@article {pmid41806005,
year = {2026},
author = {Dong, X and Zhang, T and Tang, B and Zeng, Q and Hu, Z and Huang, P and Xiong, X and Wang, X and Dong, W and Cai, Y},
title = {Microbial and metabolic profiles in autism spectrum disorder with atopic dermatitis in children.},
journal = {AMB Express},
volume = {16},
number = {1},
pages = {},
pmid = {41806005},
issn = {2191-0855},
abstract = {Atopic dermatitis (AD), an inflammatory skin disease, exhibits increased incidence with autism spectrum disorders (ASD) in children. However, the mechanism underlying the ASD-AD comorbidity remains unclear. Here, we integrated the metagenomic and metabolomics analysis to characterize the compositions and functional profiles of gut microbiome in ASD children with AD. We found significant alteration in the composition of the intestinal microbial species between ASD-AD group and ASD group based on beta diversity analysis. LEfSe analysis showed tyzzerella_nexilis, eubacterium_sp_OM08_24 and clostridium_nexile_CAG348 were significantly increased in ASD children with AD. In addition, metabolite profiles showed that differentially expressed metabolites were mainly lipids and organic acids. Meanwhile, functional profiles showed that the pathway of cholesterol metabolism and biosynthesis of unsaturated fatty acids was abundant in ASD children with AD. Furthermore, the correlation analysis revealed that bacteroides_sp_CAG443, limosilactobacillus_mucosae had a positive correlation with traumatic acid and ricinoleic acid that were decreased in ASD-AD group, respectively. Eubacterium_ramulus and lachnospiraceae_bacterium were positively correlated with 11,14-eicosadienoic acid (EDA). Taken together, our results propose that altered gut microbiota regulates metabolites to affect the development of atopic dermatitis in ASD children.},
}

@article {pmid41968359,
year = {2026},
author = {Senousy, MA and Abo-Elmaaty, RM and Nabil Omar, N and Abdelgawad, HM},
title = {Dapagliflozin-intermittent fasting combination maximizes weight and metabolic regulation through AMPK/sirtuins/clock genes and gut microbiota signaling in high-fat diet-induced obesity: a novel anti-obesity approach.},
journal = {Cell & bioscience},
volume = {16},
number = {1},
pages = {},
pmid = {41968359},
issn = {2045-3701},
abstract = {UNLABELLED: Innovative and affordable treatment options are required to combat obesity and its detrimental impact on health economics. Dapagliflozin (Dapa), an antidiabetic medication, promotes weight loss; however, the extent of weight reduction may be limited. Intermittent fasting (IF) is a dietary approach regarded as a cost-effective and readily accessible regimen. This study investigated the beneficial effects of Dapa, IF, and their combination on weight loss and metabolic derangements in high-fat diet (HFD)-induced obesity in rats. Male Sprague-Dawley rats were allocated into 6 groups: groups 1 (normal control) and 2 (drug control) were administered a normal chow diet, while the obesity groups 3, 4, 5, and 6 were subjected to HFD for 8 weeks. Rats in groups 4, 5, and 6 underwent a further 8-week treatment with Dapa (5 mg/kg, p.o) daily, IF (16/8), or a combination of both, respectively. The HFD group exhibited elevated anthropometric measurements and adiposity index. Upon histopathological examination, the HFD group showed adipocyte hypertrophy, hypercellularity, and possible necrosis, along with hepatic fat accumulation and elevated serum liver enzymes. The HFD group showed a downregulation of p-AMPK/SIRT1 and an upregulation of SIRT7, GPR43, and clock genes BMAL1, CLOCK, and CRY1 expression in adipose tissue, along with a drop in the gut microbiome diversity, serum short-chain fatty acids (SCFAs), POMC, and PYY levels. Dapa and IF combination demonstrated favorable outcomes over monotherapy, as evidenced by normalized anthropometric measurements, improved histopathological and biochemical derangements, regulated p-AMPK/SIRT1, SIRT7, and clock genes expression, and restored gut microbiome and SCFA levels. Conclusively, this study suggests the concurrent administration of Dapa and IF as a new, beneficial, cost-effective anti-obesity strategy.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13578-026-01557-4.},
}

@article {pmid41981675,
year = {2026},
author = {Zhang, W and Zhao, W and Ye, L and Wang, H and Chen, Z and Liu, X and Li, Y and Zhang, Q and Zhang, H and Liu, Y and Chen, X and Chen, S and Zeng, J and Huang, R and Li, Y and He, Y},
title = {Profiling the tumor-resident microbiota in small cell lung cancer and its influence on clinical outcomes.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41981675},
issn = {1479-5876},
support = {2022YFF0705300//National Key Research and Development Program of China/ ; Fkcy2515//"Young Eagle Soaring" Youth Talent Funding Program of Shanghai Pulmonary Hospital/ ; },
abstract = {BACKGROUND: Increasing evidence has confirmed the existence of resident microbial communities within solid tumors and indicates that the tumor microbiota may represent a novel component of the tumor microenvironment, actively regulating cancer initiation, progression, metastasis, and therapeutic responsiveness. However, the role of tumor microbiota in small cell lung cancer (SCLC) has not been well explored.

METHODS: Tumor samples were collected from 71 patients with SCLC at Shanghai Pulmonary Hospital between 2019 and 2023. A comprehensive analysis of the tumor-resident microbiota in SCLC was conducted using 16 S rRNA sequencing. The bacterial communities were profiled, and their correlation with clinical outcomes was assessed.

RESULTS: A total of 28 phyla, 79 classes, 135 orders, 251 families, and 428 genera were identified, revealing a diverse tumor microbiota in SCLC. It was shown that tumor microbiota varied markedly among patients. SCLC patients with a smoking history exhibited distinct tumor microbiota, with significantly higher abundances of Brevundimonas and Gemmatimonadetes. When patients were stratified by progression-free survival (PFS) into long-PFS (L-PFS) and short-PFS (S-PFS) cohorts, their tumor microbiota segregated distinctly. LEfSe analysis showed that Lactobacillus, Clostridium, Rothia, and Staphylococcus were selectively enriched in the L-PFS group, whereas Stenotrophomonas, Cetobacterium, and Aerococcus dominated the S-PFS group. Kaplan–Meier analysis confirmed that carriage of Lactobacillus, Clostridium, or Staphylococcus was associated with prolonged survival relative to negative status, while positivity for Stenotrophomonas, Cetobacterium, or Aerococcus conferred a reduction in survival. Subsequent response-stratified analysis revealed that Clostridium- and Lactobacillus-positive SCLC was associated with a significantly higher response rate. Conversely, positivity for Methylobacterium, Pelomonas, Ralstonia, Bradyrhizobium, Variovorax, Microbacterium, Comamonas, or Sphingomonas markedly reduced response. The intersection of survival and response results identify Clostridium and Lactobacillus as promising prognostic tumor microbiota markers in SCLC. In vitro assays demonstrated that the Clostridium and Lactobacillus metabolites, butyrate and lactic acid, lacked direct cytotoxicity against SCLC cells. However, in the syngeneic mouse model, systemic supplementation of butyrate or lactic acid significantly potentiated the anti-tumor efficacy of standard chemotherapy. Notably, flow cytometric analysis revealed that this in vivo synergistic effect was closely associated with a profound increase in CD8 + T cell infiltration within the tumor microenvironment. Furthermore, integrating these two tumor microbiota with key clinical variables (sex, age, smoking, stage, radiotherapy), we constructed three models—therapeutic-response, 1-year PFS, and 1-year overall survival—that maintained robust performance in both training and validation cohorts.

CONCLUSIONS: In conclusion, the tumor-resident microbiota constitutes a critical component of the SCLC tumor microenvironment, exerting profound influence on the therapeutic response and patient prognosis. In detail, Clostridium and Lactobacillus—two pivotal tumor-resident taxa significantly linked to enhanced therapeutic responses and favorable prognosis—indicate their potential as predictive biomarkers for treatment outcomes and patient prognosis, and highlight them as candidate targets for microbiome-directed therapeutic strategies against SCLC, which warrants further functional validation.

GRAPHICAL ABSTRACT: [Image: see text]

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-08109-x.},
}

@article {pmid41993062,
year = {2026},
author = {Nuraini, P and Nelwan, SC and Pradopo, S and Pronorahardjo, AS and Andarini, PQ and Antonius, Y and Aljunaid, MA},
title = {Fractionated ethanolic red ginger extract as antibacterial agent against Aggregatibacter actinomycetemcommitans and Porphyromonas gingivalis: In silico and in vitro studies.},
journal = {Journal of oral biology and craniofacial research},
volume = {16},
number = {3},
pages = {101446},
pmid = {41993062},
issn = {2212-4268},
abstract = {BACKGROUND: Periodontitis is a chronic inflammatory disease associated with oral microbiome dysbiosis, where Aggregatibacter actinomycetemcomitans and Porphyromonas gingivalis contribute through adhesion, biofilm formation, and tissue-destructive virulence factors. Although chlorhexidine is widely used as an adjunctive antimicrobial agent, its long-term use is limited by adverse effects, highlighting the need for safer natural alternatives. Red ginger (Zingiber officinale var. rubrum) exhibits antibacterial potential; however, data on fractionated extracts and their interaction with specific virulence proteins remain limited.

OBJECTIVE: To evaluate the antibacterial activity of fractionated ethanolic red ginger extract against A. actinomycetemcomitans and P. gingivalis using integrated in silico and in vitro approaches.

METHODS: Twenty-two bioactive compounds identified from the fractionated extract were analyzed via molecular docking against cytolethal distending toxin (Cdt) of A. actinomycetemcomitans and fimbrial protein Mfa5 of P. gingivalis, with chlorhexidine as reference. In vitro assays determined minimum inhibitory concentration (MIC), minimum bactericidal concentration (MBC), bacterial adherence, biofilm formation, and viability.

RESULTS: Docking analysis showed that cyclooctacosane and gamma-sitosterol demonstrated binding affinities comparable to chlorhexidine toward both target proteins. The extract exhibited MIC/MBC values of 0.062/0.125 mg/mL for A. actinomycetemcomitans and 0.031/0.062 mg/mL for P. gingivalis. Significant reductions in bacterial adherence, biofilm formation, and viability were observed at concentrations of 0.031-0.125 mg/mL.

CONCLUSION: Fractionated ethanolic red ginger extract demonstrates promising antibacterial activity against key periodontal pathogens by targeting virulence mechanisms related to adhesion and biofilm formation, supporting its potential as a natural adjunct in periodontal therapy.},
}

@article {pmid41993122,
year = {2026},
author = {Saez-Torillo, SN and Danielsson, R and Nguyen, TQ and Lima, J and Cleveland, MA and Roehe, R and Martínez-Álvaro, M},
title = {Predicting beef diet nutritional composition and intake from rumen metagenomic profiles.},
journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)},
volume = {25},
number = {},
pages = {297-309},
pmid = {41993122},
issn = {2405-6383},
abstract = {Knowledge of diet composition and intake levels in beef cattle is valuable for post hoc feed traceability and for more accurate modelling of the diet impact on methane emissions and performance traits. However, a direct measure of this information can be costly and labour-intensive and is not always feasible. In this study, rumen metagenomic data combined with machine learning algorithms were used to predict diet type, nutritional composition, and intake levels. An external validation to assess the generalizability of the models was also performed. Rumen samples were collected from 142 animals belonging to two breeds, Luing (n = 70) and Charolais crossbred (n = 72), with 425.6 ± 43.5 d old and 461.9 ± 70.2 kg body weight. The animals participated in a 56-d feeding trial and were assigned to diets differing in forage-to-concentrate ratio, with 72 animals receiving a concentrate-based diet and 70 receiving a forage-based diet. Liquid ruminal contents were collected immediately postmortem and subsequently subjected to metagenomic sequencing. Based on these sequences, the relative abundance of microbial genes (MGs), microbial genera (MTs), and phyla were determined. The log-ratio between the abundances of Verrucomicrobia and Chlorobi discriminated diet type with an average classification accuracy of 0.86 ± 0.05, while using the log-ratio transformed abundances of 4769 MTs and MGs as predictors reached 0.90 ± 0.05. All this microbiome information was used in a random forest model to predict continuous values for nutritional diet components starch, crude protein, neutral and acid detergent fibre, and metabolizable and gross energy with external validation prediction accuracy values between 0.77 and 0.83. Microbiome features important for prediction of diet components such as fibre and starch included Mitsuokella, Selenomonas, and MGs involved in flagellar assembly and aminoacyl-tRNA biosynthesis. Microbiome data were more informative for predicting the feed composition than the amount of feed consumed, which reached a prediction accuracy of 0.27 ± 0.12 for dry matter intake (DMI). However, microbiome data can still be used as a screening tool to classify DMI into low, medium, or high with a classification accuracy of 0.74. Incorporating dietary information into linear phenotypic and genetic models to predict methane production (MP) and DMI reduced root mean square error (RMSE) by 26.9% and 9.6%, respectively, in the phenotypic model. In the genetic model, only MP showed a reduction in RMSE, with a 31% improvement. These findings highlight rumen microbiome data as a valuable tool for the post hoc prediction of feed composition in beef cattle.},
}

@article {pmid41993168,
year = {2026},
author = {Goto, Y and Dolton, G and Thomas, H and Morin, T and Tajima, Y and Imamura, K and Sakata, S and Oka, K and Hayashi, A and Takahashi, M and Ueno, T and Sakagami, T and Tomita, Y and Sewell, AK and Motozono, C},
title = {A probiotic bacterium modulates antitumour γδ T-cell responses in lung cancer.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1750569},
pmid = {41993168},
issn = {1664-3224},
mesh = {Humans ; *Lung Neoplasms/immunology/therapy ; *Probiotics/therapeutic use/administration & dosage ; *Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism ; Cell Line, Tumor ; Immune Checkpoint Inhibitors/therapeutic use ; Female ; Male ; *T-Lymphocytes/immunology ; *Carcinoma, Non-Small-Cell Lung/immunology ; Aged ; Middle Aged ; Gastrointestinal Microbiome/immunology ; Antigens, CD/metabolism ; Lymphocyte Activation ; },
abstract = {The link between the intestinal microflora and cancer outcomes has been recognized for over a decade. Several recent studies have demonstrated that the gut microbiome is associated with the efficiency of T-cell checkpoint blockade therapy for cancer, raising interest in strategies to harness this effect via consumption of live microorganisms (probiotics). The probiotic Clostridium butyricum strain MIYAIRI 588 (CBM588) improves response rates and overall survival in patients receiving immune checkpoint inhibitor (ICI) therapy for non-small cell lung cancer and metastatic renal cell carcinoma but the mechanism underlying this benefit remains unclear. Here, we show that CBM588 spores induce a population of Vγ9Vδ2 T-cells from the peripheral blood of healthy donors and lung cancer patients. A subset of these T-cells responded to, and directly lysed, cancer cell lines via a butyrophilin 3A-dependent mechanism. In patients taking CBM588 alongside checkpoint blockade, using samples from a cohort of 38 patients, peripheral blood Vδ2[+] T-cells expressed the activation marker CD69 more frequently than in those receiving checkpoint blockade alone and the frequency of Vδ2[+]CD69[+] cells increased following initiation of CBM588 treatment (p = 0.0041). Pleural effusions from patients receiving ICI with CBM588, although available from only three individuals, also showed a notable shift in the local γδ T-cell compartment from the expected Vδ1 dominance towards Vδ2 cells, suggesting altered recruitment or retention of Vδ2 cells at the tumour site. Across the patient cohort, higher post-treatment frequencies of CD69[+] Vδ2 T-cells were associated with improved survival and more favourable clinical outcomes. These findings provide a potential mechanism by which manipulation of the intestinal microflora might contribute to cancer prognosis through effects on immune effector cells with intrinsic anticancer properties.},
}

Humans
*Lung Neoplasms/immunology/therapy
*Probiotics/therapeutic use/administration & dosage
*Receptors, Antigen, T-Cell, gamma-delta/immunology/metabolism
Cell Line, Tumor
Immune Checkpoint Inhibitors/therapeutic use
Female
Male
*T-Lymphocytes/immunology
*Carcinoma, Non-Small-Cell Lung/immunology
Aged
Middle Aged
Gastrointestinal Microbiome/immunology
Antigens, CD/metabolism
Lymphocyte Activation

@article {pmid41993185,
year = {2026},
author = {Kaźmierczak-Siedlecka, K and Kucharski, R and Kosiński, A and Marano, L and Makarewicz, W and Kalinowski, L},
title = {Red-complex bacteria: immunological background leading to the development of head and neck cancers.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1804268},
pmid = {41993185},
issn = {1664-3224},
mesh = {Humans ; *Head and Neck Neoplasms/immunology/microbiology/etiology ; *Microbiota/immunology ; Animals ; Porphyromonas gingivalis/immunology ; Periodontitis/microbiology/immunology ; },
abstract = {Oral microbiome imbalance is involved in the development of head and neck cancers (HNCs). There is a group of oral pathogens, such as Porphyromonas gingivalis, Tannerella forsythia, and Treponema denticola, that creates red-complex. Currently, the oral pathogens' role in the pathogenesis of periodontitis is well-described; nevertheless, data regarding the link between HNCs and periopathogens are still limited, especially considering T. forsythia and T. denticola. These microbes utilise various virulence factors to promote the carcinogenesis process, affecting the immunological background. This paper presents modern insights into the role of red-complex bacteria in the development of HNCs, concentrating on the immunological aspects.},
}

Humans
*Head and Neck Neoplasms/immunology/microbiology/etiology
*Microbiota/immunology
Animals
Porphyromonas gingivalis/immunology
Periodontitis/microbiology/immunology

@article {pmid41993272,
year = {2026},
author = {Wei, Z and Hong, Q and Chen, G and Hartert, TV and Rosas-Salazar, C and Das, SR and Shilts, MH and Levin, AM and Tang, ZZ},
title = {Fast and reliable association discovery in large-scale microbiome studies and meta-analyses using PALM.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.09.717497},
pmid = {41993272},
issn = {2692-8205},
abstract = {Identifying microbial features associated with various covariates is a long-standing goal in microbiome research. Modern association studies incorporate an ever-increasing number of microbial features, covariates, and datasets from diverse cohorts. However, the complexity of microbiome data challenges analysis, often leading to poor replication of findings. We introduce PALM, a quasi-Poisson regression framework that enables fast and reliable association discovery in large-scale studies and meta-analyses. Extensive, realistic simulations demonstrate PALM's advantages in controlling false discovery rates, boosting power, improving computational efficiency, and preserving cross-study homogeneity of association effects. Three real-world applications at different scales illustrate PALM's utility, underscoring its potential to advance microbiome research.},
}

@article {pmid41993317,
year = {2026},
author = {Chaki, T and Maruyama, D and Doan, TN and Xiaoli, T and Prakash, A},
title = {Dietary tryptophan mitigates lung ischemia-reperfusion injury via microbiota-derived indole-3-propionate and aryl hydrocarbon receptor signaling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.714281},
pmid = {41993317},
issn = {2692-8205},
abstract = {BACKGROUND: Lung ischemia-reperfusion (IR) injury drives early morbidity after lung transplantation and cardiothoracic surgery, yet targeted preventive therapies are lacking. The gut-lung axis and microbiota-derived tryptophan metabolites, including indole-3-propionate (IPA), may regulate pulmonary immunity and inflammation. We investigated whether a tryptophan-rich (Trp-Rich) diet attenuates sterile lung IR injury by increasing microbiota-derived indole metabolites and reprogramming alveolar macrophage (AM) inflammatory responses.

METHODS: C57BL/6 mice received isocaloric tryptophan-standard (Trp-Std; 0.18%) or Trp-Rich (0.60%) diets for 14 days, then underwent unilateral left lung IR (60 min ischemia followed by 60 min reperfusion). Oxygen saturation, lung cytokines, and aryl hydrocarbon receptor (AhR) signaling readouts (Cyp1a1 / Cyp1b1) were evaluated. Gut microbiota was profiled by 16S rRNA sequencing, and targeted metabolomics quantified tryptophan metabolites in feces, portal vein (PV) plasma, and lung tissue. To further assess inflammatory priming in vivo , mice were additionally challenged with intratracheal lipopolysaccharide (LPS). Mechanistic studies compared IPA with related indole metabolites in MH-S cells and primary human AMs, including ex vivo nutritional IR, LPS stimulation, and AhR stimulation and blockade using synthetic agonists and antagonists.

RESULTS: Trp-Rich feeding improved post-IR oxygenation, reduced lung IL-1β, and increased pulmonary Cyp1a1 / Cyp1b1 gene expression. Trp-Rich diet remodeled the gut microbiota, including enrichment of Bifidobacterium and Lactobacillus , and increased IPA levels across feces, PV plasma, and lung tissue, with lower kynurenine/IPA ratios across matrices. In the LPS intratracheal challenge, Trp-Rich feeding reduced IL-6 levels in lung tissue and systemic plasma. Primary murine AMs isolated from Trp-Rich mice also showed reduced IL-1β and IL-6 release in an ex vivo nutritional IR model. Among tested indole metabolites, IPA showed the strongest dose-dependent suppression of LPS-induced cytokines and chemokines in MH-S cells and primary human AMs, remained active in the ex vivo nutritional IR model, and its anti-inflammatory effect was abrogated by AhR blockade and enhanced by co-treatment with other indole metabolites.

CONCLUSIONS: A Trp-Rich diet attenuated sterile lung IR injury, coinciding with gut microbiota remodeling, increased systemic and pulmonary IPA, reduced inflammatory priming, and reprogrammed AM responses. These data support diet- or microbiome-directed strategies targeting IPA-AhR signaling to mitigate perioperative lung IR injury.},
}

@article {pmid41993357,
year = {2026},
author = {Malarney, KP and Scott, SA and Chang, PV},
title = {A class of metallohydrolases expands bile salt hydrolase activity in the gut.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716488},
pmid = {41993357},
issn = {2692-8205},
abstract = {Bile acids are steroidal metabolites produced by host and microbial metabolism that shape gut microbiome ecology and influence host physiology [1,2] . Bile acid structural diversification requires gut microbial bile salt hydrolase (BSH) activities, which cleave the amide bond of liver-derived bile acid amidates (BAAs) [3] . Beyond this gatekeeping metabolic function, BSHs expand the bile acid pool via their amine N -acyltransferase activity to produce numerous microbially derived BAAs that signal via host receptors and are further metabolized [4,5] . To date, all BSH activity has been attributed to a family of N-terminal nucleophile (Ntn) cysteine hydrolases. However, numerous gut anaerobic bacteria possess BSH activity but do not encode bsh genes from the Ntn family. Here, we describe a previously unknown class of m etal-dependent BSHs (mBSHs) broadly distributed in the gut microbiome. These metalloenzymes have a distinct active site architecture from the canonical Ntn superfamily of cysteine hydolase BSHs (cBSHs) and are selective for taurine-conjugated BAAs. The discovery of this heretofore unappreciated class of BSHs overturns the paradigm that this important, conserved biochemical activity of the gut microbiota is provided exclusively by canonical cysteine hydrolases, greatly expands the known landscape of bile acid metabolism, and reveals a previously unrecognized link connecting host-microbiota bile acid co-metabolism with microbial taurine utilization pathways.},
}

@article {pmid41993390,
year = {2026},
author = {Hutchinson, NT and Ye, N and Jennings, M and Fang, C and Qi, N and Li, J},
title = {Engineered Lactate Catabolizing Probiotics Reveal Timescale Dependent Microbiome-Host Metabolic Coupling.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.07.716956},
pmid = {41993390},
issn = {2692-8205},
abstract = {The exchange of lactate, a metabolic substrate and regulator, between the gut lumen and systemic circulation for use in host and microbial processes is well documented, but tools capable of uncovering whether this process influences host metabolic status across acute and chronic contexts are lacking. In our prior work, we engineered probiotic Bacillus subtilis PY79 to produce lactate oxidase (LOX) intracellularly, allowing it to rapidly convert intestinal lactate to pyruvate. Following oral administration, LOX reduced systemic lactate concentrations at rest and under challenge conditions, providing a platform for investigating lactate's influence on host metabolism and microbiota. In the present work, we demonstrate that acute LOX administration effectively rewired microbiota function and host energy balance, as revealed by 16S sequencing and indirect calorimetry. In silico microbial community modeling via MICOM and metagenomic inference via PICRUSt2 suggested that acute shunting of lactate to pyruvate induced microbiota remodeling towards anabolic processes, reflected by increased flux of pyruvate, acetate, and formate, alongside moderate to large increases (Cohen's d = 0.60-1.00) in pathways for fructan degradation, B-vitamin biosynthesis, and lipid synthesis. These anabolic shifts temporally aligned with transient increases in host energy expenditure (β = 1.08, p<0.05) via glucose oxidation (β = 0.01, p<0.05), hinting at functional coupling between microbial biosynthesis and host energy balance via lactate exchange. Of note, acute LOX administration also improved thermoregulation and survival following LPS-induced sepsis, demonstrating functional relevance of these metabolic effects during acute inflammatory challenge. To assess chronic effects, we administered LOX for 6 weeks during diet-induced obesity. LOX treatment persistently reduced blood lactate. However, this chronic lactate reduction did not curtail the progression of diet-induced obesity or induce sustained modulation of host energy expenditure. This disconnect between acute and chronic findings suggests that gut-centric lactate conversion affects energy balance through microbiome and/or host-dependent mechanisms, but cannot override homeostatic forces in the long term to produce clinical benefit during chronic disease. Our results validate LOX probiotics as a tool for acute metabolic augmentation, and highlight a clear homeostatic limit to gut-centric therapies. This platform may enable targeted design of probiotic interventions matched to therapeutic timescale and inform synbiotic formulations that overcome homeostatic compensation.},
}

@article {pmid41993507,
year = {2026},
author = {Coleman, I and Ma, J and Qian, G and Jiang, Y and Brown Kav, A and Korem, T},
title = {End-to-end evaluation of pipelines for metagenome-assembled genomes reveals hidden performance gaps.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.06.712906},
pmid = {41993507},
issn = {2692-8205},
abstract = {The generation of Metagenome Assembled Genomes (MAGs) has become a standard and basic step in the analysis of metagenomic data. This multi-step process, which includes assembly, binning, refinement, and quality control, has many alternative approaches, algorithms, and parameters. Determining the ideal approach for a given ecosystem and study, or highlighting algorithmic gaps in need of additional research and development, requires rigorous benchmarking. We present MAG-E (MAG pipeline E valuator), a generalizable and expandable framework for end-to-end evaluation of entire MAG pipelines: from assembly, through binning, to quality control and filtering. MAG-E relies on simulations that are built to match an ecosystem of interest and provide a ground truth for accurate evaluation. To demonstrate the capabilities of MAG-E, we benchmark two assemblers, six binning algorithms, three binning modes, and three quality control and refinement methods in the context of the human gut microbiome. Our findings offer multiple insights into optimal MAG generation in this context. We find that metaSPAdes consistently outperforms MEGAHIT in terms of recall (completeness), and that COMEBin overall outperforms alternative binning algorithms, but has lower precision than SemiBin2. While multi-sample binning results in higher precision, as previously shown, single-sample binning has higher recall and leads to better overall performance with modern binners. Binning refinement, which combines bins from multiple different algorithms, leads to reduced performance. We further show that CheckM2 systematically overestimates completeness and underestimates contamination, and that this is partially ameliorated when using GUNC. Finally, we analyze performance at the contig level, and demonstrate that binning algorithms systematically underperform for prophages and fail to bin contigs that are shared between genomes. Overall, MAG-E offers deep insights into successes and gaps in this important analytic process.},
}

@article {pmid41993513,
year = {2026},
author = {Cui, Z and Meng, CJ and Irwin, SM and Augustijn, HE and Papageorgiou, PP and Nguyen, ATP and Yu, R and Aguilar Ramos, MA and Kulik, HJ and Balskus, EP},
title = {A previously unappreciated class of metal-dependent bile salt hydrolases from the human gut microbiome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716592},
pmid = {41993513},
issn = {2692-8205},
abstract = {Bile salt hydrolases (BSHs) are gut microbial enzymes that catalyze the deconjugation of glycine-or taurine-conjugated bile acids (BAs), a key step in shaping the BA pool in the human gastrointestinal tract and modulating host-gut microbiome interactions. [1-3] All known BSHs are members of the N-terminal nucleophile (Ntn) hydrolase superfamily and share a conserved architecture and mechanism involving a nucleophilic active site cysteine. [4,5] This knowledge has guided predictions and study of BSH activity in the gut microbiome [6,7] as well as the development of BSH inhibitors [8] . Here, we report the discovery and characterization of a previously unknown BSH from the human gut bacterium Bilophila wadsworthia that belongs to the metal-dependent amidohydrolase superfamily and exhibits robust and specific activity toward taurine-conjugated bile salts. We show this secreted enzyme, metalloBSH, utilizes a metallocofactor for BA deconjugation, a mechanism distinct from that of canonical Ntn-type BSHs. MetalloBSHs are conserved in B. wadsworthia and present in many other Desulfovibrionaceae found in vertebrate gut microbiomes. Analysis of multi-omic datasets indicates metalloBSHs are expressed in vivo and correlate with BA metabolism. Overall, our findings reshape our understanding of BSH activity in the gut microbiome and highlight the promise of activity guided discovery in revealing previously overlooked gut microbial enzymes.},
}

@article {pmid41993533,
year = {2026},
author = {Awan, A and Blakeley-Ruiz, JA and Kleiner, M and Hinzke, T},
title = {Area under the curve quantification outperforms spectral counting in metaproteomics, but matching between runs is detrimental.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716595},
pmid = {41993533},
issn = {2692-8205},
support = {R35 GM138362/GM/NIGMS NIH HHS/United States ; },
abstract = {UNLABELLED: Metaproteomics enables the functional characterization of microbiomes and host-microbe interactions by detecting and quantifying thousands of proteins. In data-dependent acquisition metaproteomics, protein quantification is commonly performed using either MS1-based area under the curve (AUC) or MS2-based peptide spectral counts (SpC). In AUC quantification, match between runs (MBR) is frequently employed to minimize data sparsity, yet its impact on metaproteomic data remains unclear. Understanding MBR's impact on metaproteomics data is especially important due to the high peak density in the MS1 mass spectra and the potential presence of not only proteins, but even entire organisms, in one sample and their absence in the other, which would complicate accurate feature mapping and transfer. While accurate quantification is essential for deriving meaningful biological inferences from metaproteomic analyses, systematic evaluations of AUC and SpC quantification in metaproteomics remain scarce. In this study, we used defined complex metaproteomic samples to perform a ground truth-based evaluation of AUC and SpC quantification and to determine the impact of MBR on AUC quantification. We found that MBR led to a substantial number of falsely identified proteins in complex samples. Protein identifications from an organism not present in the sample were wrongly transferred from other samples when MBR was used. We found that MBR-free AUC data had a wider dynamic range, higher quantitative accuracy, and more sensitive detection of abundance differences.

SIGNIFICANCE OF THE STUDY: Although metaproteomics is increasingly used to advance microbiome research, quantification strategies in metaproteomics are mostly selected based on convention rather than evidence, due to a lack of ground truth-based evaluation of quantification strategies in metaproteomics. Accurate protein quantification is key to deriving meaningful biological inferences from metaproteomic samples, yet it remains challenging due to their high complexity and uneven protein abundances. Here, we used defined metaproteomic samples to evaluate widely used quantification strategies in metaproteomics and to determine the effects of match between runs (MBR) on quantitative accuracy. Based on our findings, MBR adds falsely identified proteins to metaproteomic data. While MBR-free AUC offers a broader dynamic range and higher quantitative accuracy, SpC offers better proteome coverage. With this study, we provide an evidence-based framework for the informed selection of quantification strategies in metaproteomics, and highlight the strengths and limitations of these approaches with respect to proteome coverage, dynamic range, quantitative accuracy, and error propagation. Our findings also have important implications for the biological interpretation of data derived from these strategies and lay the groundwork for future studies validating quantitative approaches in data-independent acquisition workflows.},
}

@article {pmid41993548,
year = {2026},
author = {Fodor, KE and Ritter, AC and Schmieley, RA and Ricart Arbona, RJ and Miranda, IC and Lipman, NS},
title = {Microbiome-Dependent Protection Against Corynebacterium bovis -Associated Hyperkeratosis in Nude Mice (Mus musculus).},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.11.716586},
pmid = {41993548},
issn = {2692-8205},
abstract = {Corynebacterium bovis , the cause of Corynebacterium -associated hyperkeratosis (CAH), is an important pathogen in immunocompromised mice that is difficult to eliminate and can confound research outcomes. We recently observed that CAH severity varies among outbred athymic nude mouse stocks, but the relative contributions of host genetics and the microbiome remain unclear. We hypothesized that disease course and severity vary based on host genetic stock and/or microbiome composition. Three nude mouse stocks were rederived into the axenic state and either monoinfected with a pathogenic C. bovis isolate (10 [4] ; CFU) or given sterile media (n=6/group). Axenic mice were also reassociated with their source microbiome or microbiomes from three other stocks with known differences in CAH severity, then inoculated with C. bovis (n=6) or sterile media (n=2). In a separate experiment, one axenic stock was used to assess the role of C. amycolatum via monoinfection, monoinfection followed by C. bovis challenge, or addition to a nonprotective microbiome followed by C. bovis challenge. Mice were monitored daily for 21 days and scored for skin lesions (0-5). C. bovis monoinfected mice developed disease comparable in severity and timing to conventionally raised controls. Notably, reassociation with Vendor A2's microbiome prevented clinical lesions and reduced histopathologic changes across all stocks. While C. amycolatum as a monoinfection did not cause disease nor reduce disease severity following C. bovis challenge, it delayed the onset and lowered peak scores when added to a non-protective microbiome. These findings demonstrate that C. bovis can cause CAH as a monoinfection, that both host genetics and microbiome composition influence disease progression, and, together with prior work, support its role as the etiologic agent consistent with Koch's postulates. Identifying protective microbiome constituents may inform strategies to reduce disease burden in susceptible mice.},
}

@article {pmid41993554,
year = {2026},
author = {Rivas, JA and Scieszka, DP and Peralta-Herrera, E and Enriquez, CM and Merkley, SD and Nava, AL and Gullapalli, RR and Castillo, EF},
title = {Colonic metabolomic and transcriptomic alterations in a mouse model of metabolic syndrome.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.02.716131},
pmid = {41993554},
issn = {2692-8205},
abstract = {UNLABELLED: Metabolic syndrome (MetS), characterized by abdominal obesity, insulin resistance, dyslipidemia, and hypertension, affects a substantial proportion of the global population and increases the risk for cardiovascular disease, diabetes, and metabolic dysfunction-associated steatotic liver disease (MASLD). Despite its prevalence, there are currently no effective pharmacological therapies targeting MetS, highlighting the need to identify novel etiological mechanisms, particularly within the gastrointestinal (GI) tract. Using a mouse model of MetS and healthy lean controls, we assessed the colonic microenvironment through metabolomic, transcriptomic, and microbiome analyses. Colonic organoids were cultured to further explore epithelial alterations. Additionally, human MetS fecal metabolomics data were cross-compared with the mouse model to validate translational relevance. MetS mice exhibited upregulation of colonic anabolic pathways, including glycolysis, the pentose phosphate pathway, and the tryptophan/kynurenine pathway, without evidence of intestinal inflammation. Microbiome analysis revealed an increased abundance of the genus Lactobacillus in MS NASH mice. Colonic organoids from MetS mice showed altered goblet cell differentiation. Comparative analysis with human MetS fecal metabolomics demonstrated similar dysregulated pathways, underscoring the translational relevance of these findings. Our study reveals significant metabolic and microbial alterations in the colon of MS NASH mice, implicating a dysfunctional GI tract as a potential etiological factor in MetS. These findings highlight specific metabolic pathways and microbial signatures that could serve as future therapeutic targets for MetS.

NEW & NOTEWORTHY: This study identifies the colon as a metabolically active tissue affected in metabolic syndrome. Despite the absence of intestinal inflammation, MS NASH mice displayed altered colonic metabolism and microbiota composition, with conserved metabolite changes matching those seen in humans with metabolic syndrome. These findings highlight colonic metabolic dysfunction as a potential driver of gut dysbiosis and disease progression in metabolic syndrome and MASLD.},
}

@article {pmid41993555,
year = {2026},
author = {Herzog, HM and Fang, C and Lam, L and Jin, K and Zamarioli, A and Dinh, E and Gupta, CL and Sharma, A and Moody, T and Pierce, JL and Hohl, MS and Takimoto, SW and Lyalina, S and Wentworth, KL and Yu, K and Lu, VF and Mamikunian, I and Hunt, NK and Lynch, S and Pollard, KS and Hernandez, CJ and Perrien, DS and Hsiao, EC},
title = {Gut microbiome-dependent IL-1 signaling is a mediator of ACVR1 [R206H] -driven heterotopic ossification.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.05.716562},
pmid = {41993555},
issn = {2692-8205},
abstract = {UNLABELLED: Inflammatory diseases cause significant morbidity and mortality, but their pathobiology is often difficult to dissect due to complex genetic-environmental interactions. Genetic forms of heterotopic ossification, such as fibrodysplasia ossificans progressiva (FOP), reduce genetic variability, allowing careful dissection of non-genetic drivers of inflammation. While >95% of FOP patients harbor the ACVR1 [R206H] mutation, patients exhibit significant variability in disease progression, suggesting a role of environmental drivers. Here, we identify the gut microbiome as a regulator of inflammation-driven HO in FOP. Metagenomic profiling of cohabitating FOP/unaffected sibling pairs revealed a pathogenic gut microbiome profile in FOP patients (Bray-Curtis, p < 0.05). In Pdgfrα-Cre/Acvr1 [R206H] (FOP) mice, gut microbiome ablation by antibiotics reduced spontaneous HO formation (47.4% reduction, p < 0.05) and reduced plasma IL-1 pathway activity. IL-1β blockade in FOP mice suppressed trauma-induced HO formation. These findings identify a gut microbiome-IL-1-HO axis with modifiable targets for developing treatments for HO and related inflammatory conditions.

ONE SENTENCE SUMMARY: Antibiotic disruption of the gut microbiome reduces HO in FOP mice via an IL-1 mediated pathway.},
}

@article {pmid41993569,
year = {2026},
author = {Wang, S and Hullar, MA and Curtis, K and Kwee, S and Park, SY and Rettenmeier, C and Monroe, KR and Ernst, T and Shepard, J and Wilkens, LR and Le Marchand, L and Lampe, JW and Lim, U and Randolph, TW},
title = {Gut Microbiota Mediates the Association between Diet Quality and Ectopic Adiposity: The Multiethnic Cohort Adiposity Phenotype Study.},
journal = {bioRxiv : the preprint server for biology},
volume = {},
number = {},
pages = {},
doi = {10.64898/2026.04.10.717245},
pmid = {41993569},
issn = {2692-8205},
support = {P01 CA168530/CA/NCI NIH HHS/United States ; R01 MD018265/MD/NIMHD NIH HHS/United States ; U01 CA164973/CA/NCI NIH HHS/United States ; },
abstract = {BACKGROUND: Higher-quality diets have been associated with lower levels of ectopic fat deposited in the viscera and liver, which is hypothesized to be mediated in part by the gut microbiota.

OBJECTIVES: We tested this hypothesis in a multi-ethnic imaging study using global (microbiome-wide) testing as well as a high-dimensional multiple-mediators regression framework to identify bacterial genera in the human gut that mediate the association between diet quality and ectopic adiposity.

METHODS: We analyzed the cross-sectional data of 1,400 older adults (age 60-77) from five racial/ethnic groups in the Multiethnic Cohort Adiposity Phenotype Study (2013-2016). Overall diet quality was defined by adherence to the MIND diet. The relative abundance of 151 bacterial genera was quantified from 16S rRNA gene sequencing of the stool samples. Visceral fat, liver fat, and the presence of MASLD (metabolic dysfunction-associated steatotic liver disease) were determined based on magnetic resonance imaging (MRI). We used high-dimensional mediation analysis (HDMA) to estimate gut microbial mediation in the linear regression of visceral fat or liver fat, or in logistic regression of MASLD, on the MIND adherence score, adjusted for potential confounders.

RESULTS: Higher diet quality was associated with lower ectopic adiposity: 12% less visceral fat area, 23% less liver fat, and a 49% less likelihood of having MASLD, comparing the highest to the lowest quartile of the MIND score. Using a distance-based global test, we confirmed overall significant microbial mediation of the inverse diet-ectopic fat association. From HDMA, four bacterial genera were identified as mediating the protective association with visceral fat, with the largest mediation conferred by Lachnospiraceae UCG.001 (12.2%). Two genera (Lachnoclostridium , Weissella) were shown to mediate the MIND association with both liver fat and MASLD. In particular, Lachnoclostridium mediated 13.6% of the liver fat association and 10.8% of the MASLD association, and Lachnospiraceae UCG.001 additionally mediated 12.1% of the liver fat association.

CONCLUSIONS: Our results support the hypothesis that the gut microbiota contributes to conveying the effect of diet quality on preferred body fat distribution, e.g., involving bacteria that are known to produce short-chain fatty acids (Lachnospiraceae) or secondary bile acids (Lachnoclostridium).},
}

@article {pmid41993570,
year = {2026},
author = {He, F and Bai, S and Xie, J and Zhang, Y and Xu, K and Wang, J and Ren, Y and Ren, Z and Chen, J and Wang, Y and Xie, P},
title = {Akkermansia muciniphila improving depression-like behaviors by regulating glycerophospholipid metabolism in gut-brain axis.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1790866},
pmid = {41993570},
issn = {1663-9812},
abstract = {BACKGROUND: Akkermansia muciniphila (AKK) is a potential probiotic. Our previous studies have shown that it could alleviate depressive-like behaviors (DLBs) in mice by inhibiting neuroinflammation in brain. To further explore its antidepressant effect, this study focused on the effects of AKK on the metabolic activities in gut-brain axis.

METHODS: After chronic restraint stress (CRS) depression model was successfully built, AKK was used as intervention method for 3 weeks. The gut microbiome in feces and two intestinal permeability proteins in colon (Claudin-1, Occludin) were measured, and the metabolites in feces, colon, liver, and prefrontal cortex were also measured. In addition, two inflammation-related factors in hippocampus (Free fatty acid receptors 3 (FFAR3), phosphorylated NF-κB p65 (p-p65)) were measured.

RESULTS: AKK was successfully colonized in gut of chronic restraint stress (CRS) mice. The DLBs in CRS mice receiving AKK (CRS + AKK) were significantly improved, along with the improved gut microbiome. Both Claudin-1 and Occludin in colon were significantly increased in CRS + AKK mice compared to CRS mice receiving phosphate buffer saline (PBS) (CRS + p). Metabolomics analysis indicated that AKK could significantly improve the changed lipids and lipid-like molecules in gut-brain axis of CRS mice; and function analysis using differential metabolites showed that AKK could significantly improve the disordered glycerophospholipid metabolism in feces, colon, liver, and prefrontal cortex of CRS mice. Additionally, we found that FFAR3 and phosphorylated NF-κB p65 were increased and decreased, respectively, in hippocampus of CRS + AKK mice compared to CRS + p mice.

CONCLUSION: Our results suggested that AKK might improve the disturbances of gut microbiome, intestinal permeability, host's lipid metabolism and inflammation levels in hippocampus. Glycerophospholipid metabolism in gut-brain axis might be the important mediator in the process of AKK producing antidepressants effects.},
}

@article {pmid41993582,
year = {2026},
author = {Simões, JLB and Braga, GC and Assmann, CE and Bagatini, MD},
title = {Targeting the gut-immune-brain axis: pharmacological insights from depression in inflammatory bowel disease.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1793292},
pmid = {41993582},
issn = {1663-9812},
abstract = {Inflammatory Bowel Disease (IBD), comprising Crohn's Disease and Ulcerative Colitis, is a chronic inflammatory condition of the gastrointestinal tract with a remarkably high prevalence of psychiatric comorbidities, particularly Major Depressive Disorder (MDD). The traditional monoaminergic hypothesis of depression is insufficient to explain the complex etiology of MDD, paving the way for new paradigms, such as the inflammatory hypothesis of depression. This narrative review critically explores IBD as a human clinical model to investigate the connection between chronic inflammation and depression. It is argued that gut dysbiosis, a central feature of IBD, is a fundamental trigger that, through a compromised gut barrier, drives systemic inflammation and, subsequently, neuroinflammation. We detail the molecular and cellular mechanisms that link intestinal inflammation to central nervous system (CNS) dysfunction, including microglial activation, hypothalamic-pituitary-adrenal (HPA) axis dysregulation, and kynurenine pathway activation, which diverts tryptophan metabolism from serotonin synthesis to the production of neurotoxic metabolites. Robust epidemiological evidence demonstrating a bidirectional association between IBD and depression is discussed, suggesting a shared pathophysiology rather than a simple cause-and-effect relationship. Furthermore, we review the implications and emerging therapeutics, highlighting the antidepressant effects of immunobiologicals, such as anti-TNF therapies, and the potential of emerging interventions that target the microbiome, such as probiotics, psychobiotics, fecal microbiota transplantation, and anti-inflammatory diets. Furthermore, we address the limitations of the current literature, such as the lack of a quantitative definition for dysbiosis and the scarcity of clinical trials with integrated neuropsychiatric outcomes, and propose directions for future translational research. We conclude that IBD should be considered a systemic disease with significant psychiatric repercussions, advocating for an integrated therapeutic approach that combines immunomodulatory, neuromodulatory, and microbiological interventions to treat both gut and brain pathology effectively.},
}

@article {pmid41993584,
year = {2026},
author = {Liang, X and He, J and Wu, Q and Fu, L and Liu, Y},
title = {Gut microbiome in alcohol-associated liver disease: interactions and therapeutic strategies.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1770833},
pmid = {41993584},
issn = {1663-9812},
abstract = {Alcohol-associated liver disease (ALD), a significant cause of chronic liver disease worldwide, is strongly linked to gut microbiome dysregulation. Heavy alcohol use disrupts the gut bacterial equilibrium and damages the intestinal barrier, making it more permeable to microbial toxins (e.g., endotoxins) that trigger liver inflammation. Many studies have investigated ALD, but no single microbial marker has yet been identified as diagnostic. Results from microbiome studies on this condition have been inconsistent; consequently, scientists are developing new microbiome-based indices and multi-omics approaches to improve their ability to predict diseases. The review evaluates current findings on how disturbances in the gut microbiome and deterioration of the intestinal barrier contribute to the development of ALD. The assessment includes microbiome-based treatments such as probiotics, fecal microbiota transplantation (FMT), and bacteriophage therapy. Research indicates that probiotics and FMT treatments may enhance liver function and reduce inflammation in patients with ALD. The studies present conflicting results because researchers used different methods and worked with limited numbers of participants. Bacteriophage therapy exists as an experimental treatment method. The development of personalized microbiome treatments, along with biomarker standardization and solutions to technical and ethical challenges, will enable these strategies to enter medical practice. The review integrates existing knowledge of the gut-liver axis in ALD to demonstrate the clinical potential of microbiome-based treatments while highlighting the need for additional research to enhance treatment outcomes.},
}

@article {pmid41993800,
year = {2026},
author = {Pande, PM and Tremblay, J and St-Arnaud, M and Yergeau, E},
title = {The metatranscriptomic response of the wheat rhizosphere to drought varies with growth stages.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag065},
pmid = {41993800},
issn = {2730-6151},
abstract = {Microbes can help plant sustain abiotic stresses, such as drought. Plant-microbe interactions are, however, dynamic and the timing of the stress will affect both partners, directly and indirectly. Here, we hypothesize that the effect of drought stress on the wheat rhizosphere microbiome would change between key growth stages. We grew wheat in pots and reduced soil water content for two weeks at stem elongation, booting, or heading. We then sampled the rhizosphere soil and sequenced its metatranscriptome. The timing of the drought strongly affected the transcriptional response of the microbes, but few differentially abundant transcripts were shared across all stages. Some common patterns were, however, observed at higher taxonomical or functional levels. Drought also affected the normal succession across wheat growth stages. Many of the differentially abundant transcripts, taxa, and functions between growth stages of the control plants were not significant anymore for plants that experienced drought. Our results suggest that the timing of the drought event is paramount to the microbial rhizosphere communities and that it could explain the heightened sensitivity of younger plants to stresses.},
}

@article {pmid41993915,
year = {2026},
author = {Hoedt, EC and Burns, GL and Hedley, KE and Waller, S and Sanchez, TC and Chisolm, O and MacCallum, H and Richardson, S and Suthers, B and Pepper, E and Keely, S and Talley, NJ},
title = {Shared functional microbiome signatures in Parkinson's disease and constipation predominate irritable bowel syndrome despite taxonomic divergence.},
journal = {Brain, behavior, & immunity - health},
volume = {53},
number = {},
pages = {101218},
pmid = {41993915},
issn = {2666-3546},
abstract = {BACKGROUND: Gastrointestinal dysfunction, including constipation, is a common non-motor feature of Parkinson's disease (PD) and often precedes motor symptoms. The gut microbiome interacts with the host through neural, hormonal, and immune pathways, yet whether constipation represents a cause or consequence of PD remains unclear. Therefore, we aimed to interrogate the associations between microbiome and immune alterations in relation to constipation to provide novel insight into microbiome-gut-brain axis mechanisms in PD.

METHODS: We analysed peripheral blood mononuclear cells (PBMCs) for circulating gut-homing T cell populations and used shotgun metagenomics to profile the stool microbiome composition and functional capacity in PD patients (n = 18), healthy controls (n = 21), and individuals with constipation-predominant irritable bowel syndrome (IBS-C; n = 8). Associations between immune markers and microbial taxa were assessed, and functional pathway differences were evaluated.

RESULTS: Circulating gut-homing T cell frequencies did not differ significantly between PD and controls, but constipated PD patients showed a trend toward increased circulating gut-homing T cells. Microbiome beta-diversity analyses revealed distinct taxonomic shifts in PD and IBS-C, while functional capacity was largely conserved. Of the differential functional pathways tryptophan biosynthesis, polyamine production, and vitamin B metabolism, processes critical for neurotransmitter synthesis, epithelial integrity, and neuroimmune regulation were reduced in PD compared to IBS-C.

CONCLUSION: Our findings highlight unique microbial and immune signatures in PD, partially overlapping with IBS-C, and underscore the importance of microbial metabolic pathways in gut-brain axis disorders. Collectively our findings suggest a contribution to dopaminergic dysfunction, neuroinflammation, and impaired gut motility. Future longitudinal studies are needed to clarify causal relationships and inform targeted interventions for PD-related gastrointestinal dysfunction.},
}

@article {pmid41993944,
year = {2026},
author = {Shalmon, G and Shapira, G and Ibrahim, R and Israel-Elgali, I and Grad, M and Shlayem, R and Youngster, I and Scheinowitz, M and Shomron, N},
title = {Gut microbiota composition correlates with PBMC microRNA expression following maximal exercise testing in endurance athletes.},
journal = {Frontiers in microbiomes},
volume = {5},
number = {},
pages = {1734737},
pmid = {41993944},
issn = {2813-4338},
abstract = {INTRODUCTION: MicroRNAs (miRNAs) are key post-transcriptional regulators that also take part in immune responses and recovery processes following exercise. While both gut microbiota composition and peripheral blood mononuclear cell (PBMC)-derived miRNAs are known to be influenced by endurance training, potential correlations between these two systems in athletes remain largely unexplored.

OBJECTIVE: This study aimed to investigate correlations between gut microbiota composition and PBMC miRNA expression following a maximal exercise stress test in endurance athletes.

METHODS: Fifty-eight participants (22 runners, 18 cyclists, and 18 controls) underwent maximal exercise testing, with blood samples collected pre- and post-maximal exercise stress test for small RNA sequencing of PBMCs. Baseline fecal samples were analyzed via 16S rRNA gene sequencing to characterize gut microbiota. Expression data of PBMC miRNAs and microbial taxonomic profiles were integrated to assess potential correlations.

RESULTS: Thirteen significant correlations (|r| = 0.41-0.51, p < 0.005) were identified between gut bacterial taxa known to produce short-chain fatty acids (SCFAs)-including Veillonella, Blautia, Coprococcus, Butyrivibrio, Propionibacterium, and Parabacteroides-and the expression of PBMC miRNAs following a maximal exercise test. The significantly expressed PBMC microRNAs included hsa-miR-545-3p, hsa-miR-126-3p, hsa-miR-1292-3p, hsa-miR-6805-5p, hsa-miR-3668, hsa-miR-196b-5p, hsa-miR-602, hsa-miR-324-5p, and hsa-miR-365a-3p, some of which are known to modulate inflammatory pathways and immune cell signaling.

CONCLUSION: This is the first study demonstrating an association between resting gut microbiota composition and PBMC miRNA expression following maximal exercise stress test in endurance athletes. These findings raise the possibility of a complex association between gut microbial composition and PBMC miRNA expression in response to exercise. While causality cannot be inferred, the observed correlations suggest a candidate microbiota-miRNA that warrants further investigation in the context of exercise-induced immune regulation and recovery in athletes.},
}

@article {pmid41993958,
year = {2026},
author = {Meng, H and Zhao, S and Jin, H and Zhang, H and Li, Q and Zhang, L and Hu, J and Kong, F and Du, X and Li, Q and Ajwad Rahim, M and Xu, L and Xue, Y},
title = {Unveiling the Role of Rumen Microbiome in Modulating Intramuscular Fat Deposition of Pingliang Red Cattle.},
journal = {Food science & nutrition},
volume = {14},
number = {4},
pages = {e71681},
pmid = {41993958},
issn = {2048-7177},
abstract = {Pingliang Red cattle is renowned for its tender meat and symmetrical intramuscular fat (IMF) deposition. Rumen microbiota are crucial for energy metabolism and nutrient acquisition in cattle, significantly influencing IMF deposition. Therefore, this study aimed to explore how rumen microbiota impact IMF deposition in Pingliang Red cattle. 34 castrated Pingliang Red cattle were subjected to the same management for 2 months, followed by centralized and unified slaughtering. Based on the measured IMF content in the longissimus dorsi, 18 cattle were selected and divided into a high-intramuscular-fat group (HIMF, n = 9) and a low-intramuscular-fat group (LIMF, n = 9). Rumen fluid was subsequently collected for metagenomic sequencing. Results showed significant differences in taxonomic abundance at both the genus and species levels, the relative abundance of carbohydrate-active enzyme (CAZy) families, and functional profiles (p < 0.05). Specific rumen microbes, such as Limosilactobacillus panis (AUC = 0.765) and Fibrobacter succinogenes (AUC = 0.753), served as potential biomarkers for HIMF deposition in Pingliang Red cattle. With the exception of Bacillus, Fibrobacter succinogenes, Limosilactobacillus panis, Prevotella intermedia, and Streptomyces exhibited positive correlations with IMF content. Functional analysis based on KEGG orthology (KO) indicated that specific enzymes promote IMF deposition by regulating the metabolism of short-chain fatty acids (SCFAs), long-chain fatty acids (LCFAs), and lipopolysaccharides, as well as insulin signaling. These findings provide a theoretical reference for regulating rumen microbial communities to improve IMF deposition.},
}

@article {pmid41993996,
year = {2026},
author = {Au Yong, SJ and Lestari Lee, AS and Subramaniyan, V and Long, CM and Husain, S and Reginald, K and Ser, HL},
title = {Gut microbiome modulation in allergic rhinitis: from current evidence to emerging therapies.},
journal = {Frontiers in allergy},
volume = {7},
number = {},
pages = {1761840},
pmid = {41993996},
issn = {2673-6101},
abstract = {Allergic rhinitis (AR) is a common inflammatory disorder of the upper airway that is primarily managed with pharmacotherapy, biologics and allergen immunotherapy. However, a substantial proportion of patients experience incomplete or insufficient symptom control, treatment-related adverse effects, or poor adherence. Increasing evidence has linked AR with alterations in microbial composition across multiple mucosal sites, including the gut, highlighting potential roles for host-microbiome interactions in the regulation of allergic inflammation, although causal relationships remain incompletely defined. This narrative mini-review synthesizes current evidence on gut microbiome-based interventions for allergic rhinitis (AR), including probiotics, prebiotics, synbiotics, postbiotics, and emerging approaches such as fecal microbiota transplantation, engineered microbes, and bacteriophage-based therapies. It examines proposed immunological mechanisms involving type 2 inflammation, regulatory immune pathways, and gut-airway axis signalling, while distinguishing clinically evaluated strategies from experimental or preclinical and assessing their translational readiness. Collectively, available evidence suggests that microbiome-targeted therapies represent a promising conceptual avenue for understanding and potentially modulating AR. However, their clinical application remains constrained by heterogeneous study designs, reliance on extrapolated data from preclinical studies, limited standardized outcome measures, insufficient long-term safety data, and evolving regulatory frameworks. Addressing these challenges through well-designed clinical trials and improved mechanistic characterization will be essential to clarify the role of microbiome-based interventions as adjunctive strategies in AR management.},
}

@article {pmid41994099,
year = {2026},
author = {Hossain, MA and Agyei, D and Reynolds, AN and Kebede, B},
title = {Legume intake on gut microbiome and glycemia in type 2 diabetes management: narrative review.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1785186},
pmid = {41994099},
issn = {2296-861X},
abstract = {Legumes are rich in dietary fiber, plant proteins, micronutrients, and bioactive compounds, offering a sustainable and affordable addition to the diet. However, the extent to which legume-induced modulation of the gut microbiota contributes to glycemic regulation in type 2 diabetes (T2D), relative to microbiota-independent physiological mechanisms, remains insufficiently defined. This narrative review synthesizes current evidence on legume-based interventions and their effects on gut microbiota composition and function in relation to glycemic control. Relevant studies were identified through structured searches of MEDLINE and the Cochrane Central Register of Controlled Trials via Ovid, complemented by manual screening of reference lists. Seventeen studies (three human and 14 animal trials) were considered in this review. Human studies report that consuming legumes is associated with improved glucose tolerance and blood glucose levels, although effects on microbiota composition are variable and modest. Conversely, animal studies demonstrate improvements in insulin sensitivity, glucose tolerance, and microbial diversity with higher dose legume interventions. Legume consumption has been associated with enrichment of beneficial microbial taxa, such as Bifidobacterium, Akkermansia, Ruminococcus, and Bacteroides, as well as increased concentrations of microbial metabolites such as short-chain fatty acids (SCFAs). These microbial features are implicated in metabolic pathways relevant to insulin signaling and glycemic regulation; however, current human evidence does not establish that microbiota alterations causally mediate glycemic improvements. Well-designed, adequately powered clinical studies incorporating functional microbiome analyses and formal mediation approaches are required to clarify microbiota-dependent and microbiota-independent mechanisms.},
}

@article {pmid41994117,
year = {2026},
author = {Byrareddy, S and Kumar, N and Acharya, A and Das, R and Sardarni, U and Olasunkanmi, O and Murakonda, S and Sutar, D and Venkatesan, A and Ampasala, D and Cohen, S and Samuelson, M and Sajja, B and Dettmer, U and Ramalingam, N and Chand, H},
title = {Sex- and Age-Dependent Neuroimmune Dysregulation and Early Neurodegenerative Signatures Following SARS-CoV-2 Infection in Golden Syrian Hamsters.},
journal = {Research square},
volume = {},
number = {},
pages = {},
doi = {10.21203/rs.3.rs-9130692/v1},
pmid = {41994117},
issn = {2693-5015},
abstract = {Post-acute sequelae of SARS-CoV-2 infection, or Long-COVID, affects millions globally and is characterized by persistent symptoms affecting multiple organs, yet the underlying mechanisms remain poorly defined. Here, we used Golden Syrian Hamsters (GSH) infected with the SARS-CoV-2 to investigate how sex and age shape viral persistence, organ-specific pathology, immune responses, and neurological outcomes during acute infection and Long-COVID. We show that during Long-COVID, viral RNA persists only in the lungs of male hamsters. Lung pathology revealed sustained inflammation and tissue remodeling, with young females exhibiting greater fibrosis. Transcriptomic profiling across brain, lung, and heart identified pronounced sex- and age-dependent regulation of gene expression spanning immune, neuroinflammatory, and neurotransmitter signaling pathways. These transcriptomic alterations were accompanied by sex-specific behavioral changes and persistent microstructural remodeling in cognition-associated brain regions. Additionally, SARS-CoV-2 altered α-synuclein homeostasis and microglial activation alongside gut microbiome composition in a sex- and age-dependent manner. Together, our findings demonstrate that, in GSH Long-COVID is strongly modulated by sex and age, influencing viral RNA persistence, immune and neurobiological responses, and gut microbiota composition mirroring clinical outcomes reported in human cohorts. This study establishes SARS-CoV-2-infected GSH as a model for dissecting the mechanisms of Long-COVID and informing targeted prevention strategies.},
}

@article {pmid41774319,
year = {2026},
author = {Pereira, EJ and de Souza, V and da Silva Braulio, C and de Jesus Santos, AF},
title = {Epiphytic bacteria from Tacinga inamoena (K. Schum.) N.P. Taylor & Stuppy improve plant growth in cucumber seedlings.},
journal = {International microbiology : the official journal of the Spanish Society for Microbiology},
volume = {29},
number = {4},
pages = {415-422},
pmid = {41774319},
issn = {1618-1905},
abstract = {The phyllosphere of host plants harbors microorganisms that represent a novel source of agricultural bioinputs. This unique microbiome opens a promising frontier for developing innovative agricultural alternatives. In this study, we evaluated the potential of Brevibacillus sp. UPT4 and Pantoea sp. SPM1, two epiphytic bacterial strains of Tacinga inamoena isolated from the Caatinga biome. In vitro assays exhibited plant growth-promoting traits, such as auxin production, nitrogen fixation, and tolerance to abiotic stresses. Under greenhouse conditions, cucumber plants inoculated with the strains and their consortium exhibited significant increases (p < 0.05) in shoot and root parameters, ranging from 13.58% to 194.86% when compared to the control treatment. Redundancy analysis (RDA) indicated that most of the variability observed in the biometric parameters is associated with the plant growth-promoting reported in this study. These results highlight the potential of epiphytic bacteria from semi-arid land as a promising candidate for the development of new bioinputs, offering an innovative tool for sustainable agriculture.},
}

@article {pmid41803694,
year = {2026},
author = {Sun, F and Lu, J and Qiu, J and Jiao, Y and Zhuang, J and Meng, B and Kwok, LY and Zhong, Z},
title = {Temporal dynamics and functional maturation of the infant gut microbiota during the first year of life.},
journal = {BMC microbiology},
volume = {26},
number = {1},
pages = {},
pmid = {41803694},
issn = {1471-2180},
support = {BR250107//the Inner Mongolia Agricultural University Young Faculty Research Capacity Enhancement Program/ ; NJYT24055//the Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region/ ; },
abstract = {BACKGROUND: The infant gut microbiota undergoes structured, time-dependent succession during the first year of life, yet high-resolution longitudinal characterization remains limited. Here, full-length 16S rRNA gene sequencing was performed using PacBio long-read technology on 68 fecal samples from 12 exclusively breastfed infants in Hohhot, China, across six time points from birth to one year (7, 30, 60, 100, 200, and 360 days).

RESULTS: In this study, 68 fecal samples from 12 infants were analyzed. A total of 16 bacterial phyla, 192 genera and 251 species were annotated, with the dominant phyla being Firmicutes, Actinobacteriota and Proteobacteria; the dominant genera including Bifidobacterium, Streptococcus and Escherichia-Shigella; and the dominant species comprising Streptococcus_salivarius, Bifidobacterium_longum and Bifidobacterium_pseudocatenulatum. Alpha diversity generally increased by days 360, while community composition shifted from early Bifidobacterium dominance toward greater taxonomic and functional complexity. Permutational multivariate analysis of variance (PERMANOVA) revealed that host and environmental factors collectively explained 33.92% of community variation (P = 0.001). Six temporal colonization patterns were observed through MaAsLin2 analyses., including mid-term explosive and sustained increasing trajectories. Functional profiling using Tax4Fun2 revealed time-specific enrichment of metabolic pathways, including fatty acid biosynthesis, xenobiotic degradation, and autophagy regulation at day 360. The findings of this longitudinal study be interpreted considering its modest sample size (n = 68). Future studies with larger cohorts are needed to validate and generalize these observations.

CONCLUSIONS: These findings demonstrate that infant gut microbiota assembly follows a non-random, host-guided trajectory, with dietary transitions and microbial interactions driving structural and functional maturation, providing a high-resolution framework for understanding early-life microbiome development and its implications for infant health. However, due to the limited sample size, the relevant research results have certain limitations. In the future, it is necessary to expand the sample scale and conduct more convincing studies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12866-026-04930-y.},
}

@article {pmid41803805,
year = {2026},
author = {Park, SY and Jung, MY and Nguyen, CD},
title = {Effect of biodegradable microneedle acupuncture for symptom relief moderate or milder atopic dermatitis: a study protocol for a multicenter, randomized, sham-controlled trial.},
journal = {BMC complementary medicine and therapies},
volume = {26},
number = {1},
pages = {},
pmid = {41803805},
issn = {2662-7671},
abstract = {BACKGROUND: Atopic dermatitis (AD) has no definitive cure; therefore, alternative treatments should be developed. We have demonstrated in preliminary clinical trials that Biodegradable Microneedle Acupuncture (BMA) treatment improves symptoms and is safe for mild to moderate AD.

AIMS: The study focused on evaluating the effectiveness and safety of a new medical device called BMA for AD, while also assessing its cost-effectiveness. It also explored the gut microbiome of patients with AD before and after BMA treatment.

METHODS: This multicenter, participant-assessor-blinded, sham-controlled trial will be conducted from January 10, 2025, to January 10, 2026. In total, 184 participants with AD (n = 92 per group) will be recruited. Participants will be assigned randomly to two equal-sized groups: the BMA and sham groups. Treatment will be administered three times per weekduring the 4-week intervention phase. The primary outcome measure will be the objective SCORing Atopic Dermatitis index. Secondary outcome measures will include the Eczema Area and Severity Index, Dermatology Life Quality Index, Patient-Oriented Eczema Measure, and pruritus Visual Analog Scale scores. Other outcome measures will include gut microbiome, economic and safety evaluations.

DISCUSSION: This study protocol will provide an important and thorough assessment of the effectiveness of BMA treatment in improving the symptoms of moderate or milder AD. In addition, we will evaluate the safety and costeffectiveness of BMA. We will also determine the link between AD and the microbiome. This clinical trial has been registered with the Korean Clinical Trial Registry (registration number: KCT0009870; date of registration: 25 October 2024).},
}

@article {pmid41803883,
year = {2026},
author = {Wei, Z and Xu, T and Gu, X and He, Q and Feng, Q and Li, M},
title = {Single-cell RNA-seq and in vitro study reveal Fusobacterium nucleatum impairs β-cell identity in type 2 diabetes via the NF-κB-CDKN1C axis.},
journal = {Journal of translational medicine},
volume = {24},
number = {1},
pages = {},
pmid = {41803883},
issn = {1479-5876},
abstract = {BACKGROUND: The pathogenesis of type 2 diabetes is characterized by insulin resistance and a progressive decline in β-cell function. A key driver of this dysfunction is the loss of β-cell identity, which reduces functional β-cell mass and leads to inadequate insulin secretion. Periodontal pathogens have been implicated in promoting insulin resistance; however, their role in the transformation of β-cell identity remains poorly understood. This study aims to investigate the impact of periodontal pathogen Fusobacterium nucleatum (F. nucleatum) on β-cell identity maintenance and the underlying molecular mechanisms.

METHOD: Single-cell RNA sequencing (scRNA-seq) data from human pancreatic islets of nondiabetic (ND), prediabetic (Pre-T2D), and type 2 diabetes (T2D) donors were analyzed to assess changes in β-cell proportion, differentiation trajectory, and associated molecular pathways. The Single-cell Analysis of Host-Microbiome Interactions (SAHMI) method was used to detect F. nucleatum sequences in pancreatic islets. Pearson correlation analysis identified key genes associated with the action of F. nucleatum, followed by in vitro validation using a co-culture model of F. nucleatum and MIN6 cells to elucidate the underlying mechanisms.

RESULTS: scRNA-seq analysis revealed a reduced proportion of β-cells and decreased expression of key β-cell identity-maintenance genes in the T2D group. The expression levels of transdifferentiation markers and β-cell disallowed genes were elevated, alongside a trend toward α-cell transdifferentiation. The NF-κB signaling pathway was significantly activated in the T2D group, accompanied by a significant increase in the SPP1 inflammatory signal, while the WNT pathway was markedly diminished. Integrated Pearson correlation and in vitro analyses identified the cell cycle regulator CDKN1C as a central mediator through which F. nucleatum promotes β-cell identity loss. Mechanistically, F. nucleatum activated the NF-κB pathway, leading to downregulation of CDKN1C expression and thereby promoting loss of β-cell identity, which played an important role in the progression of diabetes associated with periodontitis.

CONCLUSION: This study demonstrates that β-cells in T2D primarily undergo transdifferentiation towards α-cells, and the periodontal pathogen F. nucleatum promotes β-cell identity loss via NF-κB-mediated downregulation of CDKN1C.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12967-026-07981-x.},
}

@article {pmid41917955,
year = {2026},
author = {Nazir, SM and Saied, SMM and Eskander, ME and Mansour, MM and Abdelrahman, H and Elbackly, RM and Elnawam, HM},
title = {Is apical periodontitis a matter of microbial diversity or time? A scoping review.},
journal = {Head & face medicine},
volume = {22},
number = {1},
pages = {},
pmid = {41917955},
issn = {1746-160X},
abstract = {BACKGROUND: The pathophysiology of apical periodontitis is complicated involving host immunological response, virulence factors, and a diverse microbiome. Understanding how microbial diversity influences lesion size is crucial for improving therapeutic strategies.

OBJECTIVE: This scoping review aimed to have an insight through literature to determine whether primary or secondary apical periodontitis lesions of different sizes are correlated with the quantity and diversity of microorganisms or the duration of the disease.

METHODS: The Joanna Briggs Institute (JBI) methodology for conducting scoping reviews was followed. A comprehensive electronic search was conducted through PubMed, Scopus, Web of Science, and Google Scholar to identify relevant studies published up to February 2025. In addition, handsearching was performed to identify additional studies that were not retrieved in the electronic search. Eligibility criteria of the screened papers included clinical studies performed in healthy patients with symptomatic or asymptomatic apical periodontitis where microbial analysis was performed. The EndNote Web reference manager (EndNote X9; Thomson Reuters) was used to ingest articles from various sources, categorize the references, and automatically eliminate duplicates.

RESULTS: Out of 4010 papers, 132 studies met the inclusion requirements and were added to the current review. Approximately half of the papers examined bacterial diversity in endodontic infections, while just a small percentage discussed lesion size and were identified as randomized clinical trials. Brazil, USA, Germany and China were found to have the highest frequency of published articles. Fusobacteria, Streptococcus, Enterococcus faecalis and Porphyromonas species were the most detected microorganisms responsible for apical pathosis regardless of lesion size, while other microbiomes were associated with large lesions only, such as Olsenella, Lactococcus lactus and HHV-6 with 3% each and HPV with 6.1%. Other microbiomes such as Candida albicans, Filifactor alocis, HSV1, Pyramidobacter piscolens and Phocaeicola abscessus were seen only associated with small sized lesions with 4.3% each.

CONCLUSIONS: Microbial diversity and microbial load seem to be a strong determinant of apical lesion size while lesion duration could not be adequately assessed due to cross-sectional study designs. Lesion size is an important variant to be recorded to give insight into microbial diversity and provide the basis for personalized targeted antimicrobial therapies in the future. This scoping review was registered in the open science framework; DOI: 10.17605/OSF.IO/DC95Z.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13005-026-00610-4.},
}

@article {pmid41981054,
year = {2026},
author = {Mansour, NY and Ismail, MF and Sayed, NH and El-Ansary, AR and Mohanad, M},
title = {Serum metabolomics identifies gut-derived uremic toxins and bile acid dysregulation associated with chronic kidney disease severity.},
journal = {Scientific reports},
volume = {16},
number = {1},
pages = {},
pmid = {41981054},
issn = {2045-2322},
abstract = {UNLABELLED: Chronic kidney disease (CKD) affects more than 700 million people worldwide, however conventional biomarkers like creatinine cannot identify early-stage disease or accurately predict progression. In this study, untargeted and targeted metabolomic approaches were combined to identify novel biomarkers relevant for CKD staging and early detection in an underrepresented Egyptian population. Untargeted ultra-high-performance liquid chromatography–mass spectrometry analyses in both ionization modes were performed on serum samples of 50 CKD patients [25 early-stage CKD (eCKD), 25 end-stage kidney disease (ESKD)] and 20 controls. Differential metabolites were determined by univariate and multivariate analyses, coupled with pathway analysis and correlations with estimated glomerular filtration rate (eGFR). Five discriminating metabolites (p-hydroxyphenyllactic acid, indoxyl sulfate, xanthurenic acid, trimethylamine-N-oxide, and glycochenodeoxycholate) were subjected to targeted LC-MS/MS validation in an independent cohort (35 eCKD, 35 ESKD, 15 controls). Gut-derived uremic toxins, bile acid and tryptophan–kynurenine metabolic dysregulation were associated with CKD severity. p-hydroxyphenyllactic acid, xanthurenic acid, glutamyl-valine and indoxyl sulfate showed strong inverse correlations with eGFR (r = -0.75 to -0.85). A five-metabolite panel (indoxyl sulfate, p-hydroxyphenyllactic acid, trimethylamine-N-oxide, glycochenodeoxycholate, xanthurenic acid), demonstrated superior discriminatory performance compared with creatinine alone for distinguishing ESKD, especially indoxyl sulfate and p-hydroxyphenyllactic acid (AUC 0.847 and 0.828, respectively vs. 0.688). This first comprehensive metabolomics study in Egyptian CKD patients identifies alterations in gut microbiome–derived metabolites and bile acid metabolism associated with CKD severity. The multi-metabolite panel demonstrates potential for non-invasive discrimination between CKD stages and supports future longitudinal metabolomic studies aimed at improving CKD risk stratification and patient management.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1038/s41598-026-44271-4.},
}

@article {pmid41982989,
year = {2026},
author = {Yoon, KN and Lee, HG and Yeom, SJ and Kim, SS and Park, JH and Song, BS and Yi, SW and Hur, TY and Eun, JB and Park, SH and Lee, JH and Kim, HB and Lee, JH and Kim, JK},
title = {Modulation of microbial community and metabolism through Lactiplantibacillus argentoratensis AGMB00912 supplementation in weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {562-585},
pmid = {41982989},
issn = {2055-0391},
abstract = {Dietary supplementation effects with Lactiplantibacillus argentoratensis strain AGMB00912 (LA) on gut microbiota and metabolic functions of weaned piglets were investigated. Eight 25-day-old weaned piglets were evenly divided into a control group and an LA-supplemented group, with the LA group receiving 1.0 × 10[8] CFU/mL of LA daily for 10 days. Fecal samples taken on the 10[th] day were analyzed using 16S rRNA gene sequencing to assess microbial composition and metabolic function prediction. Supplementation with LA promoted a stable microbial environment by increasing the relative abundance of short-chain fatty acid-producing bacteria, including Faecalitalea, Catenibacterium, and Butyrivibrio, while reducing harmful genera like Treponema and Campylobacter. Administration of LA significantly influenced the metabolic activity of the microbial community, particularly by upregulating carbohydrate metabolism pathways, which enhanced the capacity for short-chain fatty acid production. This shift in microbial metabolism also extended to pathways involved in the biosynthesis of amino acids, lipids, cofactors, and vitamins, indicating an improved capacity for microbial-driven nutrient assimilation and utilization. Furthermore, LA supplementation promoted the biosynthesis of antimicrobial non-ribosomal peptides within the microbiome, crucial for inhibiting the growth of pathogenic microorganisms and maintaining microbial balance. The modulation of microbial metabolism is also predicted to reduce glycan degradation and increase peptidoglycan biosynthesis, contributing to enhanced gut barrier function and a more regulated immune response. These metabolic changes within the microbial community are predicted to stabilize the gut microbiota, providing enhanced disease resistance and supporting the overall health and growth of weaned piglets.},
}

@article {pmid41983000,
year = {2026},
author = {Lee, JY and Lim, C and Seo, YJ and Kyoung, H and Lee, S and Kim, Y and Shin, M and Song, M and Ryu, Y and Kim, JM},
title = {Multi-omics integrated approach reveals host-microbiome interactions in the adaptive mechanisms of weaning piglets.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {603-628},
pmid = {41983000},
issn = {2055-0391},
abstract = {The weaning transition is a critical phase in piglet development, marked by physiological challenges that influence growth and health. Therefore, this study aims to investigate host-microbiome interactions during the weaning transition using a multi-omics integrated approach. Fecal samples were collected from piglets on the weaning day (W0), 7 days post-weaning (W7), and 14 days post-weaning (W14). Ileal microbiota, microbial-derived metabolites, and tissue samples (ileum, thymus, and mesenteric lymph nodes) were collected at W0 and W14. Fecal microbiota analysis revealed a more stable community at W14 than at W7, with increased presence of fiber-degrading bacteria, including Prevotella, Treponema, Muribaculaceae, and Lachnospiraceae. The ileal microbiota exhibited an adaptive pattern with increases in Lactobacillus, Clostridium_sensu stricto_1, and Enterobacteriaceae, optimized for solid feed digestion and gut stabilization. Morphological analysis of the ileum showed changes in villus architecture between W0 and W14, including increased crypt depth and villus area and decreased villus width, while villus height and goblet cell counts were numerically higher at W14. Transcriptomic profiling revealed the ileum as the primary site of molecular adaptation, with 506 differentially expressed genes (DEGs) involved in immune response pathways, including viral protein interactions with cytokine and cytokine receptor pathways and T cell receptor signaling. The thymus (158 DEGs) and mesenteric lymph nodes (30 DEGs) exhibited modulation of structural pathways linked to systemic immune development, indicating tissue-specific molecular adaptation. Integrated analysis of the host transcriptome and microbial-derived metabolites revealed upregulated glycerophospholipid and glutathione metabolic pathways in piglets 14 days post-weaning, consistent with modulation of membrane structure, barrier function, and antioxidant defense during gut adaptation. Overall, the multi-omics findings provide a comprehensive description of molecular changes associated with weaning adaptation and identify candidate targets for piglet health management during the weaning transition.},
}

@article {pmid41983002,
year = {2026},
author = {Jeong, JY and Kim, J and Kim, M and Kim, YB and Park, C and Song, J and Kim, DW and Kim, M and Park, NG},
title = {Effect of probiotics on growth performance, cytokine levels, and gut microbiome composition of broiler chickens for 7 and 35 days.},
journal = {Journal of animal science and technology},
volume = {68},
number = {2},
pages = {586-602},
pmid = {41983002},
issn = {2055-0391},
abstract = {Through microbial fermentation, probiotics are essential for improving growth performance and gut health in broiler chickens. This study aimed to assess the effects of three additives on growth performance, cytokine levels, and cecal microbiota in broiler chickens. One-day-old Arbor Acres chicks (total 300) were randomized into four groups: (1) control: basal diet, (2) Bacillus subtilis (BS) + basal diet, (3) essential oil + basal diet, and (4) Bacillus velezensis + basal diet. All chickens were fed and watered ad libitum throughout the experiment. Feed intake and body weight were measured weekly. On days 7 and 35, cecal contents of one bird per replicate, based on average body weight, were collected and analyzed for microbiota using 16S rRNA gene amplicon sequencing. The BS group exhibited enhanced growth performance, including increased final body weight, average daily gain, and reduced feed conversion ratio compared to that of the other groups. On day 7, the BS group exhibited a higher abundance of Eisenbergiella (8.24%), and on day 35, there was an increased abundance of Firmicutes (99.63%) and Lachnoclostridium (1.4%). These results indicate that B. subtilis may be a promising probiotic for enhancing broiler health by modulating gut microbiota.},
}

@article {pmid41983140,
year = {2026},
author = {Liu, P and Cui, L and Peng, G and Han, X},
title = {Molecular insights into the role of vitamin D in atopic dermatitis: pathogenesis, diagnosis, and emerging therapies.},
journal = {Frontiers in immunology},
volume = {17},
number = {},
pages = {1739412},
pmid = {41983140},
issn = {1664-3224},
mesh = {Humans ; *Vitamin D/metabolism/therapeutic use/analogs & derivatives ; *Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology ; *Vitamin D Deficiency/immunology/epidemiology ; Skin/immunology/metabolism/pathology ; Animals ; Receptors, Calcitriol/metabolism ; Biomarkers ; Microbiota/immunology ; },
abstract = {Atopic dermatitis (AD) is a chronic inflammatory skin disease characterized by skin barrier dysfunction, immune dysregulation, and microbial imbalance. Increasing evidence suggests that vitamin D, a secosteroid hormone with pleiotropic effects, plays a key role in modulating the pathogenesis of AD. This review provides a comprehensive overview of the molecular mechanisms through which vitamin D influences skin integrity and immune function, focusing on vitamin D receptor-mediated pathways, genetic and epigenetic modifiers, and the interplay with immune cells and microbiota. We also examine the epidemiological correlations between vitamin D deficiency and AD prevalence, diagnostic considerations including biomarkers and serum 25-hydroxyvitamin D evaluation, and therapeutic strategies involving systemic and topical vitamin D interventions. The review further discusses ongoing controversies regarding optimal dosing and evaluates the limitations of current clinical evidence. Finally, emerging research directions, such as vitamin D-microbiota-skin axis and personalized vitamin D therapy, are proposed as promising avenues for advancing AD management.},
}

Humans
*Vitamin D/metabolism/therapeutic use/analogs & derivatives
*Dermatitis, Atopic/diagnosis/etiology/therapy/epidemiology/metabolism/immunology
*Vitamin D Deficiency/immunology/epidemiology
Skin/immunology/metabolism/pathology
Animals
Receptors, Calcitriol/metabolism
Biomarkers
Microbiota/immunology

@article {pmid41983252,
year = {2026},
author = {O'Sullivan, TA and Nicholl, A},
title = {Exploring the dairy milk matrix beyond isolated nutrients-a narrative review.},
journal = {Critical reviews in food science and nutrition},
volume = {},
number = {},
pages = {1-21},
doi = {10.1080/10408398.2026.2648097},
pmid = {41983252},
issn = {1549-7852},
abstract = {The concept of the food matrix considers individual components along with how they are structured, interact, and are modified during processing. There is increasing interest around the health effects of individual nutrients versus whole foods, creating a need to better understand how the matrix may influence health outcomes. This narrative review explores the dairy milk matrix and compares health effects with those of isolated components, with additional comparisons to plant-based milk alternatives. Comparative evidence suggests that while calcium from food and supplements generally has similar effects (depending on the form of the supplemental calcium), consumption of food-based sources such as milk may have fewer adverse effects associated with high-dose supplemental intake. Fermented milk products appear to offer additional health benefits compared with unfermented milk, likely due to bioactive compounds produced during fermentation. Structural and functional manipulation of milk proteins, such as whey and lactoferrin, can also modify matrix functionality; for example, appropriate processing conditions can preserve lactoferrin's iron-binding capacity, supporting iron transport and bioavailability. Compared with plant-based milks, which often require fortification and extensive processing, the dairy milk matrix is particularly effective at promoting nutrient absorption. Our findings highlight the importance of adopting a whole food perspective when considering milk in dietary recommendations and research.},
}

@article {pmid41983715,
year = {2026},
author = {Zhu, K and Zhao, J and Li, T and Zhang, S and Liu, C and Xu, Z and Lv, C and Zhang, G and Kang, Y and Huang, J},
title = {ROS-Responsive Hydrogel Delivering Bio-Nanoselenium for Targeted Therapy of UVB-Induced Skin Photodamage.},
journal = {ACS applied materials & interfaces},
volume = {},
number = {},
pages = {},
doi = {10.1021/acsami.6c00317},
pmid = {41983715},
issn = {1944-8252},
abstract = {Ultraviolet B (UVB) radiation is a major environmental factor that induces skin photodamage through oxidative stress and inflammation. To address this, we developed a reactive oxygen species (ROS)-responsive hydrogel, SeNPs@HPTA, for the intelligent delivery of biogenic selenium nanoparticles (BioSeNPs) synthesized by Bifidobacterium animalis. The hydrogel was fabricated by cross-linking phenylboronic acid-grafted hyaluronic acid (HA-PBA) with tannic acid (TA), forming dynamic boronic ester bonds that cleave under high ROS conditions to enable on-demand BioSeNPs release. Transcriptomic analysis revealed that B. lactis H15 efficiently reduces selenite (Se(IV)) to elemental SeNPs by upregulating ion transport and NADPH-regenerating pathways. In vitro, SeNPs@HPTA enhanced HaCaT cell viability, scavenged ROS, and promoted cell migration post-UVB irradiation. In vivo, topical application alleviated skin lesions, improved hydration, reduced epidermal hyperplasia, and suppressed collagen degradation. Mechanistically, the hydrogel conferred therapeutic effects by enhancing antioxidant defenses, inhibiting inflammation and attenuating ferroptosis via GPx4/Nrf2 activation. Critically, genetic knockdown of GPx4 abolished its therapeutic effects, establishing a strict dependence on this key selenoenzyme. The formulation exhibited an excellent biosafety profile. This study presents a microbiome-inspired, stimulus-responsive strategy for precise skin photodamage treatment. We anticipate this microbiome-inspired, intelligent delivery system will offer a powerful and precise strategy for treating oxidative stress-related dermatoses.},
}

@article {pmid41983734,
year = {2026},
author = {Andrade, C},
title = {Proton Pump Inhibitors and the Risk of Dementia.},
journal = {The Journal of clinical psychiatry},
volume = {87},
number = {2},
pages = {},
doi = {10.4088/JCP.26f16420},
pmid = {41983734},
issn = {1555-2101},
mesh = {Humans ; *Proton Pump Inhibitors/adverse effects ; *Dementia/chemically induced/epidemiology ; Risk Factors ; Cognitive Dysfunction/chemically induced ; Aged ; },
abstract = {Proton pump inhibitors (PPIs) are the most prescribed gastric acid suppressant drugs; the category includes omeprazole, esomeprazole, lansoprazole, dexlansoprazole, pantoprazole, and rabeprazole. In 2015, a study suggested that PPI use was associated with an increased risk of dementia. An early meta-analysis confirmed this concern, but the findings were inconsistent in subsequent meta-analyses. Also problematic is that these meta-analyses used questionable approaches, and their findings were characterized by very high heterogeneity. Notably, the high heterogeneity appeared to be driven by large studies with widely different outcomes. Nonetheless, one finding stands out in the body of research examined: older subjects who initiated and continued PPIs (implying chronic use) were at a significantly increased risk of dementia and mild cognitive impairment. Although there are causal and non-causal pathways that associate PPI use with dementia, for reasons that are explained in this article, a cause-effect relationship cannot at present be presumed; so, PPI use is best considered to be a marker of future dementia risk. However, because chronic use of PPIs has been associated with many adverse medical outcomes (eg, disturbances of the gut microbiome, orthopedic complications), and because some PPIs are associated with pharmacokinetic drug interactions (mainly inhibition of CYP2C19), it would be wise to limit the use of PPIs to the shortest duration necessary and to deprescribe PPIs when there does not appear to be need for their continuation.},
}

Humans
*Proton Pump Inhibitors/adverse effects
*Dementia/chemically induced/epidemiology
Risk Factors
Cognitive Dysfunction/chemically induced
Aged

@article {pmid41983840,
year = {2026},
author = {Ibadullayeva, A and Khamzina, A and Smagulov, D and Khamzin, K},
title = {An overview of the livestock microbiome: sheep, horses, cattle, camels, and chickens.},
journal = {Brazilian journal of biology = Revista brasleira de biologia},
volume = {86},
number = {},
pages = {e299936},
doi = {10.1590/1519-6984.299936},
pmid = {41983840},
issn = {1678-4375},
mesh = {Animals ; Cattle/microbiology ; *Livestock/microbiology ; Camelus/microbiology ; Sheep/microbiology ; *Microbiota/genetics/physiology ; Chickens/microbiology ; Horses/microbiology ; },
abstract = {The animal microbiome plays a crucial role in determining the health, productivity, and welfare of livestock species, including sheep, horses, cattle, camel, and chicken. These animal species were selected due to the high consumption of their products in Kazakhstan. Enhancing their productivity, while maintaining the safety and quality of meat and milk derived from them, represents a pressing research priority. This review article includes current research on the composition, diversity, and purposes of the microbiota found within different organ systems of these species. This study focuses on recent advancements in sequencing technology, including metagenomics, 16S rRNA sequencing, and multiomic methods, to combine data on microbial diversity, composition, and functionality within the gastrointestinal tract and other organs. The key findings show differences in microbial communities associated with breed, age, and diet, the impact of microbiota on methane emissions and feed efficiency in ruminants, and the possibility of using microbiome management techniques (e.g., probiotics, prebiotics, and feed additives) to enhance livestock production. The microbiome influences various species, extending its effects beyond digestion and immunity to reproductive health and behavior. Despite advancements, translating microbiome data into actionable interventions is interfered by variability resulting from genetic, environmental, and management factors. Integrating microbiome research more closely with animal genetics and livestock production methods could lead to innovative approaches for improving the health, efficiency, and welfare of farm animals, ultimately supporting sustainable livestock farming practices.},
}

Animals
Cattle/microbiology
*Livestock/microbiology
Camelus/microbiology
Sheep/microbiology
*Microbiota/genetics/physiology
Chickens/microbiology
Horses/microbiology

@article {pmid41983959,
year = {2026},
author = {Li, C and Yang, J and Wang, X and Tan, C and Luo, Y and Jin, Z and Zhou, X and Zhang, G},
title = {Maternal Exposure to Bisphenol A Bis(diphenyl Phosphate) Induces Offspring Colitis through Disrupting the Gut Microbiome-Metabolite Axis.},
journal = {Environmental science & technology},
volume = {},
number = {},
pages = {},
doi = {10.1021/acs.est.5c11474},
pmid = {41983959},
issn = {1520-5851},
abstract = {Bisphenol-A bis(diphenyl phosphate) (BDP) has been detected in biological organisms, but its toxicological effects remain unclear. In this study of 4376 participants, the characteristic BDP metabolite diphenyl phosphate was associated with gastrointestinal diseases via a nonlinear dose-response relationship, and was identified as a risk factor (OR = 1.02; 95% CI: 1.01-1.04; P = 0.013). Pregnant rats received 50 mg/kg/day BDP during gestation (GD 14-20) or gestation plus lactation (GD 14-PND 35). Both regimens triggered colonic inflammation and gut microbiome dysbiosis in offspring. The combined exposure group showed more severe effects, including persistent histopathological damage, elevated Il-1β and Il-6, and reduced microbial diversity. LC-MS/MS and 16S rRNA sequencing were used to assess BDP distribution and gut microbiome alterations. BDP crossed the placental barrier. SourceTracker analysis confirmed maternal microbiome transmission as the primary source (>70%) of offspring gut microbiome, accompanied by Streptococcus enrichment and Bifidobacterium depletion. Metabolite-inflammation network analysis showed positive correlations of butyrate and negative correlations of propionate with proinflammatory cytokines (IL-1β, IL-6, and TNF-α), which were subsequently confirmed by in vitro experiments. These findings demonstrate a transgenerational mechanism whereby prenatal BDP exposure induces offspring colonic inflammation via the gut microbiome-metabolite axis, informing maternal-infant intervention strategies.},
}

@article {pmid41983965,
year = {2026},
author = {Nguyen, J and Nguyen, J and Chau, T and Murphy, R and Richardson, J and Evans, E and Tiller, G},
title = {The campus microbiome: insights into soil bacterial diversity from 16S V3-V4 rRNA amplicon sequencing.},
journal = {Microbiology resource announcements},
volume = {},
number = {},
pages = {e0129325},
doi = {10.1128/mra.01293-25},
pmid = {41983965},
issn = {2576-098X},
abstract = {This study consisted of characterizing soil bacterial diversity via 16S V3-V4 amplicon sequencing on CCLA's campus, with a focus on analyzing samples collected near college dormitories. The data provides a sufficient starting point for us to characterize bacterial diversity both on and off campus in Northwest Louisiana.},
}

@article {pmid41984040,
year = {2026},
author = {Sordillo, A and Heldrich, J and Turcotte, R and Sheth, RU},
title = {A Postbiotic Positively Shifts the Canine Oral Microbiome.},
journal = {Journal of veterinary dentistry},
volume = {},
number = {},
pages = {8987564261439741},
doi = {10.1177/08987564261439741},
pmid = {41984040},
issn = {2470-4083},
abstract = {The oral microbiome is an important aspect of overall oral health in dogs. To investigate the ability of a postbiotic, canine oral health postbiotic (COHP), to support oral health, a double-blind, placebo-controlled study was conducted with a dirty tooth model to assess its ability to reduce volatile sulfur compound (VSC) producing microbes that cause halitosis and modulate canine oral microbiome composition. Ten client-owned dogs were randomly split into 2 groups. The groups received either the COHP or a placebo as a powder topper on food for 7 days. Oral microbiome samples were collected on day 0 and day 7 along with the buccal gingival margin. Hydrogen sulfide (H2S)-producing colonies were quantified by plating the oral microbiome samples and counting pigment-producing colonies. Additionally, oral microbiome samples were sequenced, and taxa abundance was quantified. A trend toward a reduction in H2S-producing colonies was observed in the COHP group (P = .06), but not in the placebo group (P = .9). Canine oral health postbiotic reduced the abundance of 9 times as many taxa as the placebo, including taxa that form biofilms and produce VSCs. The placebo reduced the abundance of only one taxon, which is not associated with biofilms or VSCs. The findings provide evidence for COHP's ability to promote a positive shift in the canine oral microbiome, and, together with previous results, provides evidence that it may broadly help to maintain canine oral health.},
}

@article {pmid41984077,
year = {2026},
author = {De Wilde, M and Maarsingh, B and de Monte, LGG and Dekinga, A and Bijleveld, AI and Kressin, H and Zomer, AL and Piersma, T},
title = {Molluscivorous red knots rapidly adjust to a plant diet.},
journal = {Biology open},
volume = {15},
number = {4},
pages = {},
doi = {10.1242/bio.062365},
pmid = {41984077},
issn = {2046-6390},
support = {NZ4543.24//Universiteit Utrecht/ ; //Koninklijk Nederlands Instituut voor Onderzoek der Zee/ ; },
mesh = {Animals ; *Diet ; Feces/chemistry ; *Adaptation, Physiological ; *Feeding Behavior ; },
abstract = {Dietary flexibility is key to adjusting to environmental change. In Mauritania, the seemingly obligatory molluscivorous red knots Calidris canutus were observed to eat seagrass rhizomes. To study the ability of knots to live on plant material, we performed a diet-change experiment on captive individuals. Two groups of five were fed protein-rich pellets for 13 weeks, then plant-based pellets for 6 weeks, then reversed back to protein-rich pellets for 4.5 weeks. During the first days following the shift to the plant diet, body mass declined by 14% before increasing and stabilizing to lower levels. Faecal colour changed from green (i.e. gall, suggesting starvation) to brown and was produced in larger quantities when the birds ate plant pellets. These experimental data prove that knots can indeed live on a plant-based diet, with the observed changes suggesting that adjustments of the digestive system, i.e. gut morphology and microbiome, take only a few days.},
}

Animals
*Diet
Feces/chemistry
*Adaptation, Physiological
*Feeding Behavior

@article {pmid41984345,
year = {2026},
author = {Brienza, M and Peña-Herrera, JM and Trotta, V and Chiron, S and Sauvêtre, A},
title = {Trichoderma harzianum enhances lettuce biomass and modulates plant-soil emerging contaminant dynamics under reclaimed wastewater irrigation.},
journal = {Biodegradation},
volume = {37},
number = {3},
pages = {},
pmid = {41984345},
issn = {1572-9729},
mesh = {*Lactuca/growth & development/metabolism/microbiology ; *Wastewater/chemistry ; Biodegradation, Environmental ; Agricultural Irrigation ; Biomass ; *Soil Pollutants/metabolism ; Plant Roots/metabolism/microbiology ; Soil/chemistry ; *Hypocreales ; Plant Leaves/metabolism ; Carbamazepine/metabolism ; Soil Microbiology ; Plant Growth Regulators/metabolism ; },
abstract = {The use of wastewater for irrigation in agricultural soils offers a sustainable means to reduce freshwater consumption and recycle nutrients, but also poses contamination risks associated with emerging pollutants. Furthermore, potentially toxic transformation products may form in soil and rhizosphere, and could subsequently be taken up by plants. Several products containing spores of symbiotic fungi are available and could serve as effective solutions to enhance the biodegradation of micropollutants in agricultural soils irrigated with treated wastewater. In this study, the effect of the fungus Trichoderma harzianum on the distribution of two emerging contaminants, carbamazepine and climbazole, and their main transformation products among soil and lettuce tissues was investigated under controlled conditions. Physiological effects were also investigated by quantifying phytohormones in roots and leaves. Inoculation with Trichoderma harzianum did not significantly affect the uptake of the parent compounds but increased the concentration of their transformation products in soil and reduced their levels in plant leaves after three weeks. The fungus enhanced plant biomass and altered certain phytohormones involved in defense mechanisms such as salicylic acid and microbiome recruitment in roots and soils. Findings of this study provide valuable insights that can be effectively applied to crop cultivation using reclaimed wastewater, leveraging readily available biological products for improved sustainable practices.},
}

*Lactuca/growth & development/metabolism/microbiology
*Wastewater/chemistry
Biodegradation, Environmental
Agricultural Irrigation
Biomass
*Soil Pollutants/metabolism
Plant Roots/metabolism/microbiology
Soil/chemistry
*Hypocreales
Plant Leaves/metabolism
Carbamazepine/metabolism
Soil Microbiology
Plant Growth Regulators/metabolism

@article {pmid41984779,
year = {2026},
author = {Sun, Z and Shi, M and Zheng, Y},
title = {Interpreting circulating microbiome-related metabolites in coronary heart disease.},
journal = {PLoS medicine},
volume = {23},
number = {4},
pages = {e1005056},
pmid = {41984779},
issn = {1549-1676},
mesh = {Humans ; Biomarkers/blood ; *Coronary Disease/microbiology/blood/metabolism/diagnosis ; *Gastrointestinal Microbiome ; *Microbiota ; },
abstract = {Circulating microbiome-related metabolites have emerged as promising biomarkers for coronary heart disease. A recent multi-stage study in PLOS Medicine strengthens signal prioritization but highlights the persistent gap between association and causality.},
}

Humans
Biomarkers/blood
*Coronary Disease/microbiology/blood/metabolism/diagnosis
*Gastrointestinal Microbiome
*Microbiota

@article {pmid41984783,
year = {2026},
author = {Calderón-Romero, P and Valderrama, B and Bastiaanssen, TFS and Lillo, P and Thumala-Dockendorff, D and Clarke, G and Cryan, JF and Slachevsky, A and González-Billault, C and Court, FA},
title = {The neuroactive potential of the elderly human gut microbiome is associated with mental health status.},
journal = {PloS one},
volume = {21},
number = {4},
pages = {e0343493},
pmid = {41984783},
issn = {1932-6203},
mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Male ; Female ; Aged ; *Mental Health ; Cognition/physiology ; *Aging/psychology ; Aged, 80 and over ; Depression/microbiology ; Middle Aged ; Chile ; Cohort Studies ; },
abstract = {Ageing is usually associated with physiological decline, increased mental health issues, and cognitive. deterioration, alongside specific changes in the gut microbiome. However, the relationship between the neuroactive potential of the gut microbiome and mental health and cognition among the elderly remains less explored. This study examines a cohort of 153 older Chilean adults with cognitive complaints, assessing anthropometric data, mental health via five distinct tests, and gut microbiome composition through 16SV4 sequencing. Our findings reveal associations between anthropometric factors and depression scores in mental tests of participants with their gut microbiome composition. Notably, depression was associated with changes in the abundance of Lachnospiraceae Eubacterium xylanophilum group and Fusobacteriaceae Fusobacterium. Additionally, bacterial pathways involved in metabolising neuroactive compounds such as tryptophan, short-chain fatty acids, p-cresol, glutamate, and nitric oxide were associated with participant age, sex, and cognitive performance. Moreover, participants' sex was associated with the neuroactive potential of specific bacteria, suggesting a role of the gut microbiome in sex-related mental health differences in the elderly. Altogether, this study provides the first evidence from a South American cohort linking the inferred neuroactive potential of the gut microbiome to cognitive and psychological function in older adults with cognitive complaints, offering novel insights into microbiota-based mechanisms that may contribute to mental health and ageing.},
}

Humans
*Gastrointestinal Microbiome/physiology
Male
Female
Aged
*Mental Health
Cognition/physiology
*Aging/psychology
Aged, 80 and over
Depression/microbiology
Middle Aged
Chile
Cohort Studies

@article {pmid41984912,
year = {2026},
author = {Fri, J and Njanje, I and Mahopo, TC and Mavhandu-Ramarumo, LG and Bessong, PO and , },
title = {The Gut Bacterial Resistome in the First Two Years of Life: Protocol for a Longitudinal Observational Birth Cohort Study.},
journal = {JMIR research protocols},
volume = {15},
number = {},
pages = {e86058},
pmid = {41984912},
issn = {1929-0748},
mesh = {Humans ; *Gastrointestinal Microbiome/drug effects ; Infant, Newborn ; Female ; Infant ; Longitudinal Studies ; Prospective Studies ; Birth Cohort ; South Africa ; *Drug Resistance, Bacterial ; Anti-Bacterial Agents/pharmacology ; Observational Studies as Topic ; Rural Population ; Milk, Human/microbiology/chemistry ; Male ; Risk Factors ; },
abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health threat that increases the burden of infectious diseases and disproportionately affects communities of low socioeconomic status. Despite the call for community-level AMR data, prospective studies from rural sub-Saharan African communities to inform appropriate targeted interventions remain scarce. Given the role of enteric bacteria in AMR transmission dynamics, there is a need to understand the timing, risk factors, and ecological drivers of gut resistome acquisition and development during infancy.

OBJECTIVE: This study aimed to characterize the temporal dynamics of enteric bacterial resistomes during the first 2 years of life and to identify drivers of AMR acquisition and development in a community-based, prospective, observational birth cohort study in a rural South African community.

METHODS: The study aims to enroll 200 newborns and their mothers within 17 days post partum. Data on key exposures and variables include sociodemographics; perinatal and anthropometrics; feeding practices and dietary exposures; illness, medication, and vaccination history; breast milk metabolomic profiles; household socioeconomic status; maternal psychosocial and behavioral factors; hygiene and sanitation practices; and environmental exposures including hydro-meteorological variables, in-house livestock and pets, and drinking water quality. Biological samples include stools from monthly collections and diarrhea episodes for metagenomic analysis and breast milk for metabolomics. Planned analyses include assessing the infant microbiome and resistome structure (diversity, abundance, and composition) across time points and modeling associations between risk factors and AMR outcomes. Additionally, a cross-sectional community survey on knowledge, attitudes, and practices regarding antimicrobial use is conducted to inform knowledge translation through responsive dialogues, thereby developing ethnographically relevant packages for community-level AMR stewardship.

RESULTS: Participant identification and enrollment began in August 2023. By October 2025, 167 newborns had been enrolled, with 20 having completed the 24-month follow-up. The characteristics of the enrolled participants are presented in this protocol.

CONCLUSIONS: This study will offer a unique opportunity to generate longitudinal resistome data from a rural sub-Saharan African setting. The study is expected to contribute knowledge on the microbiome and resistome structure dynamics and trajectories associated with key risk factors of acquisition and development. In addition, co-produced ethnographically tailored educational packages, informed by knowledge, attitudes, and practices and bacterial resistome data, will drive sustainable community-centered AMR awareness interventions.},
}

Humans
*Gastrointestinal Microbiome/drug effects
Infant, Newborn
Female
Infant
Longitudinal Studies
Prospective Studies
Birth Cohort
South Africa
*Drug Resistance, Bacterial
Anti-Bacterial Agents/pharmacology
Observational Studies as Topic
Rural Population
Milk, Human/microbiology/chemistry
Male
Risk Factors

@article {pmid41985067,
year = {2026},
author = {Sarmah, MP and Zoramthara, K and Manngaihsiam, R and Boro, HH and Baraka, AGA and Saeed, AL and Gurusubramanian, G and Kharat, KR},
title = {Microbiome Simplification During Metamorphosis in Larva and Adults of Armigeres subalbatus (Coquillett, 1898) (Culicidae) Revealed by Shotgun Metagenomics.},
journal = {Archives of insect biochemistry and physiology},
volume = {121},
number = {4},
pages = {e70159},
doi = {10.1002/arch.70159},
pmid = {41985067},
issn = {1520-6327},
support = {EM/Dev/11/SG/01993/2024//Indian Council of Medical Research/ ; DST/INSPIRE Fellowship/[IF240039]//Department of Science & Technology, New Delhi, India (INSPIRE-JRF)/ ; },
mesh = {Animals ; Larva/microbiology/growth & development ; *Microbiota ; Metagenomics ; *Culicidae/microbiology/growth & development ; *Metamorphosis, Biological ; Bacteria/genetics/classification ; Metagenome ; },
abstract = {Armigeres subalbatus is medically significant vector for filarial worms and the Japanese encephalitis virus. Shotgun metagenomic sequencing was employed to investigate the bacterial communities in A. subalbatus mosquitoes. The diversity metrics (Shannon H', Simpson 1-D, Berger-Parker) were calculated for larval and adult stages. De novo assembly and binning were used to recover metagenome-assembled genomes (MAGs) with > 82% completeness and < 4% contamination. Functional profiling assessed gene expression via transcripts per million (TPM) and clusters of orthologous groups (COG) categories. Larval microbiomes showed high alpha diversity (Shannon H' ≈ 1.336 ± 0.163, Simpson 1-D = 0.684 ± 0.046), dominated by Gammaproteobacteria (Aeromonas, Morganella, and Yersinia) and Bacteroidota, with persistent Shewanella and Acinetobacter. Adult microbiomes exhibited low diversity (Shannon H' = 0.637 ± 0.100, Berger-Parker = 0.682 ± 0.026), near-monoculture dominated by Aeromonas hydrophila, alongside low-abundance Stenotrophomonas, Pseudomonas, and Microbacterium. Six high-quality MAGs were recovered: larval (Bacteroidota, Shewanella, and Acinetobacter); adult (Acinetobacter, Stenotrophomonas, and Shewanella), confirming persistence of Shewanella and Acinetobacter, absence of Bacteroidota, and emergence of Stenotrophomonas in adults. Adult microbiomes displayed metabolic hyperactivity, with 1.5-4 times higher transcriptional output across COG categories compared to larvae. Chemotaxis [Methyl-accepting chemotaxis protein (MCP), K03406: ~6000 TPM in adults vs. < 1000 TPM in larvae] and ABC transporters (PF00005: > 10,000 TPM in adults) dominated adults, while larval expression was balanced among housekeeping functions. The microbiome undergoes significant restructuring during mosquito development, shifting from diverse larval communities to metabolically active, low-diversity adult assemblages. Recovered MAGs provide a genomic basis for future studies on mosquito microbiota dynamics and functions.},
}

Animals
Larva/microbiology/growth & development
*Microbiota
Metagenomics
*Culicidae/microbiology/growth & development
*Metamorphosis, Biological
Bacteria/genetics/classification
Metagenome

@article {pmid41985313,
year = {2026},
author = {Khushbu, and Das, S and Debanth, N},
title = {From bench to gut: Translational horizons in probiotic nanoencapsulation for enhanced host-microbiome synergy.},
journal = {Biomaterials advances},
volume = {185},
number = {},
pages = {214871},
doi = {10.1016/j.bioadv.2026.214871},
pmid = {41985313},
issn = {2772-9508},
abstract = {Delivering viable probiotics to the gastrointestinal tract remains a challenge due to harsh physicochemical conditions and limited stability during processing and storage. Conventional microencapsulation techniques, such as spray drying, lyophilization, and emulsification, enhance survival but face scalability and efficiency constraints. Emerging nanostructured delivery platforms overcome these barriers by leveraging unique physicochemical properties of nanomaterials, including high surface area, enhanced solubility, and stimuli-responsive release. Functionalized nanocarriers enable site-specific adhesion, systemic delivery, and prolonged mucosal residence, thereby enhancing therapeutic precision and reducing off-target effects. This article highlights the potential of co-encapsulating probiotics with microbial metabolites, prebiotic carbohydrates, and polyphenolic compounds within biopolymeric matrices, which can significantly enhance translational applications and strengthen conventional probiotic nanoencapsulation strategies. This review consolidates current advancements in probiotic nanoencapsulation, emphasizing the design of multifunctional matrices that preserve microbial integrity, extend shelf life, and optimize host-microbiome interactions. By elucidating nanoparticle-probiotic interfacial dynamics, it lays the groundwork for next-generation probiotic therapeutics with improved efficacy and translational potential.},
}

@article {pmid41985330,
year = {2026},
author = {Kwiendacz, H and Cembrowska-Lech, D and Skonieczna-Żydecka, K and Klimontowicz, K and Podsiadło, K and Wierzbicka-Woś, A and Styburski, D and Kaczmarczyk, M and Gumprecht, J and Łoniewski, I and Nabrdalik, K},
title = {Multi-strain probiotic enhances metformin tolerance by modulating gut microbiome and bile acid pathways: Insight from multi-omics post-hoc analysis (ProGasMet trial).},
journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie},
volume = {198},
number = {},
pages = {119370},
doi = {10.1016/j.biopha.2026.119370},
pmid = {41985330},
issn = {1950-6007},
abstract = {BACKGROUND: Metformin is the cornerstone therapy for type 2 diabetes, but gastrointestinal intolerance commonly limits dose escalation and long-term adherence. In the ProGasMet trial, multi-strain probiotic supplementation improved metformin tolerability. However, the underlying microbiome-metabolome mechanisms remain unclear.

METHODS AND ANALYSIS: We performed an exploratory multi-omics analysis using Period 1 of a randomized, double-blind, placebo-controlled trial. Participants with metformin intolerance received a multi-strain probiotic or placebo for 12 weeks. Paired stool samples collected at baseline and end of treatment were available from 34 participants (68 samples). We integrated shotgun metagenomic species profiles, predicted gut metabolic modules, and untargeted faecal LC-MS metabolomics using multi-block sparse PLS (DIABLO), complemented by longitudinal covariate-adjusted feature-level analyses and associations with gastrointestinal symptom burden (QACSMI and a simplified GI score).

RESULTS: In multi-omics integration at 12 weeks, bile acid-related metabolites were among the strongest contributors to group separation, with hyodeoxycholic acid and related compounds enriched in the probiotic arm. Global biodiversity and community-wide turnover did not differ between groups. Feature-level analyses suggested modest, directionally coherent changes in selected taxa, functional modules, and metabolites. Higher hyodeoxycholic acid concentrations were associated with lower gastrointestinal symptom burden in probiotic-treated participants, a pattern not observed under placebo.

CONCLUSION: Probiotic supplementation may be associated with coordinated microbiome-metabolome shifts in metformin-intolerant type 2 diabetes, highlighting bile acid remodelling, particularly hyodeoxycholic acid, as a plausible candidate for improved tolerability. These results support prioritising secondary bile acid-microbiome pathways for confirmation in larger trials incorporating targeted bile acid quantification and causal modelling.},
}

@article {pmid41985576,
year = {2026},
author = {Weitekamp, CA and Watson, C and Hata, E and Hester, K and Kodavanti, UP and Lau, C and Lehmann, DM and Miller, CN and Shaffer, RM and Soliman, F and Powers, M and Branch, FM},
title = {A systematic literature inventory on the interaction between dietary factors and environmental chemical exposures for nervous system health outcomes.},
journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association},
volume = {213},
number = {},
pages = {116096},
doi = {10.1016/j.fct.2026.116096},
pmid = {41985576},
issn = {1873-6351},
abstract = {Environmental health research from the last seven decades suggests that dietary factors can modify adverse health outcomes associated with chemical exposures. However, the interplay between diet, chemical exposures, and health is complex and remains poorly understood. Here, to survey the existing evidence and stimulate future research, we systematically identified and cataloged available literature on the interactions between chemical exposures and dietary factors for one health outcome category, neurotoxicity. The goal of this systematic literature inventory was to identify the relationship of dietary factors on chemical exposure mediated health outcomes related to central nervous system toxicity, given the importance of the microbiome-gut-brain axis in mediating these interactions. From an initial set of 32,529 references, we identified 80 epidemiological studies, 707 toxicological studies, and 175 in vitro studies that met inclusion criteria. Study design information was captured for the 80 epidemiological studies and for 113 toxicological studies that met additional scoping criteria. The most frequently studied chemical-diet interactions across the human and animal evidence streams were metals/metalloids and micronutrients. Knowledge gaps included dietary components known to be central to microbiome function, as well as adverse dietary modifiers compared to protective dietary factors. This systematic literature inventory is intended to support future research.},
}

@article {pmid41985591,
year = {2026},
author = {Ma, R and Wang, C},
title = {Microbiome analysis reveals the positive effects of exercise on the gut microbiota in horse.},
journal = {Microbial pathogenesis},
volume = {},
number = {},
pages = {108501},
doi = {10.1016/j.micpath.2026.108501},
pmid = {41985591},
issn = {1096-1208},
abstract = {Gut microbiota is vital to host health, involving many aspects including immunity, metabolism and digestion. Exercise is recognized as a significant factor influencing the gut microbiota. However, the effects of exercise on the gut microbiota in horses remain unclear. Here, this study aims to investigate the effects of exercise on the gut bacterial and fungal communities in the horses using 16S rDNA and ITS genes amplicon sequencing. Results indicated that exercise significantly increased the ACE, Chao1 and Shannon indices of the gut bacterial community, accompanied by significant alterations in the primary components of the gut bacterial community. Conversely, exercise did not affect the diversity and abundance of the gut fungal community. Although exercise did not change the dominant bacterial phyla and genera, it resulted in significant changes in the abundance of some bacteria and fungi. Bacterial taxonomic analysis revealed that exercise significantly increased the relative abundance of 8 phyla and 187 genera, while the relative abundance of three phyla and 197 genera decreased markedly. Moreover, exercise also resulted in a significant increase in the relative abundance of five phyla and 105 genera, whereas the relative abundance of two phyla and 82 genera decreased significantly in the gut fungal community. In summary, this study indicated that exercise can affect the composition and structure of gut microbiota. Moreover, this study also conveys an important message that exercise may exert health benefits to the host by affecting the gut microbiota. Future research could investigate the effects of various types and intensities of exercise on gut microbiota to optimize health management strategies.},
}

@article {pmid41985731,
year = {2026},
author = {Lee, E and Han, K and Mun, S},
title = {CST-Based Molecular Profiling of Vaginal Microbiota Validated by qRT-PCR and 16S Amplicon Sequencing.},
journal = {Methods (San Diego, Calif.)},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.ymeth.2026.03.015},
pmid = {41985731},
issn = {1095-9130},
abstract = {The vaginal microbiome is commonly classified into five Community State Types (CSTs) based on the dominance and relative abundance of Lactobacillus species, which play a central role in maintaining vaginal homeostasis through the production of lactic acid and hydrogen peroxide. Disruption or depletion of Lactobacillus spp. Leads to elevated vaginal pH, thereby promoting the overgrowth of anaerobic bacteria associated with bacterial vaginosis (BV). Although next-generation sequencing (NGS)-based microbiome profiling has been widely used to characterize vaginal microbial communities, its routine clinical application remains limited by high cost, long turnaround time, and reduced suitability for rapid, species-specific quantification. In this study, we developed and validated species-specific quantitative real-time polymerase chain reaction (qRT-PCR) primer sets targeting four health-associated Lactobacillus species (Lactobacillus crispatus, Lactobacillus. gasseri, Lactobacillus. iners, and Lactobacillus. jensenii) and four BV-associated bacterial taxa (Atopobium vaginae, Clostridiales genomosp. BVAB1, Prevotella bivia, and Megasphaera type 1). Quantitative results obtained by qRT-PCR were systematically compared with relative abundance profiles derived from 16S rRNA gene V3-V4 sequencing, revealing a strong concordance between the two platforms in identifying key vaginal microbial signatures. Collectively, these findings demonstrate that qRT-PCR represents a rapid, cost-effective, and sensitive approach for targeted vaginal microbiome assessment and supports its potential utility as a molecular diagnostic tool for the precise detection of vaginal microbiota imbalance.},
}

@article {pmid41985795,
year = {2026},
author = {Shen, X and Gibson-Kueh, S and Nelson, SP and Poon, ZWJ and Terence, C and Vu, NT and Carrai, M and Awate, S and Vij, S and Tan, MR and Jerry, DR and Domingos, JA},
title = {Scale drop disease virus (SDDV) infection induces intestinal dysbiosis and secondary Vibrio expansion in Asian seabass (Lates calcarifer).},
journal = {Fish & shellfish immunology},
volume = {},
number = {},
pages = {111344},
doi = {10.1016/j.fsi.2026.111344},
pmid = {41985795},
issn = {1095-9947},
abstract = {Scale drop disease virus (SDDV) is a major viral pathogen causing high mortality in farmed Asian seabass (Lates calcarifer), yet its impacts on host-associated microbiota remain poorly understood. In this study, juvenile L. calcarifer were intraperitoneally challenged with 10[7] viral copies (0.1 ml SDDV), resulting in 94.2% cumulative mortality over a 24-day experimental period. A total of 36 intestinal content samples were collected at defined time points relative to challenge (dpc) from clinically healthy (H) and sick (S) fish, representing five stages: pre-infection baseline (H0 dpc), early infection (H6 dpc), peak mortality (H10 dpc and S10 dpc), declining mortality (S15 dpc) and recovery (H24 dpc). Histopathological examination revealed progressive intestinal pathology, characterised by multifocal vesicle formation and epithelial necrosis, consistent with SDDV-associated enteropathy. 16S rRNA gene sequencing demonstrated pronounced intestinal dysbiosis during infection, with a significant collapse of alpha diversity at peak mortality (10 dpc; Kruskal-Wallis test with Dunn's post-hoc comparisons, p < 0.05) where Chao1 decreased from 942 at baseline to 416 and Shannon from 4.3 to 1.9. At peak disease, the gut microbiome was overwhelmingly dominated by Vibrio (>80% relative abundance), suggesting secondary opportunistic expansion associated with virus-induced intestinal damage. Co-occurrence network analysis further revealed fragmentation of microbial interactions during peak infection, followed by partial restoration of network connectivity and re-emergence of taxa such as Photobacterium and Rhodobacteraceae during recovery from infection. Collectively, these findings demonstrated that SDDV infection induced severe intestinal pathology accompanied by dynamic restructuring of the gut microbiome in L. calcarifer, linking viral epithelial damage to destabilization of the intestinal microbial homeostasis and secondary Vibrio overgrowth. Distinct microbiome features, including reduced community diversity and Vibrio dominance at peak disease, as well as recovery-associated taxa in surviving fish, may represent potential microbial indicators of disease progression and intestinal recovery, providing a reference framework for future microbiome-informed health management strategies aimed at mitigating SDDV impacts in L. calcarifer aquaculture.},
}

@article {pmid41986005,
year = {2026},
author = {Ansari, A and Shete, O and Ghosh, TS},
title = {Artificial intelligence in microbial metagenomics.},
journal = {Progress in molecular biology and translational science},
volume = {221},
number = {},
pages = {255-276},
doi = {10.1016/bs.pmbts.2026.01.009},
pmid = {41986005},
issn = {1878-0814},
mesh = {*Metagenomics/methods ; *Artificial Intelligence ; Humans ; Microbiota/genetics ; Machine Learning ; },
abstract = {Rapid advancements in genomic sequencing technologies and similar technological advancements in the area of accessing, isolating, extracting and functional probing of microbes residing in diverse environments has resulted in a deluge of microbiome sequencing and microbial genomic sequencing data. Concomitant developments in the area of data science, specifically in the domains of advanced statistics, and artificial intelligence (AI) can facilitate mining this data to answer complex biological questions and developing translational applications in diverse areas, ranging from health-care to industrial microbiology. For most researchers, information on which AI tools address specific biological questions is scattered across disparate sources. In this chapter, we explore the various applications of AI-based methodologies (using case-studies) in answering different biological questions using microbial genomics and metagenomic data. We also discuss different AI and machine-learning (ML) based approaches to integrate metagenomic data with other "omics" data. Finally, we highlight both challenges and possibilities with this rapidly progressing field.},
}

*Metagenomics/methods
*Artificial Intelligence
Humans
Microbiota/genetics
Machine Learning

@article {pmid41986382,
year = {2026},
author = {Dahmouni, S and Benabdelmoumene, D and Bengharbi, Z and Fodil, MK and Umar, KM and Qadi, WSM and Krache, F and Waqar, M and Tong, X and Han, R and Abu Bakar, ZH and Sarian, MN and Mediani, A and Jam, FA and Hamezah, HS},
title = {Postbiotics and paraprobiotics in food biochemistry mechanisms stability and nutritional applications.},
journal = {NPJ science of food},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41538-026-00838-z},
pmid = {41986382},
issn = {2396-8370},
support = {DIP-2024-021//Universiti Kebangsaan Malaysia/ ; },
abstract = {Postbiotics, defined as preparations of inanimate microorganisms and their components that confer health benefits, are emerging as stable and safe alternatives to probiotics. This review summarizes recent advances in the biochemical composition, mechanisms of action, and applications of postbiotics and paraprobiotics in human and animal nutrition. It also highlights innovations in omics technologies, artificial intelligence, and sustainable production strategies that are shaping next-generation microbiome-based functional foods and therapeutic interventions.},
}

@article {pmid41986393,
year = {2026},
author = {Gimeno-Molina, B and Correia, GDS and Ng, S and Lee, YS and Bayar, E and Love, RL and Zhao, S and Mountain, KE and Teoh, TG and Brown, RG and David, AL and Lewis, HV and Terzidou, V and Botto, M and Kropf, P and MacIntyre, DA and Bennett, PR and Sykes, L},
title = {Complement and neutrophils are actively involved at the cervicovaginal interface in cases of adverse microbial composition, cervical shortening and spontaneous preterm birth.},
journal = {NPJ biofilms and microbiomes},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41522-026-00969-x},
pmid = {41986393},
issn = {2055-5008},
abstract = {Microbial-driven spontaneous preterm birth (sPTB) is linked to adverse vaginal microbiome and dysregulated immune responses, yet this knowledge has not translated into predictive tools or therapies. We sampled 186 high-risk pregnant women and assessed 14 complement proteins and the neutrophil immunophenotype at the cervicovaginal interface to expand potential targets. Alterations in classical and alternative complement pathway components were associated with bacterial community composition and preceded cervical shortening and sPTB. At 12[+0]-16[+6] weeks, women with Community State Type (CST) IV had significantly higher concentrations of C1q, C4, C4b, Factor B, D, C3b/iC3b, and Factor H, I than those with CST I. Women who later developed a short cervix and delivered preterm showed lower L. crispatus abundance and elevated complement activation. Neutrophils were the dominant local immune cell and exhibited enhanced activation relative to peripheral neutrophils, with altered expression of CD11b, CD62L, CD63 and CD66b. Cervical neutrophil CD63, CD66b, and CD88 differed between CST IV and CST I, though not by pregnancy outcome. Neutrophil abundance correlated with cytokines, complement proteins, and MMPs, suggesting roles in inflammation and tissue remodelling. These findings highlight a microbiota-driven complement-neutrophil axis present before cervical remodelling and sPTB, identifying potential complement-based predictors and therapeutic targets.},
}

@article {pmid41986507,
year = {2026},
author = {Venkidesh, BS and Acharya, M and Narasimhamurthy, RK and Murali, TS and Rao, BSS and Mumbrekar, KD},
title = {Multi-strain bacterial combination mitigates pelvic irradiation-induced gut damage by preserving gut integrity, inhibiting inflammation and apoptosis.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-47773-3},
pmid = {41986507},
issn = {2045-2322},
}

@article {pmid41986930,
year = {2026},
author = {Raghav, S and Frishman, WH},
title = {Childhood Obesity, Medications, and Surgeries.},
journal = {Cardiology in review},
volume = {},
number = {},
pages = {},
doi = {10.1097/CRD.0000000000001230},
pmid = {41986930},
issn = {1538-4683},
abstract = {The obesity pandemic continues to increase in prevalence in children and adolescents, with its increase outpacing the rate of adult obesity; the human developmental index, body mass index, and family income all display associations to childhood obesity. There are numerous adverse complications of childhood obesity, including cardiovascular, endocrine, and gastrointestinal manifestations. Obesity is thought to be an interaction of several different factors, such as leptin, proopiomelanocortin, glucose uptake in adipocytes, melanocortin receptor 4, protein convertase 1/3, brain-derived neurotrophic factor, fat-mass and obesity-associated gene, melanocortin receptor 4, tumor necrosis factor, interleukin-6, and long noncoding RNA. Epigenetic regulation, the unique gut microbiome role in contributing to obesity, environmental factors, and the social context of a child can precipitation of childhood obesity. In this review, we hope to explore the different medications for obesity, orlistat, glucagon-like peptide-1 agonists, liraglutide, semaglutide, exenatide, setmelanotide, metreleptin, naltrexone, lorcaserin, phentermine, metformin, fluoxetine, lisdexamfetamine, and zonisamide, while also reviewing surgeries such as the Roux-en-Y gastric bypass, laparoscopic or vertical sleeve gastrectomy, and adjustable gastric banding.},
}

@article {pmid41986966,
year = {2026},
author = {Sourij, C and Müller, A and Al-Baghdadi, A and Aziz, F and Tripolt, NJ and Pferschy, PN and Andritz, E and Kojzar, H and Stadlbauer, V and Garcia, SL and Sourij, H},
title = {Safety and efficacy of intermittent fasting with or without exercise in people living with overweight or obesity and type 2 diabetes-The INTERFAST-3 study design.},
journal = {Diabetic medicine : a journal of the British Diabetic Association},
volume = {},
number = {},
pages = {e70328},
doi = {10.1111/dme.70328},
pmid = {41986966},
issn = {1464-5491},
support = {//Austrian Science Fund/ ; },
abstract = {AIMS: Lifestyle modification, including caloric restriction and exercise, is fundamental in the treatment of people living with overweight and type 2 diabetes mellitus (T2D). The overall aim of lifestyle intervention schemes is to reduce body weight and improve glycaemic control to reduce the future risk of diabetes-associated complications. The aim of this study is to determine whether intermittent energy restriction, exercise or their combination is best suited for reaching these targets in individuals with T2D not treated with insulin.

METHODS: This randomized, controlled, monocentric parallel-group trial is designed to investigate participants living with T2D, body mass index >27 kg/m[2], HbA1c ≥53 mmol/mol (≥7.0%) and ≤86 mmol/mol (≤10.0%) and without insulin therapy. Participants are equally and randomly allocated to one of four study groups: (1) intermittent energy restriction group, (2) exercise group, (3) combined intermittent energy restriction and exercise group and (4) control group. The intervention phase lasts 12 weeks, followed by a two-year follow-up phase. In addition to assessing body weight and glycaemic parameters, resting energy expenditure (REE) and body composition are measured. An oral glucose tolerance test is carried out at baseline and at the end of the intervention. Additionally, stool samples for microbiome analyses and individual-related outcomes are collected, and all participants are equipped with continuous glucose monitoring (CGM). The primary outcome measure is the change in bodyweight from baseline to day 84.

TRIAL REGISTRATION: The study was registered at DRKS (Deutsches Register Klinischer Studien-German Clinical Trial Register DRKS-ID: DRKS00032036)-Date of registration: 11.10.2023.},
}

@article {pmid41987215,
year = {2026},
author = {Yan, M and Firkins, J and Guo, J and Relling, A and Yu, Z},
title = {Genome-resolved multi-omics provide new insights into microbial nitrogen utilization by the rumen microbiota.},
journal = {Microbiome},
volume = {},
number = {},
pages = {},
doi = {10.1186/s40168-026-02422-9},
pmid = {41987215},
issn = {2049-2618},
abstract = {BACKGROUND: Optimizing nitrogen (N) utilization in ruminant production systems holds both economic and environmental significance. However, traditional paradigms of N metabolism, derived primarily from well-studied model rumen bacteria, do not fully reflect the diverse and complex N metabolism in the rumen ecosystem.

RESULTS: To address this gap, we utilized comparative genomics and genome-resolved multi-omics analyses using a curated set of microbial genomes to investigate N assimilation and regulation in rumen microbes. We discovered that well-established mechanisms of ammonia assimilation and regulation, such as the glutamine synthetase (GS)/glutamate synthase (GOGAT) pathways and their regulatory proteins, are absent in many of the predominant rumen microbes, which likely utilize alternative pathways for ammonia assimilation. These findings challenge the applicability of E. coli-based N regulation models to rumen bacteria in response to ammonia availability. We further linked polysaccharide utilization and ammonia assimilation across hundreds of rumen microbial species. Furthermore, we identified specific microbial species involved in ureolysis and denitrification, as well as phages carrying auxiliary metabolic genes involved in N assimilation. Using an animal trial involving 11 pairs of lamb twins in a crossover design, we demonstrated that dietary crude protein (CP) at 10% and 13% had minimal impact on rumen microbiome composition and expression of N assimilation genes. Instead, changes in concentrate levels altered N assimilation, notably increasing expression of amino acid biosynthesis pathways.

CONCLUSION: These findings indicate a nuanced, species-specific microbial response to dietary interventions, highlighting the limitations of traditional N metabolism models applied to rumen microbes and the need for more granular studies of rumen microbial ecosystems.},
}

@article {pmid41987241,
year = {2026},
author = {Zhong, Y and Peng, Y and Zhang, S and Wen, L and Liu, G and Xu, B and Liang, Y and Huang, H and He, J and Feng, Y and Zeng, J and Liang, J},
title = {An integrated microbiome-drug interaction and bioinformatics approach identifies active deglycosylated and glycosidic chain metabolites of Platycodin D targeting PTPN2/HIF1A in acute lung injury.},
journal = {Biology direct},
volume = {},
number = {},
pages = {},
doi = {10.1186/s13062-026-00779-3},
pmid = {41987241},
issn = {1745-6150},
}

@article {pmid41987825,
year = {2026},
author = {Haque, S and Ponton, F and Allen, AP and Gamage, HKAH and Encinas-Viso, F and Paulsen, IT and Dudaniec, RY},
title = {Environment and Pollen Diversity Differentially Affect the Gut Microbiomes of Introduced Honeybees and Bumblebees.},
journal = {Evolutionary applications},
volume = {19},
number = {4},
pages = {e70234},
pmid = {41987825},
issn = {1752-4571},
abstract = {Invasive species may exhibit shifts in their gut microbiome in response to novel environments and diet, but this may differ across host species and their time since colonisation. We investigate if site environmental variables and foraged pollen resources differentially shape the gut microbiomes of two bee species with contrasting introduction histories: The European honeybee, Apis mellifera (introduced 1831), and the recently invasive bumblebee, Bombus terrestris (invaded 1992). Using landscape-scale metabarcoding across the island state of Tasmania in Australia, we characterised gut bacteria (16S rRNA) and corbicular pollen diversity (ITS2) for each species. Gut bacterial composition was significantly associated with mean annual temperature for A. mellifera and with mean annual precipitation and percentage of pasture for B. terrestris. In B. terrestris, the core and facultative gut microbial diversity and richness showed associations with precipitation, foraged pollen diversity, wind velocity and temperature. Foraged pollen diversity of native plants more strongly predicted the facultative gut microbiome across species. Overall, the gut microbiome of B. terrestris showed a stronger response to abiotic and biotic predictors compared to A. mellifera. Our findings advance understanding of how environmental and dietary factors shape pollinator gut microbiomes at landscape scales, with implications for pollinator health and survival.},
}

@article {pmid41987827,
year = {2026},
author = {Bornbusch, SL and Thacher, PR and Francisque, M and DeCandia, AL and Bortner, R and Garelle, D and Kendrick, EL and Maslanka, MT and Muletz-Wolz, CR},
title = {How "pro" are probiotics for wildlife species? Novel data, lack of evidence, and future directions.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag036},
pmid = {41987827},
issn = {2730-6151},
abstract = {Treatments that aim to purposefully manipulate host-associated microbiomes are now prevalent in human and animal medicine. Probiotics that contain live bacteria are purported to improve microbiome function and host health. Although research is advancing, commercial probiotic development has outpaced empirical study of probiotic efficacy. Probiotics are widely used in ex-situ wildlife care despite a lack of empirical study or support. We interrogate the relevance of commercial probiotics in ex-situ wildlife by (a) sequencing the composition of commercial probiotics used to treat wildlife, (b) comparing the probiotic sequences to data on the microbiomes of >900 animal species, and (c) characterizing the effects of a commercial probiotic on probiotic colonization, prevalence of a potential enteric pathogen (Clostridium perfringens), and metagenomic function in endangered black-footed ferrets (Mustela nigripes). We found mislabeling and potential contaminants in probiotics marketed for a range of species. The probiotic bacteria were rare or absent in published animal microbiomes. In black-footed ferrets, probiotic treatment induced minimal probiotic colonization, negligible functional change, and limited influence on the potential enteric pathogen. Given our findings, which reiterate concerns about the efficacy of commercial probiotics across human and animal sectors, greater effort must be put towards identifying species-specific probiotic candidates and studying alternative microbial therapies for wildlife under human care.},
}

@article {pmid41987828,
year = {2026},
author = {Martino, ME and Gallo, M and Nai, I and Quagliariello, A and Rovere, GD and Babbucci, M and Monticelli, G and Graziano, M and Franch, R and Racaku, M and Cardazzo, B and Milan, M and Peruzza, L and Bargelloni, L},
title = {Standing on the shoulders of microbes: microbiome thermal priming buffers the effects of heatwaves on clams by preventing stress overreaction.},
journal = {ISME communications},
volume = {6},
number = {1},
pages = {ycag059},
pmid = {41987828},
issn = {2730-6151},
abstract = {In the context of rapidly accelerating global warming, the rising frequency of heatwaves is driving large-scale ecological shifts, profoundly affecting organismal physiology and ecosystem functioning. Thermal tolerance is a key determinant of species resilience. Evidence from diverse model systems indicates that this tolerance can be enhanced through thermal priming, a pre-adaptive process in which organisms are exposed to sublethal heat stress. Beyond intrinsic host factors, the adaptive potential of host-associated microbiomes is increasingly recognised as a critical role in shaping organismal thermal resilience. However, the extent to which microbiomes alone can enhance host thermal tolerance remains largely unknown. Here, we used the Manila clam (Ruditapes philippinarum), one of the most widely farmed bivalves, as a model system to test whether thermal pre-adaptation of the microbiome is sufficient to improve host thermal tolerance. Clams were thermally primed, their microbiota isolated, and subsequently transplanted into non-acclimated individuals, which were then exposed to simulated heatwave conditions. By integrating microbial community profiling, host physiological measurements, and transcriptomic analyses, we demonstrate that transplantation of a microbiome from animals previously exposed to heat stress is sufficient to enhance host resilience during subsequent heat stress. This effect arises from adaptive shifts in microbiome composition that promote energy conservation and survival through elevated antioxidant activity and a broad downregulation of host transcriptional pathways, placing the host in an energy-efficient, stress-mitigating state. Our findings provide novel insights into holobiont-level adaptive mechanisms to stress adaptation and hold practical potential for developing microbiome-based interventions to enhance thermal tolerance in aquaculture systems.},
}

@article {pmid41987880,
year = {2026},
author = {Cipriano, GL and Grimaldi, A and Marra, A and Quartarone, A and Maresca, G},
title = {Gut microbiota and cognitive decline: a scoping review of microbial mechanisms and adaptive responses in dementia.},
journal = {Frontiers in aging neuroscience},
volume = {18},
number = {},
pages = {1782720},
pmid = {41987880},
issn = {1663-4365},
abstract = {Dementia is a progressive disease that results in a loss of mental capacity. Some of the most affected cognitive skills are memory, orientation, and language. These skills are also associated with behavioral shifts such as increased agitation and apathy, worsening the affected person's quality of life. The most common type of dementia is Alzheimer's disease, and it is especially concerning in older adults. Alzheimer's is characterized by the formation of beta-amyloid plaques and neurofibrillary tangles that are made of hyperphosphorylated tau proteins. These plaques and tangles lead to inflammation in the central nervous system, damage to the connections between neurons, and overall degeneration of the nervous system. Newer studies have started to identify the gut microbiome and the gut-brain axis as components critical to the progression of neurodegenerative diseases. Dysbiosis, which is characterized by an imbalance or loss of microbial diversity in the gut, has been attributed to the worsening of neurodegenerative diseases. The gut microbiome has been shown to have a large impact on the brain and how it responds neurochemically. An imbalance in the gut microbiome has also been shown to lead a person to emotional and cognitive dysfunction. It has been shown that in dementia patients, there is also an associated intestinal dysbiosis and increased inflammation systemically and within the brain. Certain gut bacteria stimulate the production of pro- inflammatory cytokines and neuroinflammation, which is a defining characteristic of diseases associated with dementia. This review is focused on three main aspects in which dysbiosis is related to cognitive decline.},
}

@article {pmid41987902,
year = {2026},
author = {De, R and Kanungo, S and Mukhopadhyay, AK and Dutta, S},
title = {Comparative metagenomic analysis of diarrheal and non-diarrheal gut microbiome delineating the identification of prospective prognostic markers and probiotics to protect from diarrhea: a brief report.},
journal = {Frontiers in cellular and infection microbiology},
volume = {16},
number = {},
pages = {1729497},
pmid = {41987902},
issn = {2235-2988},
mesh = {*Diarrhea/microbiology/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Cross-Sectional Studies ; *Probiotics/therapeutic use ; Feces/microbiology ; Pilot Projects ; Female ; Prognosis ; Male ; High-Throughput Nucleotide Sequencing ; Adult ; *Bacteria/classification/genetics/isolation & purification ; Middle Aged ; Prospective Studies ; Biomarkers/analysis ; DNA, Bacterial/genetics ; },
abstract = {INTRODUCTION: Diarrhea is a leading contributor of mortality globally. To mitigate its disease burden, improved prognosis and alternative therapeutic approaches must be deployed. A cross-sectional gut microbiome analysis of 23 non-diarrheal and 5 diarrheal fecal samples was conducted with the aim of meeting the WHO's GAPPD (Global Action Plan for Pneumonia and Diarrhea) goals.

HYPOTHESIS: Next-generation sequencing is a potent tool being increasingly used for epidemiological surveillance. It can help in the comparison of the structural diversity of the gut microbiome between diarrheal and non-diarrheal samples, thereby aiding in the identification of prospective prognostic and therapeutic candidates.

AIM: The pilot study was designed to identify prospective taxa that were comparatively enriched in non-diarrheal samples and to predict gut microbial community interactions.

METHODOLOGY: 16S rRNA amplicon sequencing and subsequent analysis were undertaken for taxonomic profiling and abundance interpretation of OTUs.

RESULTS: Significant differences between the two groups with respect to structural composition was revealed. Firmicutes was the most abundant phylum in the majority of the samples. The B/F ratio was consistently <1 in all diarrheal samples. A significant difference in the mean B/F ratio of the two groups was found. Proteobacteria was significantly more abundant in the diarrheal group. On the other hand, Prevotellaceae was the most abundant family in non-diarrheal samples and was suppressed significantly in diarrheal samples. Streptococcaceae was the most abundant family in 60% of diarrheal samples; where Streptococcaceae was suppressed, Bacteroideaceae and Nocardiaceae were the most abundant. In non-diarrheal samples, where Streptococcaceae was almost completely suppressed, Bifidobacteriaceae was the most abundant and significantly suppressed other families. A negative correlation was observed between Prevotellaceae and Bacteroideaceae in the non-diarrheal group. Prevotella copri was the most abundant species in 70% of non-diarrheal samples and was significantly suppressed in diarrheal samples. Proteus mirabilis was identified in all the non-diarrheal samples, while they were absent in diarrheal samples.

CONCLUSION: The OTUs associated with diarrheal dysbiosis can serve as prognostic markers. To our knowledge, this is the first report on the comparative analysis of diarrheal and non-diarrheal microbiome, distinctly addressing the gut microbiome dysbiosis from the context that can lead to the development of prognostic markers and probiotics to protect the endemic population from diarrhea and help in achieving Sustainable Development Goals 2 and 3.},
}

*Diarrhea/microbiology/prevention & control
*Gastrointestinal Microbiome/genetics
Humans
RNA, Ribosomal, 16S/genetics
*Metagenomics/methods
Cross-Sectional Studies
*Probiotics/therapeutic use
Feces/microbiology
Pilot Projects
Female
Prognosis
Male
High-Throughput Nucleotide Sequencing
Adult
*Bacteria/classification/genetics/isolation & purification
Middle Aged
Prospective Studies
Biomarkers/analysis
DNA, Bacterial/genetics

@article {pmid41987918,
year = {2026},
author = {Wang, Y and Ni, M and Zheng, A and Peng, Y and Liu, J and Xiong, Q and Wang, X and Savkovic, V and Kang, S},
title = {A stage-based framework to interpret regulatory T cell biology after heart transplantation.},
journal = {Frontiers in cardiovascular medicine},
volume = {13},
number = {},
pages = {1777360},
pmid = {41987918},
issn = {2297-055X},
abstract = {Regulatory T cells play a pivotal role in immune responses following heart transplantation, influencing the entire post-transplant process. This article examines Treg dynamics in a stage-specific framework and their clinical implications. In the early phase (0-30 days), dominated by injury-related sterile inflammation, Treg recruitment affects local inflammation resolution and tissue repair, potentially altering risks of early immune injury and rejection. The intermediate phase (1-6 months) features high acute cellular rejection risk with ongoing immunosuppression adjustments; Treg quantity, phenotype, and suppressive function are closely associated with the regulation of anti-donor immune responses. In the late phase (>6 months), chronic low-grade inflammation and progressive vascular remodeling predominate, where Tregs suppress persistent immune attacks but may promote fibrosis via repair pathways, exhibiting bidirectional effects. This article highlights Treg detection limitations, including FOXP3 specificity, epigenetic stability, and blood-graft discrepancies. Future directions encompass multimarker monitoring, dynamic risk models, Treg cell therapy, and interventions like cytokine/microbiome modulation to achieve precise immunoregulation, reduce rejection, minimize complications, and improve long-term graft survival.},
}

@article {pmid41988036,
year = {2026},
author = {Alzahrani, SS},
title = {Gut microbiome-epigenetic crosstalk in obesity and type 2 diabetes: mechanisms, evidence, and translational opportunities.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1805937},
pmid = {41988036},
issn = {1664-302X},
abstract = {Obesity and type 2 diabetes mellitus are closely linked metabolic disorders in which gut microbial alterations interact with host epigenetic regulation to influence inflammation, insulin sensitivity, and energy homeostasis. This review examines the gut microbiome-epigenetics interface in these conditions by integrating mechanistic evidence with a Scopus-based bibliometric analysis of publications from 2016 to 2025, thereby providing both disease-focused synthesis and field-level context. Bibliometric mapping identified 1,153 documents from 515 sources authored by 5,445 researchers, with a marked annual growth rate of 27.79%, indicating rapid expansion of this interdisciplinary area. Mechanistically, current evidence converges on three major epigenetic domains: DNA methylation, histone modifications, and non-coding RNA regulation. Microbiota-derived metabolites, particularly short-chain fatty acids, folate-related methyl donors, and other bioactive compounds, influence enzymes such as DNA methyltransferases and histone deacetylases, as well as downstream chromatin marks and microRNA networks relevant to metabolic dysfunction. In obesity and type 2 diabetes, recurrent findings include reduced abundance of butyrate-producing taxa and enrichment of pro-inflammatory or endotoxin-associated bacteria, although these patterns remain heterogeneous across populations, study designs, and analytical methods. Accordingly, the review emphasizes that phylum-level or taxa-level associations should be interpreted cautiously and that causality remains incompletely resolved. A key contribution of this review is the combined evaluation of mechanistic pathways, context-dependent microbial signatures, and translational limitations within a single framework. Overall, microbiome-targeted interventions remain promising but insufficiently validated, and progress toward clinical application will require longitudinal, multi-omics, and interventional studies that directly link specific taxa, metabolites, and epigenetic modifications.},
}

@article {pmid41988038,
year = {2026},
author = {Qin, H and Gong, H and Wang, X and Liu, Y and Song, W and Li, Z and Xiang, H},
title = {Rhizosphere microbial patterns and climatic correlates of phenotypic variation in Rosa roxburghii.},
journal = {Frontiers in microbiology},
volume = {17},
number = {},
pages = {1762588},
pmid = {41988038},
issn = {1664-302X},
abstract = {Plant phenotypic variation represents an important expression of diversity among populations and their responses to heterogeneous environments. However, the factors associated with such variation remain incompletely characterized. In this study, we examined eight phenotypic traits of Rosa roxburghii across environmentally heterogeneous sites and characterized rhizosphere bacterial and fungal communities using 16S rRNA and ITS high-throughput sequencing. Marker taxa were identified, and statistical analyses were applied to explore associations between microbial patterns, climatic context, and phenotypic traits. Our results revealed significant differences among populations in fruit length, fruit width, and stem diameter. Microbial community analyses indicated inter-population divergence in both bacterial and fungal communities, with fungi showing relatively stronger compositional differentiation. Using complementary analytical approaches (LEfSe, LASSO, and sPLS-DA), we identified a consensus set of 12 marker taxa, including six bacterial and six fungal genera. Correlation analyses suggested that fungal markers exhibited broader associations with phenotypic traits than bacterial markers, and regression analyses indicated that fungal markers were statistically associated with variation in fruit size. Stem diameter showed associations with both climatic variables and microbial markers. Overall, phenotypic variation in R. roxburghii was associated with patterns in rhizosphere microbial communities and climatic context, highlighting complex relationships that warrant further investigation. This study contributes descriptive insights into plant-microbe and environment-phenotype associations and provides a foundation for future work aimed at elucidating underlying mechanisms.},
}

@article {pmid41988103,
year = {2025},
author = {Cheng, C and Ma, H and Zhong, Y and Uhlemann, AC and Feng, X and Hu, J},
title = {BIOMARKER DETECTION FOR DISEASE CLASSIFICATION IN LONGITUDINAL MICROBIOME DATA.},
journal = {The annals of applied statistics},
volume = {19},
number = {2},
pages = {943-966},
pmid = {41988103},
issn = {1932-6157},
support = {P30 CA013696/CA/NCI NIH HHS/United States ; R01 AI143886/AI/NIAID NIH HHS/United States ; },
abstract = {The microbiome has been found to have a close relationship with human health. Advancements in sequencing technologies have enabled in-depth studies of microbial communities and their associations with various diseases. When analyzing microbiome data, it is common to perform compositional scale normalization to ensure statistical validity. This requires special treatment to address the unique characteristics of microbiome data. Furthermore, biomedical studies often involve repeated measurements of microbial samples, which adds complexity to the data analysis. In this paper we focus on a liver transplant microbiome study. The main objective is to investigate the association between the colonization status of multidrug-resistant bacteria (MDRB) and the longitudinal microbial abundance profile. To accomplish this, we employ a regularized functional logistic regression model in our analysis. Specifically, we utilize the log-contrast model with a low-rank approximation to handle the compositional covariates and nonconvex penalties to select the important components in the covariate space. We propose an efficient estimation algorithm and establish the oracle property of the estimator. We name this new development as Functional Compositional data Quadratic Method (FCQM). We demonstrate the promise of the proposed method with extensive simulation studies and the liver transplant application.},
}

@article {pmid41988382,
year = {2026},
author = {Dong, H and Cao, H and Gong, Y and Zhao, Z and Wang, K and Zhang, X and Zhang, F},
title = {Chronic kidney disease as an active driver of digestive tract tumors: mechanistic insights and emerging management strategies.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1797181},
pmid = {41988382},
issn = {2296-634X},
abstract = {Digestive tract tumors (DTT), particularly gastric cancer (GC) and colorectal cancer (CRC), remain among the leading causes of cancer-related morbidity and mortality worldwide. Accumulating epidemiological evidence indicates that patients with chronic kidney disease (CKD) exhibit a significantly increased risk of developing gastrointestinal malignancies and experience worse clinical outcomes. However, the biological mechanisms underlying this association have not been comprehensively synthesized. In this review, we integrate clinical and experimental evidence to delineate how CKD functions as a systemic pro-tumorigenic condition rather than a passive comorbidity. We highlight three interrelated mechanistic axes linking CKD to DTT: (i) persistent systemic inflammation and oxidative stress, (ii) metabolic and endocrine dysregulation driven by uremic toxin accumulation, vitamin D deficiency, and mineral imbalance, and (iii) immune perturbations associated with dialysis modalities and post-transplant immunosuppression. These processes converge to disrupt gastrointestinal barrier integrity, reshape the gut microbiota, impair antitumor immune surveillance, and promote malignant transformation and tumor progression. Importantly, we discuss how CKD-specific interventions, including dialysis strategies, kidney transplantation, dietary management, and modulation of gut microbiota, may further modify gastrointestinal cancer risk. Finally, we propose CKD-oriented preventive and screening strategies for GC and CRC, emphasizing the need for risk stratification based on renal function, proteinuria, and metabolic profiles. By framing CKD as an active driver of gastrointestinal carcinogenesis, this review provides a novel integrative framework that synthesizes interconnected mechanistic pathways and explicitly links them to CKD-specific clinical management strategies, a translational perspective that informs early detection, prevention, and integrated care of DTT in patients with CKD.},
}

@article {pmid41988384,
year = {2026},
author = {Zhang, C and Tang, X and Chen, S and Akanyibah, FA and Mao, F},
title = {The role of extracellular vesicles in the transport and regulation of novel inflammatory mediators in IBD and its associated CRC.},
journal = {Frontiers in cell and developmental biology},
volume = {14},
number = {},
pages = {1760517},
pmid = {41988384},
issn = {2296-634X},
abstract = {Inflammatory bowel disease (IBD), comprising ulcerative colitis (UC) and Crohn's disease (CD), is a chronic inflammation of the gut characterized by an imbalance in the intestinal microbiome and ecology. IBD raises the risk of developing colorectal cancer (CRC). CRC is one of the most commonly diagnosed cancers in the world, with high incidence rates. Extracellular vesicles (EVs) play a crucial role in intercellular communication and are vital for maintaining intestinal homeostasis. Recent research highlights novel inflammatory mediators, such as specialized pro-resolving mediators (SPMs), damage-associated molecular patterns (DAMPs), alarmins, non-coding RNAs (ncRNAs), and metabolic intermediates, as crucial in the pathophysiology of IBD and CRC. These novel inflammatory mediators are transported by EVs, influencing the pathogenesis of IBD and associated CRC. Therefore, this article examines the role of novel inflammatory mediators transported by EVs in the pathogenesis of IBD and related CRC, as well as the interaction between EVs and the tumor microenvironment. We also review new research on EV use as a diagnostic indicator and on the potential of EVs, such as mesenchymal stem cell-derived EVs (MSC-EVs), as therapeutic delivery channels for cancer treatment targeting unique inflammatory mediators.},
}

@article {pmid41988471,
year = {2026},
author = {Gonzalez, AM and Townsend, JR and Sapp, PA and Edwards, C and Kirby, TO and Wright, J and Lamendella, R and Esposito, R},
title = {Effect of AG1[®] supplementation on nutritional adequacy and gut microbial composition in trained adults.},
journal = {Frontiers in nutrition},
volume = {13},
number = {},
pages = {1783951},
pmid = {41988471},
issn = {2296-861X},
abstract = {BACKGROUND: Dietary supplements that combine vitamins, minerals, phytonutrients, prebiotics, and probiotics have gained popularity among health-oriented consumers seeking convenient ways to fill nutritional gaps and support gut health.

METHODS: This randomized, double-blind, placebo-controlled crossover study examined the effects of two weeks of the nutritional supplement (AG1[®]) on gut microbial composition, nutritional adequacy, and tolerability. Twenty resistance-trained men (n = 10; 26.4 ± 6.5 y) and women (n = 10; 26.9 ± 5.3 y) supplemented daily with either AG1[®] or placebo (PL) for 14 days. Following a 2-week washout, participants crossed over to the other condition. Participants provided stool samples for gut microbial composition analysis, completed the Digestion-associated Quality of Life Questionnaire (DQLQ), and completed a 24-h dietary intake assessment at the beginning and end of each 14-day supplementation period. Outcomes were analyzed using repeated-measures and multivariate statistical approaches for dietary intake, gut microbiota, metabolomics, and questionnaire data.

RESULTS: AG1[®] did not produce large, global shifts in microbial alpha or beta diversity, supplementation was associated with selective enrichment of key bacterial taxa commonly linked to gut health, including Lactiplantibacillus plantarum, Lacticaseibacillus rhamnosus, and Bifidobacterium animalis. AG1[®] supplementation significantly improved nutritional adequacy by increasing the total number of micronutrient Estimated Average Requirements (EARs) met compared to placebo (2.8; p = 0.0011), with no significant differences in digestive quality of life between groups (p = 0.777). Vitamins A, C, and E were the most common nutrient gaps filled by AG1 supplementation.

CONCLUSIONS: Two weeks of AG1[®] supplementation improved micronutrient adequacy in healthy resistance-trained adults by reducing nutrient gaps. Supplementation also selectively enriched key beneficial gut microbial taxa and putative microbial functional without inducing major disruptions to overall community structure. Importantly, AG1[®] was well tolerated and did not negatively impact digestion-associated quality of life.

CLINICAL TRIAL REGISTRATION: ClinicalTrials.gov, identifier: NCT06521424.},
}

@article {pmid41988516,
year = {2026},
author = {Liang, Y and Chen, H and Ren, G and Jiang, G},
title = {Research progress on the role and therapeutic applications of traditional Chinese medicine in radiation enteropathy.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1747735},
pmid = {41988516},
issn = {1663-9812},
abstract = {Radiation enteropathy (RE) is a debilitating complication following radiotherapy, with currently limited treatment options. Multi-target intervention strategies such as Traditional Chinese Medicine (TCM) botanical formulas and acupuncture have been investigated as potential complementary approaches for its management. This review systematically synthesizes the evidence on TCM botanical formulas (e.g., Modified Baitouweng Decoction, Xihuang Pill, TJ-14) and acupuncture for the treatment of RE. Existing studies suggest multiple mechanisms of action, including anti-inflammatory and antioxidant effects, regulation of apoptosis and proliferation, restoration of intestinal barrier integrity, and modulation of gut microbiota. Clinical studies have reported improvements in symptoms and reductions in inflammatory markers, while preclinical models have demonstrated protective effects against radiation-induced intestinal injury. However, the current body of evidence is generally constrained by methodological limitations. Many clinical studies have small sample sizes and lack rigorous designs (e.g., absence of randomized controls), while mechanistic research often provides limited causal inference and relies on models with questionable clinical relevance, resulting in a significant translational gap. Based on this appraisal, we critically evaluate the limitations of existing research and propose future directions. These include: (i) employing CRISPR-based microbiome editing to investigate causal mechanisms; (ii) developing pharmacokinetic-pharmacodynamic (PK-PD) models for dose individualization; and (iii) utilizing innovative trial designs such as Bayesian adaptive trials to bridge the gap between empirical practice and evidence-based medicine. Rigorous further investigation is essential to define the role of these TCM interventions within the integrative treatment strategy for RE.},
}

@article {pmid41988525,
year = {2026},
author = {Kong, L and Wang, C},
title = {A machine learning model integrating gut microbiota biomarkers for predicting neurological recovery after cerebral hypoxia-ischemia: a single-center study augmented with public data.},
journal = {Frontiers in pharmacology},
volume = {17},
number = {},
pages = {1756017},
pmid = {41988525},
issn = {1663-9812},
abstract = {OBJECTIVE: To evaluate the predictive value of gut microbiota biomarkers for neurological recovery after cerebral hypoxia-ischemia and to develop a clinically oriented, validated machine learning (ML) for early outcome prediction.

METHODS: In this single-center cohort study, 772 patients (2022-2024) were stratified according to 1-year neurological outcomes into favorable (n = 538) and poor recovery (n = 234) groups, gut microbiota composition, microbial metabolites, systemic inflammatory and oxidative stress markers, and selected gene expression profiles were assessed using blood and fecal samples. Microbial profiling was assessed via 16S rRNA sequencing and whole-genome sequencing. LASSO regression, random forest (RF), and neural networks models were constructed and evaluated using internal validation strategies and augmented with publicly available datasets.

RESULTS: Patients with favorable neurological recovery exhibited significantly higher levels of short-chain fatty acids, increased superoxide dismutase activity, and upregulated neuroprotective gene expression, along with reduced pro-inflammatory cytokines and harmful metabolites (all P < 0.001). Microbiota analysis demonstrated enrichment of beneficial taxa (e.g., Bifidobacterium longum) and depletion of pro-inflammatory species (e.g., Clostridium difficile). Across ML approaches, IL-6 consistently emerged as a key predictive feature, with RF confirmed its prelative importance. The neural network model showed stable predictive performance across validation analyses, indicating robustness for high-dimensional biomarker integration.

CONCLUSION: Gut microbiota-associated biomarkers, when combined with systemic inflammatory indicators such as IL-6, enable robust early prediction of neurological recovery following cerebral hypoxia-ischemia. ML-based integration of multi-modal biomarkers may facilitate clinically applicable prognostic assessment, while also providing a foundation for future investigations into microbiota-targeted interventions.},
}

@article {pmid41988834,
year = {2026},
author = {Taléns-Visconti, R and Diez-Sales, O and Nácher, A},
title = {Cosmetic Interventions for Skin Microbiome Modulation: Current Strategies and Future Directions.},
journal = {Skin research and technology : official journal of International Society for Bioengineering and the Skin (ISBS) [and] International Society for Digital Imaging of Skin (ISDIS) [and] International Society for Skin Imaging (ISSI)},
volume = {32},
number = {4},
pages = {e70352},
pmid = {41988834},
issn = {1600-0846},
mesh = {Humans ; *Microbiota/drug effects/physiology ; *Skin/microbiology/drug effects ; *Cosmetics/pharmacology ; Dysbiosis ; Probiotics ; Prebiotics ; Skin Microbiome ; },
abstract = {BACKGROUND: Human skin harbors a highly diverse and dynamic microbiome that maintains barrier function and homeostasis, while endogenous/exogenous factors and cosmetic products modulate microbial balance. Dysbiosis contributes to inflammatory diseases like atopic dermatitis and acne; however, evidence for microbiome-targeted cosmetics remains preliminary. This article critically examines the impact of cosmetic products on the skin microbiota, distinguishing between potentially harmful formulations and those specifically developed to preserve microbial balance, collectively termed "microbiome-friendly" cosmetics.

MATERIALS AND METHODS: This narrative review synthesizes clinical, microbiological, and mechanistic studies on the skin microbiome's composition, endogenous/exogenous determinants, dysbiosis in skin diseases, and the impact of conventional and microbiome‑targeted cosmetics. Databases were searched up to January 2026 for peer‑reviewed studies, with emphasis on human clinical trials and systematic analyses.

RESULTS: Most conventional cosmetics do not induce major dysbiosis in healthy skin when properly formulated. For advanced formulations, including ingredients such as probiotics, prebiotics, postbiotics, and paraprobiotics, early clinical and microbiological studies report promising benefits without compromising microbial diversity. However, evidence is limited by heterogeneous designs, small sample sizes, and the lack of standardized criteria for "microbiome‑friendly" claims.

CONCLUSIONS: The evidence indicates that informed cosmetic selection and use of skincare products support microbiome balance as a complementary skin health strategy as may be key for both preventative and therapeutic strategies in managing skin disorders, just as allowing a dynamic understanding of the skin microbiome to improve human health.},
}

Humans
*Microbiota/drug effects/physiology
*Skin/microbiology/drug effects
*Cosmetics/pharmacology
Dysbiosis
Probiotics
Prebiotics
Skin Microbiome

@article {pmid41989100,
year = {2026},
author = {Yang, J and Du, H and Tao, F and Ashraf, MA and Gao, X and Huang, X and Zhu, K and Li, G and Zheng, J and Bonfante, P and Cardinale, F and Liu, J},
title = {Rhizosphere microbial shifts drive amygdalin detoxification and jasmonate-mediated alleviation of peach autotoxicity.},
journal = {The ISME journal},
volume = {},
number = {},
pages = {},
doi = {10.1093/ismejo/wrag095},
pmid = {41989100},
issn = {1751-7370},
abstract = {Plant-associated microbes play essential roles in maintaining plant health and modulating responses to environmental stresses. Autotoxicity from allelopathic compounds is a major constraint on perennial crop production, yet the potential for plants to recruit microbiota to counteract such toxicity remains understudied. Our research combined field sampling from a multi-replant peach system, multi-omics, pot, and hydroponic experiments to elucidate plant-microbe interactions that alleviate amygdalin-induced autotoxicity. Metabolomic analysis of peach orchard soils showed that amygdalin accumulated progressively in the rhizosphere with longer continuous cultivation. Exogenous amygdalin inhibited plant growth, with stronger suppression observed in sterilized soil, suggesting a protective role of soil microbes. Amygdalin application altered rhizobacterial community structure and enriched several taxa, including Burkholderia-Caballeronia-Paraburkholderia and Sinomonas. In vitro assays confirmed that amygdalin serves as a selective substrate for these enriched bacteria. We further found that three strains isolated from the amygdalin-stressed peach rhizosphere significantly alleviated autotoxic inhibition, and their co-inoculation showed the greatest enhancement of plant performance. Metabolomic and transcriptomic analyses revealed activation of plant jasmonic acid (JA) pathway. Its involvement was confirmed by the alleviation of amygdalin-induced stress upon exogenous JA application and by the attenuation of microbiota-mediated stress relief upon JA pathway inhibition. Our study reveals a critical mechanism by which host plants enrich specialized microbes that can alleviate autotoxicity by direct amygdalin degradation, activation of the JA pathway, and modulation of redox homeostasis in peach. These findings provide new insights into plant-microbe interactions in perennial systems and highlight the potential of microbiome-informed microbial interventions for mitigating replant disease.},
}

@article {pmid41989132,
year = {2026},
author = {Parhi, P and Banerjee, A and Thatoi, H},
title = {The role of gut microbiome in chemoresistance property development in colorectal cancer tissue and its novel therapeutic strategies.},
journal = {Journal of chemotherapy (Florence, Italy)},
volume = {},
number = {},
pages = {1-28},
doi = {10.1080/1120009X.2026.2653339},
pmid = {41989132},
issn = {1973-9478},
abstract = {Colorectal cancer remains the second contributor to cancer-related mortality worldwide. Despite various advances in chemotherapeutic approaches, chemoresistance still poses a significant risk, hampering the effectiveness of the treatment. Recent researches have explored the crucial role of dysbiotic gut microbiota in the progression of CRC. Specific dysbiosed gut microbiota plays a key role in enhancing chemoresistance in CRC patients through different mechanisms by metabolizing drugs, and modulating the immune system, creating a barrier between CRC tissue and chemotherapeutic drugs. Various microbial genes have been linked to chemoresistance that code for different enzymes, resulting in the degradation of chemotherapeutic drugs, thus reducing drug's efficiency and identifying these genes can provide insight into various resistance pathways. Therefore, identifying the microbial signature for predetection of chemoresistance in patient, prevention of colonizing chemoresistance inducing bacteria and interventions like modification of gut flora for enhancing the effectiveness of chemotherapeutics is essential to overcome these challenges.},
}

@article {pmid41989202,
year = {2026},
author = {Mankel, D and Maierhaba, Y and Momjian, C and Calabrese, F and Duhamel, S and Marlow, J},
title = {Dual-BONCAT reveals distinct subpopulations of anabolically active cells.},
journal = {Applied and environmental microbiology},
volume = {},
number = {},
pages = {e0239125},
doi = {10.1128/aem.02391-25},
pmid = {41989202},
issn = {1098-5336},
abstract = {Bio-orthogonal non-canonical amino acid tagging (BONCAT) has emerged as a prominent molecular technique that enables microbial ecologists to visualize and identify metabolically active cells in cultures and complex microbial communities. To date, researchers have used just one non-canonical amino acid (ncAA) in a given experiment; here, we validate a novel approach using two different ncAAs in a single experiment. This advancement facilitates the detection of differentially active subpopulations within the same experimental context, thereby reducing the uncertainty and variability associated with parallel treatments and providing precise spatial information about organisms that are active under distinct conditions or at different times. We show that both ncAAs can be taken up by E. coli cultures and by constituents of the Little Sippewissett Salt Marsh microbiome, resulting in fluorescence signals that are significantly higher than background and ncAA-free control experiments, as well as differential labeling patterns reflective of distinct subpopulations. As a proof of concept, we implemented this "dual-BONCAT" approach in salt marsh sediments, adding one ncAA during daytime hours and the other at night. Subpopulations of cells that were anabolically active during the day and/or night were distinguishable by both fluorescence microscopy and by fluorescence-activated cell sorting. Subsequent high-throughput 16S rRNA gene amplicon sequencing of active subpopulations revealed that Methylobacterium, potentially feeding on plant exudate carbon, was preferentially active during the day, while sulfur-cycling taxa dominated the night-active population. Dual-BONCAT offers an important advancement in multiplexing substrate analog probing techniques, providing a more realistic understanding of metabolic activity under distinct environmental conditions.IMPORTANCEMicrobial communities are complex and dynamic, with different groups of microbes active under distinct conditions. Bio-orthogonal non-canonical amino acid tagging (BONCAT) uses synthetic amino acids to tag newly made proteins, allowing researchers to see and identify the active subset of a community. While BONCAT studies to date have used a single synthetic amino acid to evaluate cell activity in a single experimental context, here, we introduce a new approach, "dual-BONCAT," using two synthetic amino acids to track differential responses to changing conditions. After validating the approach with E. coli, we deployed it in a salt marsh sediment community, finding that organisms potentially feeding on plant root sugars were more active during the day, while microbes likely metabolizing sulfur were more active at night. We believe dual-BONCAT will prove useful in many studies, as it illuminates microbial community responses to changing conditions, which has important implications for ecosystem dynamics.},
}

@article {pmid41989380,
year = {2026},
author = {Hontelez, S and Guthrie, M and Stobernack, T and van Baarlen, P and Rousseau, C and Boks, MP and Pereira, RR and Boekhorst, J and Kleerebezem, M},
title = {Microbiome signatures correlate with diet-mediated ADHD symptom reduction.},
journal = {Gut microbes},
volume = {18},
number = {1},
pages = {2659400},
doi = {10.1080/19490976.2026.2659400},
pmid = {41989380},
issn = {1949-0984},
mesh = {Humans ; *Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology ; Child ; Male ; *Gastrointestinal Microbiome ; Female ; Feces/microbiology ; *Diet ; Bacteria/classification/genetics/isolation & purification ; },
abstract = {Attention-deficit hyperactivity disorder (ADHD) is one of the most common childhood neuropsychiatric conditions. Both (epi)genetic and environmental factors are suggested to contribute to the etiology of ADHD. In the last decade, nutrition has received considerable attention as a potential environmental factor triggering ADHD behavior, particularly applying a few-foods diet (FFD) has been shown to elicit considerable behavioral improvements. These studies are observational rather than investigating underlying molecular mechanisms. The present study included 79 children (boys aged 8-10) with ADHD following a progressive, i.e., increasingly restrictive, FFD diet for 5 weeks. Minimally invasive samples (feces, urine, blood, and buccal swabs) were collected before and after the intervention to obtain a multi-omics perspective of the dietary responses in the participating children. For 63% of the participating children, a more than 40% behavior score improvement was observed, with an average improvement of 73%. The strength of diet-induced changes in ADHD symptoms among children was significantly associated with the gut microbiome composition, particularly when analyzing species-stratified abundance profiles of previously characterized gut-brain modules in the fecal metagenomic data. While integrative multi-omics analysis did not identify composite signatures linked to symptom changes, the strongest multi-omics signal confirmed compliance with the dietary intervention. Our findings implicate a role of the gut microbiome and its metabolic capacity to communicate with the central nervous system in children with food-associated ADHD.},
}

Humans
*Attention Deficit Disorder with Hyperactivity/diet therapy/microbiology
Child
Male
*Gastrointestinal Microbiome
Female
Feces/microbiology
*Diet
Bacteria/classification/genetics/isolation & purification

@article {pmid41989563,
year = {2026},
author = {Saini, V and Verma, A and Kumari, S and Chaudhary, S and Mishra, A and Kumar, A and Jha, HC},
title = {The gut microbiome axis: how Lactobacillus-fermented soymilk orchestrates health.},
journal = {Archives of microbiology},
volume = {208},
number = {7},
pages = {},
pmid = {41989563},
issn = {1432-072X},
support = {2103365//PMRF (IN)/ ; IITI/CRDT/2022-23/05//CRDT-IIT Indore/ ; ANRF/PAIR/2025/000018/PAIR-A(G)//Anusandhan National Research Foundation (IN)/ ; },
}

@article {pmid41989595,
year = {2026},
author = {Walker, MR and Schwarzfischer, M and Scharl, M},
title = {The cancer-microbiome axis: Mechanisms and emerging therapeutic strategies.},
journal = {Seminars in immunopathology},
volume = {48},
number = {1},
pages = {},
pmid = {41989595},
issn = {1863-2300},
}

@article {pmid41990128,
year = {2026},
author = {Giagnoni, L and Deb, S and Tondello, A and De Noni, M and Borella, M and Stevanato, P and Cecchinato, A and Squartini, A and Spanu, C},
title = {The legacy of raw milk storage temperature is associated with cheese microbiome composition, notwithstanding pasteurization and starter addition.},
journal = {FEMS microbiology letters},
volume = {},
number = {},
pages = {},
doi = {10.1093/femsle/fnag046},
pmid = {41990128},
issn = {1574-6968},
abstract = {Using DNA metabarcoding, we assessed the relative impact of two variables: (a) raw milk storage temperature and (b) cheese maturation duration, on a semi-fresh cheese bacteriome composition under authentic factory-scale industrial conditions. The study is compared to a prior literature report run at a high-quality milk facility, whilst in the present case, milk from an average-quality farm, better reflecting typical local standards, was used. We tested three milk storage temperatures (4 °C, 7 °C, 9 °C) and sampled cheese at six maturation stages (0, 10, 25, 30, 45, and 60 days). Results showed that raw milk storage temperature was the variable most strongly associated with microbial community composition across the sampled stages, exceeding the variation associated with maturation time. Even the pasteurization step and the addition of a Streptococcus thermophilus starter culture did not erase the microbial 'memory' of initial milk conditions. Interestingly, the cheese bacterial community shaping associated with different milk tank temperatures was moreover compositionally uncoupled from the dominant taxonomical pattern of the starting milk. Additionally, the study provided insights into balancing milk quality and storage temperatures to prevent spoilage by psychrotrophic pseudomonads. Under the conditions tested here, the findings suggest that the 4°C storage benchmark may warrant re-evaluation.},
}

@article {pmid41990265,
year = {2026},
author = {Liang, CL and Chen, Y and Lu, C and Liu, H and Qin, F and Dai, S and Qiu, F and Chen, H and Lu, W and Bromberg, JS and Dai, Z},
title = {High Humidity Exacerbates Psoriasiform Skin Disease Relapse by Increasing Tissue-Resident Memory T Cells via Altering Skin Microbiota.},
journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)},
volume = {},
number = {},
pages = {e04061},
doi = {10.1002/advs.202504061},
pmid = {41990265},
issn = {2198-3844},
support = {82104867//National Natural Science Foundation of China/ ; 82004377//National Natural Science Foundation of China/ ; 2023B1212060063//Science and Technology Planning Project of Guangzhou/ ; 2025A03J1082//Science and Technology Planning Project of Guangzhou/ ; 2022A1515011704//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010807//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2025A1515010295//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2026A1515012112//Basic and Applied Basic Research Foundation of Guangdong Province/ ; },
abstract = {Psoriasis recurrence remains a common and difficult medical problem, while environmental humidity appears to have an impact on psoriasis morbidity. However, it remains unknown whether and how high humidity impacts psoriasis relapse. Using unique mouse models of psoriasis relapse, we found that high humidity exposure exacerbated psoriasis recurrence by increasing skin-resident memory CD8[+] T (TRM) cells through a mechanism depending on its upregulation of IL-15Rα on keratinocytes. Keratinocyte-specific knockout of IL-15Rα or administrating soluble sIL-15Rα to block IL-15 abrogated these effects. Moreover, the effects of high humidity on psoriasis relapse, IL-15Rα expression and skin TRM cell formation were attributed to cutaneous Staphylococcus nepalensis since its recolonization or its specific metabolite, asymmetric dimethylarginine (ADMA), upregulated IL-15Rα expression on keratinocytes, increased skin CD8[+] TRM cells and worsened psoriasis relapse. However, treatment with mupirocin, an antibiotic, alleviated recurrent psoriasis. In vitro experiments showed that culture supernatant of Staphylococcus nepalensis upregulated IL-15Rα expression on keratinocytes, while IL-15Rα-expressing keratinocytes promoted formation of CD8[+] TRM phenotypes. Finally, high humidity also aggravated psoriatic skin lesions in humanized mice. Thus, our findings enhanced a new understanding of how climatic factors govern psoriasis recurrence and unveiled a role for IL-15Rα-expressing keratinocytes in skin CD8[+] TRM formation and psoriasis relapse.},
}

@article {pmid41990601,
year = {2026},
author = {Kholif, AE and Olafadehan, OA and Anele, UY},
title = {Tannins in ruminant feeding: effects of tannin type and dosage on rumen fermentation, production performance, health, and sustainability.},
journal = {Research in veterinary science},
volume = {206},
number = {},
pages = {106181},
doi = {10.1016/j.rvsc.2026.106181},
pmid = {41990601},
issn = {1532-2661},
abstract = {Tannins are plant-derived polyphenolic compounds of variable molecular weights that have attracted considerable attention as natural feed additives in ruminant nutrition. Their ability to modulate rumen microbial ecology, improve nutrient utilization, mitigate enteric methane (CH4) emissions, and promote animal health has positioned them as potential tools for improved, sustainable ruminant production systems. This review critically evaluates and synthesizes published evidence on the effects of tannins on rumen fermentation dynamics, nutrient digestibility, hematological and biochemical parameters, production performance, and overall health status of ruminants. A systematic literature search was conducted using Scopus, Web of Science, ScienceDirect, Google Scholar, and PubMed, targeting peer-reviewed English-language studies published between January 2000 and September 2025. Search terms were organized using Boolean operators across tannin chemistry and type, ruminant species, and production-, environmental-, or health-related outcomes. Studies were included if they reported in vitro or in vivo responses of ruminants to tannins, while non-ruminant studies, conference abstracts, and non-English publications were excluded to ensure comprehensive comparability. Collectively, available evidence indicates that hydrolyzable tannins generally exert more consistent positive effects on feed intake, nutrient digestibility, and CH4 mitigation than condensed tannins, although responses remain highly dependent on tannin source, chemical structure, diet composition, dietary inclusion level, and the extent of animal adaptation. Low to moderate inclusion levels (generally <3% of dietary dry matter [DM]) were associated with neutral to beneficial effects on feed intake, rumen fermentation characteristics, nitrogen utilization, and animal performance. In contrast, higher rates (>5% of dietary DM) frequently impair digestibility, depress feed intake, compromise nitrogen efficiency, and reduce productive performance, indicating dose-dependent responses. Besides nutritional modulation, other ancillary benefits of tannins include reduced internal parasite burden and decreased incidence of ruminal bloat. Positive changes in hematological and biochemical indices further suggest potential improvements in physiological response and health status at moderate levels, although high rates may induce adverse metabolic alterations. In summary, tannins represent a promising nutritional strategy for improving the sustainability of ruminant production systems; however, their successful application depends on careful selection of tannin type, strategic dosage optimization, and feeding strategy. Future research should prioritize defining optimal inclusion thresholds, elucidating rumen microbiome adaptation mechanisms at the molecular level, and assessing long-term production and health outcomes under practical production conditions.},
}

@article {pmid41990662,
year = {2026},
author = {Wen, X and Fu, Y and Xiang, L and Liao, M and Harindintwali, JD and Wang, Y and He, C and Gao, Z and Jiang, J and Jiang, X and Wang, F},
title = {Rhizosphere reprogramming by integrated bio‑organic fertilizer and seed coating mitigates atrazine phytotoxicity in soybeans.},
journal = {Journal of hazardous materials},
volume = {509},
number = {},
pages = {142058},
doi = {10.1016/j.jhazmat.2026.142058},
pmid = {41990662},
issn = {1873-3336},
abstract = {The widespread use of atrazine in maize fields poses a persistent threat to subsequent soybean production due to its soil persistence and phytotoxicity. Here, we present an integrated field strategy by synergistically combining a vermicompost-based bio-organic fertilizer with a targeted seed coating, both delivering the efficient atrazine‑degrading Paenarthrobacter sp. AT5. This synergy thereby provides a dual guarantee of precise rhizosphere colonization and a conducive soil environment for atrazine degradation. The combined treatment significantly reduced atrazine concentrations in roots, stems, and leaves by 38.8%, 23.2%, and 35.5%, respectively, while elevating hydroxyatrazine to 8.2-31.0 times the levels in the atrazine-only treatment. Soil atrazine residues decreased while hydroxyatrazine accumulated, particularly in the rhizosphere. Microbiome analyses revealed that the combined treatment enriched key bacterial genera, including Flavobacterium and Bacillus, potentially harboring atrazine-degrading capabilities, and increased the abundance of the functional gene trzN. In parallel, it restored deterministic community assembly processes and re-established cooperative interactions within the rhizosphere bacterial network. Together, these findings elucidate the mechanistic basis by which synergistic inoculation mitigates atrazine phytotoxicity under field conditions and highlight a scalable, microbiome-based strategy for sustaining soybean productivity in herbicide-impacted agroecosystems.},
}

@article {pmid41990710,
year = {2026},
author = {Moeckli, B and Rocha, M and Wassmer, CH and El Hajji, S and Collet, TH and Lacotte, S and Toso, C},
title = {Maternal obesity and the intergenerational risk of cancer: Epidemiologic evidence and mechanistic insights.},
journal = {Cancer epidemiology},
volume = {102},
number = {},
pages = {103079},
doi = {10.1016/j.canep.2026.103079},
pmid = {41990710},
issn = {1877-783X},
abstract = {Over recent decades, the prevalence of obesity has markedly surged. While excess maternal weight is a well-established risk factor for adverse pregnancy outcomes, growing evidence suggests that maternal obesity may also increase the long-term risk of cancer in offspring. This comprehensive review synthesizes epidemiological and experimental data linking maternal obesity to heightened cancer susceptibility in the next generation. Observational studies demonstrate increased risks of childhood leukemia and colorectal cancer in offspring of obese mothers, whereas preclinical models support associations with breast, liver, colon, and pancreatic cancers. Mechanistically, maternal obesity induces epigenetic reprogramming, immune dysregulation, and vertical transmission of a dysbiotic gut microbiota, which may lead to persistent alterations in metabolic and inflammatory signaling pathways in offspring, thereby promoting a pro-tumorigenic environment and potentially increasing cancer susceptibility. Given the global burden of obesity, this intergenerational risk has critical public health implications. Lifestyle modifications, weight-loss interventions, and targeted approaches such as probiotic supplementation may offer promising strategies to mitigate cancer risk in offspring, but require scientific confirmation in further studies. Future research should prioritize mechanistic dissection of exposure windows, identification of predictive biomarkers, and the development of effective, scalable preventive therapies.},
}

@article {pmid41990750,
year = {2026},
author = {Gonzalez Pastor, B and Shkoporov, AN and Hill, C},
title = {Not just passengers: Phages as agents of genetic exchange in fecal microbiota transplantation.},
journal = {Cell host & microbe},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.chom.2026.03.017},
pmid = {41990750},
issn = {1934-6069},
abstract = {Fecal microbiota transplantation (FMT) is an effective therapy for recurrent Clostridioides difficile infection and is increasingly being explored for other microbiota-associated diseases. However, general research has largely focused on bacterial engraftment, overlooking the contribution of the gut virome. In this perspective, we highlight phage-mediated horizontal gene transfer (HGT) as a potentially influential process occurring following FMT. Donor-derived phages may potentially influence community structure, engraft in resident bacteria, and modulate microbial functions or host physiology. In addition, temperate phages are well-equipped to mobilize bacterial genes, such as metabolic functions, stress-response traits, and antibiotic resistance determinants, raising the possibility that gene flow could well contribute to FMT outcomes. We propose a conceptual model in which phages act as bidirectional mediators of adaptation, not only accompanying bacterial communities but also influencing gut ecosystems in subtle, yet potentially consequential, ways.},
}

@article {pmid41990911,
year = {2026},
author = {Espín-Sánchez, D and Russo, L and Diambra, L and Mannino, MC and Scorsetti, AC and Huarte-Bonnet, C and Pedrini, N},
title = {Host transcriptional and microbiome metatranscriptomic changes in soybean plants carrying the insect-pathogenic fungus Beauveria bassiana as an endophyte.},
journal = {Journal of invertebrate pathology},
volume = {},
number = {},
pages = {108629},
doi = {10.1016/j.jip.2026.108629},
pmid = {41990911},
issn = {1096-0805},
abstract = {Entomopathogenic fungi, such as Beauveria bassiana, have been naturally isolated from various plant species and have also been introduced as endophytes to enhance plant health and resilience. These fungal endophytes are often associated with improved plant defense against insect pest herbivory. This study aimed to assess the endophytic capacity of B. bassiana ARSEF 2860 in soybean plants and to investigate the associated changes in gene expression and leaf microbiome activity one-week post-inoculation. The results showed that B. bassiana successfully colonized the leaves, stems, and roots of soybean plants and induced gene expression changes in both the host leaves and their associated microbiome. In the soybean leaves, the fungal endophyte down-regulated genes related to responses to far-red light and the abscisic acid pathway, while up-regulating genes involved in photosynthesis, lipid and carbohydrate biosynthesis, and stress response. Additionally, plant inoculation with B. bassiana was associated with a reduction in total microbiome transcript abundance. This shift was characterized by a relative decrease in reads mapping to potentially pathogenic bacteria, alongside a relative increase in transcripts from bacteria commonly associated with beneficial functions. Total fungal reads were also lower in B. bassiana-colonized plants compared to control samples, with plant-pathogenic fungal reads being reduced. These findings highlight the role of entomopathogenic fungal endophytes to promote plant growth by potentially enhancing photosynthesis and strengthening plant defense mechanisms. The shift in the microbial activity highlights the capacity of endophytes to modulate plant-associated microbiota towards communities that may enhance health and resilience.},
}

@article {pmid41991203,
year = {2026},
author = {Sefer, AP and Aydiner, EK},
title = {From bench to bedside: advances in standardized oral immunotherapy and early predictors of persistent cow's milk allergy in children.},
journal = {Allergologia et immunopathologia},
volume = {54},
number = {S Pt 1},
pages = {18-27},
pmid = {41991203},
issn = {1578-1267},
support = {//None./ ; },
mesh = {Humans ; *Milk Hypersensitivity/therapy/immunology/diagnosis ; *Desensitization, Immunologic/methods/standards ; Child ; Animals ; *Allergens/immunology/administration & dosage ; Administration, Oral ; Immunoglobulin E/immunology ; Cattle ; },
abstract = {Immunoglobulin E (IgE)-mediated cow's milk allergy (CMA) remains the most prevalent pediatric food allergy and a major cause of early-life anaphylaxis, with a substantial proportion of children developing persistent disease despite traditional avoidance-based management. Oral immunotherapy (OIT) has emerged as a proactive strategy that modulates the allergic immune response through controlled and sustained allergen exposure, shifting immunity from T-helper (Th) 2-dominant pathways toward a more regulatory and tolerogenic profile. Current evidence from randomized trials and real-world cohorts demonstrates that cow's milk oral immunotherapy (CM-OIT) achieves desensitization in most treated children, reduces accidental reaction risk, and improves quality of life, although sustained unresponsiveness remains variable and protocol-dependent. Marked heterogeneity exists across protocols regarding dosing, antigen formulation, maintenance targets, and escalation speed, reflecting differing therapeutic philosophies rather than standardized practice. Safety concerns, including dose-related reactions and rare cases of eosinophilic esophagitis, underscore the need for careful patient selection, optimization of comorbid atopic diseases, and shared decision-making. Advances in precision immunology, including component-resolved diagnostics, epitope mapping, basophil activation testing, and emerging transcriptomic and microbiome signatures, now enable the earlier identification of children at high risk of persistent CMA who may benefit most from OIT, while low-risk phenotypes can be safely observed. Adjunctive biologic therapy, particularly anti-IgE agents, has improved tolerability and expanded eligibility in high-risk patients. This review synthesizes current evidence on efficacy, safety, biomarkers, protocols, and adjunctive strategies, emphasizing a personalized, risk-adapted approach to CM-OIT and outlining future directions toward standardized formulations, biomarker-guided stratification, and integrated biologic-assisted immunomodulation.},
}

Humans
*Milk Hypersensitivity/therapy/immunology/diagnosis
*Desensitization, Immunologic/methods/standards
Child
Animals
*Allergens/immunology/administration & dosage
Administration, Oral
Immunoglobulin E/immunology
Cattle

@article {pmid41991444,
year = {2026},
author = {Simpson, RC and Cutler, HB and James, DE and Masson, SWC},
title = {The gut microbiome as an effector of metabolic disease gene variants.},
journal = {Trends in genetics : TIG},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tig.2026.03.011},
pmid = {41991444},
issn = {0168-9525},
abstract = {Here, we discuss emerging studies that have identified overlap in the genetic drivers of the gut microbiome and metabolic disease, and we evaluate the possibility that some genes affecting host metabolic function do so by first manipulating the microbiome.},
}

@article {pmid41991448,
year = {2026},
author = {Diab, E and Thome, NU and Elsayed, SS and Raaijmakers, JM and van Wezel, GP},
title = {Chemical dialogues at the crossroads of host-bacteria interactions.},
journal = {Trends in microbiology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tim.2026.03.013},
pmid = {41991448},
issn = {1878-4380},
abstract = {Microbiomes are now recognised as the second genome of eukaryotes, providing diverse life-support functions for their hosts. The impact of microbiome members on the growth and health of their hosts is determined by chemical cues from the host that modulate microbial physiology, virulence, and the biosynthesis of specialised metabolites. In this review, we provide a cross-kingdom comparison of the role of human and plant molecules in regulating bacterial gene expression. We highlight specific feedback loops and discuss common mechanisms of bidirectional cueing in human- and plant-associated bacteria. Despite the different taxonomies of human- and plant-associated bacteria, we find striking functional similarities in the chemical dialogues at the crossroads of host-bacteria interactions.},
}

@article {pmid41991462,
year = {2026},
author = {Zang, Y and Guo, Z and Ledesma-Amaro, R and Xin, Y and Wu, Y and Gu, Z and Zhang, L},
title = {Engineering Bacillus subtilis as a sustainable platform for the production of functional bile acids.},
journal = {Trends in biotechnology},
volume = {},
number = {},
pages = {},
doi = {10.1016/j.tibtech.2026.03.021},
pmid = {41991462},
issn = {1879-3096},
abstract = {Bile acids and their derivatives are key regulators of host metabolism, immunity, and microbiome interactions, with growing therapeutic potential. Conventional production methods of bile acids relying on animal extraction or chemical synthesis are inefficient, costly, and environmentally unfriendly. Microbial synthesis offers a sustainable alternative but is limited by the absence of genetic tools for native anaerobic producers. Here, we reconstructed the bile acid 7α-dehydroxylation pathway in Bacillus subtilis, a safe and tractable host. We characterized the key Bai enzymes and performed comprehensive analyses of the bile acids generated through in vitro assays and whole-cell catalysis. Multiple intermediates and end products, including cholyl-CoA, 3-oxo-cholic acid, 3-oxo-4,5-6,7-didehydro-deoxycholic acid, 3-oxo-4,5-dehydro-deoxycholic acid, 3-oxo-deoxycholic acid, and deoxycholic acid, were identified. This work establishes a functional heterologous platform for bile acid biosynthesis, enabling sustainable production and future applications in therapeutics and microbiome engineering.},
}

@article {pmid41991481,
year = {2026},
author = {Pyrzanowska, KI and Smith, EN and Ramalingam, C and Greig, M and Gandhi, RA and Heyes, S and Sanger, D and Smith, T and Partridge, DG and Stafford, GP},
title = {A Survey of the Microbiome, Culturome and ARG Profile of a Cohort of Chronic Diabetic Foot Lesions.},
journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica},
volume = {134},
number = {4},
pages = {e70203},
doi = {10.1111/apm.70203},
pmid = {41991481},
issn = {1600-0463},
support = {BB/T007222/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; NIHR203321//NIHR Sheffield Biomedical Research Centre/ ; },
mesh = {*Diabetic Foot/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Middle Aged ; Male ; Aged ; Female ; *Bacteria/isolation & purification/genetics/classification/drug effects ; Anti-Bacterial Agents/pharmacology ; Cohort Studies ; Drug Resistance, Bacterial ; Adult ; },
abstract = {This study aimed to analyse the microbiome of chronic infected diabetic foot ulcers (DFUs) using parallel methods: traditional culture (the culturome), 16S rRNA gene sequencing (the microbiome) as well as the Antibiotic Resistance Gene (ARG) profile of isolated strains. Swab samples were collected in parallel from affected ulcers. The microbiome sequencing results identified that all patients had a polymicrobial flora with the five most frequent genus level OTUs as Escherichia, Staphylococcus, Streptococcus, Pseudomonas and the anaerobe Anaerococcus. Microbiological culture from the same swabs identified multiple species in all but two patient samples and revealed the most common isolates as CoNS Staphylococcus (17%), Enterococcus faecalis (14.3%), Corynebacterium spp. (10.7%), Anaerococcus spp. (7%), Staphylococcus aureus (8%) and Pseudomonas aeruginosa (6%). Enteric pathogens such as Klebsiella spp. were also frequently isolated. Attempts to revive anaerobes were largely unsuccessful, identifying a limitation in clinical microbiology storage protocols. Genome sequencing of 55 isolates revealed a high number of ARGs relating to β-lactams and tetracyclines, indicating multi-drug-resistant organisms (MDROs). This was confirmed by phenotypic antimicrobial susceptibility data that included several highly resistant Gram-negative bacteria. Overall, our data add to the picture of DFU microbiome as complex and displaying high levels of anti-microbial resistance (AMR).},
}

*Diabetic Foot/microbiology
Humans
*Microbiota
RNA, Ribosomal, 16S/genetics
Middle Aged
Male
Aged
Female
*Bacteria/isolation & purification/genetics/classification/drug effects
Anti-Bacterial Agents/pharmacology
Cohort Studies
Drug Resistance, Bacterial
Adult

@article {pmid41991624,
year = {2026},
author = {Garg, PM and Malhotra, A},
title = {Emerging role of non-coding RNAs as biomarkers and therapeutic targets in preterm infants with necrotizing enterocolitis.},
journal = {Pediatric research},
volume = {},
number = {},
pages = {},
pmid = {41991624},
issn = {1530-0447},
abstract = {Necrotizing enterocolitis (NEC) is a leading cause of morbidity and mortality in preterm infants, marked by intestinal necrosis, inflammation, hemorrhage, and impaired repair. Despite advances in neonatal care, early diagnostics and targeted therapies remain limited. Emerging evidence shows that non-coding RNAs (ncRNAs), including microRNAs, long ncRNAs, and tRNA-derived fragments, regulate key inflammatory, cell-death, angiogenic, and immune pathways in NEC. Distinct ncRNA signatures correlate with histopathology, and plasma-derived exosomal ncRNAs show promise as early biomarkers. Human milk exosomal microRNAs exhibit protective effects, while ncRNA-microbiome interactions may influence disease susceptibility. Larger studies using high-throughput sequencing are needed to advance biomarker-driven precision care.},
}

@article {pmid41991647,
year = {2026},
author = {Liu, CC and Grencewicz, D and Chakravarthy, K and Li, L and Liepold, R and Wolf, M and Marcho, LM and Sangwan, N and Tzeng, A and Hoyd, R and Jhawar, SR and Grobmyer, SR and Al-Hilli, Z and Sciallis, AP and Spakowicz, D and Ni, Y and Eng, C},
title = {Breast tumor microbiome regulates anti-tumor immunity and T cell-associated metabolites.},
journal = {Scientific reports},
volume = {},
number = {},
pages = {},
doi = {10.1038/s41598-026-48719-5},
pmid = {41991647},
issn = {2045-2322},
support = {K01AG070310/AG/NIA NIH HHS/United States ; Innovator Award (1046611)//American Lung Association/ ; Research Scholar Award (RSG-23-1023205)//American Cancer Society/ ; P30CA016058//National Institutes of Health, United States/ ; 8UL1TR000090-05/TR/NCATS NIH HHS/United States ; GRAYFDN1908CE//Gray Foundation/ ; },
}