@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.},
}

@article {pmid42824567,
year = {2026},
author = {Wu, B and Wei, W and Zhang, K and Zhang, S},
title = {Pancreatic microbiota composition and diversity in pancreatitis-associated infection: a systematic review with focus on infected pancreatic necrosis.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1916175},
pmid = {42824567},
issn = {1664-302X},
abstract = {UNLABELLED: Pancreatitis-associated intra-abdominal infection (PA-IAI), particularly infected pancreatic necrosis (IPN), is a serious complication of severe acute pancreatitis and contributes substantially to late morbidity and mortality. Sequencing-based technologies have expanded the detection of microorganisms in pancreatic infection; however, the characteristics of pancreatic microbiota and their clinical relevance have not been systematically summarized. A systematic literature search was conducted in seven electronic databases to identify studies evaluating pancreatic microbiota in patients with pancreatitis-associated infection. Studies reporting microbial composition or diversity using sequencing-based approaches were included. Study characteristics, microbial findings, diversity patterns, clinical outcomes, and methodological details were systematically extracted and synthesized. Six studies involving 235 participants were included; 188 participants contributed pancreatic or peripancreatic microbiota data. Most available evidence was derived from patients with IPN. Sequencing-based approaches generally detected a broader range of microbial taxa than conventional culture, with enteric-associated microorganisms frequently detected, while phylum-level dominance varied among studies. Reported diversity patterns varied between studies and could not be directly compared because of methodological heterogeneity. Although IPN was associated with worse clinical outcomes, current evidence did not demonstrate that specific microbial taxa or microbiota characteristics independently predicted mortality, organ failure, or treatment response. Current evidence indicates that pancreatic microbiota in pancreatitis-associated infection, particularly IPN, are characterized by frequent detection of enteric-associated microorganisms and substantial methodological heterogeneity. Sequencing-based approaches may provide additional microbiological information beyond conventional culture and may influence clinical management; however, whether sequencing-guided management changes improve antimicrobial stewardship or patient-centered outcomes remains uncertain. Future prospective studies using standardized microbiome workflows are required to determine the clinical significance of pancreatic microbial characteristics.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420261295285, identifier: CRD420261295285.},
}

@article {pmid42824651,
year = {2026},
author = {Gadaleta, D and Ghironi, S and Maggi, F and Tiddia, M and Funari, F and Paffetti, A and Caiola, E and Roncaglioni, A and Benfenati, E and Brunelli, L},
title = {Exploring Hippuric Acid's Putative Protective Role in Aging through In Silico and In Vitro Screening.},
journal = {ACS omega},
volume = {11},
number = {38},
pages = {56923-56934},
pmid = {42824651},
issn = {2470-1343},
abstract = {Hippuric acid (HA) is a diet- and microbiome-derived metabolite consistently associated with healthy aging, yet whether it is a passive biomarker or an active effector remains unresolved. To investigate mechanisms underlying its protective role, in silico screening of large bioactivity data sets was performed and integrated with results from in vitro assays. A multifingerprint similarity approach was employed to identify close HA analogues and their reported targets. HA analogues were identified with reported potencies in the low-micromolar or nanomolar range toward transporters (solute carriers, organic anion transporters, multidrug resistance-associated proteins), epigenetic regulators (histone deacetylases), and enzymes linked to inflammation, proteostasis, or vascular homeostasis (carbonic anhydrases, cyclooxygenase-2, soluble epoxide hydrolase, neprilysin). Additional evidence pointed to proteins involved in detoxification, energy metabolism, and neurodegeneration (kynureninase, microtubule-associated protein tau, 2-amino-3-carboxymuconate-6-semialdehyde decarboxylase), supporting their plausibility as candidate HA targets. By contrast, database screenings for direct antioxidant or anti-inflammatory activity were mostly inconclusive, whereas in vitro assays suggested limited radical-scavenging activity and no modulation of nitric oxide production pathways. Results suggest that HA's protective associations with aging might involve modulation of specific proteins or transporter-mediated mechanisms, rather than acting solely through target-nonspecific pathways. While these findings remain exploratory and require further confirmation, this integrated in silico and in vitro analysis provides an initial, hypothesis-generating strategy to narrow the spectrum of potential molecular interactions, offering candidate targets to guide future functional in silico, in vitro, and in vivo validation experiments.},
}

@article {pmid42824673,
year = {2026},
author = {Aoyama, T and Cho, H and Yoshikawa, T},
title = {Small Intestinal Bacterial Overgrowth Following Gastrointestinal Cancer Surgery: Current Evidence and Future Perspectives.},
journal = {Annals of gastroenterological surgery},
volume = {},
number = {},
pages = {},
pmid = {42824673},
issn = {2475-0328},
abstract = {Small intestinal bacterial overgrowth (SIBO) has recently gained increasing attention as a potential cause of postoperative gastrointestinal symptoms following gastrointestinal cancer surgery. Surgical procedures can disrupt normal gastrointestinal physiology through anatomical reconstruction, impaired motility, reduced gastric acid secretion, vagal nerve injury, and alterations in the gut microbiota, thereby predisposing patients to bacterial overgrowth. Although positive breath tests for SIBO have frequently been reported after esophageal, gastric, and colorectal cancer surgery, the reported positivity rates vary widely because of differences in patient selection, surgical procedures, and diagnostic methods. Importantly, several studies evaluated selected symptomatic or referred patients; therefore, these rates should not necessarily be interpreted as the true prevalence of SIBO in the overall postoperative population. Breath testing is widely used because of its simplicity and non-invasive nature; however, altered gastrointestinal anatomy and accelerated postoperative transit may affect test specificity and potentially produce false-positive results. Evidence regarding treatment specifically in patients after gastrointestinal cancer surgery remains limited, and most data regarding rifaximin and other therapeutic approaches are extrapolated from general SIBO populations. This review summarizes the current evidence regarding the epidemiology, pathophysiology, diagnosis, and treatment of SIBO following gastrointestinal cancer surgery. We discuss future perspectives, including standardization of diagnostic criteria, optimization of breath testing, microbiome-based approaches, refinement of rifaximin therapy, and strategies for recurrence prevention. A better understanding of SIBO may improve the recognition and management of postoperative gastrointestinal symptoms and nutritional abnormalities; however, whether SIBO-directed management improves body composition, treatment tolerance, postoperative recovery, or long-term outcomes remains to be established.},
}

@article {pmid42824830,
year = {2026},
author = {Wu, S and Fu, S and Shi, H and Gong, Y and Chen, P and Zhang, X and Jiang, E and Wang, H},
title = {Mechanisms of microbiome-immune interactions in bladder cancer and targeted regulatory strategies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1920567},
pmid = {42824830},
issn = {1664-3224},
mesh = {Humans ; *Microbiota/immunology ; *Urinary Bladder Neoplasms/immunology/microbiology/therapy ; Animals ; Immunotherapy/methods ; Epigenesis, Genetic ; Non-Muscle Invasive Bladder Neoplasms ; Dysbiosis/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; BCG Vaccine/therapeutic use ; },
abstract = {Bladder cancer (BC), a highly prevalent malignancy of the urinary tract, imposes a considerable clinical burden because of its high recurrence rates and a substantial risk of disease progression. Accumulating evidence suggests that microbiome dysbiosis is associated with the initiation and progression of BC through potentially bidirectional interactions. Recent advances in high-throughput sequencing technologies have facilitated a more comprehensive characterization of the urinary microbiome, thereby revealing its potential involvement in the pathogenesis of BC. This review summarizes the proposed mechanisms through which microbial communities may contribute to BC carcinogenesis, including chronic inflammation, microbial metabolite production, and epigenetic regulation. We further critically evaluate the established mechanisms of Bacillus Calmette-Guérin (BCG) immunotherapy-a standard intravesical immunotherapy for patients with intermediate- and high-risk non-muscle-invasive bladder cancer (NMIBC)-and examine the emerging application of microbiome profiling as a source of candidate noninvasive biomarkers and potential correlates or modulators of immune checkpoint inhibitor (ICI) response. Additionally, we elucidate the associations between microbiota heterogeneity and immunotherapy response, offering novel insights into microbiome-targeted therapeutic strategies for BC.},
}

Humans
*Microbiota/immunology
*Urinary Bladder Neoplasms/immunology/microbiology/therapy
Animals
Immunotherapy/methods
Epigenesis, Genetic
Non-Muscle Invasive Bladder Neoplasms
Dysbiosis/immunology
Immune Checkpoint Inhibitors/therapeutic use
BCG Vaccine/therapeutic use

@article {pmid42824881,
year = {2026},
author = {Esberg, A and Jönsson, D and Persson, P and Eriksson, L and Haworth, S and Johansson, I},
title = {Cross-platform, multi-cohort identification of a caries microbial signature.},
journal = {Journal of oral microbiology},
volume = {18},
number = {1},
pages = {2737699},
pmid = {42824881},
issn = {2000-2297},
abstract = {OBJECTIVE: To identify a robust salivary microbial signature associated with caries using a cross-platform, multi-cohort design.

DESIGN: Full-length 16S rRNA gene sequencing (ONT) and shotgun metagenomics (MET) were performed in a derivation cohort with matched data (n = 463). Associations between the oral microbiome and caries were evaluated using confounder-adjusted linear models with nested cross-validation. Identified species were incorporated into microbial risk scores and tested in two independent ONT-based cohorts (n = 3,457 and n = 215).

RESULTS: ONT and MET shared community structure despite differences in sequencing depth and detection sensitivity. Inter-individual ecological distances were moderately correlated (Spearman ρ = 0.48), with significant Procrustes alignment (r = 0.60), and mean relative abundances of shared species were strongly correlated (ρ = 0.75), but agreement at the individual species level was more variable. Ten species were consistently associated with caries across platforms and analytical approaches. Risk scores based on these species were strongly associated with caries burden in the derivation cohort (R[2] = 0.46 for MET; R[2] = 0.42 for ONT) and replicated in independent cohorts (mean R[2] = 0.27 and 0.10). Detection- and abundance-based scores performed similarly and combining them provided minimal additional predictive value. Detection-based scores showed a slightly greater incremental contribution to model fit. Leave-one-out analyses confirmed that associations were not strongly driven by individual species.

CONCLUSIONS: Key ecological features of the oral microbiome are reproducible across sequencing platforms. The microbial signature of caries can be summarised using a detection-based risk score which may have potential uses in caries risk assessment.},
}

@article {pmid42824883,
year = {2026},
author = {Logan, CM and Menko, AS},
title = {Ocular immune homeostasis-mechanisms of precise regulation through coordination of the eye, visual system and beyond: a narrative review.},
journal = {Annals of eye science},
volume = {11},
number = {},
pages = {16},
pmid = {42824883},
issn = {2520-4122},
abstract = {BACKGROUND AND OBJECTIVE: The visual system relies on clarity, organization, and interactivity to allow for sight. While in the past, the eye was thought to be immune-privileged, newer insights reframe this hypothesis. Recent studies demonstrate that the eye relies on a precise regulation of immunosurveillance to function. Here, we aim to highlight the multiple layers of coordination and regulation that allow for ocular immune homeostasis and how this understanding can shape future research and clinical directions.

METHODS: The PubMed database was utilized to find recent developments in the field of ocular immunology and immune homeostasis. This review covers research in the English language from 1 January 1980 to 20 December 2025.

KEY CONTENT AND FINDINGS: Ocular immune regulation is multilevel, including systems outside the eye itself. Similar to other previously accepted immune-privileged tissues, the eye hosts a variety of tissue-resident immune cells. These cells have proven necessary for the proper development of the eye as well as the activation of a protective immune response to injury and the evolution of ocular pathology. This involves a complex system of immunoregulation aimed at global homeostasis that protects vision integrity when one eye is compromised and can also involve an immune response in the contralateral eye, further evidence of the tight coordination of the visual system. In looking at diseases of immune overactivation, models highlight the involvement of recruited inflammatory cells in the evolution of the disease, including from beyond the eye itself, as occurs in uveitis. When such inflammation occurs, regulatory T cells (Tregs) and macrophages with an immunoregulatory phenotype are necessary for the regulation and recovery of the eye. Additionally, newer studies have also demonstrated a role for the microbiome in ocular health and disease, creating yet another link between systems at play in immunoregulation of the eye.

CONCLUSIONS: The future holds multiple opportunities for capitalizing on the multiple layers of immune involvement and coordination of the immune system in ocular health and disease to advance treatments and preserve vision. By understanding the interactions of the eye, the visual system and the immune system, targeted therapies can better promote homeostasis and visual recovery.},
}

@article {pmid42824884,
year = {2026},
author = {Deshmukh, P and Jauhari, D and Gupta, P and Mishra, R and Patil, P and Bhatia, M},
title = {Revisiting Ayurveda for Pediatric Oral Health: A Randomized Controlled Trial Evaluating the Effects of Coconut Oil and Castor Oil Pulling on Plaque Accumulation, Gingival Health, and Salivary Bacterial Load in Children.},
journal = {Cureus},
volume = {18},
number = {9},
pages = {e115573},
pmid = {42824884},
issn = {2168-8184},
abstract = {Background and aim Oil pulling (OP) has been studied as an adjunct to routine oral hygiene, but pediatric evidence - especially for castor oil - is limited. The registered primary outcome broadly covered gingival health and bacterial flora at two weeks; no secondary outcome was registered. This report compared those components after virgin coconut oil (VCO), virgin castor oil, or distilled-water rinsing. Plaque Index and the direct VCO-versus-castor comparison were exploratory. Materials and methods This exploratory randomized controlled trial enrolled 70 children, of whom 51 met the eligibility criteria and were allocated equally to VCO, castor-oil, or distilled-water groups (n = 17 each). Participants performed the assigned intervention once daily for two weeks. The Turesky modification of the Quigley-Hein Plaque Index, the Löe-Silness Gingival Index, and salivary MacConkey-culturable bacterial counts were assessed at baseline (T0) and after two weeks (T2). Intergroup values were compared using one-way analysis of variance (ANOVA) followed by Tukey HSD tests (p < 0.05). Results Forty-five children (n = 15 per group) completed the study. Both oil-pulling groups showed statistically significant reductions in Plaque Index, Gingival Index, and bacterial load from baseline to the two-week follow-up (p < 0.05). At postoperative evaluation, Group B (castor oil) demonstrated the greatest reduction in Plaque Index (3.90 ± 0.46 to 2.50 ± 0.38) and Gingival Index (2.00 ± 0.32 to 0.90 ± 0.28). Bacterial counts decreased markedly in both Groups A and B (from approximately 6.75 and 6.65 to 5.70 and 5.65 × 10[3] CFU/mL, respectively), whereas Group C showed negligible change (6.55 to 6.50 × 10[3] CFU/mL). Intergroup comparisons confirmed significantly better outcomes in both intervention groups relative to the control. Conclusion Over two weeks, VCO and castor-OP were associated with lower mean plaque and gingival-index scores and lower salivary MacConkey-culturable bacterial counts than distilled-water rinsing. The small sample, baseline imbalances, short follow-up, and restricted microbiological method limited causal and clinical interpretation. Larger trials using baseline-adjusted analyses and oral-microbiome-specific methods are required before routine paediatric use can be recommended.},
}

@article {pmid42813812,
year = {2026},
author = {Pasqualetti, SM and Atwood, J and Aderibigbe, A and Russell, E and O'Keefe, K and Rosario, V and Ireland, K and Sparks, K and Campbell, K and Isenberg, RY and Lucas, R and Milligan-McClellan, K},
title = {Cold-water gut isolate from threespine stickleback (Gasterosteus aculeatus) reveals polypropylene surface oxidation and co-culture inhibition.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0059926},
doi = {10.1128/msystems.00599-26},
pmid = {42813812},
issn = {2379-5077},
abstract = {Polyethylene terephthalate (PET) and polypropylene (PP), two of the most widely produced plastics in the United States, persist in diverse environments worldwide and may persist longer in cold-water environments where plastic-degrading microbial taxa have been poorly characterized. Understanding how gut microbes interact and contribute to plastic degradation is essential for developing potential microbiome-based bioremediation strategies. We isolated 184 microbes from wild Alaskan threespine stickleback (Gasterosteus aculeatus) guts across six bodies of water and screened them for their plastic-degrading potential using lipase/esterase assays and biofilm formation on PET and PP. We discovered that while some members of the stickleback gut microbiota have high lipase, esterase, and biofilm activity, that activity is enhanced or suppressed by other microbes. Isolates with the highest plastic-degrading potential were incubated in minimal media with PET or PP as the primary carbon source to determine whether plastic degradation occurs. While no detectable changes were observed on PET, surface analysis identified a Pseudomonas trivialis strain that exhibited evidence of PP surface oxidation in monoculture; however, this activity was suppressed in the presence of another gut isolate, Pseudomonas germanica. These results demonstrate that microbes associated with the gut microbiome of a cold-water fish possess plastic-degrading potential and provide insights into how microbial interactions can inhibit bioremediation of plastic pollution in cold-water environments.IMPORTANCEPlastic pollution persists in cold, freshwater environments and presents a significant challenge to the ecosystem, where low temperatures slow abiotic degradation, and microbial contributions remain poorly understood and understudied. Here, we isolated 184 microbes from adult Alaskan threespine stickleback guts across six bodies of water and screened for plastic-degradation potential using plate-based assays under both monoculture and co-culture conditions. We identified a stickleback gut-associated microbe that can oxidize polypropylene and identified a second microbe, isolated from the same environment, that can significantly suppress polymer oxidation when in co-culture. Together, these findings demonstrate that microbial interactions influence plastic-degradation abilities and support efforts to identify ecologically relevant microbes or enzymes for bioremediation efforts.},
}

@article {pmid42813815,
year = {2026},
author = {Schloss, PD},
title = {Rarefaction is better than robust Aitchison PCA and other compositional data analysis methods at controlling for uneven sequencing effort.},
journal = {mSystems},
volume = {},
number = {},
pages = {e0093026},
doi = {10.1128/msystems.00930-26},
pmid = {42813815},
issn = {2379-5077},
abstract = {UNLABELLED: Amplicon sequencing typically results in a wide distribution in the number of sequences obtained from each sample. How best to account for this variation has been a persistent problem in the microbial ecology literature. Historically, rarefaction has been used in ecology and this practice was adopted by microbial ecologists. However, rarefaction has been strongly criticized, leading to the development of compositional data analysis and normalization methods. Therefore, I reassessed the benchmarking data that were generated by the developers of one such method, robust Aitchison PCA. I found numerous problems in the Python code that led to the support of robust Aitchison PCA. These problems extended to the creation of simulated data sets, implementation of machine learning methods, and choice of analysis parameters. Furthermore, the analysis of the simulated and case study data sets was done in a manner that was foreign to standard microbiome analyses. I corrected the problems in the original code, added data sets with smaller effect sizes, and expanded the collection of methods that purport to correct for uneven sequencing effort. Contrary to the claims of the original analysis, robust Aitchison PCA was not insensitive to uneven sequencing effort and did not perform as well as rarefaction. In fact, even using the benchmarking framework from the original analysis, rarefaction outperformed robust Aitchison PCA, other compositional data analysis methods, and other normalization methods. Rarefaction remains the preferred method of controlling for uneven sampling effort in amplicon sequence studies.

IMPORTANCE: Efforts to connect the structure of microbial communities with environmental processes and host health have captured widespread interest among scientists and the general public. The methods used to generate the sequencing data that are fundamental to these efforts result in wide variation in the number of sequences per sample. This variation and how to account for it can have detrimental effects on the ability to draw valid conclusions. Compositional data analysis methods, including robust Aitchison principal component analysis (PCA), have grown in popularity for mitigating these effects and have been proposed as alternatives to rarefaction. In this study, I reviewed and fixed the code that was used to benchmark robust Aitchison PCA and expanded the analysis. With this improved and expanded analysis, I found that rarefaction was still superior to robust Aitchison PCA and other methods of controlling for uneven sequencing effort.},
}

@article {pmid42813839,
year = {2026},
author = {Chau, KD and Sless, TJL and Nguyen, PN and Rehan, SM},
title = {Variation in Microbial and Plant Associations Across Wild Bee Families, Functional Groups, and Urban Environments.},
journal = {FEMS microbiology ecology},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsec/fiag109},
pmid = {42813839},
issn = {1574-6941},
abstract = {Bees harbour diverse microbiomes and floral associations which may shift in response to several biological and environmental factors. We examined the diversity of bacterial, fungal, and plant associates (i.e., from foraging or nesting material) across 32 bee species from five families (Apidae, Megachilidae, Halictidae, Colletidae, and Andrenidae) using 16S rRNA, ITS1, and rbcL amplicon sequencing. The included bee species represent multiple axes of variation across functional traits including body size, nesting behaviour, sociality, diet, and native status, and response to urbanization. Apidae, Colletidae, and Andrenidae bee families had richer communities of bacterial and plant associates than Halictidae and Megachilidae, while fungal diversity and composition were similar across families. Common microbes and plant associations were detected across the bee community, but certain taxa were common only to specific bee species. Plant associations more often shifted significantly in diversity depending on functional trait and urban intensity, whereas bacterial and fungal diversity were largely consistent across bee families, functional traits, and urban intensities. Our findings show that while microbial communities are fairly stable across bee lineages and functional groups, bee-associated plant communities vary with urbanization and are the primary factor differentiating bee species in urban landscapes.},
}

@article {pmid42813894,
year = {2026},
author = {Usmani, MW and Shakir, MZ and Khan, MA and Usman, M and Ullah, I and Mengjie, Y and Wang, N and Liu, X},
title = {Microglial State Reprogramming Across the Gut-Brain-Immune Axis: Limitations and Therapeutic Prospects of Traditional Chinese Medicine.},
journal = {Developmental neurobiology},
volume = {86},
number = {4},
pages = {e70060},
doi = {10.1002/dneu.70060},
pmid = {42813894},
issn = {1932-846X},
support = {2023AA503//NGHJG project of Xinjiang Production and Construction Crops/ ; 215-432094250//Ningbo Top Talent Project/ ; H2024000279//Health Fund of Translational Biomedicine/ ; },
mesh = {Humans ; Animals ; *Microglia/immunology/drug effects/physiology ; *Medicine, Chinese Traditional/methods ; *Brain/immunology/drug effects ; *Gastrointestinal Microbiome/physiology ; *Neuroimmunomodulation/physiology ; *Brain-Gut Axis/physiology ; },
abstract = {Bidirectional communication among the gut microbiota, immune system, and central nervous system shapes microglial maturation and responsiveness. This review evaluates microglia as context-dependent neuroimmune integrators rather than fixed M1/M2 populations. It organizes the literature into three linked layers: gut-derived signals and barrier physiology, microglial state transitions, and therapeutic modulation by Traditional Chinese Medicine (TCM). Experimental depletion, colonization, and metabolite studies provide causal evidence that the microbiota can modify microglial biology in animals; however, human evidence remains predominantly associative. Herbal formulations, isolated constituents, and acupuncture may alter microbial ecology, intestinal permeability, metabolite production, systemic inflammation, and microglial signaling. Yet most intervention studies measure only selected links in this chain and rely on rodent behavior, bulk cytokines, or limited polarization markers rather than direct, state-resolved microglial profiling. Therefore, improvements in cognition or inflammatory markers cannot by themselves, establish microbiota-mediated microglial reprogramming. We critically distinguish direct from indirect evidence, replace binary polarization language with state-specific terminology, and evaluate formulation standardization, bioavailability, safety, experimental confounding, and clinical generalizability. A credible translational program will require chemically defined interventions, causal perturbation of candidate microbes or metabolites, microglia-resolved multi-omics, preregistered clinical trials, and mediation analyses that connect target engagement to patient-relevant outcomes. TCM is thus best regarded as a testable source of multicomponent interventions, not yet a validated systems-level therapy for the gut-brain-immune axis.},
}

Humans
Animals
*Microglia/immunology/drug effects/physiology
*Medicine, Chinese Traditional/methods
*Brain/immunology/drug effects
*Gastrointestinal Microbiome/physiology
*Neuroimmunomodulation/physiology
*Brain-Gut Axis/physiology

@article {pmid42814189,
year = {2026},
author = {Banaee, M and Shakeri, R and Günal, AÇ and Yüce, PA and Trivedi, A and Faggio, C},
title = {Integrated toxicological approach to microplastics and nanoplastics in crustaceans.},
journal = {Ecotoxicology (London, England)},
volume = {35},
number = {8},
pages = {},
pmid = {42814189},
issn = {1573-3017},
mesh = {Animals ; *Microplastics/toxicity ; *Water Pollutants, Chemical/toxicity ; *Crustacea/physiology/drug effects ; *Environmental Monitoring/methods ; },
abstract = {Microplastics (MPs) and nanoplastics (NPs) have emerged as pervasive contaminants in aquatic ecosystems, with global inputs to the oceans projected to rise from 11 million metric tons in 2016 to 44 million tons by 2060. Originating from single-use plastics, textiles, fishing gear, industrial waste, and other sources, these particles enter water bodies via urban runoff, wastewater effluents, and atmospheric deposition, ultimately accumulating in sediments. Crustaceans, due to their benthic foraging behavior, wide ecological distribution, and trophic relevance, are highly susceptible to MP/NP exposure and serve as effective bioindicators of plastic pollution. This review synthesizes current knowledge on the occurrence, bioaccumulation, and multifaceted toxicological impacts of MPs and NPs in crustaceans. Evidence confirms uptake through ingestion, gill filtration, and dermal contact (primarily during the molting period), leading to biodistribution in the hepatopancreas, gut, gills, and hemolymph, even in edible tissues. Exposure triggers a broad range of sublethal effects, progressing from physical obstruction and cellular-level damage (oxidative stress, DNA damage, and histopathological lesions) to physiological disruptions (immune suppression, gut microbiome dysbiosis, endocrine disruption, osmoregulatory dysfunction, metabolic imbalance, and impaired growth and molting), and ultimately manifesting as behavioral alterations and reproductive disorders. Critically, the toxicity of MPs/NPs is often exacerbated by co-exposure to environmental stressors such as heavy metals, pesticides, pharmaceuticals, and other pollutants, with plastics acting as vectors that enhance contaminant bioavailability. Despite growing research, significant gaps remain in standardized methodologies, long-term monitoring, and understanding of trophic transfer, particularly in freshwater and aquaculture settings. This review emphasizes the urgent need for integrated risk assessment frameworks that account for particle characteristics, environmental variables, and multi-stressor interactions to safeguard aquatic ecosystems and the services they provide.},
}

Animals
*Microplastics/toxicity
*Water Pollutants, Chemical/toxicity
*Crustacea/physiology/drug effects
*Environmental Monitoring/methods

@article {pmid42814390,
year = {2026},
author = {Dhanush, R and Naveen, DK and Sneha, HR and Mudhol, S and Raghunathanaidu, BD},
title = {An integrative review of wound healing: anatomy, molecular mediators, and indigenous therapies.},
journal = {Molecular biology reports},
volume = {53},
number = {1},
pages = {},
pmid = {42814390},
issn = {1573-4978},
mesh = {Humans ; *Wound Healing/physiology ; Signal Transduction ; Skin/metabolism ; Intercellular Signaling Peptides and Proteins/metabolism ; Animals ; *Medicine, Traditional/methods ; Wounds and Injuries/therapy ; },
abstract = {BACKGROUND: Wound healing, an important biological process, is a process through which the human body repairs its skin from injuries through organized cell function, molecular signaling, and tissue remodeling. Chronic or delayed wound healing remains a major public health challenge around the world.

METHODS: A narrative review was conducted through searches in PubMed/MEDLINE, Scopus, Web of Science, and Cochrane Library for articles published between January 2005 and June 2026 by searching keywords such as "wound healing," "hemostasis," "growth factors," "signaling pathways," "chronic wound," "scar," "wound microbiome," and specific traditional treatments. Non-peer-reviewed papers, conference abstracts, and duplicate records were excluded. Only peer-reviewed primary studies, systematic reviews, meta-analysis, and Cochrane reviews published in English were included. The quality of selected articles was assessed by applying SANRA guidelines for narrative reviews and AMSTAR-2 checklist for cited systematic reviews.

RESULTS: Growth factors (PDGF, TGF-β, EGF, FGF, VEGF), their receptors and signaling pathways (SMAD, MAPK, PI3K/AKT, JAK/STAT, Wnt/β-catenin, Notch, Hippo/YAP-TAZ, mTOR and NF-κB) regulate the four overlapping stages of human skin wound healing (hemostasis, inflammation, and remodeling). Some bioactive substances which are antibacterial and regenerative in nature are contained in the local treatment methods like honey, Aloe vera, frog skin and maggot therapy; some of these treatments are backed up by Cochrane review-level evidence.

CONCLUSION: A path to safer and more effective wound treatment can be seen by integrating the molecular pathway, chronic wound biology, current biological therapies and evidence-based traditional medicine.},
}

Humans
*Wound Healing/physiology
Signal Transduction
Skin/metabolism
Intercellular Signaling Peptides and Proteins/metabolism
Animals
*Medicine, Traditional/methods
Wounds and Injuries/therapy

@article {pmid42814861,
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},
doi = {10.1158/0008-5472.CAN-25-5143},
pmid = {42814861},
issn = {1538-7445},
support = {1R37CA237384//National Cancer Institute (NCI)/ ; 1R01CA282786//National Cancer Institute (NCI)/ ; RP190256//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP200173//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; RP210227//Cancer Prevention and Research Institute of Texas (CPRIT)/ ; 13723124//U.S. Department of War (DOW)/ ; P30CA125123//National Cancer Institute (NCI)/ ; },
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 {pmid42815142,
year = {2026},
author = {Morrell, JM and Ntallaris, T and Hansson, I and Cojkic, A},
title = {The seminal microbiome/microbiota and implications for antibiotics in semen extenders.},
journal = {Animal reproduction science},
volume = {294},
number = {},
pages = {108347},
doi = {10.1016/j.anireprosci.2026.108347},
pmid = {42815142},
issn = {1873-2232},
abstract = {The seminal microbiota is an integral component of fertility, both through its role in maintaining the health of the male reproductive tract and its contribution to the microbiota of the female reproductive tract. Many factors affect the dynamics of the seminal microbiota, such as the age and breed of the animal, and the husbandry conditions under which it is kept. Animal breeders introduce semen storage, representing an additional potential source of contamination. It is during this storage that the seminal microbiota can have an additional influence on sperm quality, permitting some bacteria to flourish whilst others are suppressed. Factors such as type of semen extender and temperature of storage exert an impact on the microbiota, but the predominant influence is the inclusion of antibiotics in the semen extender. Apart from a direct effect on sperm quality, these antibiotics may also alter the microbiota of the female reproductive tract, thus impacting on fertility. These factors should be borne in mind when deciding to include antibiotics in insemination doses. Alternatives to antibiotics do exist, such as physical separation of the sperm component from bacteria in the ejaculate, for example, with colloid centrifugation, and should be incorporated into prudent animal breeding strategies from a One Health perspective.},
}

@article {pmid42815168,
year = {2026},
author = {Wang, J and Zheng, F and Zhang, Y and Lu, Z},
title = {Deconstructing the microbiota-gut-brain axis in multiple sclerosis: from a barrier-immune-metabolic framework to emerging therapeutics.},
journal = {Multiple sclerosis and related disorders},
volume = {115},
number = {},
pages = {107948},
doi = {10.1016/j.msard.2026.107948},
pmid = {42815168},
issn = {2211-0356},
abstract = {BACKGROUND: Multiple sclerosis (MS) is a chronic immune-mediated disease of the central nervous system characterized by progressive neuroinflammation and demyelination. Increasing evidence suggests that the gut microbiota contributes to MS pathogenesis through bidirectional gut-brain interactions; however, the underlying mechanistic framework remains incompletely defined.

METHODS: We performed a narrative synthesis of literature published from March 2010 to March 2026 using PubMed, Web of Science, the Cochrane Library, CNKI, and Wanfang Data. Relevant studies were critically evaluated to integrate current mechanistic and translational evidence regarding gut microbiota involvement in MS.

RESULTS: Gut microbial dysbiosis in MS is associated with impaired intestinal barrier function, immune dysregulation, and altered host metabolic signaling. Emerging evidence further suggests that other microbial niches, including the oral microbiome, may contribute to systemic immune activation through microbial translocation and inflammatory signaling. Microbial metabolites, particularly short-chain fatty acids and tryptophan-related compounds, represent important molecular mediators within the gut-brain axis. Emerging multi-omics studies suggest potential regulatory roles of specific microbial communities, including ileal taxa, alongside core host signaling targets such as Caspase 3 (CASP3) and E1A binding protein p300 (EP300), although evidence remains largely associative.

CONCLUSIONS: The gut microbiota may influence MS pathophysiology through a coordinated barrier-immune-metabolic axis. Emerging evidence from additional microbial niches, including the oral microbiome, further supports a broader microbial ecosystem perspective on MS immunopathology, although causal relationships remain to be established. Although microbiome-targeted interventions show promising therapeutic potential, translation into clinical practice requires further mechanistic validation and well-controlled human studies.},
}

@article {pmid42815260,
year = {2026},
author = {Zhao, Y and Zhao, X and Lian, J and Wang, S and Ning, Q and Xu, Q and Zhang, Z and Zong, J and Wang, S},
title = {Microbiome-guided prioritization of Corynebacterium striatum in diabetic foot ulcers and preclinical evaluation of tanshinone IIA.},
journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology},
volume = {162},
number = {},
pages = {158803},
doi = {10.1016/j.phymed.2026.158803},
pmid = {42815260},
issn = {1618-095X},
abstract = {BACKGROUND: Diabetic foot ulcers (DFUs) are characterized by impaired healing and infection, but microbial signatures linked to glycemic status and their therapeutic relevance remain unclear.

PURPOSE: To identify DFU taxa associated with glycemic status and test whether microbiome-guided prioritization can inform evaluation of Tanshinone IIA (Tan IIA).

STUDY DESIGN: Clinical metagenomic discovery followed by in vitro functional and multi-omics analyses, biophysical studies, and in vivo evaluation.

METHODS: Wound samples from 54 DFU patients underwent HbA1c-stratified shotgun metagenomics. A prioritized patient-derived Corynebacterium striatum isolate was assessed for Tan IIA antibacterial and antibiofilm activity, multi-omics responses, and candidate-protein binding. Topical Tan IIA was tested in non-inoculated and C. striatum-inoculated diabetic wounds.

RESULTS: C. striatum was enriched in higher-HbA1c wounds and positively associated with continuous HbA1c (β = 0.422, 95% CI 0.095-0.748; P = 0.011; q = 0.064). Tan IIA inhibited the isolate (MIC = 64 μ g/ml), reduced biofilm biomass, and induced stress, redox, cell-envelope, and metabolic responses. SPR supported binding to MurD and TrxB. On day 14, wound closure was significantly greater in inoculated wounds (93.40% vs. 78.80%; adjusted P = 0.0187). In inoculated wounds, Tan IIA reduced EUB338-positive bacterial signal and viable counts versus vehicle (8.587 vs. 8.847 log10 CFU/g; adjusted P =  0.0480).

CONCLUSION: HbA1c-stratified metagenomics prioritized C. striatum as a glycemic-status-associated candidate. These findings support microbiome-guided preclinical evaluation of plant-derived Tan IIA as a topical candidate for infected DFUs.},
}

@article {pmid42815460,
year = {2026},
author = {Tao, EW and Fang, JY and Chen, YX},
title = {Beyond BMI: The diet-microbiome context of the obesity paradox.},
journal = {Cancer cell},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ccell.2026.08.019},
pmid = {42815460},
issn = {1878-3686},
abstract = {In Nature, Desharnais et al. show that in diverse mouse models, anti-PD-1 sensitivity is more closely linked to the diet-microbiome-metabolite ecosystem than to obesity-associated metabolic dysfunction. Their findings reinforce body mass index (BMI) as an incomplete proxy for host biology and suggest strategies to improve anti-PD-1 efficacy without inducing obesity.},
}

@article {pmid42815656,
year = {2026},
author = {Negahdari, R and Pouyanfar, N and Masoudifar, R and Aftabi, P and Fendereski, F and Anvari Rostami, Z and Masoumi, N and Faizi, M and Ghorbani-Bidkorpeh, F},
title = {Nanoparticles and the gut-microbiome: a dual strategy for oral brain delivery.},
journal = {International journal of pharmaceutics},
volume = {},
number = {},
pages = {127477},
doi = {10.1016/j.ijpharm.2026.127477},
pmid = {42815656},
issn = {1873-3476},
abstract = {The blood-brain barrier (BBB) remains a major physiological challenge in the treatment of central nervous system (CNS) disorders. Most existing drug delivery strategies primarily focus on overcoming the BBB itself, while largely neglecting upstream barriers encountered during oral administration, including the intestinal mucus layer and microbiome-derived metabolism (MDM). In this review, we propose a broader conceptual framework in which the BBB is viewed as an integral component of a continuous and dynamic system shaped by the gut-microbiota-brain axis. Herein, current oral-to-brain delivery platforms are critically evaluated, ranging from synthetic organic and inorganic nanoparticles to emerging pathogen-inspired systems, with particular emphasis on bacterial extracellular vesicles (BEVs). Owing to their biological origin, BEVs exhibit intrinsic barrier-navigation capabilities, enabling efficient translocation across intestinal and cerebral interfaces. However, effective CNS drug delivery also requires consideration of inter-individual variability in microbiome composition and metabolic function, which can profoundly influence drug bioavailability and efficacy. By integrating advances in synthetic biology and human-relevant organ-on-chip platforms, this review highlights emerging strategies to address microbiome-driven variability and improve translational predictability. Collectively, these approaches support the development of next-generation oral CNS therapeutics that move beyond standardized formulations toward precision microbiome-pharmacology, with potential implications for the treatment of neurodegenerative and neuropsychiatric disorders.},
}

@article {pmid42815760,
year = {2026},
author = {Jakštienė, G and Koida, A and Kavoliūnas, J and Pleskytė, S and Prigodina Lukošienė, I and Lastauskienė, E},
title = {Inverse Relationship Between Microplastic Abundance and Microplastic Biodegradation Potential in Soils from Both Natural and Anthropogenic Sites in Lithuania.},
journal = {Environmental pollution (Barking, Essex : 1987)},
volume = {},
number = {},
pages = {129265},
doi = {10.1016/j.envpol.2026.129265},
pmid = {42815760},
issn = {1873-6424},
abstract = {Biodegradation is a sustainable strategy for removing microplastics (MP), owing to its environmental compatibility and cost-effectiveness. This study investigated MP distribution, characterized microbial communities, and assessed the presence of plastic-degradation-associated genes across three locations in Lithuania: an operating Kazokiškės landfill, a closed Kariotiškės landfill, and a natural grassland. Polyamide was the most abundant plastic across all locations, followed by polyethylene, with the highest MP concentrations detected in the operating landfill. Sequencing of 16S rRNA and ITS genes revealed site-specific microbial communities with significantly different β-diversity. Operating landfill soils were enriched in plastic-associated genera, including Methylocaldum, Rhizobium, Brevundimonas, Aspergillus, and Malassezia. Based on the microbiome analysis, both studied landfills had distinct communities yet shared some plastic-degradation-associated genera. The key novel finding is contrary to conventional assumptions: the active landfill had the most MP and the highest number of plastic-associated microbial genera, yet the narrowest range of plastic-degradation-associated genes was limited to alkane hydroxylases and styrene monooxygenases, possibly due to suppression by constant input of fresh, labile organic waste. The grassland and closed landfill, despite lower MP abundance, hosted a broader diversity of studied genes: cutinases in both and urethanases exclusively in the grassland, suggesting broader plastic polymer utilization potential in non-operating landfill soils. These findings suggest that ordinary and closed-landfill soils are an underappreciated reservoir of plastic-degradation potential, and that the closed-landfill topsoil microbiome may be influenced by buried waste beneath it.},
}

@article {pmid42815780,
year = {2026},
author = {Dorscheid, D and Aegerter, H and Caminati, M and Eckl-Dorna, J and Hopkins, C and Hynds, RE and Jackson, DJ and Marone, G and Nawijn, MC and O'Callaghan, C and Palomares, O and Rabe, KF and Renz, H and Brightling, CE and , },
title = {Restoring epithelial health in epithelial-driven disease through an early treat-to-target approach: improving patient care towards clinical remission.},
journal = {The Journal of allergy and clinical immunology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.jaci.2026.09.019},
pmid = {42815780},
issn = {1097-6825},
abstract = {The structure and function of the airway epithelium are central in protecting against harmful environmental insults and conserving respiratory health; however, epithelial dysfunction can contribute to airway disease. Epithelial health represents a state of equilibrium where the airway epithelial barrier, immune activity and mucociliary dynamics work in concert to maintain tissue integrity and prevent inflammation. An invited Epithelial Science Expert Group met in London in March 2025 to discuss the current understanding of epithelial health in the airways and ways in which epithelial health may be restored in upper and lower inflammatory airway disease. This review summarises the key concepts raised during the meeting. The group discussed the benefits and drawbacks of currently available biomarkers of respiratory epithelial disruption, including mucus plugs, ventilation defects, mucin glycoproteins, cilia beat frequency, tight junction proteins and inflammatory biomarkers. These discussions highlighted a need for biomarkers with the ability to directly assess epithelial function to improve the understanding of epithelial-driven airway disease. Approaches to restore epithelial health were also reviewed, focusing on normalisation of mucin production, restoration of epithelial tight junctions, improvement of the epithelial microbiome, and stem cell therapy, all of which show clinical promise. Attendees highlighted the need for a united airways approach to respiratory disease management, involving multidisciplinary, cross-speciality care. Finally, the trajectory of respiratory epithelial injury and repair over time was explored, focusing on the role of a treat-to-target approach, and early intervention to restore epithelial health and achieve clinical remission in patients with epithelial-driven inflammatory airway disease.},
}

@article {pmid42815789,
year = {2026},
author = {Yao, D and Lin, X and Jiang, C},
title = {From dysbiosis to precision supportive care: the gut microbiota-immune axis in pediatric acute lymphoblastic leukemia.},
journal = {Critical reviews in oncology/hematology},
volume = {},
number = {},
pages = {105631},
doi = {10.1016/j.critrevonc.2026.105631},
pmid = {42815789},
issn = {1879-0461},
abstract = {Long-term survival in pediatric acute lymphoblastic leukemia (ALL) exceeds 90% in high-income countries, yet life-threatening infections, chemotherapy-induced mucositis, and impaired hematopoietic recovery remain major challenges. The gut microbiota-immune axis offers a framework for investigating these complications, but its contribution in pediatric ALL remains uncertain. This critical review distinguishes direct pediatric ALL observations from pediatric transplantation evidence and external mechanistic studies. A structured revision-stage search retained 156 clinical reports for design-specific appraisal. We examine intestinal barrier injury, innate immune signaling, regulatory T-cell (Treg)/T helper 17-cell (Th17) regulation, microbial metabolites, and associations with hematopoietic recovery without assuming causality in affected children. Pediatric studies associate microbial features with infection-related outcomes and neutrophil recovery; adult transplantation and chimeric antigen receptor T-cell (CAR-T) findings remain indirect. Small cohorts, heterogeneous sampling and sequencing, age-dependent microbiome maturation, and treatment-related confounding limit interpretation. Proposed priorities include longitudinal ALL cohorts, paired microbial and host measurements, independent biomarker validation, and safety-focused evaluation of antimicrobial and microbiota-targeted interventions. Microbiome associations alone do not justify changes to supportive care.},
}

@article {pmid42815826,
year = {2026},
author = {Evbuomwan, EM and Khanna, S and Xi, C and Rottinghaus, AG and Ferreiro, A and Kwak, S and Butler, B and Ning, J and Najari, J and Liao, J and Diao, H and Moon, TS and Dantas, G},
title = {Engineered Escherichia coli Nissle with an Inducible Phenylalanine Degrading Cassette and a Multi-input Kill Switch.},
journal = {New biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.nbt.2026.09.007},
pmid = {42815826},
issn = {1876-4347},
abstract = {Engineered probiotics provide new avenues for disease management through diagnostic sensing, delivery of bioactive molecules, and modulation of host-microbiome interactions. However, successful clinical translation requires rational safeguards preventing unintended environmental release. We report an integrated phenylalanine (Phe) sensor and CRISPR-based kill-switch biocontainment system for phenylketonuria (PKU) management. We engineered KSPAL, a strain of Escherichia coli Nissle (EcN) 1917, to sense gut Phe levels and responsively express phenylalanine ammonia lyase (PAL). The kill switch triggers bacterial death below 33°C or upon anhydrotetracycline (aTc) administration, ensuring post-excretion clearance. In vitro, KSPAL demonstrated dose-dependent degradation, achieving more than 60-fold Phe reduction following a 1000 µmol/L Phe spike, and bacterial death upon aTc or temperature induction. In vivo, KSPAL treatment reduced serum Phe by threefold 2-hours post Phe bolus, and KSPAL death 24-hours post aTc induction. This work presents a tunable therapeutic platform for PKU disease management via engineered probiotics.},
}

@article {pmid42816164,
year = {2026},
author = {Rangel, G and Panomket, P and Panya, M and Maneenin, C and Sinthuchao, P and Seawsakul, S and Maneenin, N and Jirapornkul, C and Wanram, S},
title = {Clinical translation of gut microbiome biomarkers and host immune dysregulation in colorectal neoplasia: a systematic review with Clinical and Molecular Pathology Prioritisation.},
journal = {Journal of clinical pathology},
volume = {},
number = {},
pages = {},
doi = {10.1136/jcp-2026-210946},
pmid = {42816164},
issn = {1472-4146},
abstract = {AIMS: Gut microbiome signatures are promising non-invasive biomarkers for colorectal neoplasia, but clinical translation is limited by heterogeneity in populations, platforms, validation and comparator tests. We evaluated microbiome-based biomarkers and microbiome-host immune associations, emphasising applicability.

METHODS: We systematically reviewed human studies published from 1 January 2020 to 15 July 2026 evaluating gut microbiome-associated biomarkers in colorectal adenoma or colorectal cancer. Diagnostic studies were summarised by biomarker, target lesion, comparator, validation and performance, with Quality Assessment of Diagnostic Accuracy Studies-2 appraisal. A predefined seven-domain framework provided secondary translational prioritisation. Mechanistic and prognostic microbiome-immune studies were synthesised separately.

RESULTS: Recurrent signals included Fusobacterium nucleatum, multispecies panels, microbial gene and single-nucleotide-variant classifiers, multikingdom signatures and metabolite profiles. Some integrated models combining microbial biomarkers with faecal immunochemical testing, methylated DNA, clinical variables or metabolomics showed improved performance measures, but benefits were inconsistent. External validation was limited. Microbiome-immune studies linked microbial profiles with immune-related expression, immune-cell infiltration and treatment-response phenotypes without establishing improved screening accuracy.

CONCLUSIONS: Microbiome biomarkers show promise for colorectal neoplasia detection, but evidence does not establish universal multimodal superiority. Routine translation requires prospective validation, analytical standardisation, reproducibility, cost-effectiveness and demonstrated incremental utility.

PROSPERO REGISTRATION NUMBER: CRD420261457983.},
}

@article {pmid42816166,
year = {2026},
author = {},
title = {Correction to: A Non-Metaproteomics Researchers' View on Metaproteomics in Microbiome Research.},
journal = {Proteomics},
volume = {},
number = {},
pages = {e70187},
doi = {10.1002/pmic.70187},
pmid = {42816166},
issn = {1615-9861},
}

@article {pmid42816241,
year = {2026},
author = {Thomas, VE and Cernava, T and Pieterse, CMJ and Roesch, LFW and Garrett, KA and Martins, SJ},
title = {Dysbiotic microbiomes and the collapse of plant health.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.09.003},
pmid = {42816241},
issn = {1878-4380},
abstract = {Dysbiosis, the disruption of plant-associated microbial communities, is increasingly recognized as a driver of impaired plant health. Notably, plant dysbiosis parallels disruptions of the human gut microbiome, where imbalances similarly contribute to host dysfunction and disease. Here, we discuss the current understanding of plant dysbiosis by integrating host-microbiome interactions and emerging analytical methods. Dysbiosis can extend beyond local compartments, affecting systemic processes such as immunity and nutrient acquisition. Advances in sequencing and quantitative metrics now enable its measurement at the population level, while experimental evidence shows that restoring microbial balance can recover plant function. We highlight translational strategies, including microbiome-informed breeding (Microbiome genes or M genes), synthetic microbial communities (SynComs), and soil microbial priming, to enhance plant resilience. We propose a three-tiered framework for studying and interpreting plant microbiome dysbiosis that integrates compositional profiling, functional omics, and host-performance assessment, and we introduce the concept of functional dysbiosis. We also outline how host-genome-informed M-gene selection, metabolite monitoring, and rationally defined microbial community (SynCom) design can translate this framework into practical crop management strategies.},
}

@article {pmid42816498,
year = {2026},
author = {Wu, Z and Tong, Y and Chen, W and Chen, W and Li, L and Huang, D and Li, Z and Song, Z and Cai, X},
title = {16S rRNA Datasets of Gut Microbiota in Stent-Based Diverting Technique and Ileostomy from A Prospective, Open-Label, Multicenter Randomized Controlled Trial.},
journal = {Scientific data},
volume = {13},
number = {1},
pages = {},
pmid = {42816498},
issn = {2052-4463},
support = {LQ22H030003//Zhejiang Provincial Natural Science Foundation of China/ ; 2023C03171//"Pioneer" and "Leading Goose" R&D Program of Zhejiang, China/ ; 2024DB008//Science and Technology Plan Project of XPCC/ ; U24A20762//National Natural Science Foundation of China/ ; },
mesh = {Humans ; *RNA, Ribosomal, 16S/genetics ; *Ileostomy ; *Stents ; *Gastrointestinal Microbiome ; Prospective Studies ; Rectal Neoplasms/surgery ; },
abstract = {Accumulating evidence implicates gut dysbiosis in postoperative complications and delayed intestinal recovery after rectal cancer surgery. Although stent-based diverting technique (SDT) and conventional ileostomy exert divergent impacts on gut microbial balance, high-quality comparative microbiome data from randomized trials are lacking. We report a 16S rRNA amplicon dataset from 80 patients randomized to SDT (n = 37) or ileostomy (n = 43), with fecal samples collected preoperatively and on postoperative day 90. We characterized phylum-level taxonomic composition, α-diversity and intergroup β-diversity across four subgroups, and identified discriminatory taxa via LEfSe. Functional prediction detected differential metabolic pathways after surgery. We additionally performed correlation analyses to link clinical covariates with microbial signatures. This public dataset enables independent reprocessing and cross-study comparisons, facilitating exploration of diversion-strategy-specific microbial remodeling and validation of SDT's gut microbiota-preserving capacity.},
}

Humans
*RNA, Ribosomal, 16S/genetics
*Ileostomy
*Stents
*Gastrointestinal Microbiome
Prospective Studies
Rectal Neoplasms/surgery

@article {pmid42816540,
year = {2026},
author = {He, Y and Salles, JF},
title = {Rethinking soil microbiome interventions through an ecological lens.},
journal = {Nature reviews. Microbiology},
volume = {},
number = {},
pages = {},
pmid = {42816540},
issn = {1740-1534},
}

@article {pmid42816543,
year = {2026},
author = {Lim, YJ and Kim, TS},
title = {The dynamic landscape of T helper cell plasticity and Th17-Treg instability in periodontitis.},
journal = {Experimental & molecular medicine},
volume = {},
number = {},
pages = {},
pmid = {42816543},
issn = {2092-6413},
support = {RS-2026-25483514//National Research Foundation of Korea (NRF)/ ; },
abstract = {Periodontitis is a chronic inflammatory disease initiated by a dysbiotic microbiome, yet tissue destruction is primarily driven by an exaggerated host immune response. CD4[+] T helper (Th) cell subsets play important roles in regulating periodontal inflammation and osteoclast-mediated bone resorption through distinct cytokine networks. Th1 and Th17 responses are closely associated with pro-inflammatory signaling and alveolar bone loss, whereas Th2 and regulatory T (Treg) cells exert context-dependent immunomodulatory functions. Beyond these subsets, Th9 and Th22 cells further expand the complexity of T cell-mediated regulation in periodontal lesions. Importantly, accumulating evidence supports T helper cell plasticity, exemplified by the emergence of IL-17[+] Treg, suggesting that periodontal disease reflects immune imbalance and functional instability rather than the dominance of a single lineage. Clarifying these mechanisms may support the development of targeted immunomodulatory strategies aimed at restoring oral mucosal immune homeostasis. This review shifts the focus from static T cell subsets to their dynamic phenotypic flexibility, highlighting how maladaptive transitions drive chronic tissue destruction.},
}

@article {pmid42816582,
year = {2026},
author = {Chang, J and Wang, D and Yao, Z and Pang, Y and Zhang, H and Wang, C and Xie, Y and Sun, Y and Zhang, J and Li, W and Liang, A and Li, X and Chen, D and Chen, H and Chen, X and Wang, E and Tran, LP and Wang, J and Raaijmakers, JM and Tian, C and Kuramae, EE},
title = {Wild rice locus enables microbiome re-domestication for enhanced nitrogen-use efficiency.},
journal = {Nature microbiology},
volume = {},
number = {},
pages = {},
pmid = {42816582},
issn = {2058-5276},
support = {32401436//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024YFD1501004//National Natural Science Foundation of China (National Science Foundation of China)/ ; U22A20593//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2024M753212//China Postdoctoral Science Foundation/ ; },
abstract = {Domestication of crops, such as rice, has resulted in the loss of beneficial root-associated microbiota central to plant nitrogen-use efficiency. Whether these microbes can be inherited through hybridization of wild and cultivated plants and the host genes involved is unclear. Here we used two recombinant inbred line populations, derived from cultivated rice (Oryza sativa) and its wild relative Oryza rufipogon to map host quantitative trait loci associated with core bacterial taxa. Integrating microbiome profiling, quantitative trait loci mapping, population genomics and transgenic validation, we identified 113 candidate plant genes. The receptor-like kinase-encoding gene OsRLK, found predominantly in wild rice, was significantly associated with Acinetobacter, which enhances plant nitrogen uptake. Knockout and overexpression of OsRLK, inoculated with an Acinetobacter synthetic community, validated their role in nitrogen-use efficiency. In field trials, the overexpression line significantly increased yield-related traits. These findings establish the genetic basis of microbiome re-domestication and provide a framework for microbiome-guided breeding of nutrient-efficient crops.},
}

@article {pmid42816625,
year = {2026},
author = {Dai, A and Ballweg, A and Jogia, W and Rangesa, M and Adintori, PA and Baichoo, M and Funnell, T and Fei, T and Waters, NR and Swartz, A and Sahu, S and Gipson, B and Raj, SS and Hayase, E and Pierce, Z and Wu, K and Smith, N and Neuberger, J and Warren, A and da Silva, MB and Miltiadous, O and Zuanelli Brambilla, C and Buchan, ML and Peets, TK and Gradissimo, A and Amoretti, LA and Duan, C and Zhang, C and Matheis, F and Sullivan, AP and Slingerland, JB and Clurman, AG and Brereton, DG and Giardina, PA and Gomes, ALC and Johnson, AJ and Knights, D and Jenq, RR and Markey, KA and Perales, MA and Giralt, SA and van den Brink, MRM and Schluter, J and Peled, JU},
title = {Sugar-rich foods exacerbate antibiotic-induced microbiome disruption.},
journal = {Nature},
volume = {},
number = {},
pages = {},
pmid = {42816625},
issn = {1476-4687},
abstract = {Diet shapes the composition of the gut microbiota[1]; however, the specific effects of distinct food groups on microbiome dynamics are unclear, particularly in circumstances of extreme perturbation. Here we evaluated the relationship between diet and intestinal microbiome dynamics by precisely tracking 9,419 meals consumed by 173 patients who were hospitalized for haematopoietic cell transplantation and analysing subsequent microbiome changes. Bayesian inference applied to data from 158 patients with paired longitudinal microbiome samples revealed that the intake of sweets and sugars during antibiotic exposure predicted exacerbated microbial dysbiosis, manifesting as lowered α-diversity and greater expansion of the pathobiont Enterococcus. Experiments in mice also showed that sucrose supplementation increased and prolonged antibiotic-induced Enterococcus expansion. These data suggest that avoiding a diet rich in simple sugars during antibiotic treatment may mitigate microbiota disruption. Further studies in independent cohorts will offer opportunities to generalize these findings and evaluate microbiota-sparing interventions.},
}

@article {pmid42816763,
year = {2026},
author = {Bhuiyan, MNI and Momtaj, M},
title = {Post-Microbial Therapeutics for the Next Generation of Medicine.},
journal = {MicrobiologyOpen},
volume = {15},
number = {5},
pages = {e70427},
pmid = {42816763},
issn = {2045-8827},
mesh = {*Bacteriophages/physiology/genetics ; Humans ; *Bacteria/virology ; *Bacterial Infections/therapy/microbiology ; },
abstract = {Post-microbial therapeutics is proposed here as an integrative, function-centered framework rather than a new therapeutic class. It asks whether a defined microbial perturbation can produce a reproducible change in a microbial function, biochemical output, and clinically relevant host phenotype. Bacteriophages provide a perturbation model because their host dependence permits strain-selective intervention, but the framework also distinguishes between whole phages and engineered phages, lysins, depolymerases, delivery systems, and combination products. A central requirement is that a microbial module must be defined by experimentally testable functional contribution rather than by statistical co-occurrence alone. Computationally inferred modules are therefore treated as hypotheses until supported by perturbation, reconstruction, removal/add-back, flux, or rescue experiments. Evidence reviewed across infection, gastrointestinal, biofilm, and cardiometabolic contexts shows a recurring pattern: phage exposure can alter bacterial abundance, resistance phenotypes, community interactions, and metabolism, but the strength of evidence diminishes as claims shift from bacterial killing to ecosystem restoration and host benefit. Engineering and delivery technologies can improve targeting or exposure, yet they introduce additional constraints in genetic stability, resistance, formulation, pharmacology, and regulation. The framework is consequently best viewed as a testable translational architecture that connects intervention to function and outcome while separating established evidence from emerging hypotheses.},
}

*Bacteriophages/physiology/genetics
Humans
*Bacteria/virology
*Bacterial Infections/therapy/microbiology

@article {pmid42817661,
year = {2026},
author = {Wang, X and Zheng, H and Feng, Y and Zhang, F},
title = {Hu Mei Qing Yan Ke Li Alleviates Periodontitis by Modulating the Oral Microbiome.},
journal = {Molecular oral microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1111/omi.70040},
pmid = {42817661},
issn = {2041-1014},
support = {W20243222//Health Research Project of the Hunan Provincial Health Commission of China/ ; 2025JJ50687//Natural Science Foundation of Hunan Province/ ; 2025JJ50631//Natural Science Foundation of Hunan Province/ ; },
abstract = {BACKGROUND: Periodontitis is a prevalent chronic inflammatory disease driven by dysbiosis of the oral microbiota. Hu Mei Qing Yan Ke Li (HM), a modern herbal formulation derived from Reynoutria japonica Houtt and Prunus mume Siebold & Zucc, exhibits anti-inflammatory, antioxidant, and antibacterial properties, suggesting promising therapeutic potential for periodontitis therapy. This study aimed to investigate the protective effects of HM against experimental periodontitis and further explore its underlying mechanisms.

METHODS: Periodontitis was induced by ligature placement in C57BL/6 mice. Mice were randomly assigned to the untreated periodontitis (P) and HM-treated (P + HM) groups. Mice in the P + HM group received HM via daily oral gavage at 6.58 mg/g body weight for 2 weeks. Alveolar bone loss was assessed by micro-CT analysis. Periodontal tissue destruction and osteoclast activity were evaluated by H&E, Masson's, and TRAP staining. Expression of OPG and RANKL was detected by immunofluorescence. Subgingival microbiota composition was analyzed by 16S rRNA sequencing.

RESULTS: HM treatment significantly inhibited osteoclastogenesis and alleviated alveolar bone resorption, while preserving periodontal tissue integrity. Quantitatively, HM treatment significantly increased BV/TV from 41.89% to 54.41% (p = 0.0019), Tb.Th from 111.5 to 131.2 µm (p = 0.0028), and Tb.Sp from 119.2 to 153.6 µm (p = 0.0015), while decreasing BS/BV from 0.03166 to 0.02655 1/µm (p = 0.0004). Mechanistically, HM upregulated OPG and downregulated RANKL expression in periodontal tissues. Notably, HM restructured the subgingival microbial community, suppressing the pathobiont Streptococcus acidominimus (16.95%-9.37%, p = 0.0411) and Rodentibacter_A_734545pneumotropicus (70.32%-16.46%, p < 0.0001), while enriching a beneficial consortium including Streptococcus danieliae (0.75%-30.68%, p < 0.0001), unclassified Corynebacterium (0.00%-6.50%, p = 0.0022), and unclassified Ligilactobacillus (1.57%-22.74%, p = 0.0063).

CONCLUSION: HM alleviates periodontitis by remodeling the dysbiotic oral microbiome toward homeostasis and favorably modulating the OPG/RANKL axis in a murine ligature-induced periodontitis model.},
}

@article {pmid42817792,
year = {2026},
author = {Wang, NY and Bi, XY and Yang, ZG and Dou, GL and Li, SH and Lu, SR and Huang, Y and Wang, ZX and Piao, HJ and Dong, WW and Ji, WX and Li, XJ},
title = {In Vitro Digestion and Fermentation Characteristics of Cordyceps militaris Mycelial Polysaccharide and Its Regulatory Effects on the Intestinal Environment.},
journal = {Journal of food science},
volume = {91},
number = {10},
pages = {e71418},
doi = {10.1111/1750-3841.71418},
pmid = {42817792},
issn = {1750-3841},
support = {YDZJ202201ZYTS635//Jilin Provincial Science and Technology Department Project/ ; },
mesh = {*Cordyceps/chemistry/metabolism ; Fermentation ; *Digestion ; *Mycelium/chemistry ; *Polysaccharides/metabolism/chemistry/pharmacology ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/drug effects ; Hydrogen-Ion Concentration ; Bacteria/classification/genetics/isolation & purification/metabolism ; Humans ; *Intestines/microbiology ; },
abstract = {Cordyceps militaris mycelial polysaccharides (IPS) possess diverse metabolic and bioactive properties, yet existing studies on their gastrointestinal digestion and prebiotic potential remain scarce. This study aims to investigate the changes of IPS at different digestive stages and its interactions with the gut microbiota. During simulated salivary digestion, no significant changes were observed in IPS. During simulated gastric digestion, the reducing sugar content of IPS significantly increased, while in simulated intestinal digestion, this value decreased. After in vitro fermentation, the total carbohydrate, reducing sugar levels, and pH of digested IPS declined to different extents. Microbiome profiling demonstrated that IPS markedly elevated the relative abundance of Firmicutes, whereas it suppressed the levels of Proteobacteria, especially the pathogenic genus Shigella. Furthermore, total short-chain fatty acids (SCFAs) increased from 0.77 mmol/L to 3.58 mmol/L after 24 h fermentation. Collectively, these results verify that IPS holds great potential to improve intestinal homeostasis and alleviate gut-related disorders.},
}

*Cordyceps/chemistry/metabolism
Fermentation
*Digestion
*Mycelium/chemistry
*Polysaccharides/metabolism/chemistry/pharmacology
Fatty Acids, Volatile/metabolism
*Gastrointestinal Microbiome/drug effects
Hydrogen-Ion Concentration
Bacteria/classification/genetics/isolation & purification/metabolism
Humans
*Intestines/microbiology

@article {pmid42817813,
year = {2026},
author = {Wang, L and Yu, S and Huang, J and Meng, Y and Zhao, C and Gan, Y and Hu, W and Yang, Y},
title = {Ecological Boundaries Shape Microbial Diversity and Microbiome Similarity Across Host Communities in Mixed Pastoral Systems.},
journal = {Molecular ecology},
volume = {35},
number = {19},
pages = {e70579},
doi = {10.1111/mec.70579},
pmid = {42817813},
issn = {1365-294X},
support = {2023YFD1801900//National Key Research and Development Program of China/ ; 2025KYPT0066//National Key Laboratory of Reproductive Regulation and Breeding of Grassland Livestock/ ; 32460897//National Natural Science Foundation of China/ ; Q2022002//'Grassland Talents' Youth Innovation and Entrepreneurship Talent Project of Inner Mongolia Autonomous Region/ ; 2025-Gui-Yan-1-36//Hohhot R&D Investment Incentive Program/ ; },
mesh = {Animals ; *Microbiota/genetics ; Birds/microbiology/virology ; *Ecosystem ; Bacteria/genetics/classification ; *Biodiversity ; Arthropod Vectors/microbiology/virology ; Fungi/genetics/classification ; Phylogeny ; Grassland ; Sequence Analysis, DNA ; Virome ; Viruses/classification/genetics ; },
abstract = {Mixed pastoral ecosystems provide natural settings in which wildlife, livestock, humans and arthropod vectors interact, creating opportunities for microbial exchange across host communities. However, the ecological factors shaping microbial diversity and microbiome similarity across hosts remain poorly understood. We conducted field surveys and sampled 1527 individuals across 20 sites spanning pastures and natural grasslands. Metagenomic and metatranscriptomic sequencing generated over 30.5 million contigs, identifying 41 bacterial genera, 24 fungal genera, 28 parasitic genera and 174 viral species. Arthropod vectors and wild birds harboured the highest viral diversity, including 11 novel viruses. Virome analyses revealed viral sharing among host groups, particularly within mosquito- and bird-associated communities. Ecological network analyses revealed substantial cross-host microbiome similarity among phylogenetically distant hosts, especially involving arthropod vectors and resident birds. Generalized linear and additive models identified livestock density, habitat overlap and host traits as key predictors of microbial richness, relative microbial abundance and microbiome similarity. Random forest models further showed that host clusters and livestock density were among the strongest predictors of microbial connectivity. This study provides a system-wide view of microbial diversity and microbiome similarity in mixed pastoral systems. Arthropod vectors and resident birds occupied central positions in host-associated microbial networks and acted as ecological bridges linking otherwise distinct host communities. Together, our results demonstrate that ecological structure and livestock density are major determinants of microbial diversity and microbiome similarity across complex host communities.},
}

Animals
*Microbiota/genetics
Birds/microbiology/virology
*Ecosystem
Bacteria/genetics/classification
*Biodiversity
Arthropod Vectors/microbiology/virology
Fungi/genetics/classification
Phylogeny
Grassland
Sequence Analysis, DNA
Virome
Viruses/classification/genetics

@article {pmid42817815,
year = {2026},
author = {De Vrieze, L and Aerts, J and Masschelein, J},
title = {Comparative pangenomics unveils distinct host adaptation trends and conserved biosynthetic potential in microbiome Clostridia.},
journal = {Molecular biology and evolution},
volume = {},
number = {},
pages = {},
doi = {10.1093/molbev/msag247},
pmid = {42817815},
issn = {1537-1719},
abstract = {To thrive in diverse ecological niches, bacteria adopt various lifestyles that range from living freely in the soil to forming close associations with human and animal hosts. However, the impact of these adaptation processes on their genomes and metabolisms remains largely unexplored beyond the genus level. Investigating these evolutionary dynamics at higher taxonomic levels can enhance our understanding of the relationship between host adaptation and functional capabilities. Here, we examine the evolutionary trajectories and metabolic capabilities of the Clostridia class, which displays a wide variety of lifestyles and is of high importance for industry, medicine and microbiome research. First, we uncover that the clostridial orders have significantly different genomic divergence rates. Second, we show contrasting host adaptation tendencies in Oscillospirales and Lachnospirales, the two clostridial orders dominated by host-associated species. Species of the former have often undergone extensive genomic and functional specialisation toward a host-associated lifestyle, while species of the latter tend to show a lower level of host adaptation, retaining a remarkably high number of free-living trait genes and a high degree of metabolic versatility. Third, we reveal substantial differences in genomic architecture and metabolic versatility between the clostridial orders and link these to the progressing stages of host adaptation. Additionally, we identify widely conserved biosynthetic gene clusters, highlighting untapped biosynthetic potential of evolutionary significance. Hence, the beyond-genus level analyses in this study provide valuable new insights into bacterial adaptation with broad implications for evolutionary biology, microbiome research and biotechnology.},
}