particularly in the rhizosphere. The abundance of the aerobic respiration-related gene coxA was increased, while the abundance of the anaerobic fermentation gene L-lactate dehydrogenase (LDH) was decreased. Additionally, in rhizosphere soil, biochar significantly increased the abundance of norB (denitrification), GDH2 (nitrogen mineralization), and nifD (nitrogen fixation), while decreasing the abundance of genes involved in nitrogen assimilation (gltB), assimilatory nitrate reduction (nirA), nitrogen mineralization (cynS), and nitrogen uptake (nrtA, nasF, cynA, nrtC, and nasD). Together, these results suggest that biochar application may enhance nutrient availability and reshape microbial functional potential primarily in the cassava rhizosphere, providing field evidence for biochar use in continuous cassava cropping.},
}

*Manihot/growth & development
*Soil Microbiology
Rhizosphere
*Charcoal/pharmacology
*Soil/chemistry
Nitrogen/metabolism
Metagenome
*Microbiota/genetics
Nitrogen Cycle

@article {pmid42825219,
year = {2026},
author = {Sabourin, KR and Mugisha, J and Marshall, VA and Miley, WJ and Chen, T and Billodeaux, J and Whitby, D and Rochford, R and Newton, R},
title = {The association between the oral microbiome and oral Kaposi's sarcoma-associated herpesvirus (KSHV) shedding is modified by age and HIV status in a rural Ugandan cohort.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737698},
pmid = {42825219},
issn = {2000-2297},
abstract = {BACKGROUND: Kaposi's sarcoma-associated herpesvirus (KSHV) spreads through saliva. KSHV shedding is intermittent, suggesting individual-level factors affect reactivation.

OBJECTIVE: Identify associations between oral microbiome and KSHV shedding.

DESIGN: Oral mouthwash samples from 67 KSHV-seropositive participants (ages 4-78) were tested for KSHV DNA by qPCR and microbiome composition via 16S rRNA V4 region sequencing (Illumina MiSeq, Earth Microbiome Project protocols). Samples were selected on age, self-reported HIV status, and KSHV shedding. Alpha and beta diversity and relative abundances at species, genus and phylum levels were compared by KSHV shedding status. Analyses of KSHV shedding and the oral microbiome were stratified by HIV status (n = 49 adults only) and by age (n = 37 without HIV only, children <18 vs adults ≥18).

RESULTS: Neither alpha nor beta diversity differed by KSHV shedding status. Shedders had higher differential abundance of Prevotella multisaccharivorax, Bifidobacterium dentium, B. moukalabense and Bifidobacterium genus and lower Absconditabacteria G-1 bacterium HMT-875. Whether stratified by HIV and KSHV shedding or by age and KSHV shedding, alpha and beta diversity and several taxa at species, genus and phylum levels differed significantly.

CONCLUSIONS: Differences in oral microbiome were associated with KSHV shedding and possibly modified by age and HIV status. Future research should consider the multifactorial nature of the oral environment and KSHV reactivation.},
}

@article {pmid42825245,
year = {2026},
author = {Jia, M and Yang, R and Xu, Y and Wu, Z and Lu, J and Li, Z and Yan, Q and Fan, G and Gui, Y},
title = {Oral microbiome-metabolome axis links glycerophospholipid dysregulation to Alzheimer's disease.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2732297},
pmid = {42825245},
issn = {2000-2297},
abstract = {INTRODUCTION: This study aimed to evaluate the feasibility of using tongue biofilm as a non-invasive, patient-friendly, and cost-effective biomarker source for identifying early microbial and metabolic disturbances associated with Alzheimer's disease (AD).

MATERIALS AND METHODS: A total of 62 outpatients were enrolled (31 with AD and 31 cognitively normal controls). Tongue biofilm samples were analyzed using 16S rRNA sequencing and untargeted metabolomics via UPLC-Q/TOF-MS. Additionally, cerebrospinal fluid (CSF) samples from 36 individuals (18 per group) were examined under identical untargeted metabolomics processing protocols to validate the metabolomic findings.

RESULTS AND DISCUSSION: Microbiome analysis revealed an increased relative abundance of Proteobacteria in the AD group, while Firmicutes and Bacteroidetes were enriched in controls. Metabolomic profiling identified 88 significantly different metabolites between groups, 64 of which achieved area under the curve (AUC) values > 0.90 in the ROC analysis. Glycerophospholipid metabolism has emerged as a key dysregulated pathway in AD, a finding further corroborated by CSF metabolomic analysis. Tongue biofilm represents a non-invasive, cost-effective, and accessible biomarker source, offering potential for AD diagnosis and research when coupled with microbiome and metabolomic analyses. Moreover, the role of glycerophospholipid metabolism in AD pathogenesis warrants further investigation.},
}

@article {pmid42825323,
year = {2026},
author = {Cheong, P and Mangan, C and Clarke, ED and Stanford, J and Cairns, MJ and Collins, CE and Marques, FZ and Snelson, M},
title = {Personalized Nutrition for Hypertension: Current Evidence and Future Directions.},
journal = {Circulation. Genomic and precision medicine},
volume = {},
number = {},
pages = {e005566},
doi = {10.1161/CIRCGEN.125.005566},
pmid = {42825323},
issn = {2574-8300},
abstract = {Hypertension is a leading risk factor for cardiovascular disease, with lifestyle interventions, particularly diet, playing a pivotal role in its management. Recent advancements in personalized nutrition that tailor dietary recommendations based on an individual's unique biology (eg, genetics, microbiome) and lifestyle factors can potentially improve blood pressure control. Indeed, emerging evidence suggests that personalized nutrition can result in more effective and sustained blood pressure reductions than general dietary guidelines. This review explores the current evidence supporting personalized nutrition as a novel strategy for managing hypertension, while leveraging established approaches for controlling glycemia. We evaluate studies integrating genetic markers and genomics, gut microbiome profiles, and metabolic phenotypes to design personalized dietary interventions to reduce blood pressure. Specifically, we discuss how nutritional factors, including sodium and fiber intake and diets such as the Dietary Approaches to Stop Hypertension, interact with an individual's genetic predisposition and gut microbiota composition to influence blood pressure outcomes. However, challenges remain in translation to clinical practice, including the need for larger, long-term trials in real-world settings, accessibility of advanced dietary assessments, considerations of patient adherence, and equity. We highlight the potential of personalized nutrition to refine hypertension treatment and call for further research to optimize its implementation at the public health and clinical practice levels. Particularly in low- and middle-income countries, where hypertension prevalence is higher, cost is an important consideration for successful implementation. However, some personalized treatments focusing on diet are cost-effective and should be prioritized. Ultimately, a personalized nutrition approach may offer a powerful tool for mitigating the global burden of hypertension through targeted, individualized dietary strategies.},
}

@article {pmid42825349,
year = {2026},
author = {Wang, J and Liao, Z and Liu, M and Wang, Y and Cui, Y and Chen, H and Zeng, F and Zhu, Z},
title = {Novel insights into the role of the renal interstitial microenvironment in Randall's plaque formation (Review).},
journal = {International journal of molecular medicine},
volume = {58},
number = {5},
pages = {},
doi = {10.3892/ijmm.2026.6004},
pmid = {42825349},
issn = {1791-244X},
mesh = {Humans ; Animals ; *Cellular Microenvironment ; Calcium Oxalate/metabolism ; *Kidney Medulla/pathology/metabolism ; *Kidney Calculi/pathology/metabolism ; *Kidney/pathology/metabolism ; Durapatite/metabolism ; },
abstract = {Randall's plaque (RP) consists of subepithelial hydroxyapatite (HAP) deposits within renal papillae and provides a well‑established attachment substrate for a subset of idiopathic calcium oxalate (CaOx) kidney stones. However, RP has traditionally been viewed as a passive mineral surface onto which crystals accrete, with comparatively less focus on the cellular and molecular events that build the plaque itself. The renal papillary interstitium has been indicated as a dynamic microenvironment that undergoes molecular remodeling during plaque‑associated mineralization. The present review aimed to organize the current evidence regarding interconnected processes that may overlap in vivo rather than occur in a fixed sequence. Physicochemical conditions in the inner medullary interstitium favor HAP nucleation and provide the foundation for plaque formation. Epithelial injury responses, regulated cell death, osteogenic‑like fibroblasts and immune remodeling may contribute to the development of a pro‑calcific microenvironment; however, the spatial relationship, temporal order and plaque specificity of these processes remain incompletely defined. Macrophage polarization may influence whether local crystal‑associated inflammation and mineralization are amplified or reduced. As interstitial HAP deposits enlarge and become exposed through focal disruption of the renal papillary epithelium, these deposits can interact with pelvic urine and support CaOx nucleation and overgrowth. Systemic metabolic abnormalities and urinary or gut microbiome alterations are associated with stone disease and may modify the papillary microenvironment; however, direct evidence that they alter human RP burden is lacking to date. Of note, available animal and cell models demonstrate selected aspects of mineralization or crystal injury but do not reproduce the chronic, progressive interstitial HAP plaque observed in humans. In conclusion, considering RP as an interstitial microenvironmental disorder may help identify potential biomarkers of early papillary remodeling and generate potential therapeutic strategies for stone prevention in the future.},
}

Humans
Animals
*Cellular Microenvironment
Calcium Oxalate/metabolism
*Kidney Medulla/pathology/metabolism
*Kidney Calculi/pathology/metabolism
*Kidney/pathology/metabolism
Durapatite/metabolism

@article {pmid42825360,
year = {2026},
author = {Lu, F and Macpherson, CW and Haj-Husein, I and Klein, MS and Iskandar, MM and Kubow, S},
title = {Metabolomic signatures of probiotic secretomes reveal strain-specific biofunctional potential: insights from Lacticaseibacillus rhamnosus R0011 and Bifidobacterium longum R0175.},
journal = {Food & function},
volume = {},
number = {},
pages = {},
doi = {10.1039/d5fo05684e},
pmid = {42825360},
issn = {2042-650X},
abstract = {Probiotic secretomes are cell-free byproducts of bacterial growth, which contain bioactive metabolites. These metabolites have antioxidant and anti-inflammatory effects and mediate the host-microbe and microbe-microbe interactions. However, the metabolomic profiles of probiotic secretomes are strain-specific and have not been fully investigated. Untargeted metabolomic analysis was used to characterise the metabolomic profiles of Lacticaseibacillus rhamnosus R0011 (R11) secretome (LR) and Bifidobacterium longum R0175 (R175) secretome (BL). LR and BL had distinct metabolomic profiles. LR exhibits a greater relative abundance of branched-chain hydroxy and aromatic lactic acids, mannitol/sorbitol, mevalonate and flavin mononucleotide. BL is characterized by higher relative abundance of indolelactate, γ-glutamylamino acid, niacin-related metabolites, and organic acids in the citric acid cycle. This study is the first to reveal distinct metabolomic signatures of two widely used probiotic species, providing new insights into their strain-specific roles in host health and microbiome modulation.},
}

@article {pmid42825575,
year = {2026},
author = {Abeysinghe, G and Nagy, E and Wagner, T and Parunandi, S and Santos, J and Bagavathiannan, M and Antony-Babu, S},
title = {A hyphal release-capture soil microcosm for recovering hyphosphere bacterial communities.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0109626},
doi = {10.1128/msystems.01096-26},
pmid = {42825575},
issn = {2379-5077},
abstract = {Fungal hyphae form spatially confined interfaces in soil that mediate close associations with bacteria, collectively referred to as the hyphosphere. Despite its recognized ecological importance, experimental access to hyphosphere-associated microbial communities under realistic soil and plant-associated conditions has remained limited. Here, we present a soil-mimetic microcosm that enables controlled recovery of hyphosphere bacterial communities embedded within plant-associated soil. The system integrates field-derived soil, a native soil microbial inoculum, living cotton seedlings, and a spatially constrained fungal inoculum housed within sterile cell-strainer assemblies, permitting hyphal extension into soil while preserving a recoverable fungal-soil boundary. Using the soil-borne plant pathogen Fusarium oxysporum f. sp. vasinfectum as a model filamentous fungus, we show that the microcosm enables reproducible recovery of hypha-associated soil microaggregates containing physically attached bacterial cells. Full-length 16S rRNA profiling revealed pronounced reductions in bacterial richness and evenness in hyphosphere samples relative to bulk and rhizosphere soils (Shannon diversity, Kruskal-Wallis H = 15.25, P = 0.0016, with genus richness declining by 87% in bulk soil and 24% in rhizosphere soil contexts), consistent with recruitment of a restricted subset of the surrounding microbiota. Ordination analyses demonstrated clear compositional separation between soil and hyphosphere compartments (PERMANOVA F = 7.14, R[2] = 0.572, P = 0.001), with hyphosphere communities of bulk and rhizosphere origin converging to similar composition despite differing starting soils (R[2] = 0.128, P = 0.307). Phylogenetic turnover analyses (βNTI) indicated phylogenetic structuring (exceeding the +2 threshold), whereas taxonomic analyses identified a conserved set of bacterial genera consistently associated with hyphae, alongside compartment-specific taxa influenced by soil and plant context. Together, these findings establish the novel hyphal release-and-capture microcosm as a reproducible, ecologically grounded platform for studying hyphosphere-associated bacterial communities in plant-associated soils.IMPORTANCESoil fungi recruit distinct bacterial communities along their hyphae, forming a specialized microhabitat known as the hyphosphere. Despite its ecological importance, studying hyphosphere-associated bacteria under realistic plant-soil conditions has remained experimentally difficult. Here, we present a soil-mimetic hyphal release-capture microcosm that enables controlled reconstruction and recovery of bacterial communities assembled along fungal hyphae in intact plant-associated soils. Using the cotton wilt pathogen Fusarium oxysporum f. sp. vasinfectum, we show that fungal hyphae reproducibly recruit reduced and compositionally distinct bacterial assemblages from surrounding soils through strong deterministic selection. Because this pathogen is a regulated quarantine organism for which field inoculation is restricted, this system provides a tractable experimental platform for studying hyphosphere assembly under controlled yet ecologically relevant conditions. This approach provides new opportunities to investigate fungal-bacterial interactions, microbial community assembly, and plant-associated soil microbiomes at spatially resolved hyphal interfaces.},
}

@article {pmid42826055,
year = {2026},
author = {Shen, BA and Asfahl, KL and Lim, B and Bertolli, SK and Minot, SS and Radey, MC and Penewit, KM and Ngo, B and Salipante, SJ and Johnston, CD and Peterson, SB and Goodman, AL and Mougous, JD},
title = {The type VI secretion system governs strain maintenance in a wild mammalian gut microbiome.},
journal = {eLife},
volume = {15},
number = {},
pages = {},
pmid = {42826055},
issn = {2050-084X},
support = {R35GM118159/NH/NIH HHS/United States ; DE027850/NH/NIH HHS/United States ; F32 AI164853/NH/NIH HHS/United States ; },
mesh = {Animals ; *Type VI Secretion Systems/metabolism/genetics ; Mice ; *Gastrointestinal Microbiome ; *Bacteroides/genetics/metabolism/growth & development ; },
abstract = {Bacteria inhabiting the mammalian gut coexist in dense communities where contact-dependent antagonism mechanisms are widespread. The type VI secretion system (T6SS) is an interbacterial toxin delivery pathway prevalent among gut Bacteroidales, yet its function in naturally evolved microbiomes remains poorly defined. Here, we examine the role of the T6SS in Bacteroides within a physiologically relevant gut community derived from wild mice (the WildR microbiome). Using newly developed genetic tools and a strategy for functional replacement of strains within the WildR community, we demonstrate that the WildR isolate B. acidifaciens employs a T6SS to antagonize co-resident Bacteroidales. We also show that loss of T6SS function compromises the long-term maintenance of B. acidifaciens in the community but not its initial colonization, establishing the system as a determinant of strain persistence. The T6SS we identified resides on an integrative and conjugative element (ICE). ICE-seq, a targeted sequencing approach, reveals that the T6SS-ICE is distributed among select Bacteroidales and Muribaculaceae species in the WildR microbiome, between which it appears to be recently exchanged. We also show that transfer of the T6SS-ICE to WildR isolate Phocaeicola vulgatus confers transient colonization benefits in mice, but is linked to eventual population decline. Our findings demonstrate that the T6SS can stabilize the presence of specific strains within a complex, co-evolved gut microbiome, yet its value is context dependent and constrained by the ecological and physiological landscape of the host community.},
}

Animals
*Type VI Secretion Systems/metabolism/genetics
Mice
*Gastrointestinal Microbiome
*Bacteroides/genetics/metabolism/growth & development

@article {pmid42826097,
year = {2026},
author = {Shen, S and Xie, X and Lu, L and Ma, W and Tu, H and Zhang, J},
title = {Lacticaseibacillus rhamnosus GG enhances gefitinib efficacy and reduces treatment-related toxicity via propionyl-L-carnitine regulation.},
journal = {Cell reports},
volume = {45},
number = {10},
pages = {118068},
doi = {10.1016/j.celrep.2026.118068},
pmid = {42826097},
issn = {2211-1247},
abstract = {Gefitinib improves outcomes in patients with EGFR-mutant non-small cell lung cancer; however, treatment-related gastrointestinal and hepatic toxicity can limit its long-term use. Here, we investigate whether probiotic strains can improve gefitinib efficacy while reducing treatment-associated toxicity. Among the tested strains, Lacticaseibacillus rhamnosus GG (LGG) shows the strongest enhancement of gefitinib efficacy while reducing intestinal and hepatic injury without altering systemic gefitinib exposure. Metabolomic analyses identify propionyl-L-carnitine as an LGG-associated metabolite detected in both LGG culture and LGG-treated mice. Propionyl-L-carnitine treatment reproduces the antitumor effects of LGG and is associated with altered mitochondrial metabolism, decreased NF-κB/IL-6 signaling, and increased apoptosis. A gut-liver-tumor organ-on-a-chip model further supports these effects. LGG treatment also improves short-chain fatty acid profiles, intestinal barrier markers, and bile acid-related metabolism. Together, these findings suggest that LGG may represent a microbiota-based strategy to enhance gefitinib response while limiting treatment-associated toxicity.},
}

@article {pmid42826146,
year = {2026},
author = {Lio, P and Benjamin, L and Gonzalez, ME and Guénin, S and Hebert, AA and Kwong, PC and Silverberg, N and Schachner, LA},
title = {The Essential Role of Topical Targeted Therapy in Atopic Dermatitis.},
journal = {Journal of drugs in dermatology : JDD},
volume = {25},
number = {10},
pages = {898-902},
doi = {10.36849/JDD.10052},
pmid = {42826146},
issn = {1545-9616},
mesh = {Humans ; *Dermatitis, Atopic/drug therapy/immunology/microbiology ; Administration, Cutaneous ; Skin Microbiome ; *Dermatologic Agents/administration & dosage ; Staphylococcus aureus/isolation & purification/drug effects ; Anti-Inflammatory Agents/administration & dosage ; Pruritus/drug therapy/etiology/immunology ; Administration, Topical ; },
abstract = {BACKGROUND: Atopic dermatitis (AD) is a chronic inflammatory skin disorder marked by immune dysregulation, epidermal barrier dysfunction, microbiome imbalance, pruritus, and xerosis. Despite therapeutic advances, topical treatments remain the foundation of AD management across all severities. However, most existing topicals address only limited aspects of the disease such as itch or inflammation, resulting in frequent relapse and patient dissatisfaction.

METHODS: A focused literature review of topical AD therapies published between January 2015 and July 2025 was conducted, emphasizing efficacy and safety. Recent findings were synthesized in this narrative review to highlight the ongoing role of topical treatments in AD management.

RESULTS: AD is a multifactorial condition influenced by Staphylococcus aureus colonization, immune dysregulation, genetic susceptibility, and environmental factors. These contribute to disease pathogenesis, the itch-scratch cycle, and barrier disruption. While systemic therapies are important, AD treatment continues to rely heavily on topical agents. Optimal management should target inflammation, restore barrier function, and address microbiome dysbiosis. Most current treatments focus on individual disease components, with few addressing the full pathogenic spectrum. Emerging evidence on zabalafin (9.5%) hydrogel, a novel botanical topical therapy, suggests potential multi-target benefits, including anti-inflammatory, antipruritic, antimicrobial, and anti-xerotic effects.

CONCLUSION: There remains a significant unmet need for topical therapies that comprehensively address the AD continuum, including inflammation, itch, barrier dysfunction, and microbial imbalance. Novel agents such as zabalafin may help bridge this gap. &nbsp.},
}

Humans
*Dermatitis, Atopic/drug therapy/immunology/microbiology
Administration, Cutaneous
Skin Microbiome
*Dermatologic Agents/administration & dosage
Staphylococcus aureus/isolation & purification/drug effects
Anti-Inflammatory Agents/administration & dosage
Pruritus/drug therapy/etiology/immunology
Administration, Topical

@article {pmid42826147,
year = {2026},
author = {Thompson, A and Morales-Rivera, A and Patel, E and Sevilla, A and Langley, C and Wolverton, J},
title = {A Narrative Review of Seven Off-Label Treatment Options for Seborrheic Dermatitis.},
journal = {Journal of drugs in dermatology : JDD},
volume = {25},
number = {10},
pages = {943-948},
doi = {10.36849/JDD.9507},
pmid = {42826147},
issn = {1545-9616},
mesh = {Humans ; *Dermatitis, Seborrheic/drug therapy/diagnosis/microbiology ; *Off-Label Use ; Antifungal Agents/administration & dosage/therapeutic use ; *Dermatologic Agents/administration & dosage/therapeutic use/adverse effects ; Phosphodiesterase 4 Inhibitors/administration & dosage/therapeutic use ; Calcineurin Inhibitors/administration & dosage/therapeutic use ; Isotretinoin/administration & dosage/therapeutic use ; Treatment Outcome ; },
abstract = {BACKGROUND: Seborrheic dermatitis (SD) is a chronic inflammatory skin condition driven by overactive sebaceous glands, Malassezia colonization, immune dysfunction, and epidermal barrier disruption. While topical corticosteroids and antifungals are first-line treatments, rebound disease and adverse effects limit long-term use.

OBJECTIVE: To evaluate seven off-label therapies for SD: topical calcineurin inhibitors (TCI), metronidazole, phosphodiesterase-4 inhibitors (PDE4), systemic antifungals, isotretinoin, natural remedies, and microbiome-directed therapies.

METHODS: A PubMed-based narrative review included clinical trials, observational studies, and case reports when higher-level data were lacking.

RESULTS: TCIs and PDE4 inhibitors demonstrated consistent efficacy for facial SD as steroid-sparing options. Metronidazole provided modest benefit, mainly in patients with concomitant rosacea. Both systemic antifungals and low-dose isotretinoin were effective for moderate-to-severe disease, though systemic therapy requires monitoring for hepatotoxicity. Natural agents (eg, honey, tea tree oil) and microbiome-targeted therapies (eg, probiotics, Triphala) showed variable improvement.

CONCLUSION: These therapies serve as promising treatment options for SD, particularly in refractory cases or when standard treatments are unsuitable. Larger comparative trials with standardized outcomes and long-term follow-up are needed to clarify their role.},
}

Humans
*Dermatitis, Seborrheic/drug therapy/diagnosis/microbiology
*Off-Label Use
Antifungal Agents/administration & dosage/therapeutic use
*Dermatologic Agents/administration & dosage/therapeutic use/adverse effects
Phosphodiesterase 4 Inhibitors/administration & dosage/therapeutic use
Calcineurin Inhibitors/administration & dosage/therapeutic use
Isotretinoin/administration & dosage/therapeutic use
Treatment Outcome

@article {pmid42826310,
year = {2026},
author = {Lwere, K and Nakasujja, N and Muwonge, H and Sendagire, H and Gumikiriza-Onoria, JL and Buwembo, D and Buwembo, W and Kabwigu, S and Mukasa, JK and Kirya, F and Nazziwa, A and Othieno, E and Nassanga, R and Nakimbugwe, R and Munabi, IG and Sajatovic, M and Kaddumukasa, M},
title = {Systemic inflammation, gut microbiome composition, and cognitive performance among older Ugandans with Alzheimer's disease and related dementias: A cross-sectional study.},
journal = {Medicine},
volume = {105},
number = {40},
pages = {e50956},
doi = {10.1097/MD.0000000000050956},
pmid = {42826310},
issn = {1536-5964},
mesh = {Humans ; Cross-Sectional Studies ; Female ; Male ; *Gastrointestinal Microbiome/physiology ; *Alzheimer Disease/microbiology ; C-Reactive Protein/analysis/metabolism ; *Inflammation/blood ; Aged ; Uganda/epidemiology ; *Cognition/physiology ; *Cognitive Dysfunction ; Biomarkers/blood ; Aged, 80 and over ; East African People ; },
abstract = {Systemic inflammation is implicated in neurodegeneration; however, evidence linking circulating inflammatory biomarkers to cognitive decline remains inconsistent, particularly in low- and middle-income countries. High-sensitivity C-reactive protein (hs-CRP) is a standard systemic inflammatory marker; however, its relationship with cognitive performance and gut microbiome composition in sub-Saharan Africa remains underexplored. We investigated the association between hs-CRP and cognitive performance across older Ugandans diagnosed with Alzheimer disease (AD), mild cognitive impairment (MCI), and cognitively intact controls and examined whether gut microbial composition modified this relationship. We conducted a cross-sectional study of community-dwelling older adults in Wakiso District, Uganda. Cognitive performance was assessed using the Education-Adjusted Montreal Cognitive Assessment (MoCA). Systemic inflammation was quantified using plasma hs-CRP, and gut microbial profiles were generated via full-length 16S rRNA gene sequencing. Multivariable linear regression models were used to evaluate the associations between log-transformed hs-CRP concentrations and MoCA scores, adjusting for age, sex, and body mass index. Linear regression assumptions were formally tested. Exploratory analyses examined taxon-level differential abundance across diagnostic categories, hs-CRP-microbiome correlations, and hs-CRP × taxon interaction terms on MoCA scores, with multiple-testing adjustment using the false discovery rate. The analytic cohort comprised 85 participants (mean age 77.5 ± 9.2 years; 67 AD, 10 MCI, and 8 controls). Median hs-CRP was higher in AD (1.96 [0.25-3.75] mg/L) than in MCI (0.25 [0.25-2.73] mg/L) and controls (0.25 [0.25-0.84] mg/L). Higher hs-CRP showed a modest inverse trend with MoCA scores that was not statistically significant after adjustment for age, sex, and body mass index (standardized ,). Advancing age was independently associated with poorer cognitive performance (standardized ,). Several microbial genera exhibited nominal differences across diagnostic groups and hs-CRP levels; however, no individual taxon-level associations or hs-CRP × microbiome interaction terms survived false discovery rate correction (). Circulating hs-CRP was not independently associated with global cognitive performance in this cohort of older Ugandans. Genus-level microbiome analyses yielded exploratory, hypothesis-generating patterns that warrant validation in larger longitudinal cohorts investigating gut-brain axis interactions in African populations.},
}

Humans
Cross-Sectional Studies
Female
Male
*Gastrointestinal Microbiome/physiology
*Alzheimer Disease/microbiology
C-Reactive Protein/analysis/metabolism
*Inflammation/blood
Aged
Uganda/epidemiology
*Cognition/physiology
*Cognitive Dysfunction
Biomarkers/blood
Aged, 80 and over
East African People

@article {pmid42826548,
year = {2026},
author = {Huang, P and Zhang, M and Li, Q and Xu, H and Shou, H},
title = {Altered gut microbiota composition and function potential in polycystic ovary syndrome: a multicohort metagenome-assembled genomes study.},
journal = {European journal of obstetrics, gynecology, and reproductive biology},
volume = {327},
number = {},
pages = {115453},
doi = {10.1016/j.ejogrb.2026.115453},
pmid = {42826548},
issn = {1872-7654},
abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) has been associated with gut microbial dysbiosis, but cross-cohort reproducibility and genome-resolved alterations remain insufficiently characterized.

METHODS: We integrated fecal shotgun metagenomic data from three independent PCOS cohorts comprising 169 participants. Taxonomic and functional profiles were generated using MetaPhlAn4 and HUMAnN, while de novo assembly and binning were used to reconstruct species-level genome bins (SGBs). Linear mixed models accounted for cohort heterogeneity. Phylogenetic, co-occurrence network, KEGG-based functional, and prevalence-bias analyses were performed. PCOS classification was evaluated across genus, species, and SGB layers using leakage-safe nested cross-validation and leave-one-cohort-out testing.

RESULTS: PCOS was associated with reduced species richness, contraction of the core microbiota, altered community structure, and lower microbial network connectivity in the two larger cohorts. Eleven species showed differential abundance, including enrichment of Phocaeicola vulgatus and Bacteroides uniformis in PCOS. Genome-resolved analysis recovered 540 dereplicated SGBs, including 32 putative novel species. SGB prevalence bias was phylogenetically structured and remained associated with distinct KEGG Orthology profiles after adjustment for genome length and completeness. PCOS-biased SGBs were enriched in phosphotransferase-system and carbohydrate-utilization functions, whereas Healthy-biased SGBs were enriched in carbon and amino-acid metabolic pathways. Species-level XGBoost achieved the highest internal discrimination (AUC 0.757), but leave-one-cohort-out performance declined substantially, indicating limited cross-cohort generalizability.

CONCLUSIONS: PCOS is associated with multi-resolution gut microbiome alterations, with several community-level features showing cross-cohort reproducibility. These findings extend from community structure to genome-resolved functional programs, refine candidate microbial biomarkers, and highlight the need for external validation before clinical translation.},
}

@article {pmid42826571,
year = {2026},
author = {Aransiola, SA and Onyinoyi, AH and Akhigbe, JO and Onoruoiza, SI and Esenogho, E and Maddela, NR},
title = {The benefits and biases of artificial intelligence in microbiology.},
journal = {Computational biology and chemistry},
volume = {126},
number = {Pt 1},
pages = {109457},
doi = {10.1016/j.compbiolchem.2026.109457},
pmid = {42826571},
issn = {1476-928X},
abstract = {Microbiology has been greatly advanced by the incorporation of Artificial Intelligence (AI) by improving the classification, isolation and detection of microorganisms in several fields where microbial exploration is carried out. With the ability to process large volumes of data from genomic sequences, biochemical profiles and imaging, AI enables faster and more accurate microbial identification than conventional techniques. In microbiome study, AI decodes complex microbial communities in environments, the human body and air by identifying unknown species and their ecological roles. AI is a valuable tool in predicting antimicrobial resistance (AMR) by detecting resistance genes within microbial genomes and aiding in effective treatment strategies. AI-powered diagnostic tools and biosensors offer rapid pathogen detection, while Natural Language Processing (NLP) aids in tracking emerging microbial threats through scientific literature and health databases. In drug and vaccine development, AI accelerates the discovery process by simulating molecular interactions and predicting outcomes, saving time and resources. Most AI models, especially deep learning tools, however, lack transparency leading to difficult result interpretation. Additionally, over-fitting and limited generalizability of AI models are also concerns, along with ethical and legal issues like data privacy in microbiome research and clinical settings. Prior review articles have examined AI's impact in singular microbiological settings, and special attention has been paid to AI applications in medical microbiology. This review article reaches out and analyzes AI applications across general, industrial, medical, and environmental microbiology. It also outlines how mitigation strategies like inclusive dataset design, algorithm vigilance, evaluation techniques like Translational Evaluation of Healthcare AI (TEHAI) and emerging directions of analyses like federated learning and Explainable Artificial Intelligence (XAI) address the risks associated with AI use like bias and reduced interpretability.},
}

@article {pmid42826892,
year = {2026},
author = {Pan, Y and Hua, Y and Wang, T and Lin, H},
title = {Microbial community composition on polytetrafluoroethylene tape retrieved from implant screw channels: A cross-sectional high-throughput 16S rRNA sequencing study.},
journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases},
volume = {145},
number = {},
pages = {106037},
doi = {10.1016/j.meegid.2026.106037},
pmid = {42826892},
issn = {1567-7257},
abstract = {OBJECTIVES: To identify the types of microorganisms colonizing the surface of polytetrafluoroethylene (PTFE) tape used for sealing the central screw channel in implant prostheses and to evaluate their association with the duration of prosthetic functional loading.

METHODS: A cross-sectional study design was adopted. Forty patients who had received single-tooth screw-retained implant restorations using the Straumann BL implant system were recruited and allocated into four groups (n = 10 per group) according to the time elapsed since prosthetic loading: 1 month (Group A), 3 months (Group B), 1 year (Group C), and ≥ 3 years (Group D). PTFE tape samples were aseptically retrieved from the central screw channels. Total genomic DNA was extracted, and the V3-V4 hypervariable regions of the 16S rRNA gene were amplified and sequenced using the Illumina NovaSeq platform. Bioinformatic analysis was performed using the QIIME2 pipeline with amplicon sequence variant (ASV) clustering, and taxonomic assignment was conducted against the SILVA database. Alpha diversity indices, including Chao1 richness, Shannon diversity, and Simpson indices, were compared among the four groups using the Kruskal-Wallis test with pairwise post-hoc comparisons.

RESULTS: The rarefaction curves for all 40 samples plateaued, indicating sufficient sequencing depth. At the phylum level, the ten most abundant taxa across all samples were Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes, Synergistetes, Fusobacteria, Patescibacteria, Campilobacterota, Spirochaetae, and Euryarchaeota. Comparative analysis of microbial diversity among Groups A, B, C, and D revealed no statistically significant differences in Chao1 richness, Shannon diversity, or Simpson indices (P > 0.05 for all comparisons).

CONCLUSION: Bacterial DNA was detected on PTFE tape across all groups, consistent with the hypothesis that microbial ingress into the screw channel via the implant-abutment interface or screw access opening is a frequent phenomenon. The diversity of the bacterial community detected on the PTFE tape within the central screw channel was not significantly influenced by the duration of prosthetic loading.},
}

@article {pmid42826905,
year = {2026},
author = {Lam, IPY and Fong, JJ},
title = {A cross-families evaluation of using fecal samples as a method to study the amphibian gut microbiome.},
journal = {Journal of microbiological methods},
volume = {},
number = {},
pages = {107733},
doi = {10.1016/j.mimet.2026.107733},
pmid = {42826905},
issn = {1872-8359},
abstract = {The gut microbiota plays an important role in animals. Fecal samples are often used to study the gut microbiota because they are convenient to collect, allow for longitudinal sampling, and often necessary when studying rare and endangered species. In this study, we evaluate the effectiveness of using fecal samples by characterizing and comparing the microbiota of feces and the gut (small intestine mucosa, large intestine mucosa) for representatives of seven amphibian families. This includes the first data from a salamander species. Additionally, we compared fecal samples before (pre-feces) and after egestion to understand the microbiota change when there is a delay in collection and preservation (< 24 h). We find that fecal samples significantly differ from both small intestine and large intestine mucosal samples largely based on abundance. The relationship between fecal and gut microbiota differs slightly between species, indicating an influence of host identity. Also, the microbiota of pre-feces and feces significantly differ, indicating a measurable change can occur less than 24 h after egestion. These results help us better understand the relationship between gut and fecal microbiota for amphibians, as well as guide the fieldwork design and data interpretation of future studies.},
}

@article {pmid42827259,
year = {2026},
author = {Pulgar, R and Gaete, A and Mejías, M and Madrid, R and Chávez, I and Pino, L and Talamilla-Espinoza, A and Moscote, J and Pastenes, C and Mandakovic, D},
title = {Dual legacy of plant water-deficit-tolerance and watering history shapes rhizosphere microbial transplant outcomes in tomato post-drought recovery.},
journal = {Environmental microbiome},
volume = {21},
number = {1},
pages = {},
pmid = {42827259},
issn = {2524-6372},
support = {Fondecyt Regular 1221848//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt Postdoctorado 3250795//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt Regular 1250936//Agencia Nacional de Investigación y Desarrollo/ ; },
abstract = {BACKGROUND: Climate change is intensifying drought events, negatively affecting crop yields and quality. Enhancing plant recovery following drought is therefore critical for agricultural resilience. Within the holobiont framework, the plant microbiome plays a key role in modulating plant responses to environmental stress. Here, we evaluated the contribution of rhizosphere microbial transplants derived from Solanum lycopersicum cultivars differing in water-deficit-tolerance and prior exposure or not to water deficit to post-drought recovery in susceptible tomato plants.

RESULTS: Physiological measurements, including net photosynthetic rate, relative water content, and water potential, showed that microbial community transplants from water-deficit-tolerant cultivars previously exposed to water deficit significantly enhanced post-drought recovery in susceptible plants, suggesting a dual legacy effect of host phenotype and irrigation history. High-throughput metabarcoding revealed marked temporal shifts in rhizosphere microbial communities between the initial (Ti) and post-recovery (Tf) stages. Bacterial alpha diversity increased significantly at Tf only for the tolerant inoculant under deficit irrigation, whereas fungal diversity showed more stable response across conditions. Beta-diversity analyses revealed clear separation between Ti and Tf communities for both bacteria and fungi. Community structure changes were highly pronounced in the inoculation treatments that produced the most contrasting post-drought recovery phenotypes (SFI: susceptible cultivar under full irrigation and TDI: tolerant cultivar under deficit irrigation), which formed distinct clusters in hierarchical analyses. Differential abundance analysis identified bacterial taxa enriched at Tf in TDI, while fungal communities displayed stage-specific markers. Functional annotation using FAPROTAX and FUNGuild revealed enrichment of nitrate reduction and anoxygenic photoautotrophy among bacterial functions, and saprotrophic guilds among fungal communities at Tf in TDI, suggesting increased nutrient cycling activity associated with post-drought recovery. Co-occurrence network analysis revealed contrasting interaction patterns, with higher connectivity in SFI and a greater contribution of fungal taxa and positive fungi-fungi interactions in TDI.

CONCLUSIONS: These results indicate that the legacy of rhizosphere microbiomes shaped by host water-deficit-tolerance and irrigation history is associated with enhanced post-drought recovery, involving the enrichment of specific microbial taxa and functional guilds. The concept of dual legacy provides a useful framework for understanding microbiome-mediated plant resilience.},
}

@article {pmid42827267,
year = {2026},
author = {Cai, S and Tu, J and Yang, T and Qiao, S and Zeng, X},
title = {Carbohydrate and protein adaptation in low-protein diets for livestock and poultry: a nutritional revolution from static balance to dynamic synergy.},
journal = {Journal of animal science and biotechnology},
volume = {17},
number = {1},
pages = {},
pmid = {42827267},
issn = {1674-9782},
abstract = {Low-protein diet is a pivotal strategy for alleviating protein feed shortage and promoting the sustainable development of the livestock industry. However, the utilization efficiency of carbohydrate and protein nutrients in livestock and poultry remains relatively low, and carbohydrate-protein metabolism asynchrony is the core bottleneck limiting their efficient utilization. Carbohydrate and protein adaptation, based on low-protein diets, makes a shift from traditional static energy and nitrogen balance theories. By precisely aligning the digestive release patterns of carbohydrates and proteins, it enables the synergistic and efficient utilization of energy and amino acids, representing a promising concept in the low-protein diet systems. Nevertheless, current evidence supporting carbohydrate and protein adaptation remains relatively limited and largely based on indirect inference. This review summarizes the patterns of digestion and absorption of carbohydrate and protein in livestock and poultry as well as their key regulatory factors, clarifies the core technology and cutting-edge research methodologies for carbohydrate and protein adaptation, and analyzes the mechanisms by which carbohydrate and protein adaptation influences production performance, meat quality, intestinal health, and nutritional metabolism regulation. In addition, this review proposes future research directions, including quantitative and precise regulation, microbiome-targeted modulation, and multi-omics mechanism analysis, providing a theoretical basis for further research and industrial application of carbohydrate and protein adaptation in low-protein diets for livestock and poultry.},
}

@article {pmid42827404,
year = {2026},
author = {Yan, D and Collins, LB and Staley, C and Matovu, FK and Jacobson, P and Nicol, M and Cheng, S},
title = {Evaluating Vaginal Microbiome Effects on Antiretroviral Exposure in the Female Genital Tract Using Pharmacometric and Machine Learning Approaches.},
journal = {Clinical pharmacology and therapeutics},
volume = {},
number = {},
pages = {},
doi = {10.1002/cpt.70499},
pmid = {42827404},
issn = {1532-6535},
abstract = {Antiretroviral pre-exposure prophylaxis (PrEP) is less effective in women than expected, partly because drug exposure within the female genital tract is variable and may be influenced by the vaginal microbiome. We developed an integrated pharmacometrics and machine learning framework to evaluate associations between vaginal microbiome composition and cervical antiretroviral exposure in women with human immunodeficiency virus (HIV) receiving tenofovir (TFV)-, lamivudine (3TC)-, or emtricitabine (FTC)-containing regimens. Pharmacokinetic and microbiome data were obtained from two single-center studies in Uganda and the United States. Published population pharmacokinetic models were used to estimate individual parameters by maximum a posteriori Bayesian estimation and to simulate plasma and cervical tissue exposure metrics under sexual-activity-driven dosing that were not studied in these trials. Microbiome diversity was assessed using alpha and beta diversity analyses. Associations between microbial genera and cervical drug exposure were evaluated using correlation analysis, differential abundance testing, and three machine learning approaches: LASSO, random forest, and XGBoost. Overall vaginal microbiome diversity was not associated with cervical exposure to TFV, 3TC, or FTC. In contrast, specific taxa-level associations with cervical drug exposure were identified. For TFV, Gemella was positively associated with cervical TFV-diphosphate exposure, whereas Megasphaera and Falsiporphyromonas were negatively associated across multiple models. For 3TC, Dialister, Prevotella, Atopobium, Streptobacillus, and Gardnerella were repeatedly identified. For FTC, Bifidobacteriaceae was consistently selected, with Lachnospiraceae and Prevotellaceae also implicated. This pharmacometrics-machine learning framework identified specific vaginal taxa associated with cervical antiretroviral exposure, supporting the future development of microbiome-based biomarkers and precision PrEP strategies for women.},
}

@article {pmid42827448,
year = {2026},
author = {Imokhai, PO and Metellus, R and Karsten, M and Alhoda, M and Gandhi, S and Ogbuefi, C and Carranza, S and Zhang, J and Lee, D and Brooks, A},
title = {An interdisciplinary scoping review of the emerging impact of periocular skincare products on the ocular surface microbiome and tear film stability.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1898798},
pmid = {42827448},
issn = {2235-2988},
mesh = {Humans ; *Microbiota/drug effects ; *Tears/drug effects/chemistry ; *Cosmetics/adverse effects ; *Eye/microbiology/drug effects ; Personal Care Products ; Bacteria/classification/drug effects ; Meibomian Gland Dysfunction ; Meibomian Glands/drug effects ; },
abstract = {BACKGROUND: The healthy ocular surface microbiome consists of Actinobacteria, Proteobacteria, and Firmicutes phyla, with Corynebacterium, Propionibacterium, and Staphylococcus as dominant genera. This microbial environment is essential for maintaining immune homeostasis and barrier integrity.

OBJECTIVE: To synthesize existing evidence on how periocular skincare and cosmetic products affect the ocular surface microbiome, tear film stability, and downstream ocular surface disease.

METHODS: A systematic literature search was conducted across PubMed, Cochrane Library, Embase, Web of Science, and Scopus using Boolean MeSH term strategies. Studies from 2010 to present evaluating microbial composition of the ocular surface and the effects of exogenous exposures (cosmetics, contact lenses, medications) were included.

RESULTS: Preservatives (benzalkonium chloride, parabens), surfactants, retinoids, and essential oils (tea tree oil/terpinene-4-ol) disrupt the ocular surface through non-selective microbial depletion, epithelial cytotoxicity, and lipid emulsification. These mechanisms contribute to meibomian gland dysfunction (MGD), blepharitis, and evaporative dry eye - all associated with characteristic dysbiotic microbiome shifts. Advanced sequencing technologies, including 16S rRNA gene sequencing and shotgun metagenomics, reveal taxon-level changes and functional alterations linked to inflammation and tear film instability.

CONCLUSIONS: Periocular product ingredients represent an underappreciated source of ocular surface dysbiosis. Regulatory gaps under current FDA and MoCRA frameworks limit ingredient-level safety evaluation. Future longitudinal studies using functional metagenomics, metabolomics, and standardized microbiome-specific testing pipelines are urgently needed.},
}

Humans
*Microbiota/drug effects
*Tears/drug effects/chemistry
*Cosmetics/adverse effects
*Eye/microbiology/drug effects
Personal Care Products
Bacteria/classification/drug effects
Meibomian Gland Dysfunction
Meibomian Glands/drug effects

@article {pmid42827489,
year = {2026},
author = {Zhang, X and Dou, W and Cao, Q and Guo, J and Yin, Y and Zhu, Z and Zeng, M and Liu, J and Han, D and Qiang, X},
title = {Combined application of organic and microbial amendments reshapes soil microbiome diversity and improves soybean growth performance.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1939259},
doi = {10.3389/fmicb.2026.1939259},
pmid = {42827489},
issn = {1664-302X},
abstract = {Agricultural practices, including organic amendments and microbial inoculants, strongly influence soil microbial communities, which play a crucial role in maintaining soil function and structure. To identify an effective strategy for improving soil microbiome diversity and crop production, we assessed and compared the soil microbial community in fields treated with cattle manure amendment (MA), microbial inoculant (MI), and a mixture of cattle manure and microbial inoculant (MM), while an untreated field served as the control. We then evaluated treatment effects on soybean production. Microbial diversity analyses showed that MM treatment was associated with increased bacterial diversity in bulk soil, whereas a pronounced enhancement of fungal diversity was observed in the rhizosphere. Community composition analyses indicated the elevation of relative abundances of Acidobacteriota and Chloroflexi in bulk soil upon either treatment. Notably, the Proteobacteria, including the rhizobial genus Ensifer, was significantly enriched in the rhizosphere upon MM treatment, while the relative abundance of Ascomycota was increased in both bulk and rhizospheric soil upon MA treatment. To co-relate with these soil microbiome features, the MM treatment was shown to have the most significant effect on the soybean growth promotion, including the notably higher aboveground and underground fresh weight, plant height, accompanied with markedly more root nodules, than either MI or MA treatment. Collectively, our results suggest that the combined application of organic and microbial amendments effectively reshapes the soil microbiome by enhancing microbial diversity and enriching nitrogen-fixing bacteria in the rhizosphere, thereby promoting the nitrogen-fixing potential and productivity of soybean.},
}

@article {pmid42827539,
year = {2026},
author = {Guzel, M and Mukherjee, A and Assunção, R and Frias, J and Humblot, C and Laranjo, M and Savary-Auzeloux, I and Yilmaz, B and Chassard, C and Praćer, S and Vergères, G and , },
title = {Health benefits of fermented foods: a strategic roadmap from the PIMENTO initiative.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1904521},
doi = {10.3389/fnut.2026.1904521},
pmid = {42827539},
issn = {2296-861X},
abstract = {Fermented foods are receiving increasing attention as potentially beneficial components of healthy diets because they provide live microorganisms, fermentation-derived metabolites, and food matrices modified by microbial activity. However, the evidence supporting their health effects remains heterogeneous, making it difficult to translate current knowledge into clear regulatory or public health guidance. Here we present a Strategic Research and Policy Roadmap developed within Working Group 3 of the COST Action "Promoting Innovation of ferMENTed fOods" (PIMENTO) CA20128 to identify priorities for fermented foods research and policy directions in the near future. Using an approach informed by the European Food Safety Authority framework for health claim substantiation, the PIMENTO WG3 initiative synthesised evidence from a dedicated series of 17 published reviews, comprising systematic reviews, meta-analyses, systematic narrative reviews, narrative reviews, and a scoping review, preceded by a position paper setting out the WG3 strategy, covering human studies, mechanistic evidence, food characterisation, bioavailability, and safety. Across these reviews, fermented foods were associated with generally modest, and sometimes neutral, effects on diverse health outcomes. The collective evidence also highlighted recurring strengths of the field, including biological plausibility, broad health relevance, and promising functional targets for selected fermented food categories, alongside persistent challenges related to food characterisation, study heterogeneity, dose-response assessment, mechanistic validation, and long-term human evidence. Safety findings were broadly reassuring in the populations studied, although reporting was inconsistent. We translate these findings into a strategic roadmap for research and policy, reflecting the expert judgement of the author panel rather than a formal consensus procedure, organised across short-, medium-, and long-term horizons, to harmonise fermented food definitions and exposure assessment, standardise product dossiers and analytical methods, strengthen trial design, incorporate mechanistic validation, and align evidence generation with regulatory and public health needs while remaining relevant to diverse stakeholders. Overall, this work provides a structured foundation for the next phase of fermented food research by identifying evidence gaps, methodological priorities, and policy needs required to advance the field toward greater scientific and regulatory maturity. To our knowledge, this represents the first effort of its kind to consolidate evidence and knowledge gaps across the full breadth of fermented foods research into a single, actionable strategic framework.},
}

@article {pmid42827678,
year = {2026},
author = {Anitua, E and Tierno, R and Alkhraisat, MH},
title = {Platelet-rich therapies in cutaneous and mucocutaneous disorders characterized by inflammatory tissue responses: mechanistic insights and clinical evidence.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1901254},
doi = {10.3389/fmed.2026.1901254},
pmid = {42827678},
issn = {2296-858X},
abstract = {Cutaneous and mucocutaneous dermatoses comprise a heterogeneous group of inflammatory, autoimmune, infectious, and immune-mediated diseases affecting epithelial barrier tissues, including skin and mucosal surfaces. Despite their diverse etiologies these conditions frequently share convergent pathogenic mechanisms characterized by epithelial barrier dysfunction and inflammation, contributing to a substantial global health burden. At the immunopathological level, these disorders frequently involve coordinated activation of innate immune sensing pathways followed by adaptive immune polarization driven by Th1, Th2, Th17 and CD8+ T cell-associated responses. These pathways converge on shared intracellular signaling cascades, resulting in persistent cytokine production, chronic inflammation, and epithelial barrier disruption. Platelet-rich derivatives are autologous biologic therapies enriched in bioactive mediators with pleiotropic regenerative and immunomodulatory properties. Preclinical evidence indicates that these formulations modulate innate immune activation, promote macrophage polarization toward pro-regenerative phenotypes, influence dendritic cell maturation, and support regulatory T cell responses largely via modulation of NF-κB, TLR, PI3K/Akt, MAPK, and TGF-β/SMAD-dependent pathways. In addition to immunomodulation, platelet-rich derivatives enhance tissue repair by promoting cell activation, angiogenesis, and extracellular matrix remodeling. They also contribute to epidermal barrier restoration and normalization of epithelial-immune-microbiome interactions. Despite the heterogeneity of underlying pathogenic molecular pathways, the multi-level effects of platelet-rich formulations provide a rationale for targeting shared downstream processes involved in tissue injury and disease progression. Clinical evidence, although heterogeneous and largely limited to small studies, suggests potential benefit in psoriasis, atopic dermatitis, lichen planus, lichen sclerosus, vitiligo, alopecia areata, and acne, with limited evidence in other mucocutaneous dermatoses associated with substantial primary or secondary inflammation. However, variability in pathophysiological landscapes, platelet-rich formulations and experimental designs limits definitive conclusions. Overall, platelet-derived therapies represent a promising adjunctive approach for restoring immune and epithelial homeostasis in inflammatory mucocutaneous disease, underscoring the need for methodologically standardized clinical and translational research and compliance with minimum reporting standards.},
}

@article {pmid42827717,
year = {2026},
author = {Zhong, L and Purushothaman, B and Wang, X and Zhang, Y and Sun, X and Jiang, J and Karamveer, K and Zhang, Y and Tu, Q and Seenivasan, B},
title = {Effects of dietary fucoidan and exercise on the gut microbiome, fecal metabolome, and tumor-related responses in a murine colorectal cancer model.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1926528},
doi = {10.3389/fcimb.2026.1926528},
pmid = {42827717},
issn = {2235-2988},
mesh = {Animals ; *Polysaccharides/administration & dosage ; *Colorectal Neoplasms/pathology/prevention & control/metabolism/therapy ; *Feces/chemistry/microbiology ; *Metabolome/drug effects ; Mice ; *Gastrointestinal Microbiome/drug effects ; Disease Models, Animal ; *Physical Conditioning, Animal ; *Diet ; Male ; Metabolomics ; },
abstract = {Dietary fucoidan, a sulfated polysaccharide derived from brown seaweed, has attracted increasing interest for its potential to influence gut microbial and metabolic responses. However, the individual and combined effects of dietary fucoidan and exercise on host-microbiome interactions during colorectal cancer development remain incompletely understood. In this preventive study, mice received fucoidan at 300 mg/kg (F1) or 600 mg/kg (F2), alone or in combination with low-intensity exercise at 12 m/min for 30 min or moderate-intensity exercise at 15 m/min for 40 min, for six weeks before MC38 tumor induction. The interventions were associated with distinct changes in gut microbial composition and fecal metabolic profiles. Notably, the X2F1 group showed enrichment of Lactobacillus murinus together with alterations in bacterial taxa linked to short-chain fatty acid metabolism. Metabolomic analysis further revealed changes in amino acid, bile acid, and central carbon metabolism, indicating coordinated microbial and metabolic remodeling. The X2F1 group also showed a marked reduction in tumor burden, while low-dose fucoidan alone produced a clear tumor-associated response and broad changes across microbial and metabolic outcomes. Tumor gene-expression analysis showed increased p53 and Bax expression and reduced Bcl-2 and Ki67 expression in several intervention groups, consistent with apoptosis- and proliferation-related molecular responses. These findings suggest that dietary fucoidan, alone or in combination with exercise, is associated with coordinated changes in the gut microbiome, fecal metabolome, tumor burden, and tumor-related molecular profiles in an MC38 colorectal cancer model.},
}

Animals
*Polysaccharides/administration & dosage
*Colorectal Neoplasms/pathology/prevention & control/metabolism/therapy
*Feces/chemistry/microbiology
*Metabolome/drug effects
Mice
*Gastrointestinal Microbiome/drug effects
Disease Models, Animal
*Physical Conditioning, Animal
*Diet
Male
Metabolomics

@article {pmid42827880,
year = {2026},
author = {Luo, H and Xu, D and Wang, Y and He, T and Zhang, L and Jiang, D and E, Y and Hu, H and Chen, W},
title = {Soil acidification drives a massive accumulation of nitrite as a mechanistic bottleneck to inhibit maize growth and productivity.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1830432},
doi = {10.3389/fmicb.2026.1830432},
pmid = {42827880},
issn = {1664-302X},
abstract = {Soil acidification poses a critical threat to global agricultural sustainability, particularly in high-buffering Mollisol (black soil) ecosystems. However, the microbially mediated biochemical mechanisms underlying nitrogen (N) transformation blockages and subsequent phytotoxicity under acid stress remain poorly understood. Here, using a controlled soil acidification gradient (pH 2.0-7.0) combined with 16S rRNA gene sequencing, functional profiling (FAPROTAX), quantitative PCR (qPCR), and chemical N speciation, we unravel a key microbially driven mechanism governing acid-induced crop failure. Our findings demonstrate that soil acidification imposes strong deterministic environmental filtering (βNTI approaching +2) on the rhizosphere microbiome, driving a drastic collapse in microbial phylogenetic diversity (Chao1 index). This structural transition severely alters N-cycling functional guilds, inducing a profound functional bottleneck. In strong acid treatments (pH 2.0-4.0), ammonium (NH4 [+]) and nitrate (NO3 [-]) concentrations plummeted to 0.25-fold and 0.20-fold of those in circumneutral soils, respectively. Crucially, nitrite (NO2 [-]-N) underwent a 5.85-fold hyper-accumulation, reaching up to 28.52 mg kg[-1]. At the molecular level, this accumulation was driven by a transcriptional and functional decoupling between nitrifying cohorts: while ammonia oxidation genes (amoA/amoB in AOA and AOB) were upregulated or sustained under acidity, nitrite oxidoreductase (NxrC) expression and gaseous denitrification pathways were almost completely suppressed. To decouple nitrite phytotoxicity from direct proton (H[+]) stress, exogenous sodium nitrite (NaNO2) was spiked into neutral soil (pH 7.0) matching the acidification gradient (1.75-28.52 mg kg[-1]; M7-M2). Dose-response validation revealed that NO2 [-]-N exceeding 13.21 mg kg[-1] exerted severe phytotoxicity, significantly inhibiting maize germination, leaf area, and height, with total plant mortality occurring at ≥27.78 mg kg[-1] NO2 [-]-N. Collectively, this study establishes that acid-induced functional decoupling of the nitrifying community causes a massive NO2 [-]-N accumulation, acting as an relatively overlooked, independent phytotoxic driver of crop failure in acidified soils. These insights demonstrate that restoring acidified agroecosystems requires shifting from simple pH neutralization to integrated microbiome management aimed at relieving N-transformation bottlenecks.},
}

@article {pmid42827942,
year = {2026},
author = {Pereira-Santos, AR and Jesus-Faria, S and Candeias, E and Maranha, A and Tiago, I and Rodrigues-Santos, P and Empadinhas, N and Cardoso, SM},
title = {Mucosal microbiota and intraepithelial lymphocyte remodeling link maternal immune activation to neuroimmune outcomes in female and male offspring.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1945751},
doi = {10.3389/fimmu.2026.1945751},
pmid = {42827942},
issn = {1664-3224},
mesh = {Animals ; Female ; Male ; Pregnancy ; Mice ; *Prenatal Exposure Delayed Effects/immunology ; *Neuroimmunomodulation ; *Gastrointestinal Microbiome/immunology ; *Intraepithelial Lymphocytes/immunology/metabolism ; Cytokines/metabolism ; *Intestinal Mucosa/immunology/microbiology ; Prefrontal Cortex/immunology ; Lipopolysaccharides ; Developmental Origins of Health and Disease ; Mice, Inbred BALB C ; },
abstract = {BACKGROUND: Maternal immune activation (MIA) is associated with increased risk for neurodevelopmental disorders, including schizophrenia and autism spectrum disorder, yet its long-term impact on intestinal immune-microbial programming remains incompletely understood. Here, we investigated whether lipopolysaccharide (LPS)-induced MIA drives persistent alterations in the offspring mucosal immune environment, with a focus on intraepithelial lymphocytes, mucosa-associated microbiota, systemic cytokines, and prefrontal cortical immune-related readouts.

METHODS: MIA was induced in wild-type BALB/cByJ mice via intraperitoneal LPS injection at gestational day 12.5. Male and female offspring were assessed at 10 weeks of age for gut, systemic, and prefrontal cortex (PFC) immune alterations.

RESULTS: MIA offspring displayed a regionally restricted intestinal immune signature, with more pronounced alterations in the ileum than in the colon. Ileal changes included increased inflammatory cytokine signaling and remodeling of IEL populations, particularly TCRγδ CD8αα cells, together with changes in TCRαβ IEL subsets. Analysis of the mucosa-associated microbiome revealed parallel changes in ileal microbial community structure, including alterations in segmented filamentous bacteria and Lactobacillus. These mucosal alterations co-occurred with increased plasma IL-6 in both female and male offspring, while plasma IL-17 was selectively increased in females. In the PFC, MIA was associated with cytokine changes and divergent microglial morphological profiles, suggesting that prenatal immune challenge produces neuroimmune alterations that may differ in sex, timing, magnitude, or cellular expression.

CONCLUSIONS: Collectively, these findings identify the mucosa-associated microbiota-IEL interface as a previously underexplored component of MIA-induced immune remodeling. Our study provides an integrated framework in which persistent ileal immune and microbial alterations co-occur with systemic inflammation and cortical neuroimmune changes in MIA offspring, supporting future mechanistic studies of gut-brain immune communication in neurodevelopmental disorders.},
}

Animals
Female
Male
Pregnancy
Mice
*Prenatal Exposure Delayed Effects/immunology
*Neuroimmunomodulation
*Gastrointestinal Microbiome/immunology
*Intraepithelial Lymphocytes/immunology/metabolism
Cytokines/metabolism
*Intestinal Mucosa/immunology/microbiology
Prefrontal Cortex/immunology
Lipopolysaccharides
Developmental Origins of Health and Disease
Mice, Inbred BALB C

@article {pmid42827958,
year = {2026},
author = {Ni, L and Xian, B and Li, F and Zou, Q and Du, J and Lai, J and Liu, Y},
title = {Multi-omics profiling identifies intestinal microbial shifts and tissue-specific immunometabolic changes associated with experimental Nocardia seriolae challenge in hybrid sturgeon (Acipenser baerii♀ × Acipenser schrenckii♂).},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1956937},
doi = {10.3389/fmicb.2026.1956937},
pmid = {42827958},
issn = {1664-302X},
abstract = {INTRODUCTION: Nocardia seriolae is an important bacterial pathogen in aquaculture, but the intestinal microbial, transcriptional, and metabolic responses of hybrid sturgeon (Acipenser baerii♀ × Acipenser schrenckii♂) to infection remain poorly understood.

METHODS: Hybrid sturgeons were experimentally challenged with N. seriolae. PBS-injected control fish were sampled at 0 days post-infection (dpi) as the baseline reference, whereas infected fish were sampled at 7 and 14 dpi for microbiome, transcriptome, and metabolome profiling. Full-length 16S rRNA gene and ITS sequencing were used to characterize intestinal microbial communities, while RNA-seq and untargeted LC-MS metabolomics were performed on liver and spiral valve intestine tissues.

RESULTS: Compared with the baseline control group, fish sampled at 7 and 14 dpi showed differences in intestinal bacterial community composition, whereas bacterial alpha diversity did not differ significantly among the three sampled groups. ITS profiling also showed differences in fungal diversity and community composition among groups, although no fungal genus remained significant after false discovery rate (FDR) correction. RNA-seq revealed tissue-specific transcriptional responses, with the liver showing a larger number of differentially expressed genes than the spiral valve intestine. Hepatic pathways were mainly related to immune recognition, complement and coagulation cascades, antigen processing, and stress-related responses, whereas intestinal transcriptional changes involved phagosome, cell adhesion, and mucosal immune-related pathways. Metabolomic analysis showed tissue- and stage-related metabolic changes, with clearer pathway-level evidence in the spiral valve intestine at 14 dpi, particularly involving amino acid metabolism and protein digestion and absorption. Representative metabolites related to lipid and bile acid metabolism, carnitine-associated lipid utilization, energy metabolism, and purine/nicotinamide metabolism also showed sampling-stage-related variation. Genus-metabolite association analysis further identified candidate relationships between intestinal bacterial genera and representative metabolites.

DISCUSSION: These findings provide a multi-omics view of intestinal microbial and tissue-specific immunometabolic changes associated with experimental N. seriolae challenge in hybrid sturgeon. The candidate genus-metabolite relationships provide a basis for future targeted validation of microbial and metabolic features associated with nocardial infection.},
}

@article {pmid42828028,
year = {2026},
author = {Yu, Z and Peng, H and Cheng, X and Xu, W and Wang, Y and Xiao, Y and Wei, T and Huang, Z and He, Y and Wang, J},
title = {Heterogeneous mechanisms, risk stratification, and translational advances in the malignant transformation of oral potentially malignant disorders to oral squamous cell carcinoma.},
journal = {Frontiers in molecular biosciences},
volume = {13},
number = {},
pages = {1948915},
doi = {10.3389/fmolb.2026.1948915},
pmid = {42828028},
issn = {2296-889X},
abstract = {Oral potentially malignant disorders (OPMDs) represent important precursor conditions in the development of oral squamous cell carcinoma (OSCC) and provide a critical window for early prevention, risk assessment, and precision intervention of oral cancer. Oral leukoplakia, proliferative verrucous leukoplakia, oral erythroplakia, oral lichen planus, and oral submucous fibrosis are among the most common and clinically significant OPMDs. Although these disorders may contribute to malignant transformation through shared mechanisms, including chronic inflammation, oxidative stress, genetic and epigenetic alterations, immune dysregulation, epithelial-mesenchymal crosstalk, and microbiome dysbiosis, their predominant pathological processes and malignant transformation trajectories exhibit substantial heterogeneity. Oral leukoplakia is characterized by marked clinical and molecular heterogeneity, genomic instability, and field cancerization effects; Proliferative verrucous leukoplakia is characterized by progressive multifocal disease, an exceptionally high risk of malignant transformation, and a pronounced propensity to develop multiple primary oral cancers; oral erythroplakia is frequently associated with high-grade epithelial dysplasia or early invasive carcinoma; oral lichen planus represents an immune-mediated chronic inflammatory microenvironment that may facilitate tumorigenesis; and oral submucous fibrosis represents a matrix-driven precancerous condition primarily characterized by areca nut exposure and fibrotic extracellular matrix remodeling. In recent years, advances in single-cell omics, spatial omics, salivary liquid biopsy, digital pathology, artificial intelligence, and local drug delivery systems have provided emerging technological platforms for dynamic risk stratification, early diagnosis, and precision prevention of malignant transformation in OPMDs. This review summarizes the epidemiological links between major OPMDs and OSCC, disease-specific and shared mechanisms underlying malignant transformation, candidate biomarkers, risk stratification strategies, and advances in translational therapies. Furthermore, it aims to establish an integrated management framework for oral potentially malignant lesions based on the "epithelial-immune-stromal-microbial" niche.},
}

@article {pmid42828098,
year = {2026},
author = {Hanna, ME and Kartha, N and LaMantia, A and Grayson, MH and Hussain, SA},
title = {Are we there yet? understanding interactions between respiratory viral infections, atopy, and the microbiome.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1952677},
doi = {10.3389/falgy.2026.1952677},
pmid = {42828098},
issn = {2673-6101},
abstract = {Atopic disease has become an increasingly prevalent condition worldwide and a significant health concern. Similarly, due to concerns about morbidity associated with respiratory viral illness in early childhood, there has been increased exploration of the relationship between atopy and viral illnesses. Historically, studies have focused on early-life respiratory infections driving the development of atopy or post-viral airway disease, with respiratory syncytial virus (RSV) infection driving post-viral disease in those without atopy, while human rhinovirus (hRV) leading to asthma in those with pre-existing atopy. The impact of atopy on the antiviral immune response remains debated, with some studies suggesting it provides a protective role, while others suggest it impairs the immune response. Beyond the respiratory tract, the gut microbiome increasingly is recognized as a potential modulator of both local and distant immune responses, a relationship associated with lung function termed the gut-lung axis. As we continue to elucidate the biochemical mechanisms underlying these pathways in mouse models, it will be important to identify analogous human pathways. This review explores what is currently known about the relationship between atopy and respiratory viral infections focusing on knowledge about how viral infections drive atopy and, reciprocally, how atopy modulates respiratory viral induced disease. Moreover, we review published information on analogous human pathways. Utilizing this information will help us with better disease management and potential development of targeted therapeutics.},
}

@article {pmid42828144,
year = {2026},
author = {Cui, J and Li, F and Qi, Q and Qin, P and Su, X and Quan, H and Wang, D and Chen, X and Zhang, J and Liu, Z},
title = {Research progress of Rumen microbes utilizing lignocellulose for high-value chemical production.},
journal = {Biodesign research},
volume = {8},
number = {3},
pages = {100107},
doi = {10.1016/j.bidere.2026.100107},
pmid = {42828144},
issn = {2693-1257},
abstract = {Lignocellulose is the most abundant renewable carbon resource in nature. However, its structural recalcitrance, arising from the complex association of cellulose, hemicellulose, and lignin, results in high pretreatment costs and inefficient enzymatic hydrolysis, thereby limiting its high-value utilization. The rumen harbors a diverse anaerobic microbial community with efficient lignocellulose-degrading capacity, interconnected metabolic networks, and considerable functional adaptability, making the rumen microbiome a promising biological platform for lignocellulose conversion. This review systematically summarizes the mechanisms of lignocellulose degradation by rumen microorganisms, the metabolic pathways underlying value-added chemical production, and the process-, community-, and genetic-level strategies used to improve lignocellulose conversion performance. It further discusses major constraints on the development of rumen-derived bioconversion systems, including the instability of in vitro microbial communities, limited control over metabolic flux, and difficulties in process scale-up. Finally, the potential of multi-omics analyses and synthetic biology to improve community stability, metabolic controllability, and product selectivity is highlighted. This review provides theoretical and technical guidance for developing sustainable lignocellulose valorization processes based on rumen microorganisms.},
}

@article {pmid42828167,
year = {2026},
author = {Wang, H and Zhao, X and Yang, J},
title = {Spatial multi-omics-guided drug development in inflammatory bowel disease: from mucosal immune niches to precision therapy.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1951659},
doi = {10.3389/fimmu.2026.1951659},
pmid = {42828167},
issn = {1664-3224},
mesh = {Humans ; Multiomics ; *Drug Development/methods ; *Precision Medicine/methods ; *Inflammatory Bowel Diseases/drug therapy/immunology/metabolism ; *Intestinal Mucosa/immunology/drug effects/metabolism ; Animals ; Biomarkers ; *Immunity, Mucosal/drug effects ; },
abstract = {Crohn's disease and ulcerative colitis are now treated with an expanding set of biologics and small molecules, yet treatment selection remains largely empirical. Primary non-response, secondary loss of response, incomplete mucosal healing, fibrostenosis, and fistulizing disease show that conventional clinical, endoscopic, and bulk molecular markers do not capture how disease is organized within tissue. This review argues that the inflamed intestine is better viewed as a set of spatially structured mucosal immune niches rather than as uniform inflammation, with epithelial, myeloid, lymphoid, stromal, vascular, neural, and microbiome-associated cells communicating through defined cytokine and ligand-receptor circuits. In this framework, mucosal immune niches can be considered functional tissue units that link tissue-resolved mechanisms to therapeutic target discovery, pharmacodynamic assessment, biomarker qualification, and biomarker-enriched trial design. Single-cell atlases and spatial multi-omics, interpreted through computational modeling, can identify disease-driving cellular neighborhoods, ligand-receptor circuits, and compartment-specific vulnerabilities in both diseases. We discuss how these spatial features may inform target discovery, mechanism-of-action validation, patient stratification, response prediction, and trial design, using pathways such as TNF, IL-23, OSM, TL1A, integrins, JAK-STAT, and S1P as examples. At present, the realistic value of spatial data lies in generating mechanistic hypotheses, defining pharmacodynamic endpoints, and enriching trials, not in guiding routine treatment selection. Most candidate spatial biomarkers remain at the discovery or early translational stage and require standardized sampling, harmonized computation, longitudinal assessment, and multicenter validation. A staged translational path is proposed, moving from disease-specific atlases to spatial pharmacodynamic endpoints and adaptive precision trials, while also offering a comparative framework for studying chronic inflammation across mucosal organs.},
}

Humans
Multiomics
*Drug Development/methods
*Precision Medicine/methods
*Inflammatory Bowel Diseases/drug therapy/immunology/metabolism
*Intestinal Mucosa/immunology/drug effects/metabolism
Animals
Biomarkers
*Immunity, Mucosal/drug effects

@article {pmid42820741,
year = {2026},
author = {Napier, BA and Merrill, BD and Krieger, M and Gevers, D and Reid, G},
title = {Formulations containing co-biotic compounds mediate microbiome function and composition without increased gas production in an ex vivo gastrointestinal model.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0131126},
doi = {10.1128/aem.01311-26},
pmid = {42820741},
issn = {1098-5336},
abstract = {UNLABELLED: Dietary supplement formulations that contain co-biotics or compounds that modulate biological processes in both the host and microbiome to confer a health benefit are an emerging strategy to fine-tune both host physiology and gut microbiome function. Here, we evaluated three novel formulations containing co-biotic compounds (DM-02, a multivitamin; AM-02, formulated for energy and focus; and PM-02, formulated to promote sleep) for their effects on human gut microbiome composition and function. The three formulations and untreated control (Unt-Ctrl) were subjected to upper gastrointestinal digestion, after which the digesta were exposed to 24-h simulated colonic fermentation in the validated ex vivo systemic intestinal fermentation research (SIFR) technology (n = 6 healthy adults). Outcomes included pH, short-chain fatty acid (SCFA) and gas production, ultra-deep metagenomic profiling, and untargeted metabolomics of post-colonic supernatants, each compared to Unt-Ctrl. All three formulations significantly reduced pH (3%-4%) and increased total SCFAs (9%-11%) and acetate (9%-12%), with AM-02 and PM-02 also increasing butyrate by 20% and propionate by 7%-8%, without increasing gas production. Each formulation significantly enriched specific SCFA- and B-vitamin-producing taxa. AM-02 significantly increased the abundance of two pyruvate fermentation to acetate/lactate pathways. PM-02 significantly increased the abundance of two tryptophan biosynthesis pathways, accompanied by an increase in available tryptophan and the abundance of tryptophan-producing microbes. All three formulations increased the availability of microbiome-derived metabolites, indicating microbiome functional modulation by the treatments. These findings support clinical evaluation of these novel formulations as a strategy to enhance microbiome composition and function.

IMPORTANCE: The gut microbiome produces metabolites, including short-chain fatty acids, B vitamins, and tryptophan derivatives, that are critical regulators of host physiology, from energy metabolism and gut barrier integrity to sleep and immune function. While probiotics introduce live microorganisms, and prebiotics selectively feed existing microbes, co-biotics represent a distinct category of compounds that simultaneously modulate host cell biology and microbiome activity. Despite growing interest in co-biotic supplementation, the impact of complete co-biotic-containing formulations on gut microbiome composition and functional output has not been evaluated. Using a validated ex vivo gastrointestinal model inoculated with fecal microbiota from six healthy adults, we demonstrate that three supplement formulations containing co-biotic compounds consistently increased production of health-associated metabolites, selectively enriched beneficial microbial taxa, and modulated functional metabolic pathways, all without increasing gas production. These findings establish a mechanistic foundation for the clinical investigation of co-biotic formulations as targeted, tolerable interventions for optimizing gut microbiome function across diverse human populations.},
}

@article {pmid42820934,
year = {2026},
author = {Maurya Arvind, U and Maniya, H and Kumar, V},
title = {Live probiotic encapsulation: process engineering, wall materials, and the translation gap to human gastrointestinal survival.},
journal = {Critical reviews in microbiology},
volume = {},
number = {},
pages = {1-13},
doi = {10.1080/1040841X.2026.2729426},
pmid = {42820934},
issn = {1549-7828},
abstract = {Probiotic viability from manufacture to colonic delivery is compromised by thermal processing, oxidative storage conditions, and sequential gastrointestinal (GIT) stresses, with cumulative losses exceeding 8 log10 CFU in unprotected preparations. Encapsulation addresses this challenge by shielding cells within protective matrices. This review synthesizes current evidence across the full encapsulation value chain. We examine GIT stress physiology from ingestion to colonic fermentation, then analyze encapsulation architectures spanning macro-beads to single-cell metal-phenolic network (MPN) nano-coatings. Wall material performance covering sodium alginate, chitosan, whey proteins, pectin, zein, soy protein isolate, and MPNs is evaluated against six selection criteria. Four industrial processes (ionotropic gelation, spray drying, spray chilling, and freeze drying) are appraised for engineering efficiency. A critical assessment of in vitro digestion models reveals that static INFOGEST 2.0 protocols overestimate in vivo protection by 1-3 log10 CFU relative to human fecal recovery studies, owing to the absence of peristaltic mechanics, mucus interactions, and microbiome competition. Emerging frontiers including synbiotic co-encapsulation, AI-driven formulation optimization, and engineered live biotherapeutic products are discussed. A four-stage validation pipeline static in vitro screening, dynamic model validation, ex vivo/animal confirmation, and stratified human trial is proposed as a translational framework to close the gap between laboratory performance and clinical outcome. No single wall material, process, or validation stage performs optimally across all contexts; the evidence instead supports strain, matrix, and application-specific formulation, verified through staged evidence generation, as the most defensible route from laboratory protection to clinically meaningful gastrointestinal delivery.},
}

@article {pmid42821048,
year = {2026},
author = {Zhou, C and Wen, W and Ji, L and Song, F and Xing, Y and Li, Q and Li, T and Fu, X},
title = {Functional divergence of bacterial communities in root zones of Suaeda salsa in an aged petroleum-polluted area of the Yellow River Delta.},
journal = {World journal of microbiology & biotechnology},
volume = {42},
number = {10},
pages = {},
pmid = {42821048},
issn = {1573-0972},
support = {YDZX2023057//Central-guided Local Science and Technology Development Fund of Shandong Province/ ; },
mesh = {*Chenopodiaceae/microbiology ; Rhizosphere ; *Plant Roots/microbiology ; *Bacteria/classification/genetics/isolation & purification/metabolism ; *Petroleum/metabolism/analysis ; China ; Soil Microbiology ; *Soil Pollutants/metabolism ; RNA, Ribosomal, 16S/genetics ; Rivers ; *Microbiota ; *Petroleum Pollution/analysis ; Biodegradation, Environmental ; Phylogeny ; Endophytes/classification ; Salt-Tolerant Plants/microbiology ; Hydrocarbons/metabolism ; },
abstract = {Petroleum hydrocarbon pollutants pose a significant threat to the ecological security of oilfields. In these contaminated habitats, Suaeda salsa is a dominant halophyte of the coastal wetlands and oilfields, which has shown potential in remediation of petroleum polluted saline soils. However, the role of plant-associated microbial communities in pollutant attenuation remains poorly understood, particularly regarding niche-specific responses within the root zone. In this study, bacterial community structures associated with the halophyte Suaeda salsa in China's Yellow River Delta were investigated across three ecological niches comprising the endophytic tissues, rhizosphere soils, and bulk soils. A total of 54 samples from 6 sites were collected and analyzed using high-throughput absolute quantification sequencing and physicochemical analyses. Results demonstrated that petroleum hydrocarbons were the primary environmental drivers shaping bacterial community structure across all niches. Comparisons among ecological niches indicated that the rhizosphere effect further promoted the selection and enrichment of specific bacterial taxa, especially the genus Sphingomonas. Contrasting ecological strategies between niches were clearly resolved by co-occurrence network analysis, which showed highly connected networks in rhizosphere communities and modular structures in endophytic ones. Functional predictions further indicated niche-specific metabolic specialization, with endophytic communities enhancing xenobiotic degradation pathways and rhizosphere communities upregulating motility-related functions. These findings reveal the niche-dependent assembly and functional specialization of root-zone microbiomes under petroleum stress, thereby advancing our understanding of plant-microbe adaptive strategies in contaminated ecosystems.},
}

*Chenopodiaceae/microbiology
Rhizosphere
*Plant Roots/microbiology
*Bacteria/classification/genetics/isolation & purification/metabolism
*Petroleum/metabolism/analysis
China
Soil Microbiology
*Soil Pollutants/metabolism
RNA, Ribosomal, 16S/genetics
Rivers
*Microbiota
*Petroleum Pollution/analysis
Biodegradation, Environmental
Phylogeny
Endophytes/classification
Salt-Tolerant Plants/microbiology
Hydrocarbons/metabolism

@article {pmid42821103,
year = {2026},
author = {Luo, N and Yan, H and Wang, N and Fan, W and Chen, P},
title = {Gut microbiota signatures and machine learning-based candidate feature prioritization in advanced colorectal cancer.},
journal = {Archives of microbiology},
volume = {208},
number = {12},
pages = {},
pmid = {42821103},
issn = {1432-072X},
support = {2024AAC03713//Ningxia Natural Science Foundation/ ; 2024-10-2026.10//Study on the Role and Mechanism of Karyopherin Alpha 2 (KPNA2)‑Mediated Tumor‑Associated Macrophage Polarization in Gastric Cancer Progression/ ; },
mesh = {Humans ; *Colorectal Neoplasms/microbiology ; *Machine Learning ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification ; Cross-Sectional Studies ; Female ; Male ; Middle Aged ; Aged ; Random Forest ; },
abstract = {This single-center, cross-sectional case-control study aimed to characterize the gut microbiome profiles of patients with advanced colorectal cancer (CRC), identify candidate microbial features, and explore how well these features distinguished advanced CRC cases from healthy controls within the study dataset. Fecal samples were collected from 72 treatment-naïve patients with advanced CRC and 61 healthy controls. Microbial community structure was profiled using high-throughput sequencing of the V3-V4 region of the 16 S rRNA gene. The analytical pipeline included α/β-diversity analysis, multilevel taxonomic analysis, LEfSe, and machine-learning algorithms, including random forest (RF), gradient boosting machine (GBM), and LASSO, to identify key Amplicon Sequence Variants (ASVs) and evaluate their ability to discriminate between the two groups. Results showed significantly reduced α-diversity and distinct β-diversity in the CRC group. Key SCFA-producing genera (Faecalibacterium, Agathobacter, Roseburia) were consistently depleted. The RF feature-prioritization model achieved an out-of-bag (OOB) accuracy of 0.850 and an OOB AUC of 0.899. Nested five-fold cross-validation based on the prioritized ASVs yielded AUCs of 0.891, 0.900, and 0.891 for RF, GBM, and LASSO, respectively. These findings show internally reproducible case-control discriminatory patterns within the present cohort and support further evaluation of the prioritized microbial features in independent, clinically representative populations.},
}

Humans
*Colorectal Neoplasms/microbiology
*Machine Learning
Case-Control Studies
RNA, Ribosomal, 16S/genetics
Feces/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification
Cross-Sectional Studies
Female
Male
Middle Aged
Aged
Random Forest

@article {pmid42821694,
year = {2026},
author = {Venkataraman, A and Midavaine, É and Ingraham, HA},
title = {Sex-specific mechanisms of chronic pain.},
journal = {Science (New York, N.Y.)},
volume = {394},
number = {6819},
pages = {69-74},
doi = {10.1126/science.aeh4468},
pmid = {42821694},
issn = {1095-9203},
mesh = {Humans ; *Chronic Pain/physiopathology/immunology ; Female ; Gonadal Steroid Hormones/metabolism/physiology ; Gastrointestinal Microbiome ; Sex Factors ; Visceral Pain/physiopathology ; Animals ; Nociceptive Pain/physiopathology ; },
abstract = {For decades, we have known that women, especially younger women, are disproportionately affected by pain disorders, including irritable bowel syndrome, endometriosis, menstrual migraines, fibromyalgia, osteoarthritis, and neuropathic pain, all of which degrade quality of life. The adoption of sex as a biological variable in 2016 has begun to transform the field, revealing distinct sex-specific pathways that initiate, amplify, and resolve pain. In this Review, we synthesize recent advances across visceral and somatic pain, highlighting the impact of sex hormones, immune-neural cross-talk, the gut microbiome, and endogenous analgesic circuits. Rather than clinging to the historical standard that simply described the female bias in pain symptoms, these studies begin to explain why females experience heightened pain, paving the path for mechanism-based precision therapeutics.},
}

Humans
*Chronic Pain/physiopathology/immunology
Female
Gonadal Steroid Hormones/metabolism/physiology
Gastrointestinal Microbiome
Sex Factors
Visceral Pain/physiopathology
Animals
Nociceptive Pain/physiopathology

@article {pmid42822267,
year = {2026},
author = {Zhao, Y and Che, C and Hong, D and Zhuang, Y and Qin, K and Li, Y and Chen, Y and Wang, C and Mu, C and Wang, H},
title = {Long-term stress induced by low bicarbonate alkalinity causes intestinal oxidative stress, gut microbiota imbalance and metabolic disorder in Scylla paramamosain.},
journal = {Marine pollution bulletin},
volume = {233},
number = {Pt 3},
pages = {120400},
doi = {10.1016/j.marpolbul.2026.120400},
pmid = {42822267},
issn = {1879-3363},
abstract = {To investigate the effects of low bicarbonate alkalinity on intestinal health of Scylla paramamosain, we systematically evaluated the growth survival, intestinal antioxidant enzyme activities, and expression profiles of genes involved in immunity, inflammation, apoptosis and osmoregulation under low alkalinity conditions. Meanwhile, integrated intestinal microbiome and metabolome analyses were performed. The results showed that low bicarbonate alkalinity significantly reduced the survival and molting rates of S. paramamosain. It markedly elevated the activities of intestinal SOD, CAT and GSH-Px, as well as the expression levels of inflammation-related genes (IL-16, RELISH, LITAF), apoptosis-related genes (CASPASE7, BAX, BCL2) and osmoregulation-related genes (NKA, NHE, Cl[-]/HCO3[-]), while suppressing the expression of immune genes (proPO, ALF1, LZM) (P < 0.05). Low bicarbonate alkalinity disrupted the intestinal microbiota structure of S. paramamosain, accompanied by a decreased abundance of the phylum Bacteroidota and a significant increase in the abundance of the genus Klebsiella (P < 0.05). A total of 714 differential metabolites were identified by metabolomic analysis, which were mainly annotated into Fatty Acyls, Glycerophospholipids, and Steroids and steroid derivatives. Multiple carbohydrate metabolism pathways were significantly enriched and participated in the regulation of Fructose 6-Phosphate (F6P). Integrated microbiome-metabolome analysis revealed that N,N-dimethyl arachidonoyl amine (NDAA) may cooperate with intestinal microorganisms to regulate the stress tolerance of S. paramamosain under low bicarbonate alkalinity stress. Based on the physiological and biochemical characterization of the intestine, this study elucidated the adaptive characteristics of S. paramamosain under low bicarbonate alkalinity. The findings provide important theoretical basis and practical significance for the saline-alkaline aquaculture of S. paramamosain.},
}

@article {pmid42822324,
year = {2026},
author = {Johnson, MJ and Frank, DN and Salazar, AT and Nunes, MC and Madhi, SA and Weinberg, A},
title = {Association of gut microbiota and regulatory T cells with vaccine immunogenicity in HIV-exposed uninfected and HIV-unexposed infants: a longitudinal cohort study.},
journal = {EBioMedicine},
volume = {132},
number = {},
pages = {106500},
doi = {10.1016/j.ebiom.2026.106500},
pmid = {42822324},
issn = {2352-3964},
abstract = {BACKGROUND: Responses to vaccines reflect the functionality of the immune system. We measured BCG, tetanus and measles vaccine responses in HIV-exposed uninfected (HEU) and HIV-unexposed (HUU) infants to identify factors associated with HEU immunologic defects.

METHODS: We assessed cell-mediated immunity (CMI) by FluoroSpot, antibodies by ELISA, regulatory and immunologic checkpoint inhibitor-expressing T cells (Tregs/Ticis) by flow cytometry, and gut microbiota by 16S rRNA gene sequencing. CMI and antibody responses were the primary outcome measures. Associations with Tregs/Ticis and gut microbiome parameters were identified using the hurdle model, Spearman correlations and enrichment analyses.

FINDINGS: Among 123 HEUs and 117 HUUs, HEUs tended to have lower BCG-CMI than HUUs without reaching statistical significance (p = 0.07) and similar tetanus-CMI, measles-CMI, and measles-antibodies. Multiple Treg and Tici subsets had significant or marginal negative effects on CMI (p = 0.003-0.10). Treg/Tici inclusion in the hurdle model decreased the statistical significance of the negative effect of HEU status on BCG-CMI suggesting that Tregs/Ticis may have contributed to the difference between HEUs and HUUs. Enrichment of the gut microbiota in Actinobacteria and Firmicutes was significantly associated with low vaccine immunogenicity (p = 0.002-0.04), and Bacteroidetes and Proteobacteria with high immunogenicity (p < 0.0001-0.10). The Firmicute Murdochiella sp. had a higher negative effect size on BCG-CMI in HEUs than HUUs (p < 0.0001). High microbiome diversity negatively correlated with CMI responses (p = 0.002-0.03), with higher effect sizes in HEUs than HUUs (p = 0.047).

INTERPRETATION: The frequency of Tregs/Ticis and the composition of the gut microbiome are associated with immune responses to vaccines and may contribute to decreased responses in HEUs. The internally consistent association between the enrichment of gut microbiota in specific phyla and the immunogenicity of several vaccines suggests the possibility of designing mitigating interventions that target the gut microbiome.

FUNDING: National Institute of Allergy and Infectious Diseases and Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health.},
}

@article {pmid42822377,
year = {2026},
author = {Lewandowski, R},
title = {When microbial drug metabolism becomes a drug disposition variable.},
journal = {Drug metabolism and disposition: the biological fate of chemicals},
volume = {54},
number = {10},
pages = {100407},
doi = {10.1016/j.dmd.2026.100407},
pmid = {42822377},
issn = {1521-009X},
abstract = {Microbial transformation of drugs is experimentally established, but no agreed method determines when a detected pathway materially contributes to drug disposition. This minireview proposes a 5-gate framework for evaluating microbial metabolism as a source of drug-disposition variability. Evaluation begins by asking whether drug-related material reaches a microbial compartment, whether a defined drug-specific problem exists, and whether confirmation could change a development or therapeutic decision. Candidates then require demonstration of a defined microbial function, confirmation of an in vivo drug-specific consequence, comparison of effect magnitude with a prespecified pharmacologic benchmark, and evidence that the microbial measure improves prediction or decision-making beyond established covariates. The benchmark serves as the drug-specific denominator for interpreting microbial effect size. Route and formulation determine substrate access, sampling compartment, assay selection, and the relevant disposition endpoint. Transformation catalogs and genome-scale community models can prioritize pathways and estimate population heterogeneity, but predicted capacity is not equivalent to expressed activity, realized flux, or altered human exposure. A worked digoxin example compares the maximum reported increase of approximately 2-fold in serum concentration after suppression of microbial inactivation with recognized digoxin drug interactions. The framework complements existing microbiome tools by defining when mechanistic findings justify targeted drug-metabolism, pharmacokinetic, or drug-development evaluation. Microbial metabolism becomes a drug-disposition variable when measured function produces a reproducible, quantitatively material effect on drug behavior and provides information beyond established covariates. SIGNIFICANCE STATEMENT: Microbial biotransformation is increasingly detectable, but detection alone does not establish that microbial activity materially alters drug disposition. This minireview proposes a 5-gate framework that connects microbial-compartment exposure and demonstrated function to an in vivo drug-specific consequence, compares effect magnitude with a prespecified pharmacologic benchmark that serves as the drug-specific denominator, and requires incremental predictive or decision value before microbial measures advance beyond targeted drug-development evaluation.},
}

@article {pmid42822490,
year = {2026},
author = {Odendaal, ML and Binkowska, J and Zhang, J and Groot, JA and Chu, MLJ and van der Klis, FR and Bogaert, D and van den Beld, MJ},
title = {Host and environmental factors associated with upper respiratory tract mycobiota in healthy individuals: a cross-sectional observational study.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101517},
doi = {10.1016/j.lanmic.2026.101517},
pmid = {42822490},
issn = {2666-5247},
abstract = {BACKGROUND: Although the bacterial microbiome in the respiratory tract is well-characterised, the fungal microbiome or mycobiome remains underexplored. We aimed to characterise the upper respiratory tract mycobiome within the general population, assess its variation across niches and in relation to host and environmental factors, and evaluate its role as a source community for the fungal pathogens Candida auris (also called Candidozyma auris), Candida albicans, and Aspergillus fumigatus.

METHODS: In this cross-sectional population-based observational study, we characterised paired nasopharyngeal and oropharyngeal mycobiota from 108 participants in the Dutch population-based PIENTER-3 cohort using internal transcribed spacer-amplicon sequencing. Participants were recruited via municipal registers from four municipalities in the central Netherlands between Feb 1, 2016, and Oct 16, 2017. No clinical inclusion or exclusion criteria were applied. In addition, pan-Aspergillus and A fumigatus qPCR assays were performed on oropharynx samples. The primary outcome was to characterise niche-specific differences in the mycobiota.

FINDINGS: We analysed samples from 108 participants (55 [51%] female and 53 [49%] male); the participant age ranged between 10 and 87 years (median 58; IQR 30-67). After quality-control filtering, 107 nasopharyngeal and 89 oropharyngeal samples were retained for analysis. Nasopharyngeal and oropharyngeal mycobiota differed in composition (p=0·0010) and diversity (p<0·0001), with greater heterogeneity in the oropharynx and higher diversity in the nasopharynx. We identified niche-specific factors influencing community structure; sampling season, degree of urbanisation, and livestock farm exposure shaped the nasopharyngeal mycobiota, particularly influencing the abundance of ubiquitous and plant-associated genera. In contrast, age, degree of urbanisation, and recent antibiotic use were key factors influencing the oropharyngeal mycobiome composition. Candida was highly prevalent in both niches, with the genus being more prevalent in the oropharynx (prevalence=85 [96%] of 89 samples) than in the nasopharynx (58 [54%] of 107 samples). Aspergillus was detected at low relative abundance in both niches and was more prevalent in the nasopharynx (49 [46%] of 107 samples) than in the oropharynx (27 [30%] of 89 samples). Although C albicans was frequently found, with its prevalence increasing with age, A fumigatus was not identified during internal transcribed spacer-amplicon sequencing or qPCR.

INTERPRETATION: Our study identified niche-specific fungal communities, with their distinct influencing factors. Our findings also suggest that respiratory mycobiota might serve as a source community for potentially pathogenic fungi. Future studies should investigate which fungi represent commensals versus potential pathogens and elucidate the mechanisms underlying colonisation resistance and infection risk.

FUNDING: National Institute for Public Health and the Environment (RIVM), Netherlands Organization for Scientific Research, and Chief Scientist Office grant.},
}

@article {pmid42822491,
year = {2026},
author = {Vogtmann, E and Um, CY and Zouiouich, S and Absher, D and Benamouzig, R and Chan, AT and Fu, J and Garrett, WS and Greiser, KH and Havulinna, AS and Huttenhower, C and Hveem, K and Kushi, LH and Lahti, L and Liou, JM and Lituev, A and Michaëlsson, K and Milne, RL and Næss, M and Niiranen, TJ and Olsen, A and Patel, AV and Rimm, EB and Rowell, S and Salomaa, V and Sayols-Baixeras, S and Segal, E and Shrubsole, MJ and Shu, XO and Skarbinski, J and Song, M and Southey, MC and Tjønneland, A and Veiga, P and Weersma, RK and Wu, MS and Zheng, W and Zhernakova, A and Shi, J and Hong, HG and Abnet, CC and Sinha, R},
title = {Importance of faecal sample collection in prospective cohort studies to evaluate the effect of the gut microbiome on cancer development.},
journal = {The Lancet. Microbe},
volume = {},
number = {},
pages = {101525},
doi = {10.1016/j.lanmic.2026.101525},
pmid = {42822491},
issn = {2666-5247},
abstract = {The gut microbiome has been linked to cancer in many cross-sectional studies. These studies compared individuals with and without cancer, but they do not establish causation. Prospective cohort studies, with faecal samples collected before a cancer diagnosis, will be instrumental in assessing the role of the gut microbiome in human cancer risk. We identified 18 prospective cohort studies, each of which collected faecal samples from at least 5000 individuals with expected future cancer linkages, and calculated the projected numbers of colorectal, stomach, pancreatic, and female breast cancers. Larger numbers of incident cancer cases need to be evaluated to identify robust associations between the gut microbiome and cancer with sufficient power. To achieve this goal, we propose that additional cohorts collect faecal samples, particularly those with participants from various backgrounds and from under-represented world regions. Furthermore, sufficient data sharing and improved methods are needed to pool and meta-analyse microbiome data. These data can then be used to gain a better understanding of how the gut microbiome is involved in cancer development and other health outcomes at multiple body sites.},
}

@article {pmid42822514,
year = {2026},
author = {Chung, YS and Yoo, IH and Kim, EH and Jeong, JY and Kim, I and Hwang, JJ and Kim, TW and Hong, SM and Jun, E},
title = {Combined Gemcitabine and Nab-Paclitaxel Treatment Restores Gut Microbiota Homeostasis in an Orthotopic Pancreatic Ductal Adenocarcinoma Mouse Model.},
journal = {Cancer research and treatment},
volume = {},
number = {},
pages = {},
doi = {10.4143/crt.2026.0409},
pmid = {42822514},
issn = {2005-9256},
abstract = {PURPOSE: Although chemotherapy can disrupt homeostasis of gut microbiota, the role of chemotherapy affecting in gut microbiota of pancreatic ductal adenocarcinoma (PDAC) is unclear.

MATERIALS AND METHODS: We evaluated whether chemotherapy could alter the integrity of gut microbiota of PDAC-bearing mouse in vivo. Using a xenogenic orthotopic PDAC-bearing BALB/c nude mouse model by inoculation of BxPC-3-luc into the pancreas, we monitored tumor volumes and analyzed gut microbiota profiles via 16S rRNA sequencing, comparing mice systemically treated with gemcitabine/nab-paclitaxel (OC, orthotopic PDAC chemotherapy), those treated with 1× phosphate-buffered saline (ON, orthotopic PDAC non-treated), and normal controls (NC).

RESULTS: No differences were found in alpha diversity; however, phylogenetic diversity increased significantly in OC mice compared to ON mice. Phylogenetic analysis at the family level showed that abundances of Lachnospiraceae, Oscillospiraceae, and Bacteriodaceae were similar in OC and ON. However, Borkfalkiaceae and Lactobacillus significantly increased in OC compared to ON. Unclassified bacterial genera lacking formal taxonomic assignments and functional annotations, such as Clostridium, FMGN, PAC000663, and PAC001360, increased significantly in OC compared to ON. Further, a pathobiont of Escherichia increased significantly in ON compared to NC, but was depleted in OC.

CONCLUSION: This is the first study to demonstrate recovery of a partial, chemotherapy-associated shift toward a more balanced gut microbiota composition in a xenogenic orthotopic PDAC-bearing BALB/c nude mouse model after systemic chemotherapy of gemcitabine/nab-paclitaxel. Our findings provide proof-of-concept evidence that systemic chemotherapy-based approaches may be associated with amelioration of gut microbiota dysbiosis in a xenogenic orthotopic PDAC mouse model.},
}

@article {pmid42822632,
year = {2026},
author = {Qian, X and Huang, J and Liang, Z and Li, C and Yao, J and Cao, C and Xu, J},
title = {Plant-driven microbiome reorganization sustains multifunctionality of iron-biochar constructed wetlands under chronic PFOA exposure.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125826},
doi = {10.1016/j.envres.2026.125826},
pmid = {42822632},
issn = {1096-0953},
abstract = {Plant capacity to regulate treatment stability and ecological function of iron-biochar (IC) based constructed wetlands (CWs) operated under long-term PFOA exposure remains insufficiently understood. In this study, compared with unplanted system, plant (Iris pseudacorus) increased the dynamic transformation of ammonium and nitrate, limited nitrite accumulation, thus promoting total nitrogen removal, which was, on average, 12.54% higher in planted system. Besides, vegetation increased total phosphorus and chemical oxygen demand removal efficiency by 14.21% and 7.97% on average. These improvements were accompanied by vegetation-associated changes in enzyme activity, including higher dehydrogenase, phosphatase, and nitrate reductase activities during specific periods or in specific layers, greater EPS production, and improved biofilm stability with reduced bio-clogging risk. Microorganism-plant interaction also influenced greenhouse gases (GHG) emission, in which CO2 fluxes were 4.32-71.61% lower in the planted group during most sampling periods, and CH4 emissions and long-term global warming potential were also reduced. Plants also markedly increased microbial richness/diversity and enriched dominant functional taxa. Besides, Dominant genera involved in microbial carbon/nitrogen/phosphorus metabolism, iron/sulfur cycling, electron transfer, PFOA resistance, and decrease of GHG emission risk were enriched in various layers of planted group. Such variation of microbial community resulted from related gene regulation in planted group. Some other indicator bacteria also contributed substantially to optimized microbial community in planted group, including Shewanella, Thiobacillus, and Dechloromonas. These new findings provided preliminary evidence for integrating Iris pseudacorus into IC-based CWs to improve the operational stability of IC-based CWs.},
}

@article {pmid42822635,
year = {2026},
author = {Pulster, EL and Kolpin, DW and Givens, CE and Hladik, ML and Keele, LM and Meppelink, SM and Rodriguez, MD and Alvarez, DA and Williams, BM and Gordon, SE and Hubbard, LE},
title = {A Multi-State Assessment of Per- and Polyfluoroalkyl Substances (PFAS), Pesticides, and Antibiotic Resistance Genes in White-Tailed Deer (Odocoileus virginianus) of the United States.},
journal = {Environmental research},
volume = {},
number = {},
pages = {125817},
doi = {10.1016/j.envres.2026.125817},
pmid = {42822635},
issn = {1096-0953},
abstract = {Sentinel species provide a vital One Health perspective on ecosystem contamination driven by rising global chemical production. We evaluated white-tailed deer (Odocoileus virginianus; n = 54, 24 states, six matrices) as nationwide bioindicators for PFAS, pesticides, antimicrobial resistance (AMR) genes, and microbiome diversity. PFAS were detected in 100% of deer samples (26 compounds identified overall; non-detect to 12.3 ng/g ww), with preferential accumulation in the liver, indicating widespread systemic exposure. Neither region, landscape, nor source proximity predicted liver PFAS concentrations, whereas landscape had a significant, albeit weak, effect on spleen concentrations. This overall absence of strong spatial drivers suggests ubiquitous background contamination rather than localized point-source exposure. Conversely, 13 pesticides/transformation products (ranging from non-detect to 88.6 ng/g ww; highest in scat) were detected in only 28% of samples, despite widespread national use. Since not all possible transformation products were measured, these data reflect the accumulation of the target compound rather than total pesticide exposure. Driven by the rapid metabolism and excretion of herbicides, persistent insecticides dominated tissue samples. Additionally, biological threats were prevalent with eight distinct AMR genes identified in WTD scat, frequently featuring the florfenicol resistance gene (flost, 33%). The presence of synthetic compounds and AMRs in game meat and scat pose a direct One Health risk to the human food chain. These findings highlight the value of using a single, widely distributed sentinel species as an early warning system for the ecological and public health threats posed by global chemical pollution.},
}

@article {pmid42822660,
year = {2026},
author = {Welp, K and Paul, L and Froissart, R and Happel, AU and Pidwell, T and Gill, K and Bekker, LG and Jaspan, HB and Vasse, M and Passmore, JS and Kullin, BR},
title = {Antimicrobial resistance profiles and genomic diversity of vaginal Prevotella bivia isolates from South African women, including the first report of nimK in South African vaginal P. bivia isolates.},
journal = {Anaerobe},
volume = {},
number = {},
pages = {103086},
doi = {10.1016/j.anaerobe.2026.103086},
pmid = {42822660},
issn = {1095-8274},
abstract = {OBJECTIVES: To characterise the phenotypic and genotypic antimicrobial resistance (AMR) profiles and genomic diversity of vaginal Prevotella bivia isolates obtained from South African women and to compare them with publicly available genomes.

METHODS: P. bivia isolates were recovered from lateral vaginal wall swabs and identified by polymerase chain reaction (PCR) and 16S rRNA gene sequencing. Antimicrobial susceptibility testing against metronidazole, clindamycin, azithromycin, amoxicillin and doxycycline was performed using MIC test strips (MTS). Whole-genome sequencing was undertaken using the Illumina MiSeq platform to investigate genomic diversity, AMR gene carriage and mobile genetic elements.

RESULTS: Thirty-five P. bivia isolates from 30 vaginal samples underwent phenotypic characterisation, and 33 high-quality genomes were included in genomic analyses. Resistance to metronidazole and clindamycin was low (11.4% and 8.6%, respectively). The tetQ and cfxA genes were the most frequently detected AMR determinants (90.9% and 72.7% of genomes, respectively), whereas ermF and nimK were rare (3.0% each). Comparative genomic analysis revealed generally low within-sample diversity, although one participant harboured genetically distinct strains, and strain persistence was observed in another participant over a 16-week interval. South African isolates clustered separately from most publicly available isolates originating from the United States. One isolate harboured nimK within a previously described Tn6456-like mobile element, representing, to our knowledge, the first identification of nimK in a South African vaginal P. bivia isolate.

CONCLUSIONS: Vaginal P. bivia isolates from South African women exhibited low genomic diversity, evidence of strain persistence and occasional co-colonisation with multiple P. bivia strains. Although resistance to standard bacterial vaginosis therapies remained low, the presence of mobile AMR determinants highlights the importance of continued genomic and phenotypic surveillance of vaginal P. bivia populations.},
}

@article {pmid42822687,
year = {2026},
author = {Abe, S and Gondo, T and Hiraishi, N and Rujiraprasert, P and Abe, T and Okazaki, Y and Shimabukuro, M and Hayashi, F and Shimada, Y},
title = {Stannous Fluoride: NMR Characterization and Antibacterial Activity by Microbiome Analysis.},
journal = {Journal of dentistry},
volume = {},
number = {},
pages = {107089},
doi = {10.1016/j.jdent.2026.107089},
pmid = {42822687},
issn = {1879-176X},
abstract = {OBJECTIVES: This study aimed to characterize the ionization behavior and chemical speciation of stannous fluoride (SnF2) using NMR spectroscopy and to evaluate its effects on microbial viability and bacterial community composition in saliva-derived polymicrobial biofilms.

METHODS: SnF₂ speciation was characterized by ¹⁹F NMR spectroscopy. As a physicochemical assessment, biomimetically precipitated apatite samples were analyzed by solid-state ³¹P NMR. Saliva-derived polymicrobial biofilms were formed on hydroxyapatite discs and exposed to SnF₂ or NaF at final F concentrations of 38, 76, and 190 ppm. Deionized water was added instead of the fluoride stock solution, served as the control. ATP-based microbial activity was assessed by luminescence assay, and bacterial community composition was analyzed by 16S rRNA gene sequencing at 190 ppm F.

RESULTS: ¹⁹F NMR analysis showed that SnF₂ existed not only as free F⁻ ions but also partly as Sn-F complex species. Solid-state ³¹P NMR suggested that NaF promoted pronounced fluorapatite-like formation, whereas SnF₂ resulted in partial retention of lattice OH groups. SnF₂ produced a greater reduction in ATP-based microbial activity than NaF. The SnF₂ group also showed significantly lower Shannon diversity than NaF and lower abundances of Veillonella and Fusobacterium than the fluoride-free control.

CONCLUSIONS: SnF₂ exhibited complex aqueous speciation and affected both apatite formation and saliva-derived polymicrobial biofilms differently from NaF. These findings highlight complementary physicochemical and biological properties of SnF₂, although a direct mechanistic link between them was not established.

CLINICAL SIGNIFICANCE: Understanding the chemical speciation of SnF₂ may help clarify its anticaries potential, including its effects on apatite mineralization and polymicrobial biofilm control.},
}

@article {pmid42822841,
year = {2026},
author = {Yan, Y and Yuan, Z and Lin, X and Zhang, N and Lv, X and Jing, W and Zhang, J and Zhang, H},
title = {Mechanisms of Phyllosphere Microbial Regulation of Nitrogen Use in Rice.},
journal = {Physiologia plantarum},
volume = {178},
number = {5},
pages = {e71138},
doi = {10.1111/ppl.71138},
pmid = {42822841},
issn = {1399-3054},
support = {32572443//National Natural Science Foundation of China/ ; 32272197//National Natural Science Foundation of China/ ; 32071944//National Natural Science Foundation of China/ ; GRF 12101722//Hong Kong Research Grants Council/ ; 12102423//Hong Kong Research Grants Council/ ; 12105824//Hong Kong Research Grants Council/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; },
mesh = {*Oryza/microbiology/metabolism ; *Nitrogen/metabolism ; *Plant Leaves/microbiology/metabolism ; *Microbiota/physiology ; Fertilizers ; },
abstract = {Nitrogen (N) fertilizers are key drivers of high yields in rice (Oryza sativa L.), yet increasing N inputs often deliver diminishing improvements in N use efficiency (NUE) and can exacerbate N losses via volatilization, leaching, and runoffs, with associated environmental impacts. The rice phyllosphere microbiome, which consists of microbes inhabiting leaf surfaces and internal tissues, has the potential to influence foliar nutrient turnover, N metabolism, and stress responses and may therefore influence internal NUE (IEN) and, under reduced fertilizer-N input, potentially affect agronomic efficiency of applied N (AEN). Here, we summarize the major steps of rice N metabolism (uptake, assimilation, transport, redistribution, and remobilization) and discuss microbial pathways that could modulate N use, including foliar N transformations, microbially mediated N inputs, and indirect effects through hormonal regulation, stress buffering, and microbe-microbe interactions. Key knowledge gaps remain in quantification of underlying mechanistic processes, field robustness across seasons and sites, and genotype/microbiome matching under reduced-N management.},
}

*Oryza/microbiology/metabolism
*Nitrogen/metabolism
*Plant Leaves/microbiology/metabolism
*Microbiota/physiology
Fertilizers

@article {pmid42822994,
year = {2026},
author = {Hanin, A and Gopaul, MT and Navarro, V and Gaspard, N and Hirsch, LJ},
title = {Insights into new-onset refractory status epilepticus (NORSE) from biorepository-based studies.},
journal = {Seminars in pediatric neurology},
volume = {59},
number = {},
pages = {101296},
doi = {10.1016/j.spen.2026.101296},
pmid = {42822994},
issn = {1558-0776},
mesh = {Humans ; *Status Epilepticus/immunology/diagnosis/etiology/physiopathology ; *Drug Resistant Epilepsy/diagnosis/immunology ; },
abstract = {New-onset refractory status epilepticus (NORSE) is a rare clinical condition characterized by the occurrence of refractory status epilepticus in previously healthy children or adults. When preceded by a febrile illness 1-14 days prior, it is known as Febrile Infection-Related Epilepsy Syndrome (FIRES). In most cases, no underlying etiology is identified despite extensive evaluation, and these patients are classified as having cryptogenic NORSE. The NORSE Institute was established to define the condition, increase awareness, and facilitate collaborative research, notably through the creation of a biorepository designed to collect biospecimens and clinical data from patients with NORSE. In recent years, extensive research has been conducted using these samples and datasets, as well as complementary resources from additional collaborating biorepositories. In this review, we summarize recent advances in the field, namely the development of guidelines for biospecimen collection and use, the characterization of immune dysfunction and its potential link to neuronal excitability and possibly to personalized treatments, the interaction between the microbiome and inflammatory pathways, and the characterization of clinical outcomes in patients with NORSE. Together, these advances are improving our understanding of NORSE mechanisms, helping to identify prognostic biomarkers and to support the development of personalized treatments.},
}

Humans
*Status Epilepticus/immunology/diagnosis/etiology/physiopathology
*Drug Resistant Epilepsy/diagnosis/immunology

@article {pmid42823104,
year = {2026},
author = {Dunneram, Y and Hackney, E and Manning, S and Louca, P and Stewart, CJ and Taylor, GS and Koo, S and Young, GR and Mitra, S and Hampton, JS and Dobson, C and Neilson, LJ and Addison, C and Whelpton, J and , and Sharp, L and Hull, MA and Rees, C},
title = {Baseline characteristics of participants recruited into the COLO-COHORT study: a UK-wide resource for colorectal cancer prevention.},
journal = {BMJ open gastroenterology},
volume = {13},
number = {1},
pages = {},
pmid = {42823104},
issn = {2054-4774},
mesh = {Humans ; *Colorectal Neoplasms/prevention & control/diagnosis/epidemiology ; Male ; Middle Aged ; United Kingdom/epidemiology ; Colonoscopy/statistics & numerical data ; Female ; Aged ; Prospective Studies ; *Early Detection of Cancer/methods/statistics & numerical data ; Mass Screening/methods ; *Patient Selection ; Cohort Studies ; Risk Factors ; },
abstract = {OBJECTIVE: To describe the design, recruitment, and baseline characteristics of the first phase of COLO-COHORT and to establish this population as a resource for colorectal cancer (CRC) prevention research.

METHODS: COLO-COHORT is a prospective, multicentre observational study recruiting adults undergoing colonoscopy through screening and routine National Health Service referral pathways within a 32-site UK network. We present descriptive data from the first 4754 participants, recruited through 27 Phase 1 sites, including demographics, lifestyle factors, clinical characteristics, biospecimen availability and colonoscopy outcomes.

RESULTS: Participants had a median age of 64 years (IQR 57-70), and 54.3% were male. Overweight (38.0%) and obesity (30.5%) were common, and cardiometabolic comorbidities were prevalent (11.8% with type II diabetes; 39.4% with hypertension). Colorectal neoplasia was identified at colonoscopy in over half of participants (56.1%), with histologically characterised data available on polyp type, size, morphology and anatomical location. Core demographic and clinical variables were available for >95% of participants, with colonoscopy findings recorded for all. Linked blood and stool microbiome biospecimens were available for approximately 80% and 40% of participants, respectively.

CONCLUSION: This paper establishes and characterises COLO-COHORT's Phase 1 study cohort as a well-phenotyped resource, representing a population of individuals undergoing colonoscopy via UK screening and routine clinical pathways. This cohort will support and underpin future collaborative clinical, epidemiological and translational research in CRC prevention.},
}

Humans
*Colorectal Neoplasms/prevention & control/diagnosis/epidemiology
Male
Middle Aged
United Kingdom/epidemiology
Colonoscopy/statistics & numerical data
Female
Aged
Prospective Studies
*Early Detection of Cancer/methods/statistics & numerical data
Mass Screening/methods
*Patient Selection
Cohort Studies
Risk Factors

@article {pmid42823330,
year = {2026},
author = {Xu, Z and Zhang, T and Liu, Z and Jiang, H and Li, S and Qi, H and Chan, FKL and Kwok, T and Ng, SC},
title = {Diabetes status stratifies the association between gut microbiome and sarcopenia.},
journal = {Gut},
volume = {},
number = {},
pages = {},
doi = {10.1136/gutjnl-2026-340737},
pmid = {42823330},
issn = {1468-3288},
}

@article {pmid42823420,
year = {2026},
author = {Chang, L and Corsetti, M and Chey, WD and Ford, AC and Schmulson, MJ and Shin, A and Barbara, G and Ballou, S and Mayer, EA and Siah, KT and Simrén, M and Staudacher, H and Lembo, AJ},
title = {Irritable bowel syndrome.},
journal = {Nature reviews. Disease primers},
volume = {12},
number = {1},
pages = {},
pmid = {42823420},
issn = {2056-676X},
mesh = {Humans ; *Irritable Bowel Syndrome/physiopathology/diagnosis/therapy/epidemiology ; Quality of Life/psychology ; Abdominal Pain/etiology ; },
abstract = {Irritable bowel syndrome (IBS) is one of the most prevalent disorders of gut-brain interaction, characterized by recurrent abdominal pain or abdominal discomfort associated with altered bowel habits in the absence of identifiable structural disease. IBS affects ~4-11% of the global population and is associated with substantial healthcare utilization, impaired quality of life and considerable socioeconomic burden. IBS is increasingly recognized as a heterogeneous condition caused by dysregulated bidirectional communication within the gut-brain axis. Altered gastrointestinal motility, visceral hypersensitivity, epithelial barrier dysfunction, neuroimmune activation, gut microbiome and metabolome changes, central pain amplification, stress and autonomic dysregulation, and sex-related biological influences underlie pathophysiological mechanisms. IBS can develop after a gastrointestinal infection and can frequently co-occur with other disorders of gut-brain interaction, chronic pain conditions, psychological disorders and organic gastrointestinal disorders such as inflammatory bowel disease and coeliac disease. Diagnosis relies on a positive symptom-based approach using the Rome V criteria, supported by clinical assessment and limited testing to exclude differential diagnoses. Management focuses on improving symptoms and quality of life through an individualized, stepwise approach that involves patient education, dietary interventions, pharmacological therapies and gut-brain behaviour therapies. Emerging biomarkers, multi-omics approaches, digital health tools and precision medicine strategies may enable mechanism-based diagnosis and targeted treatment in the future.},
}

Humans
*Irritable Bowel Syndrome/physiopathology/diagnosis/therapy/epidemiology
Quality of Life/psychology
Abdominal Pain/etiology

@article {pmid42823534,
year = {2026},
author = {Raja-Kumar, RS and Mesny, F and Basak, AK and Newfeld, J and Chesneau, G and Entila, F and Lee, T and Rigerte, L and Carvajal Acevedo, S and Hüttel, B and Crous, PW and Maciá-Vicente, JG and Stewart, H and Ryan, M and Fakhoury, AM and Sacristán, S and Aitouguinane, M and Batisson, I and Dumontet, S and Elmer, WH and Henzelyová, J and Kruszewska, JS and Nelson, JM and Santelli, CM and Pauly, M and Molina, A and Hiruma, K and Hacquard, S},
title = {Carbohydrate-active enzymes from a core root mycobiota member enable infection of multiple plant hosts.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42823534},
issn = {2058-5276},
support = {101089198//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; SPP DECRyPT 2125//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; },
abstract = {The root microbiome includes fungal pathogens capable of colonizing multiple plant hosts, yet the underlying genetic determinants remain unknown. Here we report that Plectosphaerella cucumerina is a core member of the Arabidopsis thaliana root microbiota, which displays pathogenic potential across multiple hosts. Using a collection of 72 Plectosphaerella isolates and whole-genome sequencing, we observed subtle phenotypic and genotypic variation associated with fungal phylogeny but not host plant identity. Transcriptome profiling of a P. cucumerina isolate in roots of diverse plants revealed core and host-specific fungal responses, including induction of carbohydrate-active enzymes (CAZymes) involved in root cell wall deconstruction. A fungal gene encoding a candidate β-1,3-glucanase (GH64) was identified as a key genetic factor driving multihost infection. This gene is present across plant-colonizing fungi and functions as a disease determinant in both P. cucumerina and a Colletotrichum root pathogen. Our results indicate that host-induced CAZymes can couple fungal virulence with multihost compatibility.},
}

@article {pmid42823565,
year = {2026},
author = {Khan, I and Xie, X and Li, Z},
title = {Gut Microbiome and Fecal Metabolome Analysis Reveal Potential Non-Invasive Biomarkers For Acute Myocardial Infarction.},
journal = {Probiotics and antimicrobial proteins},
volume = {},
number = {},
pages = {},
pmid = {42823565},
issn = {1867-1314},
support = {24ZDCA004//Science and Technology Project of Gansu Province/ ; 00400/Z23115//Science and Technology Project of Gansu Province/ ; },
abstract = {Although the gut microbiome is recognized as crucial for human health, its combined effects with microbial metabolites on acute myocardial infarction (AMI) remain poorly understood. This study investigated gut microbiome composition using 16 S rRNA sequencing and untargeted LC-MS metabolomics profiles from 24 AMI patients and 24 healthy individuals to identify microbial biomarkers, metabolite signatures, and key functional pathways. No significant difference was observed in alpha diversity, whereas beta diversity differed significantly between AMI patients and controls. At the taxonomic level, Bacteroidota, Proteobacteria, Escherichia_Shigella, Collinsella, and Klebsiella were increased, while Firmicutes, Actinobacteriota, and Bifidobacterium were decreased in the AMI group compared with controls. Metabolomic profiling identified seven metabolites with strong discriminatory power for AMI, with area under the curve (AUC) values ranging from 0.91 to 0.99. Among these, S‑adenosyl‑L‑homocysteine, Cyanidin 3‑[6‑(4‑glucosylcoumaryl)sophoroside] 5‑glucoside, and 5‑Methyltetrahydrofolate were found to be upregulated, whereas Prostaglandin J2, Leukotriene A4, and 5‑HEPE were downregulated. Based on these findings, the upregulated metabolites S‑Adenosyl‑L‑homocysteine, Cyanidin 3‑[6‑(4‑glucosylcoumaryl)sophoroside] 5‑glucoside, 5‑Methyltetrahydrofolate, and the downregulated metabolites Prostaglandin J2, Leukotriene A4, and 5‑HEPE represent candidate non‑invasive biomarkers for AMI that warrant further validation. Functional pathway analysis highlighted pronounced disruptions in arginine biosynthesis and the folate-mediated one-carbon metabolism. Spearman correlation analysis showed that specific gut microbial taxa were significantly associated with clinical parameters and metabolites implicated in AMI-related pathways. These findings revealed distinct microbial and metabolic profiles in Chinese patients with AMI compared to healthy controls. Future research should investigate causal mechanisms and evaluate microbiota-targeted approaches for cardiovascular disease prevention and therapy.},
}

@article {pmid42823722,
year = {2026},
author = {Waelchli, J and Janse van Rensburg, H and Stengele, K and D'Adda, V and Cadot, S and Caggìa, V and Gfeller, V and Schlaeppi, K},
title = {Soil iron modulates beneficial maize microbiome feedbacks in rotations with wheat.},
journal = {Microbiome},
volume = {14},
number = {1},
pages = {},
pmid = {42823722},
issn = {2049-2618},
support = {189249//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; },
mesh = {*Triticum/growth & development/microbiology ; *Zea mays/microbiology/growth & development ; *Iron/metabolism/analysis ; *Soil Microbiology ; *Soil/chemistry ; *Microbiota ; Plant Roots/microbiology/metabolism ; Arabidopsis/growth & development/microbiology ; Benzoxazines/metabolism/pharmacology ; Bacteria/classification/isolation & purification/genetics ; },
abstract = {BACKGROUND: Plants change their surrounding soil microbiome by root exudates and these conditioned microbiomes impact the performance of the present as well as the next plant generation as for example in crop rotations. The big challenge is that such 'microbiome feedbacks' are highly context-dependent, i.e. they vary in strength and direction dependent on the local soil environment - of which the driving factor(s) remain unknown. Including maize in crop rotations involves benzoxazinoids (BXs), which are exuded from roots and alter the soil microbiome, which in turn affects growth and defence of the following crop.

RESULTS: Here, we grew wild-type and BX-depleted maize in the field to differentially condition their soil microbiome and we found varying feedbacks on wheat performance dependent on the local physicochemical soil parameters. Using multivariate, correlation and modelling approaches and including additional data from two previous field experiments, we identified plant-available (PA) iron to be associated with BX-dependent microbiome feedbacks on wheat. The BX-conditioned soil microbiome caused wheat to grow taller at low levels of soil PA-iron but smaller at high levels. This finding was generalized by testing these maize microbiome feedbacks on the model plant Arabidopsis thaliana using soil batches containing different levels of iron. Consistent with wheat, a significant inverse relationship between soil PA-iron levels and plant growth was found. This relationship was experimentally validated with Arabidopsis thaliana grown at low levels of soil iron where iron supplementation abolished the beneficial feedback of the BX-conditioned soil microbiome.

CONCLUSION: Together, these findings revealed that beneficial microbiome feedbacks occur at low levels of plant-available iron, i.e. when plants grow in a suboptimal soil, but they are lost when plants are nutritionally well supported. These results underscore the importance of iron availability in soil for beneficial microbial feedbacks on plant growth and predict agronomic benefits of incorporating maize in crop rotations on low iron soils. Video Abstract.},
}

*Triticum/growth & development/microbiology
*Zea mays/microbiology/growth & development
*Iron/metabolism/analysis
*Soil Microbiology
*Soil/chemistry
*Microbiota
Plant Roots/microbiology/metabolism
Arabidopsis/growth & development/microbiology
Benzoxazines/metabolism/pharmacology
Bacteria/classification/isolation & purification/genetics

@article {pmid42823781,
year = {2026},
author = {Kudjordjie, EN and Vestergård, M and Gebremikael, MT and Nielsen, O and Nicolaisen, M},
title = {Neighbour Effects and Dynamics of Plant-Associated Microbiomes in a Strip-Crop System.},
journal = {Environmental microbiology reports},
volume = {18},
number = {5},
pages = {e70423},
doi = {10.1111/1758-2229.70423},
pmid = {42823781},
issn = {1758-2229},
support = {34009-20-1703//GUDP Organic RDD 6 project/ ; },
mesh = {*Hordeum/microbiology ; *Microbiota ; *Soil Microbiology ; Bacteria/classification/genetics/isolation & purification ; *Vicia faba/microbiology ; Fungi/classification/genetics/isolation & purification ; *Crops, Agricultural/microbiology ; RNA, Ribosomal, 16S/genetics ; Agriculture/methods ; Seasons ; Plant Leaves/microbiology ; },
abstract = {While multi-cropping systems, such as strip-cropping, assemble complex microbial communities that contribute to ecosystem resilience, we have limited understanding of their assembly and functions at field scale. Here, we examined the dynamics and site-specific assembly of soil and phyllosphere microbiomes in a rotational faba bean (Vicia faba) and spring barley (Hordeum vulgare) strip-system during two seasons. Using bacterial 16S and fungal ITS amplicon sequencing, we analysed microbial communities across gradients from the centre towards strip edges. We found that phyllosphere microbiomes are more affected by strip-cropping than soil microbiomes. Neighbouring crops harbour different microbial communities, but with increasing proximity, their phyllosphere microbiomes share more specific microbial taxa. Likewise, we observed gradient-specific microbial distribution, including fungal pathogen taxa. For instance, Puccinia was more abundant in the centre of the spring barley strips and gradually declined towards the edge. Correlation and co-occurrence network analyses revealed distinct microbial interaction patterns across soil and phyllosphere gradients. These networks were more resilient at the edge of the strips compared to central networks of spring barley. Altogether, our findings revealed neighbour-effects modulating host-associated microbiomes across strips that could be harnessed for designing optimal cropping systems, for example, to reduce leaf pathogens.},
}

*Hordeum/microbiology
*Microbiota
*Soil Microbiology
Bacteria/classification/genetics/isolation & purification
*Vicia faba/microbiology
Fungi/classification/genetics/isolation & purification
*Crops, Agricultural/microbiology
RNA, Ribosomal, 16S/genetics
Agriculture/methods
Seasons
Plant Leaves/microbiology

@article {pmid42823913,
year = {2026},
author = {Alkeheli, MF and Othman, HI},
title = {Biological Biomarkers in Proliferative Verrucous Leukoplakia: A Systematic Review and Meta-Analysis.},
journal = {Oral diseases},
volume = {},
number = {},
pages = {},
doi = {10.1111/odi.70520},
pmid = {42823913},
issn = {1601-0825},
abstract = {OBJECTIVE: To synthesise biological biomarker evidence in proliferative verrucous leukoplakia/proliferative leukoplakia and quantify malignant transformation using eligible longitudinal evidence.

METHODS: Primary human biomarker studies and longitudinal studies reporting extractable malignant-transformation events and denominators were systematically reviewed. Biomarker evidence was synthesised narratively. Malignant-transformation proportions were pooled using a random-effects model, with conservative handling of potentially overlapping cohorts.

RESULTS: Forty-one publications contributed to the biomarker synthesis, spanning genetic, genomic, DNA-ploidy, epigenetic, transcriptomic, proteomic, immunohistochemical, immunologic, viral, microbiome, salivary, and circulating markers. No biomarker had sufficient independent validation for clinical diagnostic or prognostic use. Twenty independent or conservatively non-overlapping study estimates comprising 745 patients and 243 malignant-transformation events contributed to the meta-analysis. The pooled malignant-transformation proportion was 34.13% (95% confidence interval 26.62-42.53), with substantial heterogeneity and a 95% prediction interval of 13.85%-62.56%. Results remained stable in sensitivity and leave-one-out analyses.

CONCLUSIONS: Diverse biological alterations have been reported, but none currently supports routine biomarker-based diagnosis or individual risk stratification. Malignant transformation is frequent, although substantial between-study variability limits interpretation of the pooled estimate as an individual patient risk.},
}

@article {pmid42823956,
year = {2026},
author = {Kardomatea, N and Kool, J and Nicolaie, MA and van Dijken, H and Reinen, E and Konstanti, P and Eggink, D and Jaarsma, R and van Emst, L and van Woudenbergh, E and Ferreira, JA and Fuentes, S and de Jonge, MI and de Jonge, J and Verhagen, LM and Hartog, GD},
title = {Niche-specific immune and microbial signatures across the healthy upper respiratory tract mucosa.},
journal = {iScience},
volume = {29},
number = {10},
pages = {117574},
pmid = {42823956},
issn = {2589-0042},
abstract = {Host-microbe interactions in the upper respiratory tract (URT) niches that form the first line of defense against respiratory infections are incompletely understood. We profiled immune and microbial features using minimally invasive samples from 44 healthy adults (20-65 years), including nasopharyngeal (NPS), oropharyngeal (OPS), and mid-turbinate nasal swabs (MTSs), mucosal lining fluid (MLF), and saliva. Multiplex cytokine and antibody assays, 16S rRNA sequencing, and pathogen detection by PCR were performed. Immune and microbial profiles differed by niche: nasal samples showed consistently higher antiviral cytokine levels and Corynebacterium dominance. Oral samples had greater microbial diversity with distinct cytokine and antibody patterns. Saliva and MLF had the highest antibody concentrations, predominantly IgA. Integrated analyses identified site-specific microbe-immune associations. These findings show the feasibility of non-invasive, integrated profiling to uncover compartment-specific host-microbe relationships, providing a scalable framework for respiratory mucosal immunology and microbiome research with applications in infection surveillance and vaccine evaluation.},
}

@article {pmid42824003,
year = {2026},
author = {Qi, G and Wu, Z and Chen, J and Zhang, D and Wang, Q},
title = {Gut microbiota characteristics of gastric cancer patients across distinct pathological stages and their associations with tumor and paratumor mucosal microbiota.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1897107},
pmid = {42824003},
issn = {2235-2988},
mesh = {Humans ; *Stomach Neoplasms/microbiology/pathology ; *Gastrointestinal Microbiome ; Female ; Male ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; China ; Aged ; Feces/microbiology ; Metagenomics ; Neoplasm Staging ; Dysbiosis ; },
abstract = {Gastric cancer (GC) is closely associated with microbial dysbiosis; however, the spatial-temporal characteristics of the gut, paracancerous, and intratumoral microbiomes, as well as their interrelationships during tumor progression, remain insufficiently defined. This study aimed to characterize these microbiomes in 85 GC patients from Northwest China using shotgun metagenomic sequencing and functional annotation. Clinical samples included feces, tumor tissues, and paratumor mucosal tissues (≥5 cm from the tumor margin), enabling comprehensive profiling of microbial composition at the phylum, genus, and species levels, as well as functional pathway analysis. The results showed that the microbial community was dominated by Firmicutes and Bacteroidetes (combined relative abundance >75%), maintaining structural stability across tumor stages II-IV (Stage I n=2 is only descriptively reported and excluded from formal statistical testing), thereby supporting the "core microbiota resilience" hypothesis. PERMANOVA revealed that tumor stage had a statistically significant yet modest effect on community structure (R[2] = 0.039, P = 0.032). MaAsLin2 identified stage-associated differential genera: Roseburia and Megamonas decreased with advancing stage, whereas Lactobacillus and Enterobacter were enriched in advanced stages (III/IV). Functional pathway analysis revealed stage-specific metabolic remodeling: Stage II was enriched in DNA repair, glycolysis, aromatic amino acid, and nucleotide biosynthesis pathways; Stage IV showed enrichment in protein deamination/demethylation, pyruvate fermentation, and coenzyme metabolism pathways. Correlation analysis further revealed a characteristic pattern of "pathogen enrichment and beneficial bacteria depletion." Fusobacterium nucleatum and Helicobacter pylori exhibited strong positive correlations with GC, whereas short-chain fatty acid-producing bacteria such as Roseburia and Faecalibacterium prausnitzii showed significant negative correlations, particularly in paracancerous tissues. We established multi-layered taxonomic correlation profiles based on intra-cohort microbial shifts, in which Bacteroides stercoris and Bifidobacterium pseudocatenulatum exhibited the most pronounced stage-related abundance changes in the fecal microbiota across tumor stages. Overall, this study systematically delineates the structural stability, stage-specific functional remodeling, and interrelated dynamics of gut, paracancerous, and intratumoral microbiomes in gastric cancer. These findings provide descriptive baseline data of cross-compartment microbiome variation within gastric cancer patients across tumor stages, which only deliver preliminary correlative clues of GC-related microbial shifts and require further multi-cohort verification with non-cancer control populations.},
}

Humans
*Stomach Neoplasms/microbiology/pathology
*Gastrointestinal Microbiome
Female
Male
*Bacteria/classification/genetics/isolation & purification
Middle Aged
China
Aged
Feces/microbiology
Metagenomics
Neoplasm Staging
Dysbiosis

@article {pmid42824160,
year = {2026},
author = {Li, X and Zhang, J and Wu, H and Sun, B and Liu, J and Xiao, N and Xiang, H and Liu, H and Li, Q and Li, Z},
title = {Supplementary probiotic complexity modulates growth performance, physiological status, and water quality of super-intensive Pacific white shrimp (Litopenaeus vannamei) biofloc system.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1924931},
pmid = {42824160},
issn = {1664-302X},
abstract = {Supplementing biofloc systems with functionally specialized probiotics represents a promising strategy for super-intensive Pacific white shrimp (Litopenaeus vannamei) aquaculture. Nevertheless, the efficacy and the microbial mechanism are still opaque. Based on heterotrophic nitrifying bacterium Providencia rettgeri (N), which has exhibited holistically promoting effects to the shrimp biofloc system, we further compared the impacts (N) with a dual consortium (N + Bacillus subtilis; NB) and a triple consortium (NB + effective microorganisms; NBE). Our results demonstrated that survival rates from all groups exceeded 76% with no significant differences. Regarding growth performance, NB simultaneously promoted the growth speed and the feed utilization of shrimp, whilst NBE exerted negative effects on feed efficiency. Besides, NB consortium kept the lowest inorganic nitrogen in the rearing water. Microbiome profiling of biofloc revealed NB induced a distinct microbial structure, characterized by nitrifying bacteria (e.g., Nitrosomonas) and intestinal symbionts (e.g., Candidatus Bacilloplasma). Physiologically, shrimp reared in NB showed higher catalase activity. In contrast, NBE suppressed superoxide dismutase activity and induced compensatory transcription of digestion (trypsin and lipase) and lipid metabolism (peroxisome proliferator-activated receptor γ). Transcriptomic analyses further elucidated, in comparison with N, NB stimulated host energy metabolism via the TCA cycle and glycolysis, whereas NBE triggered cellular stress and macromolecular catabolism, notably enriching autophagy and ubiquitin-mediated proteolysis pathways. In conclusion, the combination of P. rettgeri and B. subtilis synergistically optimizes the output and ecology to the super-intensive L. vannamei biofloc system. Excessive microbial complexity results in a metabolic burden, forcing the host to prioritize stress responses instead of growth. Further work should concentrate on optimizing probiotic formulas in which prioritize ecological compatibility over mere strain richness.},
}

@article {pmid42824179,
year = {2026},
author = {Manoharan, RK and Han, KI and Lee, Y and Baek, S and Moon, E and Park, YB and Cho, J and Chaudhary, J and Shin, HD},
title = {Gut health and microbiome modulation by the heat-killed postbiotic beLP1[®] in adults with excess weight: a randomized, placebo-controlled trial.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1919277},
pmid = {42824179},
issn = {2296-861X},
abstract = {BACKGROUND: Overweight is linked to gut microbiota dysbiosis and gastrointestinal (GI) symptoms that impair quality of life.

METHODS: This 84-day randomized, double-blind, placebo-controlled study evaluated the gut-health effects of heat-killed Lactiplantibacillus plantarum (beLP1[®]) in otherwise healthy adults (aged 18-45 years) within the BMI range of 25-35 kg/m[2] and a ≥3-month history of mild-to-moderate GI discomfort, confirmed by Gastrointestinal Symptom Rating Scale (GSRS). In this trail 140 adults were allocated in a 1:1 ratio to receive either daily beLP1[®] (>30 billion cells) (n = 70) or placebo (n = 70). A total of 103 participants completed the study without protocol deviations and were included in the primary per-protocol (PP) analysis (beLP1[®]: n = 49; Placebo: n = 54). This predefined analysis directly compares the beLP1[®] and placebo arms using analysis of covariance (ANCOVA), supplemented by two independent-sample Student's t-tests. The primary endpoint was change in gastrointestinal symptoms via the GSRS, secondary endpoints included the Perceived Stress Scale (PSS), the Digestion-associated Quality of Life Questionnaire (DQLQ), Tumor Necrosis Factor-alpha (TNF-α), lipid parameters, Dual-Energy X-ray Absorptiometry (DEXA), and gut microbiome diversity by metagenomic Next-Generation Sequencing (NGS).

RESULTS: Compared to placebo, beLP1[®] significantly reduced total Gastrointestinal Symptom Rating Scale (GSRS) scores at Day 42 (p = 0.0215) and Day 84 (p = 0.0394), with prominent improvements in abdominal pain (p = 0.0205) and dyspeptic syndrome (p = 0.0303) domains. Significant reductions in perceived stress (p = 0.0004) and improvements in digestion-associated quality of life (p = 0.0008) were concurrently achieved. Metagenomic analysis revealed a favorable modulation of the gut microbiota, characterized by an enrichment of several short-chain fatty acid-producing bacteria and a significant reduction in multiple opportunistic pathogens. No significant changes occurred in serum TNF-α, lipid profiles, or DEXA body composition metrics.

CONCLUSION: Overall, beLP1[®] safely and progressively alleviates GI symptoms, reduces stress, and optimizes microbiome composition in adults with excess weight. ClinicalTrials.gov: NCT05820737.

CLINICAL TRIAL REGISTRATION: https://clinicaltrials.gov/study/NCT05820737?cond=NCT05820, identifier NCT05820737.},
}

@article {pmid42824488,
year = {2026},
author = {Xu, Y and Niu, Z and Zhou, L and Ding, W and Li, J},
title = {Associations of body fat percentage-based obesity with depression and comorbidity-related gut microbiota features in college students.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1906822},
pmid = {42824488},
issn = {2296-861X},
abstract = {INTRODUCTION: The association between body fat percentage (BFP)-defined obesity and depression in college students remains unclear, and gut microbiota alterations in this comorbid condition have not been fully characterized.

METHODS: A total of 906 college students were recruited to examine the prevalence of comorbid obesity and depression and the association between body fat percentage-defined obesity and depression. Logistic regression was used for association analysis. Subsequently, 104 participants balanced for age and sex distributions across groups were selected and divided into four groups: obese with depression (G1), non-obese with depression (G2), obese without depression (G3), and non-obese without depression (G4). Fecal samples were analyzed by 16S rRNA gene sequencing.

RESULTS: The prevalence of comorbid obesity and depression was 9.71%. BFP-defined obesity was significantly associated with depression after adjustment for covariates (OR = 1.62, 95% CI: 1.10-2.38). Gut microbiota analysis showed no significant differences in α-diversity among groups, whereas β-diversity differed significantly between the G1 and G4 (P < 0.05). Descriptive taxonomic profiles suggested differences in the relative abundances of several genera (e.g., decreased Akkermansia, increased Fusobacterium and Collinsella in G1). PICRUSt- based functional prediction suggested differences in inferred microbial metabolic pathways between G1 and other groups, including higher predicted lipopolysaccharide biosynthesis pathway abundance than in G2 and G4.

DISCUSSION: BFP-defined obesity was associated with depression in college students. The microbiome findings were exploratory and suggest that co-occurring obesity and depression may be associated with differences in gut microbial composition and predicted functional potential. Larger longitudinal studies with direct functional and inflammatory measurements are needed.},
}