@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.},
}

@article {pmid42818014,
year = {2026},
author = {McClure, EA and Natoli, R and Castillo, RC and Carlini, AR and Wenke, J and O'Toole, RV and Schrank, GM and Obremskey, W and Warner, S and Bosse, M and Ross, BD and Gitajn, L and , },
title = {Culture Positivity Reflects Quantitative Bacterial Bioburden in Open Fractures.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.22.753238},
pmid = {42818014},
issn = {2692-8205},
abstract = {BACKGROUND: Infection following high-energy open fractures remains a major challenge. Open fractures are exposed to environmental and skin pathogens, which, along with traumatized tissue and implanted hardware, create a favorable environment for infection. 24-83% of open fractures yield positive culture results. Despite culture-positive wounds being at higher risk for infection, culture data are rarely used in clinical decision-making. Culture-positivity in open fractures is believed to indicate higher wound bioburden, but this hypothesis remains unconfirmed. This study aimed to correlate culture positivity and quantitative wound bioburden using next-generation sequencing (NGS) and to characterize patterns of bioburden and bacterial diversity amongst patients with open fracture and Fracture Related Infection. We hypothesized that higher wound bioburden would be associated with culture positivity.

METHODS: This secondary analysis of the METRC Bioburden Study included 78 patients with severe open tibia fractures who underwent standardized tissue sampling at definitive wound closure and at later fracture site revision surgery. DNA extracted from intraoperative tissue was analyzed via 16S rRNA gene amplicon sequencing. Quantitative bioburden metrics included bacterial read percentage and bacteria-to-human read ratio (BHR). Associations between sequencing-based bioburden, culture results, and clinical infection (CDC-defined) were evaluated using Mann- Whitney U tests, McNemar's chi-squared tests, and unsupervised clustering analyses.

RESULTS: Culture-positive samples exhibited significantly higher bacterial read percentages (17.5 ± 26.7% vs. 0.8 ± 4.7%, p = 8×10□□) and higher log(BHR) values (1.73 ± 10.35 vs. 0.06 ± 0.52, p = 3×10□□) than culture-negative samples. Optimal thresholds yielded 65% sensitivity/94% specificity (bacterial reads) and 89% sensitivity/69% specificity (BHR) for predicting culture positivity. Neither baseline culture nor NGS positivity predicted later infection. However, follow-up samples from patients with established infection showed significantly higher bioburden and distinct microbiome structures. Clustering analyses identified two infection-associated microbial profiles: one with high bioburden and high diversity (polymicrobial infection) and one with low bioburden and low diversity (single-dominant pathogen).

CONCLUSIONS: Culture positivity in open fractures correlates strongly with increased bacterial bioburden, indicating that positive cultures may primarily reflect microbial load rather than specific pathogens. Quantitative NGS-based measures, including bacterial read proportion and BHR, may offer a biologically grounded approach to assess wound contamination and may inform infection risk. Distinct bioburden-diversity patterns suggest heterogeneous infection phenotypes that may require tailored surgical and antimicrobial strategies.},
}

@article {pmid42818114,
year = {2026},
author = {Mridha, S and Alam, MZ and Denny, JE and Hulit, EN and Maslanka, JR and Mdluli, NV and Tran-Ha, M and Mears, KS and Brown, DD and Alameh, MG and Abt, MC},
title = {Immunotherapy restores therapeutic efficacy of fecal microbiome transplants to treat Clostridioides difficile.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.17.752434},
pmid = {42818114},
issn = {2692-8205},
abstract = {Microbiome-based therapeutics to treat enteric bacterial infections requires stable engraftment of transplanted beneficial bacteria that target and eliminate the pathogen. The host factors that determine whether a microbiome transplant engrafts remain largely unresolved. Here we demonstrate that Interleukin-10 (IL-10) signaling deficiency leads to impaired fecal microbiota transplantation (FMT) engraftment and failure to resolve Clostridioides difficile infection in mice. In the absence of IL-10-mediated immunoregulation provided by Foxp3 [+] T reg cells, increased IFN-γ signaling in the intestine leads to elevated production of reactive oxygen/nitrogen species (ROS/RNS) by neutrophils and epithelial cells that supports the growth of inflammation-tolerant microbes, inhibits FMT engraftment, and impairs resolution of C. difficile. FMT treatment success can be restored by antibody-mediated blockade of IFN-γ signaling, neutrophil depletion or inhibition of ROS/RNS production. Lastly, we developed an Il10 -mRNA-LNP immunotherapy to boost IL-10 signaling in FMT Non-Responsive mice and demonstrate that Il10 -mRNA-LNP administration is sufficient to restore FMT engraftment and subsequent resolution of C. difficile . Combined, these data support a mechanism by which IL-10 released by T reg cells limits IFN-γ mediated intestinal inflammation thereby promoting an intestinal microenvironment receptive to FMT engraftment and resolution of C. difficile . These data demonstrate that the host's immune status can be therapeutically modulated to improve microbiome-based approaches to treat infection.},
}

@article {pmid42818157,
year = {2026},
author = {Siddiqui, NY and Diaz, NM and Burnett, L and Zemlin, J and Ma, L and Karstens, L},
title = {The Urogenital Lactobacillus Axis Across Menopause: Connections Between the Vagina, Bladder, and Urinary Metabolome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.18.751586},
pmid = {42818157},
issn = {2692-8205},
abstract = {Alterations in the female urinary microbiome have been linked to several common urinary conditions that increase in prevalence after menopause. Here we use sequencing and metabolomic data to compare the urinary bladder microenvironments between women who are premenopausal, postmenopausal, and postmenopausal using vaginal estrogen. While the urinary microbiome differs between pre- and postmenopausal women, at least 6 weeks of vaginal estrogen is associated with higher urinary lactobacilli and fewer opportunistic pathogens in the urinary postmenopausal microbiome, which closer approximates what is seen in the premenopausal context. Changes in urinary Lactobacillus species are correlated with vaginal pH and the same Lactobacillus species found in the vaginal microbiome tend to also be identified within the urinary bladder microbiome. Urinary metabolites differ by context (e.g., pre-, post-, and post-menopausal using vaginal estrogen), but the majority of metabolites that drive these differences are unannotated. Of the metabolites with shared associations among different Lactobacillus species, L. iners have consistently inverse relationships compared to L. crispatus, L. gasseri , or L. jensenii .},
}

@article {pmid42818341,
year = {2026},
author = {Li, T and Yang, Y and Cho, SH and Howell, BR and Wu, Z and Yin, W and Elison, JT and Huynh, KM and Ahmad, S and Yap, PT and Li, G and Wang, L and Zhu, H and Lin, W and , },
title = {Microbes on the Mind: Multi-modal Neuroimaging Reveals Gut-Brain Axes in Infants.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.23.753825},
pmid = {42818341},
issn = {2692-8205},
abstract = {The gut microbiome undergoes rapid maturation after birth and has been associated with cognition and mental health, yet its relation to early brain development remains poorly defined. We analyzed 223 typically developing children aged 0-3 years with multimodal MRI and paired fecal shotgun metagenomics. Microbiome-wide association analyses identified associations with cortical morphology, white-matter microstructure, and functional connectivity. Ridge-regularized canonical correlation analysis identified two principal covariance patterns: a structural-metabolic mode and a functional-taxonomic mode. Sparse canonical partial least squares recovered the principal CCA score and phenotype patterns within the same sample. Longitudinal canonical-score slopes were not significantly correlated; in autoregressive cross-lag models, however, neuroimaging CCA1 scores predicted microbiome CCA1 scores 1-6 months later. These results indicate cross-domain covariance and temporal ordering within the measured windows but do not establish causality.},
}

@article {pmid42818437,
year = {2026},
author = {Wang, L and Zhang, Y and Nguyen, SM and Peters, BA and Qi, Q and Burk, RD and Kaplan, R and Thyagarajan, B and Daviglus, M and Shu, XO and Ma, S and Dai, Q and Shrubsole, MJ and Zheng, W and Yu, D},
title = {Discovery and Validation of Gut Microbiome Features Associated with Dietary Patterns in U.S. Black/African and Hispanic/Latino Populations.},
journal = {medRxiv : the preprint server for health sciences},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.04.26362286},
pmid = {42818437},
abstract = {BACKGROUND: Large-scale studies examining dietary patterns and gut microbiome have focused predominantly on European ancestry populations; evidence from other ancestry groups remains limited.

OBJECTIVES: We conducted a two-stage study to evaluate associations of multiple dietary patterns with gut microbiome diversity and composition among Black/African American adults and validate significant findings in a Hispanic/Latino population in the US.

METHODS: Included were 514 Black participants from the Southern Community Cohort Study (SCCS) and 2,133 participants from the Hispanic Community Health Study/Study of Latinos (HCHS/SOL). Diet was collected by food frequency questionnaires or 24-h dietary recalls at cohort enrollment. Gut microbiome profiling was performed by shotgun metagenomic sequencing of stool samples collected during cohort follow-up. Five dietary patterns - Healthy Eating Index (HEI), Dietary Approaches to Stop Hypertension (DASH), Empirical Dietary Inflammatory Potential (EDIP), Empirical Dietary Index for Hyperinsulinemia (EDIH), and Ultra-Processed Foods (UPF) - were examined for associations with microbiome diversity and composition by linear regression after data transformation and confounders adjustment. Microbial taxa with FDR<0.1 and their constituent lower-level features identified in SCCS were targeted for validation in HCHS/SOL.

RESULTS: In SCCS, HEI, DASH, EDIP, or EDIH were associated with the relative abundances of 14 microbial taxa, primarily members of families Coriobacteriaceae and unclassified Firmicutes, as well as species Lactococcus lactis and Clostridium sp. AF20-17LB . Among these, the inverse associations of genus Collinsella and its species C. aerofaciens with HEI or DASH were validated in HCHS/SOL (all P <0.05). Additionally, Collinsella and C. aerofaciens were associated with higher odds of obesity in SCCS (BMI≥ 30 kg/m2; OR [95%CI]:1.24 [1.01, 1.53] and 1.32 [1.07, 1.63], respectively).

CONCLUSIONS: Healthier dietary patterns were consistently associated with lower abundances of Collinsella and C. aerofaciens in Black/African and Hispanic/Latino Americans. Further research should clarify causal pathway linking diet, gut microbiome, and health outcomes across diverse populations.},
}

@article {pmid42818523,
year = {2026},
author = {Chen, D and Wang, Y and Portik, DM and Nearing, J and Nickols, WA and Wilkinson, JE and Christiani, DC and Nguyen, LH and Franzosa, EA and Spengler, JD and Huttenhower, C and Thompson, KN},
title = {Microbial transmission and ecology of human and environmental microbial communities in childcare centers.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-10207669/v1},
pmid = {42818523},
issn = {2693-5015},
abstract = {Background Early-life microbial exposures profoundly impact lifelong health trajectories by shaping immune maturation and modulating disease risk, e.g. as described by the "hygiene hypothesis." Childcare facilities represent a critical yet understudied source of microbial exposures where preschool-aged children spend 7-10 hours daily during key developmental periods. This study presents the first multi-omic and multi-kingdom investigation of microbial transmission and community ecology across childcare environments, integrating microbiome samples from both high-touch and low-touch surfaces with children's nasal and oral microbiomes, using full-length 16S rRNA gene and internal transcribed spacer (ITS) amplicon sequencing paired with short-read (SR) and long-read (LR) metagenomic sequencing. This combination provides enhanced species-level taxonomic resolution and improved recovery of genomes and genomic elements compared to conventional short-read approaches. Results Our findings revealed distinct microbial signatures across environments, with human-associated microorganisms predominating in high-touch areas, while greater taxonomic diversity characterizes low-touch areas. Specifically, on high-touch surfaces, several bacterial and fungal species were shared between host and environmental communities, such as food-associated Lactococcus lactis and Streptococcus thermophilus , suggesting defined transmission routes via host shedding, environmental exposures, and food consumption. With improved genomic resolution and reconstruction from paired SR and LR metagenomics, we identified novel lateral gene transfer (LGT) events enriched for mobile elements, DNA-interacting domains, and adaptive elements such as antibiotic resistance and virulence factors. These methods also shed light on viral ecology, such as Caudoviricetes bacteriophages ubiquitous across host and environmental communities with phylogenetically-differentiated niche- and bacterial host-specific lineages. The positive relationship between the host prediction frequency and its community relative abundance suggested host abundance (availability)-driven phage-bacteria population dynamics. Conclusions This work highlights previously understudied components of early-life microbial exposures in childcare environments with enhanced resolution and provides methods for identifying potential pathogen reservoirs, tracking transmission routes, and developing targeted interventions.},
}

@article {pmid42818594,
year = {2026},
author = {Dennis, N and Freeman, L and Vazquez-Prada, M and Langley, I and Mortensen, MS and Karamelegos, AA and Watts, JL and Ezcurra, M},
title = {A defined microbial community remodels host metabolism and pathogen resistance in Caenorhabditis elegans.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.06.749774},
pmid = {42818594},
issn = {2692-8205},
abstract = {The microbiome is an important regulator of metabolism and health, yet the mechanisms by which microbial communities influence host physiological state remain incompletely understood. Here we used a defined host-microbiota model consisting of Caenorhabditis elegans and an 11-member bacterial consortium representative of its natural microbiota (DefNatMta). We investigated how this native microbial community influences host metabolism and physiology relative to the standard laboratory diet, E. coli OP50. Transcriptomic analyses revealed remodelling of host pathways associated with lipid metabolism, immunity and xenobiotic detoxification. Comparison with fasting-responsive transcriptional programmes showed that the DefNatMta response is distinct from fasting or caloric restriction. DefNatMta enhanced resistance to Staphylococcus aureus infection, and this protective effect was consistent with roles for the conserved host defence regulators PMK-1/p38 MAPK and HLH-30/TFEB. Additionally, DefNatMta reduced lipid accumulation, modified expression of lipid metabolism genes, and altered fatty acid composition, including enrichment of monomethyl branched-chain fatty acids and polyunsaturated fatty acids. Together, these findings demonstrate that a defined microbial community can induce transcriptional, metabolic and physiological remodelling in the host. Our results are consistent with microbial communities shaping host metabolic state and immune competence.},
}

@article {pmid42818602,
year = {2026},
author = {Lu, S and Zhao, Y and Zhao, Y and Dong, H and Qu, C and Zhong, W and Zhang, P and Ma, Z and Zhang, P},
title = {Interpretable machine learning uncovers core seminal microbial signatures in idiopathic oligoasthenospermia.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1923816},
pmid = {42818602},
issn = {2235-2988},
mesh = {Humans ; Male ; *Machine Learning ; *Semen/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Oligospermia/microbiology/diagnosis ; Phylogeny ; Adult ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {BACKGROUND: Previous studies have confirmed that changes in semen microbiota are closely related to male oligoasthenospermia(OA). However, current research only qualitatively describes the differences in the microbial community, fails to screen out core markers with independent discriminatory value, and also fails to quantitatively evaluate the diagnostic efficacy of the microbial community, resulting in insufficient research on the diagnostic value of the semen microbiota in oligoasthenospermia.

METHODS: A total of 40 untreated patients with idiopathic oligoasthenospermia (IOA) and 30 fertile control (FC) were recruited for this study. The semen samples were sequenced using 16S rRNA sequencing technology to assess the differences in microbial diversity and abundance. Subsequently, three machine learning algorithms were employed to further identify the core microorganisms and to further evaluate the diagnostic performance. Then, the SHapley Additive exPlanations(SHAP)analysis method was used to explain the contribution of these core microbiota to the disease. Additionally, the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2 (PICRUSt2) algorithm was used to predict the functions of the core microorganisms.

RESULTS: The analysis of the microbial community in semen revealed that there were differences in the internal composition structure of the semen microbiota between the IOA group and the FC group. Machine learning algorithms identified a total of 5 core bacterial genera. The area under the curve (AUC) of this model was 0.773, with a 95% confidence interval (CI) of 0.661-0.885, indicating that the model has strong discriminatory power. SHAP analysis further revealed the direction of the association between the abundance of the microbiota and disease prediction. Additionally, KEGG pathway prediction revealed that the 5 core genera were predominantly enriched in carbohydrate and nucleic acid metabolism pathways, most notably glycolysis/gluconeogenesis (P = 6.67 × 10[-3]).

CONCLUSION: This study employed a variety of machine learning algorithms to conduct a systematic characterization study on the semen microbiota of patients with idiopathic oligoasthenospermia. This method overcomes the limitations of traditional microbiota analysis and can This approach overcame the limitations of traditional microbiota analysis and constructed a risk prediction model based on core bacterial genera. It preliminarily explored the potential of the semen microbiota as a non-invasive screening candidate marker for IOA, providing a reference for subsequent research on non-invasive diagnostic markers and mechanisms., providing a basis for non-invasive precise diagnosis of the disease and the analysis of the pathogenic mechanism of the microbiome.},
}

Humans
Male
*Machine Learning
*Semen/microbiology
RNA, Ribosomal, 16S/genetics
*Microbiota/genetics
*Oligospermia/microbiology/diagnosis
Phylogeny
Adult
Bacteria/classification/genetics/isolation & purification

@article {pmid42818699,
year = {2026},
author = {Dickey, JR and Loomis, DA and Caraballo-Rodríguez, AM and Dorrestein, PC and Jackrel, SL},
title = {The caddisfly gut microbiome contributes to the consumption of riparian leaf litter within rivers.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.09.10.749941},
pmid = {42818699},
issn = {2692-8205},
abstract = {Ecosystem functions can be regulated by biodiversity ranging from broad to narrow scales, including variation within a species. For most multicellular life, intraspecific variation is determined not only by an organism's phenotype and genotype, but also variation imparted by their microbiome. Here, we investigate how leaf decomposition in rivers is affected by phenotypic variation in plant secondary metabolites (PSMs) and antibiotic-induced variation within the gut microbiomes of aquatic macroinvertebrate decomposers. We found that consumption by Dicosmoecus caddisflies was inhibited by the presence of dietary PSMs from riparian Alnus rubra trees, irrespective of the state of their gut microbiome. We further compared consumption of diets prepared from 20 different local and non-local A. rubra trees. We found that antibiotic-treated and control caddisflies consumed similar amounts of diets containing local A. rubra PSMs. However, compared to caddisflies with an intact gut microbiome, antibiotic- treated caddisflies consumed less of non-local A. rubra diets. Thus, decomposition by caddisflies could be regulated by both host adaptation to local resources and bacterial-mediated digestion of non-local resources. Overall, our study suggests that gut microbiomes can facilitate adjustment of macroinvertebrate decomposers to novel plant phenotypes, which may arise from shifting spatial distributions of plants in response to global change.},
}

@article {pmid42818782,
year = {2026},
author = {Zhang, X and Guo, Y and Gao, S and Li, S and Du, Y and Wan, D and Liu, Z},
title = {A study on oral microbiome characteristics and differences in epilepsy adults with depressive symptoms based on 16S rRNA sequencing.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1894254},
pmid = {42818782},
issn = {1664-302X},
abstract = {BACKGROUND: Depression is a common comorbidity in epilepsy, but its underlying mechanisms are poorly understood. Although the "oral-brain axis" has gained increasing attention in neuropsychiatric disorders, oral microbial characteristics in epileptic patients with depressive symptoms remain largely unexplored. This study aimed to compare the oral microbial composition between epileptic patients with and without depressive symptoms and to identify bacterial genera and functional pathways that may be associated with depressive symptoms.

METHODS: The study included 59 adult patients with epilepsy. Based on the Neuropsychiatric Depression Scale for Epilepsy (NDDI-E) scores, the participants were divided into two groups: patients with epilepsy with depressive symptoms (EDS, NDDI-E > 12, n = 28) and patients with epilepsy alone (EP, NDDI-E ≤ 12, n = 31). Tongue swab samples were collected and analyzed by 16S rRNA MiSeq sequencing. Firth-corrected logistic regression analysis was performed to identify potential factors associated with depressive symptoms in epilepsy.

RESULTS: No significant differences were found between the two groups in terms of general clinical data or oral microbial diversity (α- and β-diversity). Using an uncorrected p value < 0.05 as the screening criterion, microbial composition analysis revealed that Dialister and Olsenella were enriched in EDS, while Bacillus, Fusicatibacter, and [Eubacterium]_coprostanoligenes_group were enriched in EP. LEfSe analysis further suggested that Dialister and Bacillus were key differential genera with discriminatory capability. Based on PICRUSt2's functional prediction results, the predicted functional abundance annotated to the RIG-I-like receptor signaling pathway was higher in the EDS group than in the EP group. Multivariate Firth-corrected logistic regression analysis showed that the abundance of Dialister remained associated with EDS (OR = 1.646, 95% CI: 1.007-2.896, p = 0.047), after adjusting for potential confounding factors.

CONCLUSION: This study utilizing 16S rRNA sequencing elucidates alterations in the oral microbiome associated with epilepsy and concurrent depressive symptoms. Significantly, the enrichment of Dialister is independently correlated with depressive symptoms following adjustment for confounding variables, indicating its potential as a microbial biomarker. Functional prediction analysis further indicated that the associated oral microbial alterations may involve innate immune-related functional characteristics, particularly the RIG-I-like receptor signaling pathway. These findings provide new clues for further investigating the potential association between oral microbiota and epilepsy with depressive symptoms.},
}

@article {pmid42818860,
year = {2026},
author = {Zhang, R and Chen, Y and Hou, D},
title = {Functional organization outweighs spatial separation in structuring microbial communities across a petroleum-hydrocarbon groundwater plume.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1938677},
pmid = {42818860},
issn = {1664-302X},
abstract = {OBJECTIVE: Petroleum-hydrocarbon plumes in groundwater are shaped by hydrological transport, redox conditions, and indigenous microbial activity. However, it remains unclear whether spatial differences among groundwater microbiomes primarily reflect physical separation among wells or ecological reorganization associated with distinct attenuation states within a plume.

METHODS: We integrated hydrogeological context, petroleum-hydrocarbon concentrations, hydrochemical variables, and shotgun-metagenomic profiles from 15 groundwater monitoring wells at a petroleum-hydrocarbon-impacted site. Community beta diversity, spatial and functional distance relationships, permutation-based group tests, and exploratory composite indices of natural attenuation potential and taxonomic-functional diversity were evaluated.

RESULTS: Genus-level community dissimilarity increased with estimated spatial distance (Mantel r = 0.240, p = 0.034), but was more strongly associated with functional-module dissimilarity (r = 0.670, p = 0.001). Biodegradation potential remained associated with community dissimilarity after controlling for spatial distance (partial Mantel r = 0.428, p = 0.001). Operational attenuation states explained 35.4% of genus-level compositional variation (PERMANOVA p = 0.008). High natural attenuation potential and high taxonomic-functional diversity occurred in partly distinct wells.

CONCLUSION: The results indicate that groundwater microbiome turnover within the plume is spatially structured but is more closely coupled to functional reorganization than to distance alone. Joint consideration of hydrological setting, microbial degradation potential, and functional diversity may improve groundwater natural-attenuation assessment.},
}

@article {pmid42819031,
year = {2026},
author = {Távora, BCLF and Gimenes, SNC and de Camargo, IM and Martins, LC and Colombini, M and Clissa, PB and Sanabani, SS and Faquim-Mauro, EL},
title = {Crotoxin from Crotalus durissus terrificus impairs the establishment of chemically induced colitis in mice associated with formyl peptide receptor signaling.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1886884},
pmid = {42819031},
issn = {1664-3224},
mesh = {Animals ; *Colitis/chemically induced/metabolism/drug therapy/immunology/pathology ; Humans ; Mice ; *Receptors, Formyl Peptide/metabolism ; Caco-2 Cells ; *Crotoxin/pharmacology ; Trinitrobenzenesulfonic Acid ; Signal Transduction/drug effects ; *Crotalus ; Disease Models, Animal ; Male ; Intestinal Mucosa/drug effects/metabolism/immunology ; Intestinal Barrier Function ; Venomous Snakes ; },
abstract = {Inflammatory bowel diseases (IBDs) arise from a breakdown in tolerance to intestinal microbiota and are characterized by exacerbated inflammatory responses. Epithelial cells of the gastrointestinal tract play a central role in maintaining barrier integrity and orchestrating immune responses; however, the mechanisms underlying epithelial dysfunction and uncontrolled inflammation remain incompletely understood. Crotoxin (CTX), the main component of Crotalus d. terrificus venom, exhibits immunomodulatory activity, making it a promising tool to investigate epithelial-immune interactions in intestinal inflammation. This study evaluated the effects of CTX on acute colitis induced by trinitrobenzene sulfonic acid (TNBS) in mice, as well as its ability to modulate human epithelial responses. In Caco-2 cells stimulated with IFN-γ, CTX attenuated inflammatory responses by preserving epithelial barrier integrity, maintaining ZO-1 expression and reducing ICAM-1 expression and IL-8 secretion. Furthermore, IFN-γ-stimulated Caco-2 cultures induced neutrophil and monocyte migration, an effect reduced when CTX was present. The TNBS intrarectal instillation in mice induced acute colitis, which was ameliorated by CTX administration resulting in reduced weight loss, lower clinical scores, smaller necrotic areas, decreased recruitment of neutrophils, monocytes and macrophages into the lamina propria, and a partial reversal of TNBS-induced gut dysbiosis. Notably, the protective effects of CTX were abrogated by Boc2, an antagonist of formyl peptide receptor (FPR), indicating the role of these receptors on the effect of CTX. In conclusion, CTX prevents early events of acute colitis by regulating epithelial and immune responses and modulating the gut microbiota through FPR-mediated pathways, highlighting its promise as a novel therapeutic candidate.},
}

Animals
*Colitis/chemically induced/metabolism/drug therapy/immunology/pathology
Humans
Mice
*Receptors, Formyl Peptide/metabolism
Caco-2 Cells
*Crotoxin/pharmacology
Trinitrobenzenesulfonic Acid
Signal Transduction/drug effects
*Crotalus
Disease Models, Animal
Male
Intestinal Mucosa/drug effects/metabolism/immunology
Intestinal Barrier Function
Venomous Snakes

@article {pmid42819040,
year = {2026},
author = {Raju, S and Kookal, A and R V, M and Joshy, S and Bhavya, MSP and E A, A and Aushna, J and C, NC},
title = {Elevated CO2 and the hidden hunger crisis: mechanisms, magnitudes, and mitigation of micronutrient dilution in staple crops.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1929375},
pmid = {42819040},
issn = {1664-462X},
abstract = {Hidden hunger results from inadequate intake of iron (Fe), zinc (Zn), and other key micronutrients. Over 2 billion people worldwide are affected, especially those who rely on staple cereals for daily food. Elevated CO2 often boosts photosynthesis and yield in C3 crops. However, it also reduces grain mineral levels via multiple physiological pathways. These include less transpiration-driven mineral delivery, an imbalance between carbon accumulation and mineral uptake, and changes in mineral uptake, transport, and grain loading. This review collects current evidence for Fe, Zn, copper (Cu), manganese (Mn), boron (B), molybdenum (Mo), selenium (Se), and iodine (I). It draws on free-air CO2 enrichment (FACE) experiments, controlled studies, reviews, and meta-analyses from major cereals and legumes. Grain Fe and Zn show the most consistent and significant declines, and often drop more under combined CO2 enrichment with drought, warming, or low nitrogen. Cu and Mn show greater variability, and data for Se, I, B, and Mo remain limited. This highlights big gaps in climate-nutrition research. The review also considers other factors that affect micronutrient dilution. It identifies research priorities and assesses strategies such as breeding, biofortification, agronomic management, soil-microbiome support, fortification, and dietary diversity. Overall, the evidence indicates that rising CO2 levels threaten the nutritional quality of grains. There is a clear need to include micronutrient density in climate-resilient crop improvement and food system planning.},
}

@article {pmid42819041,
year = {2026},
author = {Lal, D and Sokal-Dembowska, A and Jarmakiewicz-Czaja, S},
title = {Editorial: Harnessing the gut microbiome: paving the way for personalized treatment of diverse disorders.},
journal = {Frontiers in medicine},
volume = {13},
number = {},
pages = {1946088},
pmid = {42819041},
issn = {2296-858X},
}

@article {pmid42819061,
year = {2026},
author = {Yengo, CK and Liu, X and Langley, RJ and Avila, F and Sagar, M and Ochsenbauer, C and Bensing, BA and Hioe, CE},
title = {HIV-1 interactions with sialic acid-binding bacterial lectins promote virus infectivity in vitro and mucosal transmission in humanized mice.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1879791},
pmid = {42819061},
issn = {2235-2988},
mesh = {*HIV-1/pathogenicity/physiology ; Animals ; Humans ; *HIV Infections/transmission/virology ; Mice ; *Mucous Membrane/virology ; *Lectins/metabolism ; *Sialic Acid Binding Immunoglobulin-like Lectins/metabolism ; Virus Attachment ; Staphylococcus aureus/metabolism ; HEK293 Cells ; Streptococcus gordonii/metabolism ; CD4-Positive T-Lymphocytes/virology ; Disease Models, Animal ; N-Acetylneuraminic Acid/metabolism ; },
abstract = {Most human immunodeficiency virus type 1 (HIV-1) transmission occurs at mucosal surfaces, which are colonized by the host microbiota. However, interactions between HIV and bacteria or bacterial products derived from the human microbiome are poorly characterized, and their biological consequences are largely unexplored. Here, we evaluated the effects of sialic acid-binding lectins expressed by bacterial species ubiquitous in the human microbiota on HIV-1 infectivity using viruses produced in 293T cells and human primary cells. We demonstrated that these bacterial lectins enhanced HIV-1 infectivity in a sialoglycan-dependent manner. Specifically, Siglec-like binding region lectins (SLBR-N, SLBR-H, and SLBR-B) from Streptococcus gordonii and staphylococcal superantigen-like lectins (SSL3, SSL4, and SSL11) from Staphylococcus aureus increased HIV-1 infectivity to varying extents, depending on lectin type and virus strain. Among these lectins, SLBR-N exhibited the greatest potency, corresponding with its superior ability to bind virions and promote virus-cell attachment. This enhancing activity was observed for direct infection of TZM-bl reporter cells and primary CD4[+] T cells, as well as trans-infection in the presence or absence of the mannose-binding host lectin DC-SIGN. Importantly, these findings were corroborated in vivo using humanized mice, in which pre-exposure to SLBR-N promoted rectal HIV-1 transmission and increased viral burdens in plasma and splenic cells. Collectively, the data show sialoglycan-binding bacterial lectins as microbial factors that can enhance HIV-1 transmission at mucosal surfaces, highlighting a potential direct role for the microbiota in modulating HIV-1 acquisition risk.},
}

*HIV-1/pathogenicity/physiology
Animals
Humans
*HIV Infections/transmission/virology
Mice
*Mucous Membrane/virology
*Lectins/metabolism
*Sialic Acid Binding Immunoglobulin-like Lectins/metabolism
Virus Attachment
Staphylococcus aureus/metabolism
HEK293 Cells
Streptococcus gordonii/metabolism
CD4-Positive T-Lymphocytes/virology
Disease Models, Animal
N-Acetylneuraminic Acid/metabolism

@article {pmid42819081,
year = {2026},
author = {Bondre, S and Shetty, V and Kumari, M and Shetty, U},
title = {Effect of probiotic interventions on oral health in children: a systematic review.},
journal = {Frontiers in dental medicine},
volume = {7},
number = {},
pages = {1914359},
pmid = {42819081},
issn = {2673-4915},
abstract = {INTRODUCTION: Early childhood caries (ECC) is one of the most prevalent chronic diseases affecting young children worldwide. Probiotic supplementation has emerged as a potential adjunctive strategy for modifying the oral microbiome and reducing caries risk; however, evidence regarding its effectiveness remains inconsistent. This review evaluated the effects of probiotic interventions on oral health outcomes in children under 6 years of age, with emphasis on probiotic-based interventions and their influence on caries incidence, microbial changes, and biological mechanisms.

METHODS: A systematic search of PubMed, Scopus, and Web of Science was conducted in accordance with the PRISMA 2020 guidelines up to June 2026. Eligible studies included randomized controlled trials, non-randomized intervention studies, and in vitro mechanistic studies evaluating probiotic interventions in children aged 0-6 years. Two independent reviewers performed study selection, data extraction, and quality assessment using the Cochrane RoB 2.0, ROBINS-I, and QUIN tools. Due to substantial clinical and methodological heterogeneity, findings were synthesized narratively, with supplementary quantitative analyses performed where appropriate. Certainty of evidence was assessed using the GRADE framework.

RESULTS: Twenty-one studies met the inclusion criteria, comprising 13 randomized controlled trials, three non-randomized intervention studies, and five in vitro studies. The clinical evidence primarily evaluated probiotic supplementation, most commonly Lactobacillus paracasei SD1, Lactobacillus rhamnosus strains, and Limosilactobacillus reuteri. Most randomized trials reported reductions in caries incidence or progression and decreases in salivary Streptococcus mutans counts, although findings were heterogeneous across probiotic strains and outcome measures. Mechanistic studies consistently demonstrated antimicrobial and antibiofilm activity of probiotic lactobacilli against cariogenic microorganisms, providing biological plausibility for the observed clinical effects. GRADE assessment indicated moderate-certainty evidence for randomized controlled trials, while evidence from non-randomized and in vitro studies was rated as low and very low certainty, respectively.

CONCLUSION: Probiotic supplementation appears to be a promising adjunct to conventional preventive strategies for improving oral microbial profiles and reducing caries progression in preschool children. However, the observed benefits appear to be strain-specific, and considerable heterogeneity across interventions and outcome measures limits definitive clinical recommendations. Further high-quality, adequately powered randomized controlled trials with standardized probiotic regimens, uniform caries assessment.

https://www.crd.york.ac.uk/PROSPERO/view/CRD420251229276, PROSPERO CRD420251229276.},
}

@article {pmid42819214,
year = {2026},
author = {Chen, Y and Li, D and Wang, Z and Li, J and Zhang, H and Xie, X},
title = {The potential role and research progress of the gut microbiota-NGF axis in postmenopausal bone homeostasis imbalance.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1933248},
pmid = {42819214},
issn = {1664-3224},
mesh = {Humans ; *Gastrointestinal Microbiome/immunology ; *Nerve Growth Factor/metabolism ; Female ; Homeostasis ; Animals ; *Osteoporosis, Postmenopausal/metabolism/microbiology/immunology ; *Bone and Bones/metabolism ; Bone Remodeling ; Signal Transduction ; },
abstract = {Postmenopausal osteoporosis(PMOP)is a common metabolic bone disease characterized by an imbalance in bone remodeling due to estrogen deficiency. Increasing evidence suggests that alterations in gut microbiota, intestinal barrier, immune response, microbial metabolites, and autonomic nervous activity are involved in postmenopausal bone loss. Nerve growth factor (NGF) and its receptors tropomyosin receptor kinase A (TrkA) and p75 neurotrophin receptor (p75 NTR) are implicated in sensory nerve innervation, inflammation regulation, bone adaptation, bone repair, and pain sensitization, thus potentially serving as a molecular interface linking microbiota, nerves, immunity, and skeletal processes. This review evaluates the proposed gut microbiota-NGF-bone relationship by distinguishing between mechanisms supported by experimental evidence, indirect evidence, and speculative hypotheses. Existing studies support the regulation of NGF by gut microbiota under specific neuroimmune contexts, the gut microbiota-immune-bone interactions in estrogen deficiency models, and the roles of NGF and its receptors in neurobiology and skeletal biology. However, these findings originate from independent experimental systems. Currently, no studies have simultaneously demonstrated that gut microbiota-induced changes in NGF signaling are a necessary or sufficient condition for the abnormal bone remodeling associated with PMOP. Therefore, the gut microbiota-NGF-bone axis should be viewed as a conceptual framework connecting the microbiome, immunity, neuroendocrine factors, and bone metabolism, rather than as an established causal pathway. This framework aids in integrating existing evidence, clarifying mechanistic gaps, and proposing testable scientific questions. Future research should combine the manipulation of gut microbiota with tissue or cell-specific regulation of NGF, TrkA, or p75 NTR, while also conducting rescue experiments, longitudinal multi-omics analyses, and systematic skeletal phenotype evaluations. Direct causal validation must be obtained before applying gut microbiota or NGF-targeting strategies for the precise prevention and treatment of PMOP.},
}

Humans
*Gastrointestinal Microbiome/immunology
*Nerve Growth Factor/metabolism
Female
Homeostasis
Animals
*Osteoporosis, Postmenopausal/metabolism/microbiology/immunology
*Bone and Bones/metabolism
Bone Remodeling
Signal Transduction

@article {pmid42819236,
year = {2026},
author = {Yan, S and Zhang, Y and Tan, W and Guo, J and Si, J and Li, H and Shi, J},
title = {A spatial-microbial-metabolic-immune framework for high-risk oral potentially malignant disorders: an evidence-ranked review for malignant transformation risk stratification.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1928595},
pmid = {42819236},
issn = {2235-2988},
mesh = {Humans ; *Mouth Neoplasms/pathology/immunology/microbiology/metabolism ; *Microbiota/immunology ; Dysbiosis/microbiology ; *Mouth Mucosa/microbiology/immunology/pathology/metabolism ; *Cell Transformation, Neoplastic/immunology ; Animals ; Carcinoma, Squamous Cell/pathology/microbiology/immunology ; },
abstract = {The oral mucosa is a microbe-exposed barrier ecosystem in which surface biofilms, epithelial differentiation programs, microbial products, metabolic stress, stromal remodeling, and immune surveillance are spatially organized. Although oral microbiome studies have associated dysbiosis with oral potentially malignant disorders (OPMDs) and oral squamous cell carcinoma (OSCC), most evidence remains saliva-based, rinse-based, swab-based, tissue-homogenate-based, or taxon-centered. These approaches can identify disease-associated microbial patterns but cannot determine whether microbial signals are locally aligned with epithelial, metabolic, stromal, and immune changes within the same mucosal microdomains. Here, we propose a spatial-microbial-metabolic-immune (SMMI) framework as an evidence-ranked and testable approach for studying malignant transformation risk in high-risk OPMDs. The acronym denotes four analytical dimensions-spatial organization, microbial signals, metabolic mediation, and immune remodeling-all interpreted within oral host tissue. The framework asks whether dysbiosis-associated microbial signals, epithelial barrier-response states, metabolic stress, stromal remodeling, macrophage-centered immunoregulation, altered epithelial immune visibility, and T-cell positioning become locally aligned within candidate mucosal microdomains. SMMI is a conceptual and validation framework rather than an established causal mechanism, fixed anatomical structure, or immediate therapeutic target. This article is an evidence-ranked conceptual review rather than a systematic review. We distinguish direct human OPMD evidence from OSCC-derived inference, preclinical perturbation data, broader cancer biology, methods papers, and speculative but testable hypotheses. We outline a modular validation roadmap that proceeds from pathology-anchored sampling and contamination-aware microbial localization to hypothesis-selected spatial modules, targeted functional testing, and longitudinal clinical validation. The near-term translational goal is improved risk stratification and risk-adapted surveillance, rather than ecological intervention. By reframing high-risk OPMDs as spatial oral microbe-host immune-metabolic ecosystems, the SMMI framework provides a cautious structure for hypothesis generation, spatial validation, and clinically relevant risk modeling.},
}

Humans
*Mouth Neoplasms/pathology/immunology/microbiology/metabolism
*Microbiota/immunology
Dysbiosis/microbiology
*Mouth Mucosa/microbiology/immunology/pathology/metabolism
*Cell Transformation, Neoplastic/immunology
Animals
Carcinoma, Squamous Cell/pathology/microbiology/immunology

@article {pmid42819299,
year = {2026},
author = {Xu, F and Deakin, G and Xu, X},
title = {Is within-field spatial variation in wheat Fusarium crown rot associated with rhizosphere microbiome and soil nutrients.},
journal = {Frontiers in plant science},
volume = {17},
number = {},
pages = {1928197},
pmid = {42819299},
issn = {1664-462X},
abstract = {Fusarium crown rot (FCR) of wheat, caused predominantly by Fusarium pseudograminearum, frequently exhibits marked spatial heterogeneity within individual fields despite uniform cultivars and agronomic management. However, the mechanisms underlying this within-field variation remain poorly understood. In this study, we investigated six commercial wheat fields in Henan Province, China, each containing distinct highly diseased (HD) and lightly diseased (LD) zones. Soil physicochemical properties and rhizosphere microbial communities (characterised via 16S rRNA and ITS amplicon sequencing) were compared between HD and LD zones. Despite identical management histories, HD and LD zones differed significantly in soil pH, nitrate nitrogen, available potassium, and magnesium. Furthermore, fungal communities in HD zones exhibited significantly lower α -diversity and distinct compositions, whereas bacterial communities showed only minor variations. Fusarium was significantly enriched in HD zones, while putatively beneficial taxa, including Acremonium and Pseudoxanthomonas, were more abundant in LD zones. These findings provide new insights into the micro-ecological factors associated with within-field disease heterogeneity and support the development of site-specific management strategies for FCR.},
}

@article {pmid42819390,
year = {2026},
author = {Morishita, S and Iida, N and Sato, T and Endo, Y and Tanno, D and Yabuki, S},
title = {The exercise-gut-muscle axis in physical frailty: A narrative review.},
journal = {JAR life},
volume = {15},
number = {},
pages = {100087},
pmid = {42819390},
issn = {2534-773X},
abstract = {The prevalence of physical frailty has increased in recent years, owing to an aging population. This geriatric syndrome is characterized by a decline in physiological reserve and physical function. Thus, the risk of adverse health outcomes amongst individuals in a state of frailty is high. Frailty development is strongly influenced by skeletal muscle dysfunction, which involves reductions in muscle mass, strength, and metabolic capacity. Exercise is the most effective approach for the maintenance of muscle function and prevention of functional decline in older adults. However, the biological mechanisms underlying its role in aging remain unclear. The gut microbiota produces various bioactive metabolites that affect metabolic regulation, immune responses, and inflammatory pathways. Exercise may modify the composition and metabolic function of the gut microbiota in some studies, although the findings remain inconsistent. These exercise-associated alterations may influence the production of microbial metabolites that may affect skeletal muscle metabolism. Recent evidence on age-related alterations in the gut microbiota is reviewed here, with a focus on how these changes relate to skeletal muscle physiology. Furthermore, the mechanisms by which exercise modifies the composition and metabolic pathways of the gut microbiota are described, highlighting the concept of the "exercise-gut-muscle axis" as a framework linking physical activity, the gut microbiome, skeletal muscle, and physical frailty trajectories. Our narrative synthesis integrates the emerging evidence on exercise-microbiome-muscle interactions. This may help identify priorities for future research on lifestyle-based strategies that support healthy aging and may help delay physical frailty in older adults.},
}

@article {pmid42819443,
year = {2026},
author = {Lutsiv, T and Thompson, HJ and Fiehn, O and Gareau, MG and Borowsky, AD and Chen, BH and Hussan, H},
title = {A Distinct Host-Microbiome Signature Underlies the Accelerated Malignant Potential of Colorectal Laterally Spreading Tumors.},
journal = {Gastro hep advances},
volume = {5},
number = {12},
pages = {101102},
pmid = {42819443},
issn = {2772-5723},
abstract = {BACKGROUND AND AIMS: Laterally spreading tumors (LST) are flat colorectal neoplasms with an accelerated risk of malignant transformation and interval colorectal cancer. Despite their clinical importance, the molecular and microbial mechanisms underlying LST's aggressive biology remain poorly understood. Thus, we aimed to characterize the transcriptomic and microbial landscape of LST in comparison with paired protruding lesions and the adjacent normal colonic tissue.

METHODS: Formalin-fixed, paraffin-embedded tissues from 36 samples were obtained from 15 adults and analyzed using RNA sequencing and 16S rRNA gene amplicon sequencing. Patterns of the differential gene expression were assessed using Gene Set Enrichment Analysis and Ingenuity Pathway Analysis. Microbial community composition and its predicted functional capacity were evaluated with analysis of compositions of microbiomes with bias correction in QIIME 2 and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2, respectively.

RESULTS: Compared with paired protruding lesions and normal tissue, LST exhibited a distinct protumorigenic transcriptomic profile marked by the activation of MYC, E2F, mTOR, DNA damage, and senescence-associated secretory phenotype pathways, as well as robust proinflammatory signaling driven by TNF, NF-κB, IL-1, and IL-17. LST tissue also demonstrated a permissive environment for genomic instability. Microbiome analysis revealed enrichment of Fusobacterium and depletion of beneficial taxa, including Lactococcus, accompanied by predicted suppression of carbohydrate fermentation and short-chain fatty acid production, as well as altered sulfur metabolism. Fusobacterium abundance correlated with increased TNF expression, supporting a microbiota-driven inflammatory niche in LST.

CONCLUSION: LST are characterized by a unique inflammatory/metabolic/senescence axis that distinguishes them from other paired colorectal tissue samples. This procarcinogenic signature is driven by a Fusobacterium-enriched and carbohydrate-fermentation-depleted microbial ecosystem. These findings highlight the gut microbial ecosystem as a critical cofactor in LST pathogenesis and further support that combined host/microbiota-targeted strategies may improve colorectal cancer prevention in this population. Given the exploratory nature and limited cohort size, these findings require validation in larger prospective cohorts with metagenomic and metabolomic integration.},
}

@article {pmid42819658,
year = {2026},
author = {Otu, N and Inyang-Otu, M},
title = {Perspectives on engineering and biomaterials in tampon design: a review of device-tissue interactions and dysmenorrhea risk.},
journal = {Frontiers in bioengineering and biotechnology},
volume = {14},
number = {},
pages = {1920190},
pmid = {42819658},
issn = {2296-4185},
abstract = {BACKGROUND: Dysmenorrhea affects approximately 71% of menstruating individuals globally and is associated with substantial losses in quality of life, work and school participation, and healthcare utilization. Tampons are among the most widely used intravaginal menstrual devices, yet their design has evolved primarily around absorbency, structural integrity, and infection risk, not around comfort or pain minimization as a formal design or regulatory endpoint. No existing review has examined tampon design, materials, or biomechanical properties through the lens of menstrual pain or discomfort.

OBJECTIVES: This review (1) synthesizes evidence on tampon-associated discomfort; (2) identifies plausible biomechanical and biological mechanisms linking device properties to pain; (3) characterizes tampon materials and biocompatibility; and (4) proposes an engineering framework for developing lower-discomfort products.

METHODS: Literature was searched across PubMed, Google Scholar, and regulatory databases. A PRISMA-informed screening process prioritized primary research and systematic reviews, identifying a core evidence base of 51 sources for narrative synthesis.

RESULTS: No randomized controlled trials or prospective clinical studies directly examining the effect of tampon use or tampon material type on menstrual cramp severity were identified. However, evidence from adjacent fields supports several plausible mechanisms: colposcopy studies of older superabsorbent tampon formulations documented mucosal desiccation and microulceration, though modern products have not been comparably characterized; tampon materials contain detectable chemical residues including metals, phthalates, and volatile organic compounds, though their bioavailability across vaginal mucosa and contribution to systemic exposure remain unquantified, and current regulatory reviews (FDA, American College of Medical Toxicology) have not identified an associated safety concern; tampon use may perturb the vaginal microbiome in ways that could increase pro-inflammatory bacterial activity; and removal dynamics plausibly generate friction and contact pressure against vaginal tissue, though this has not been directly measured. These mechanisms are mechanistically coherent hypotheses that may converge in populations with elevated pain sensitivity, not established causal pathways.

CONCLUSION: A substantial evidence gap exists at the intersection of tampon design and menstrual pain. Biomedical engineering provides a pathway to close this gap via testable design specifications. These include friction-reducing surface architectures and controlled expansion geometry, which are framed as research targets requiring further validation.},
}

@article {pmid42819668,
year = {2026},
author = {Tian, J and Chen, K and Wang, L and Wang, J},
title = {Gut microbiota-host co-metabolism in hypertriglyceridemia-associated acute pancreatitis: from causality to precision intervention.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1932634},
pmid = {42819668},
issn = {1664-3224},
mesh = {Humans ; *Hypertriglyceridemia/complications/metabolism/microbiology ; *Pancreatitis/metabolism/etiology/microbiology/therapy ; *Gastrointestinal Microbiome ; Animals ; Precision Medicine ; *Host Microbial Interactions ; },
abstract = {Clinical outcomes in hypertriglyceridemia-associated acute pancreatitis remain highly heterogeneous. Despite comparable lipid burdens, patients may experience anything from mild interstitial edema to fulminant necrotizing disease, a divergence that current models struggle to explain. Hypertriglyceridemia-associated acute pancreatitis (HTG-AP) now accounts for roughly one in nine acute pancreatitis cases worldwide, but serum triglyceride levels alone do not explain the significant East-West mortality gap (4.1% versus 1.0%). Emerging evidence shifts the focus away from the pancreas itself and toward a gut-pancreas co-metabolic circuit. Within this circuit, microbial metabolites engage host receptors and determine whether local injury escalates into systemic disease. In this review, we examine four interconnected axes that form The mechanistic backbone of this circuit: LPS-TLR4-lysophosphatidylcholine, short-chain fatty acid-GPR43/HDAC, tryptophan-aryl hydrocarbon receptor, and bile acid-FXR/TGR5-recognizing that direct HTG-AP-specific evidence is currently strongest for the LPS-TLR4-LPC axis, while the other three axes are supported by evidence from AP broadly and await HTG-AP-specific validation. We critically examine the cross-talk among these pathways and apply the Bradford Hill criteria to assess the validity of current causal inferences in the gut-pancreas axis. From a translational perspective, we introduce the concept of "functional metabolite guilds" (metabolite clusters sharing protective endpoints) to inform and streamline future postbiotic formulation designs. We also outline a co-metabolic stratification logic to guide patient selection in future trials. The ultimate goal is to move beyond descriptive microbiome catalogs toward precision interventions that match metabolic deficits with guild-based restoration strategies.},
}

Humans
*Hypertriglyceridemia/complications/metabolism/microbiology
*Pancreatitis/metabolism/etiology/microbiology/therapy
*Gastrointestinal Microbiome
Animals
Precision Medicine
*Host Microbial Interactions

@article {pmid42819723,
year = {2026},
author = {Huang, X and Yang, X and Huang, J and Tao, W and Yu, Y and Yu, R},
title = {Indoxyl sulfate in the gut-kidney axis: from diet-microbiome interactions to renal injury and targeted therapies.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1881019},
pmid = {42819723},
issn = {2296-861X},
abstract = {Indoxyl sulfate (IS) is a prototypical protein-bound uremic toxin, linking dietary tryptophan metabolism by gut microbiota to renal injury. Derived from dietary tryptophan metabolized by gut microbiota into indole, which is subsequently transported to the liver and sulfated to form IS. In circulation, IS binds serum albumin and is actively secreted into urine via renal tubular organic anion transporters. In chronic kidney disease (CKD), impaired renal clearance and altered albumin-binding capacity contribute to IS accumulation and an increased free fraction. IS exerts nephrotoxic effects through multiple mechanisms. As an endogenous ligand of the aryl hydrocarbon receptor (AHR), it activates AHR signaling and contributes to mitochondrial dysfunction, oxidative stress, inflammation, regulated cell death, and renal fibrosis through interconnected downstream pathways. Therapeutic strategies targeting IS include dietary and microbiota-based interventions, oral adsorbent AST-120, modified dialysis approaches, and traditional Chinese medicine interventions. Although these strategies may reduce IS exposure or its downstream effects, the current evidence is predominantly derived from preclinical studies and surrogate-endpoint assessment. Further well-designed clinical trials are needed to determine whether reducing IS exposure can translate into sustained improvements in renal and patient-centered outcomes.},
}

@article {pmid42819986,
year = {2026},
author = {Liu, Q and Luo, L and Yan, Z and Yang, P and Long, T and Yang, Y and He, M and Tao, L},
title = {The "pro-inflammatory imprint" of ultra-processed food exposure: a review of mechanisms affecting child and adolescent health and development via the gut microbiome-inflammation axis.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1843587},
pmid = {42819986},
issn = {2296-861X},
abstract = {The prevalence of ultra-processed food (UPF) consumption in pediatric diets has raised significant concerns regarding long-term health. This review examines evidence for a proposed 'pro-inflammatory imprint' involving the gut microbiome-inflammation axis. Using a structured narrative synthesis of pediatric observational evidence, adult intervention studies, preclinical research, multi-omics data, and public health evaluations, we examine associations between UPF exposure and metabolic, inflammatory, cognitive, and neurodevelopmental outcomes while distinguishing direct from indirect evidence. We propose the Pediatric-Specific Integrated Dietary Inflammatory Index (cP-IDII) as an unvalidated, hypothesis-generating research framework for integrating reproducible nutrient- and processing-related dietary exposures; downstream microbial, intestinal-barrier, inflammatory, metabolic, and immune measures are reserved for external validation. Furthermore, we discuss the role of commercial determinants and environmental factors in shaping child health. The synthesis identifies measurement gaps and complementary policy entry points across product composition, food environments, affordability, and marketing. Empirical development and external validation are required before the cP-IDII can be used for clinical, epidemiological, or public health decision-making.},
}

@article {pmid42820064,
year = {2026},
author = {Hajjar, J and Stephen, B and Aaroe, AE and Aiche, MM and Al-Zubidi, N and Ameri, M and Aragon, KE and Carabenciov, ID and Chambers, MS and Chaudhry, AL and Connors, JM and Davies, MA and Debnath, KC and Faiz, SA and Fuller, CD and Goepfert, RP and Gombos, DS and Gupta, S and Hadfield, M and Hutcheson, KA and Islam, S and Jalal, A and Jayasekera, M and Jazieh, KA and Khine, A and Kim, P and Lai, SY and Lei, YL and Li, YJ and Markovic, SN and McMillan, H and Moreno, AC and Muhaj, F and Nader, ME and Otun, A and Pacha, O and Palaskas, NL and Patel, AB and Patel, N and Quandt, Z and Sagiv, O and Sharon, E and Shatila, M and Sheshadri, A and Suarez-Almazor, ME and Thomas, AS and Wang, Y and Won, A and Zhang, HC and Naing, A},
title = {The Immune Checkpoint Inhibitors Journey: From Early Promise to Lasting Impact.},
journal = {Journal of immunotherapy and precision oncology},
volume = {9},
number = {4},
pages = {153-245},
pmid = {42820064},
issn = {2590-017X},
abstract = {Immune checkpoint inhibitors (ICIs) have transformed cancer therapy, yet their clinical impact is limited by immune-related adverse events (irAEs), therapeutic resistance, and the lack of reliable predictive biomarkers, contributing to a shift from early promise to a therapeutic plateau. irAEs affect multiple organ systems and may lead to treatment interruption and significant morbidity. Emerging strategies emphasize phenotype-driven and steroid-sparing approaches to control toxicity while preserving antitumor efficacy. Concurrently, primary and acquired resistance remain major challenges, driven by tumor-intrinsic mechanisms, immune microenvironment alterations, and host factors. Furthermore, current biomarkers, including programmed cell death ligand 1 (PD-L1) expression and tumor mutation burden, demonstrate inconsistent predictive performance across tumor types. Advances in immune profiling, genomics, and microbiome research are enabling more precise patient stratification and informing novel therapeutic strategies, including rational combinations and targeted immunomodulation. This position article synthesizes key barriers in ICI therapy while highlighting emerging opportunities to refine patient selection, improve safety, and enhance therapeutic durability. Together, these advances position the field to move beyond the current plateau toward a more precise, effective, and patient-centered era of immuno-oncology.},
}

@article {pmid42820090,
year = {2026},
author = {Ma, X and Lin, K and Wang, Y and Xu, Y},
title = {The microbiome-inflammasome axis in endometriosis-associated chronic pelvic pain: mechanisms and therapeutic opportunities from an immunological perspective.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1942637},
pmid = {42820090},
issn = {1664-3224},
mesh = {Humans ; Female ; *Endometriosis/immunology/microbiology/therapy/complications ; *Inflammasomes/immunology/metabolism ; *Pelvic Pain/immunology/therapy/etiology/microbiology ; *Chronic Pain/immunology/therapy/etiology/microbiology ; Animals ; *Microbiota/immunology ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Toll-Like Receptor 4/metabolism ; Signal Transduction ; },
abstract = {INTRODUCTION: Endometriosis (EMs) is increasingly recognized as a chronic inflammatory disease in which innate immune dysregulation plays an important role. Its immunopathological features include macrophage polarization imbalance, with M1-skewed activation in inflamed peritoneal fluid and lesions, reduced natural killer (NK) cell cytotoxicity, adaptive immune alterations including Th2/Treg-skewed profiles reported in some studies, and persistently elevated pro-inflammatory cytokines. The disease affects approximately 10% of women of reproductive age worldwide, and 70%-80% of these patients experience chronic pelvic pain (CPP). Conventional hormonal therapies provide limited relief and are associated with high recurrence rates after withdrawal, yet the immunological drivers of CPP remain incompletely understood.

METHODS: We conducted a narrative review of peer-reviewed literature identified through PubMed, Web of Science, and Scopus up to August 2026. Search terms covered endometriosis, chronic pelvic pain, microbiota/dysbiosis, Toll-like receptor 4, NF-κB, NLRP3 inflammasome, IL-1β/IL-18, neuroinflammation, and immunotherapy. Reference lists were screened for additional relevant studies, and evidence was synthesized by mechanistic theme and appraised according to study design, directness, and consistency.

RESULTS: Convergent preclinical and observational evidence suggests that dysbiosis of the gut and reproductive tract microbiota may activate TLR4 via lipopolysaccharide, triggering NF-κB signaling and promoting NLRP3 inflammasome priming and activation. This cascade may contribute to M1-skewed pelvic inflammation, adaptive immune alterations, pyroptosis, and neuroimmune sensitization that could facilitate CPP chronification. Host-derived damage-associated molecular patterns and metabolic stress appear to be the principal immediate Signal 2 sources, whereas microbiota-derived signals mainly provide priming and indirect contributions. Direct causal evidence in humans remains incomplete, and conflicting microbiome findings may reflect sampling site, disease stage, and methodological differences.

DISCUSSION: The microbiome-inflammasome axis represents one potentially important and testable mechanism in EMs-associated CPP rather than a dominant explanatory framework. Promising therapeutic avenues include probiotics/postbiotics, TLR4 antagonists, NF-κB inhibitors, NLRP3 inhibitors, and IL-1β/IL-18-directed therapies, but most remain exploratory and require validation in prospective, mechanism-based trials. Refining this framework may inform immune stratification and precision immunomodulatory therapy for endometriosis-associated pelvic pain.},
}

Humans
Female
*Endometriosis/immunology/microbiology/therapy/complications
*Inflammasomes/immunology/metabolism
*Pelvic Pain/immunology/therapy/etiology/microbiology
*Chronic Pain/immunology/therapy/etiology/microbiology
Animals
*Microbiota/immunology
NLR Family, Pyrin Domain-Containing 3 Protein/metabolism
Toll-Like Receptor 4/metabolism
Signal Transduction

@article {pmid42820210,
year = {2026},
author = {Handelsman, J and Emmett, B and Schadt, C and Sanders, IR and Evans, D and Beattie, GA and Martiny, JBH and Crowther, T and Salles, JF and Nicolaisen, MH and Harper, L and Stevenson, M and Edlund, A and Byck, P and Sullivan, MB and McGlashan, B and Lischer, M and Benjamin, K and Franch, J and Voss, M and Hawken, P and Hartmann, J and Dosier, GK and Garcia, V and Sauer, M and Häggblom, MM and Doyle, E and Smit, T and Ryan, D and Depledge, M and Marsden, P and Jansson, JK and Gilbert, JA},
title = {Developing global goals for soil health research and action: report on the "Soil Stars Heligan Summit," The Lost Gardens of Heligan, UK, March 2026.},
journal = {Sustainable microbiology},
volume = {3},
number = {4},
pages = {qvag038},
pmid = {42820210},
issn = {2755-1970},
abstract = {Soil underpins food production, freshwater, carbon storage and biodiversity, yet over 40% of the world's soils are now degraded, eroding at rates up to 1000 times their formation rate. Microbial technologies have matured and can now aid soil recovery, but deployment has lagged due to absent shared targets, harmonized metrics, and coherent reward structures to mobilize solvers across academia, industry, philanthropy, and government. Building on major initiatives (e.g. A Soil Deal for Europe, the FAO Global Soil Partnership, etc.) a consensus has emerged on the need for actionable, transformative advances in soil health. To translate that consensus into coordinated action, The Soil Stars, a multidisciplinary coalition of scientists, communicators, investors, policymakers, and farming-systems leaders, convened the inaugural Soil Stars Heligan Summit in March 2026 at The Lost Gardens of Heligan, Cornwall, United Kingdom, with a public launch at the Eden Project's Anthropy 2026 forum. The summit combined a grand-missions hack-a-thon with roundtables on the climate-society interface, the soil carbon-fertility-microbiome nexus, and deployment hurdles. The primary outcome is the first draft of the Heligan Grand Challenges; seven XPRIZE-inspired challenges with concrete performance thresholds achievable within 24-36 months, alongside a path toward a formal Grand Challenges paper and five-year implementation roadmap.},
}

@article {pmid42820214,
year = {2026},
author = {Sola, M and Paravel, A and Auger, S and Chatel, JM and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Veiga, P and Frioux, C and Mariadassou, M and Berland, M},
title = {NeighborFinder: an R package inferring local microbial network around a species of interest.},
journal = {Bioinformatics advances},
volume = {6},
number = {1},
pages = {vbag201},
pmid = {42820214},
issn = {2635-0041},
abstract = {MOTIVATION: Understanding interactions from microbiome data is a central aspect in microbial ecology, as it provides insights into ecosystem stability, disease mechanisms, and can be used to design synthetic communities. Current network inference tools reconstruct global networks from co-abundance data, which means they capture the overall correlation structure for the entire set of taxa considered. These approaches are computationally intensive and suboptimal when the focus is on the local neighborhood of one or a few taxa of interest.

RESULTS: We introduce NeighborFinder, a local network inference method that enables the targeted discovery of direct neighbors around a species of interest. Using cross-validated multiple linear regression with ℓ 1 penalty and microbiome-specific filters, our approach infers interpretable species-centered interactions, with F1 score ≥ 0.95 on simulated cohorts ranging from 250 to 1000 samples. This method is well-suited for large metagenomic datasets and is particularly valuable for exploratory studies where the targeted hypotheses outweigh the need for global community structure. The approach complements existing methods by being biologically intuitive and computationally efficient.

The R package is available on CRAN https://CRAN.R-project.org/package=NeighborFinder. The data and source code used to calculate performances and produce the use case example can be found respectively at: https://doi.org/10.57745/UPITJ0 and https://doi.org/10.57745/HJLWW4.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.},
}

@article {pmid42809026,
year = {2026},
author = {Akanmu, AM},
title = {Beyond the Rumen: Current Evidence and Knowledge Gaps in Microbial Diversity and Function Across the Bovine Gastrointestinal Tract.},
journal = {Current microbiology},
volume = {83},
number = {11},
pages = {},
pmid = {42809026},
issn = {1432-0991},
mesh = {Animals ; Cattle/microbiology ; *Gastrointestinal Tract/microbiology ; Rumen/microbiology ; *Gastrointestinal Microbiome ; *Bacteria/classification/genetics/isolation & purification/metabolism ; Fermentation ; Biodiversity ; },
abstract = {The bovine gastrointestinal tract (GIT) is a spatially organised microbial ecosystem, but the evidence supporting a whole-tract interpretation is highly uneven. This critical review distinguishes well-established rumen biology from emerging observations in the reticulum, omasum, abomasum, small intestine and hindgut. Comparative studies show strong regional filtering of microbial communities, yet most available datasets are cross-sectional, use digesta rather than mucosa, and infer function from DNA. Consequently, the presence of genes or taxa cannot be equated with active metabolism. Early life provides an important developmental dimension: microbial succession during the milk-to-solid-feed transition accompanies rumen maturation and region-specific immune development, although durable effects on adult productivity remain incompletely demonstrated. Across adult cattle, foregut fermentation supplies most microbially derived energy, whereas downstream compartments support residual fermentation, epithelial interactions and barrier-related processes whose quantitative contributions are less certain. Methanogenesis is therefore treated as one outcome among nutrition, immune function, pathogen resistance and gut integrity. Metagenomics, metatranscriptomics, metaproteomics and metabolomics are complementary rather than interchangeable; coordinated sampling is required to connect functional potential to activity and host phenotype. Priority should be given to longitudinal, multi-compartment, mucosa-and-digesta studies with absolute microbial measurements, metabolite fluxes and transparent causal inference. A tract-wide framework is valuable not because all compartments are equally understood, but because it makes the present evidence imbalance explicit and identifies where microbiome-targeted nutrition can be tested responsibly.},
}

Animals
Cattle/microbiology
*Gastrointestinal Tract/microbiology
Rumen/microbiology
*Gastrointestinal Microbiome
*Bacteria/classification/genetics/isolation & purification/metabolism
Fermentation
Biodiversity

@article {pmid42809046,
year = {2026},
author = {Dwivedi, S and Kumar, A and Upreti, D},
title = {Reconstructing bovine disease trajectories through integrative multi-omics: molecular decision nodes, predictive biomarkers and precision intervention.},
journal = {Veterinary research communications},
volume = {50},
number = {6},
pages = {},
pmid = {42809046},
issn = {1573-7446},
mesh = {Animals ; Cattle ; *Multiomics ; Biomarkers ; *Cattle Diseases/genetics/diagnosis ; Genomics ; },
abstract = {Bovine diseases arise from dynamic interactions among genetic susceptibility, regulatory responses, immune activity, metabolism, microbial ecology and tissue function. Although individual omics studies have identified numerous disease-associated molecular signatures, many remain context-dependent and poorly reproducible across animals, breeds, disease stages and biological matrices. Integrative multi-omics extends beyond parallel profiling of individual molecular layers by connecting genomic variation with epigenetic regulation, transcriptional activity, protein and metabolite states, and microbial ecology to reconstruct coordinated mechanisms underlying disease development and recovery. This review synthesizes integrative multi-omics data across a trajectory from pre-disease vulnerability through active disease to persistence or functional recovery, while examining ecological destabilization as a process that may arise at different points along this continuum. Across diseases, integration of multiple molecular layers identifies recurrent associations among genetic regulation of disease-response pathways, inflammatory activation, immune-metabolic and redox imbalance, tissue-barrier dysfunction and microbiome-metabolite feedback. These interacting processes have the potential to provide greater biological and predictive information than isolated molecular alterations. We therefore propose that robust biomarker development should prioritize reproducible cross-omics signals and compact panels integrating three complementary components: disease burden or causal trigger, host-response state and functional consequence. Such biomarkers require validation across independent populations, breeds, disease stages and field conditions before clinical deployment. By linking molecular layers rather than cataloguing individual signatures, multi-omics can support more reliable disease prediction, mechanistically informed diagnostics, targeted intervention and selection for improved disease resistance and resilience in cattle.},
}

Animals
Cattle
*Multiomics
Biomarkers
*Cattle Diseases/genetics/diagnosis
Genomics

@article {pmid42809189,
year = {2026},
author = {Toda, M and Wangorsch, A and Yajima, Y and Guo, Y and He, C and Vieths, S and Scheurer, S},
title = {Immunomodulatory Function of Soluble Dietary Fiber: Toward Application for Prevention and Treatment of Food Allergies.},
journal = {Current allergy and asthma reports},
volume = {26},
number = {1},
pages = {},
pmid = {42809189},
issn = {1534-6315},
mesh = {Humans ; *Dietary Fiber/metabolism ; *Food Hypersensitivity/prevention & control/immunology/diet therapy ; Animals ; Gastrointestinal Microbiome/immunology ; Receptors, Pattern Recognition/metabolism ; beta-Glucans ; Immunomodulation ; },
abstract = {PURPOSE OF REVIEW: Gastrointestinal dysbiosis is implicated in the disruption of immune homeostasis and the pathogenesis of food allergies. Consequently, dietary fibers have gained attention as key molecules modulating microbial balance and immunity. This review aims to explore the immunomodulatory functions of dietary fibers commonly found in the human diet, including pectin, inulin, β-glucan, and mannan.

RECENT FINDINGS: Dietary fibers affect the immune system through two primary pathways: direct interaction with pattern recognition receptors and indirect action via microbial metabolism. In the indirect pathway, the gut microbiome utilizes these fibers as an energy source to produce a diverse range of metabolites. Notably, these fiber-derived processes exhibit a dual nature in food allergies, showing potential to either suppress or, in some cases, promote allergic inflammation. Understanding the unique physicochemical and physiological characteristics of individual types of fibers is important for the rational development of dietary-based prevention and treatment strategies in food allergies.},
}

Humans
*Dietary Fiber/metabolism
*Food Hypersensitivity/prevention & control/immunology/diet therapy
Animals
Gastrointestinal Microbiome/immunology
Receptors, Pattern Recognition/metabolism
beta-Glucans
Immunomodulation

@article {pmid42809217,
year = {2026},
author = {Timsit, JF and Roberts, JA and Kanj, S and Bassetti, M and Canton, R and Dark, P and Fowler, R and Huttner, A and Kollef, MH and Micek, ST and Sawyer, RG and Thy, M and Yahav, D and Daneman, N},
title = {Duration of antibiotic therapy in sepsis and severe infections in critically ill patients.},
journal = {American journal of respiratory and critical care medicine},
volume = {},
number = {},
pages = {},
doi = {10.1093/ajrccm/aamag458},
pmid = {42809217},
issn = {1535-4970},
abstract = {Antibiotic treatment duration in critically ill patients has undergone major reevaluation. Historically concerns for short therapy included a lower cure rate and emergence of resistance, whereas prolonged courses raised risks of microbiome disruption, superinfection, Clostridioides difficile colitis, and resistance. Defining optimal duration of therapy in sepsis and severe infections remains challenging due to heterogeneity in host immunity, pathogen virulence, infection site and source control. Mechanistic insights from microbiology and PK/PD highlight how bacterial inoculum, biofilms, mutant selection windows and altered drug distribution in critical illness influence bacterial clearance and resistance selection. Experimental models and PK-optimized dosing strategies underscore the potential to shorten therapy by accelerating pathogen eradication. Across a range of serious infections, randomized trials consistently show that short course therapy (<7 days) is noninferior to longer courses, including bacteremia, intra-abdominal infections and ventilator-associated pneumonia. Biomarker guided strategies-particularly procalcitonin-based algorithms-might further individualize duration of therapy and safely reduce exposure. Uncertainty remains for S. aureus bacteremia, infections caused by non-fermenting Gram-negative bacilli, difficult to treat multidrug-resistant organisms, invasive candidiasis and immunocompromised patients. Robust evidence supports markedly reduced duration of therapy for uncomplicated bloodstream infections after effective source control, intra-abdominal infections and ventilator-associated pneumonia. Infections involving retained prosthetic material or devices often require prolonged therapy or long-term suppressive regimens. Future research must include adequately powered trials across diverse populations, and evaluate rapid diagnostics, host-response profiling, and individualized response-guided strategies. Optimizing antibiotic duration in critically ill patients ultimately requires integrating mechanistic understanding, individual clinical evolution, and stewardship principles to balance potential efficacy and potential harm.},
}

@article {pmid42809314,
year = {2026},
author = {Dritsa, C and Hoffmann, S and Hulme, H and Lynch, C and Taylor, V and Burchmore, R and Cole, J and Goodwin, RJA and Wall, DM},
title = {Mapping gene expression across the microbiome-gut-brain axis of germ-free and specific pathogen-free mice.},
journal = {Microbiology (Reading, England)},
volume = {172},
number = {9},
pages = {},
pmid = {42809314},
issn = {1465-2080},
mesh = {Animals ; Mice ; *Brain/metabolism ; *Gastrointestinal Microbiome/genetics ; Germ-Free Life ; Specific Pathogen-Free Organisms ; Gene Expression Profiling ; Mice, Inbred C57BL ; Male ; },
abstract = {Perturbation of the gut microbiota has been implicated in neurological diseases via communication across the microbiome-gut-brain axis. As a result, the discovery of mechanisms underlying interaction across this axis is becoming increasingly important. The germ-free (GF) mouse model has enabled an improved understanding of the influence of the gut microbiota on brain development and function. By utilizing an advanced spatial profiling approach, we determined transcriptional changes in the brain, improving our understanding of how brain cells function and interact within their microenvironment in the absence of microbiome influence. Targeted regions of interest were selected based on brain regions implicated in neurological disease or reported structural differences between GF mouse brains and those of colonized mice. In the hippocampus, 276 differentially expressed genes (DEGs) were identified, 345 DEGs in the thalamus and 21 DEGs in the pons. Contrastingly, we identified only 2 DEGs in the midbrain and 4 in the medulla oblongata, with no DEGs in the cerebellum or corpus callosum. These data provide an overview of gut microbiota influence on gene expression in the brain, highlighting multiple genes of interest for further investigation in the context of microbiome influence on brain function and their potential relevance to neurological disease.},
}

Animals
Mice
*Brain/metabolism
*Gastrointestinal Microbiome/genetics
Germ-Free Life
Specific Pathogen-Free Organisms
Gene Expression Profiling
Mice, Inbred C57BL
Male